- Volume 73, Issue 4, 2023
Volume 73, Issue 4, 2023
- Notification Lists
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- New Taxa
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Genome analysis-based union of the genera Youhaiella and Paradevosia, and proposal that Methyloterrigena soli Kim et al. 2016 is a later heterotypic synonym of Paradevosia shaoguanensis Geng et al. 2015
More LessPhylogenetic tree analysis of Youhaiella tibetensis F4T, Paradevosia shaoguanensis J5-3T and Methyloterrigena soli M48T based on 16S rRNA gene sequences revealed that the three genera did not form distinct and independent monophyletic clusters. The 16S rRNA gene sequence similarities were all higher than 99 % between each pair of the three type strains. Average nucleotide identity, digital DNA–DNA hybridization, average amino acid identity and 16S rRNA gene sequence similarity between Paradevosia shaoguanensis J5-3T and Methyloterrigena soli M48T showed that they represented the same species. Physiological and biochemical characteristics of these three strains were similar, such as motility by polar flagella, major respiratory quinone, polar lipids, and fatty acids. Polygenetic trees and other characteristic comparative analysis revealed the need to merge the genera Youhaiella and Paradevosia into one genus.
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Genome-based reclassification of Picrophilus torridus Zillig et al. 1996 as a later heterotypic synonym of Picrophilus oshimae Schleper et al. 1996
In the present study, we attempt to clarify the taxonomic positions of Picrophilus oshimae and Picrophilus torridus . The 16S rRNA gene sequence similarity between P. oshimae DSM 9789T and P. torridus DSM9790T (99.4 %) was above the threshold value (98.6 %) for bacterial species delineation. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between P. oshimae DSM 9789T and P. torridus DSM9790T were higher than the threshold values (95–96 % for ANI and 70 % for dDDH) for bacterial species delineation. The present results indicate that Picrophilus torridus Zillig et al. 1996 is a later heterotypic synonym of Picrophilus oshimae Schleper et al. 1996.
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- Actinomycetota
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Nocardia pulmonis sp. nov., an actinomycete isolated from a patient with pulmonary infection
A novel bacterial strain, CDC141T, was isolated from sputum samples of a patient with pulmonary infection in Hainan Province, PR China. We performed a polyphasic study to assess the taxonomic position of the new species. Based on the results of 16S rRNA gene sequence analyses, strain CDC141T belonged to the genus Nocardia with the highest sequence similarity to Nocardia nova NBRC 15556T (98.84 %) and Nocardia macrotermiti s RB20T (98.54 %). The dapb1 gene sequence-based phylogenetic and phylogenomic trees further showed that the novel strain was clustered in a distinct clade adjacent to Nocardia pseudobrasiliensis DSM 44290T. The DNA G+C content of strain CDC141T was 68.57 mol%. The genomic diversity analysis revealed low average nucleotide identity and in silico DNA‒DNA hybridization values (<84.7 and <28.9 %, respectively) with its closest relative. Growth occurred at 20–40 °C, pH 6.0–9.0 and with NaCl concentrations of 0.5–2.5 % (w/v). The main fatty acids of strain CDC141T were C16 : 0, C18 : 0 10-methyl, TBSA, C16 : 1 ω6c/C16 : 1 ω7c, C18 : 1 ω9c, C18 : 0, C17 : 1 iso I/anteiso B and C17 : 0. The polar lipid profile was dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, unidentified glycolipids, unidentified phospholipids and unidentified lipids. MK8 (H4ω-cycl) and MK8 (H4) were the major respiratory quinones. These characteristics were consistent with the typical chemotaxonomic properties of members of the genus Nocardia . Based on the results of phenotypic and genetic analyses, strain CDC141T was identified as representing a new species of the genus Nocardia , with the proposed name Nocardia pulmonis sp. nov. (CDC141T=JCM 34955T=GDMCC 4.207T).
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Arthrobacter caoxuetaonis sp. nov., Arthrobacter zhangbolii sp. nov. and Arthrobacter gengyunqii sp. nov., isolated from Marmota himalayana faeces from Qinghai-Tibet Plateau
Six aerobic or facultative anaerobic, motile, Gram-stain-positive, catalase-positive and oxidase-negative strains (zg-Y453T, zg-Y324, zg-Y462T, zg-Y411, zg-Y809T and zg-Y786) were isolated from different faecal samples of Marmota himalayana from the Qinghai–Tibet Plateau. Pale yellow, round, raised and moist colonies appeared 48 h after incubation at 28 °C on brain–heart infusion plates supplemented with 5 % defibrinated sheep blood. According to the 16S rRNA gene sequence alignment, two strain pairs (zg-Y453T/zg-Y324 and zg-Y462T/zg-Y411) shared the highest similarities to Arthrobacter luteolus (99.5 and 99.2 %), and the other one (zg-Y809T/zg-Y786) to Arthrobacter citreus (99.5 %). Results of phylogenetic analysis based on the 16S rRNA gene and genome sequences showed that these six strains represented three separate species within the genus Arthrobacter . The average nucleotide identity and digital DNA–DNA hybridization values between the three novel type strains (zg-Y453T/zg-Y462T/zg-Y809T) and other known species in this genus were all below respective thresholds (70.2–81.5/19.6–24.2 %, 70.6–81.8/19.8–25.0 %, and 70.4–88.2/19.9–35.3 %). Although phylogenetically related, there were obvious chemotaxonomic and phenotypic differences: strain pair zg-Y462T/zg-Y411 had anteiso-C15 : 0 as the only major fatty acid; the three novel species had different dominant quinones, MK-8(H2) in strains zg-Y462T/zg-Y809T (74.8/81.1 %) and MK-8(H2)/MK-9(H2) (43.1/53.0 %) in zg-Y453T; similarly, the ability to reduce nitrate in strains zg-Y453T and zg-Y462T could differentiate them from zg-Y809T. All strains had diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol, but differed slightly in the types of unidentified glycolipids, phospholipids and lipids. Based on the results of these polyphasic taxonomic analyses, three novel species within the genus Arthrobacter are proposed, namely Arthrobacter caoxuetaonis sp. nov. (type strain, zg-Y453T=GDMCC 1.2809T=JCM 35173T), Arthrobacter zhangbolii sp. nov. (type strain, zg-Y462T=GDMCC 1.2880T=JCM 35170T) and Arthrobacter gengyunqii sp. nov. (type strain, zg-Y809T=GDMCC 1.2808T=JCM 35168T).
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Sphaerisporangium perillae sp. nov., isolated from the root of Perilla frutescens (Linn.) Britt
A novel protease-producing actinomycete, designated strain NEAU-ZS1T, was isolated from the root of Perilla frutescens (Linn.) Britt collected from Jiamusi, Heilongjiang, PR China. Comparative 16S rRNA gene sequencing showed that strain NEAU-ZS1T belonged to the genus Sphaerisporangium and was most closely related to ‘ Sphaerisporangium corydalis ’ NEAU-YHS15T (99.2%) and Sphaerisporangium cinnabarinum JCM 3291T (99.0%). Phylogenetic tree analysis revealed that strain NEAU-ZS1T formed a monophyletic clade with ‘ S. corydalis ’ NEAU-YHS15T. The genome size was 9.3 Mbp with a DNA G+C content of 70.3 mol%. Digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values between the genome sequence of strain NEAU-ZS1T and those of ‘ S. corydalis ’ NEAU-YHS15T (28.6, 83.9 and 79.1 %) and S. cinnabarinum JCM 3291T (18.5, 70.6 and 50.2 %) were below the recommended thresholds for species delineation. The strain formed spherical spore vesicles produced on the aerial hyphae. The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were glucose and madurose. The polar lipids consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, an unidentified phospholipid and an unidentified glycolipid. The menaquinones were MK-9(H4), MK-9(H6) and MK-9(H2). The major fatty acids were iso-C16 : 0, C16 : 1 ω5c, 10-methy C17 : 0 and C17 : 1 ω7c. On the basis of the results of a polyphasic taxonomic study, it is concluded that strain NEAU-ZS1T represents a novel species of the genus Sphaerisporangium , for which the name Sphaerisporangium perillae sp. nov. is proposed. The type strain is NEAU-ZS1T (=CCTCC AA 2021019T= JCM 35655T).
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Mumia quercus sp. nov., isolated from the root of Quercus variabilis
A novel endophytic actinomycete, designated strain NEAU-365T, was isolated from the root of Quercus variabilis collected from Nanjing, Jiangsu, PR China. Comparative 16S rRNA gene sequencing showed that strain NEAU-365T belonged to the genus Mumia but clearly differs from the currently recognized species Mumia zhuanghuii Z350T (99.31 %), Mumia xiangluensis NEAU-KD1T (98.82 %) and Mumia flava MUSC 201T (97.78 %). Phylogenetic tree analysis revealed that strain NEAU-365T clustered with the type strains of the genus Mumia . The genome size was 4.1 Mbp with a DNA G+C content of 71.2 mol%. Digital DNA–DNA hybridization and average nucleotide identity values between the genome sequence of strain NEAU-365T and those of M. zhuanghuii Z350T(27.5 and 84.0 %), M. xiangluensis NEAU-KD1T(23.4 and 80.9 %) and M. flava MUSC 201T(20.9 and 77.7 %) were below the recommended thresholds for species delineation. Cells were observed to be irregular cocci shaped. The cell wall contained ll-diaminopimelic acid and the whole-cell sugars were galactose and rhamnose. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid and three unidentified phospholipids. The predominant menaquinone was detected as MK-9(H4). The major fatty acids were C16 : 0, C18 : 0, C18 : 1 ω9c and 10-methyl C18 : 0. On the basis of genotypic and phenotypic differences from members of the genus Mumia , a novel species, Mumia quercus sp. nov. is proposed. The type strain is NEAU-365T (=CCTCC AA 2021033T=JCM 35005T).
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Lolliginicoccus levis gen. nov., sp. nov., a novel bacterium isolated from the brain of the Chiroteuthis picteti squid, and reclassification of two Hoyosella species as Lolliginicoccus suaedae comb. nov. and Lolliginicoccus lacisalsi comb. nov.
A Gram-stain-positive, non-motile, mesophilic, aerobic, coccus-shaped bacterium, designated strain Y7R2T, was isolated from the brain of a Chiroteuthis picteti squid living in mesopelagic water near Muroto, Kochi, Japan. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain was most closely related to the genus Hoyosella (96.1 % similarity to the type strain of the type species Hoyosella altamirensis ) and formed a separate distinct cluster in a stable, deep-branching lineage with the type strains of Hoyosella suaedae and Hoyosella lacisalsi (98.7–99.5% similarities). The major fatty acids (>10 %) of strain Y7R2T were C17 : 1 ω8c, C15 : 0, C16 : 1 ω6c/C16 : 1 ω7c and C16 : 0, and the isoprenoid quinones were menaquinone-7 (57.8 %) and menaquinone-8 (42.2 %). The principal polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol, and the DNA G+C content was 68.0 %. These chemotaxonomic features, with the exception of the fatty acid composition, were similar to those of the phylogenetically clustered species ( H. suaedae and H. lacisalsi ) but different from those of core Hoyosella species (including H. altamirensis ). These results suggested that Y7R2T, H. suaedae and H. lacisalsi strains should be assigned to a novel genus. Furthermore, strain Y7R2T showed low average nucleotide identity values (88.0–88.2 %) and low digital DNA–DNA hybridization values (34.3–34.7 %) to the type strains of H. suaedae and H. lacisalsi . These data indicated that strain Y7R2T should be assigned to a novel genus and species, for which the name Lolliginicoccus levis gen. nov., sp. nov. is proposed. The type strain is Y7R2T (=NBRC 114883T=KCTC 49749T). Accordingly, reclassification of H. suaedae and H. lacisalsi as Lolliginicoccus suaedae comb. nov. (type species) and Lolliginicoccus lacisalsi comb. nov. is also proposed.
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Rathayibacter rubneri sp. nov. isolated from Allium cepa var. Rijnsburger, an onion landrace
More LessThe novel, aerobic, Gram-stain-positive, rod-shaped bacterial strain, ZW T2_19T, was isolated from an onion sample (Allium cepa var. Rijnsburger). Analyses of the 16S rRNA gene sequence revealed that ZW T2_19T represented a member of the genus Rathayibacter but may represent a novel species of this genus. Analyses of the whole draft genome sequences, i.e. digital DNA–DNA hybridisation (dDDH) and average nucleotide identity (ANI) of ZW T2_19T and all type strains of species of the genus Rathayibacter confirmed that ZW T2_19T represents a novel species of the genus Rathayibacter . The genome size of ZW T2_19T is 4.01 Mbp and the DNA G+C content is 71.8 mol%. Glucose, mannose, rhamnose and ribose were detected as whole-cell sugars of ZW T2_19T. The major respiratory quinone of ZW T2_19T is menaquinone MK-10, at 78.9 %. The detected peptidoglycan type in ZW T2_19T is a variant of type B2γ with {Gly} [l-diaminobutyric acid (l-DAB)/l-homoserine (l-Hse)] d-Glu-l-DAB. Polar lipids in ZW T2_19T consisted of one diphosphatidylglycerol, one phosphatidylglycerol, seven glycolipids, one phospholipid and one lipid. The fatty acid profile of ZW T2_19T predominantly consisted of anteiso-C15 : 0 (53 %), iso-C16 : 0 (21 %) and anteiso-C17 : 0 (18 %). In addition, API 20NE, API 50CH, API Coryne, API ZYM, antibiotic susceptibility, haemolysis and growth at different temperatures and with different supplements was investigated. On the basis of the results obtained using this polyphasic approach, including molecular, phenotypic and biochemical analyses, we propose the novel species Rathayibacter rubneri with the type and only strain ZW T2_19T (= DSM 114294T = LMG 32700T).
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Actinophytocola gossypii sp. nov. and Streptomyces gossypii sp. nov., two novel actinomycetes isolated from rhizosphere soil of cotton
More LessTwo Gram-positive, aerobic and non-motile actinomycetes, designated S1-96T and N2-109T, were isolated from soils collected from a cotton field. They are described as representing two novel species of genera Actinophytocola and Streptomyces through a polyphasic approach. Analysis of 16S rRNA gene sequences revealed that strains S1-96T and N2-109T showed highest similarity to Actinophytocola xinjiangensis CGMCC 4.4663T (99.10 %) and Streptomyces iconiensis BNT558T (98.21 %), respectively. Phylogenetic analyses based on 16S rRNA and core genes confirmed the close relationships of these strains. Genomic analyses further supported the novel taxonomic delimitation of these two species based on digital DNA–DNA hybridization and average nucleotide identity. Strains S1-96T and N2-109T contained MK-9(H4) and MK-9(H6) as the most abundant menaquinone, respectively. High abundances of iso-fatty acids were detected in both strains, which was similar to their close relatives. Physiological and polar lipid analyses also revealed differences between these strains and their phylogenetic neighbours, supporting their taxonomic delimitation as novel species. The names Actinophytocola gossypii sp. nov. (type strain S1-96T=JCM 34412T=CGMCC 4.7707T) and Streptomyces gossypii sp. nov. (type strain N2-109T=JCM 34628T=CGMCC 4.7717T) are proposed.
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Streptomyces phytophilus sp. nov., an endophytic actinobacterium with biosynthesis potential as an antibiotic producer
More LessAn endophytic actinobacterium, strain PIP175T, was isolated from the root sample of a native apricot tree (Pittosporum angustifolium) growing on the Bedford Park campus of Flinders University, Adelaide, South Australia. This strain is a Gram stain-positive, aerobic actinobacterium with well-developed substrate mycelia. Aerial mycelia rarely produce spores and the spore chain is spiral. Strain PIP175T showed the highest 16S rRNA gene sequence similarity to Streptomyces aculeolatus DSM 41644T (99.4 %). Other closely related phylogenetic representatives include Streptomyces synnematoformans DSM 41902T (98.3 %), Streptomyces albospinus NBRC 13846T (97.6 %), Streptomyces cacaoi subsp. cacaoi NRRL B-1220T (97.5 %) and Streptomyces ruber NBRC 14600T (97.4 %). The major cellular fatty acid of this strain was iso-C16 : 0 and the major menaquinone was MK-9(H6). The whole-cell sugar contained galactose, glucose and mannose. Chemotaxonomic data confirmed that strain PIP175T belonged to the genus Streptomyces . Digital DNA–DNA hybridization, average nucleotide identity based on blast and OrthoANIu results between strain PIP175T and S. aculeolatus DSM 41644T were 60.0, 94.1 and 94.9 %, respectively. Genotypic and phenotypic data and genome analysis results allowed the differentiation of strain PIP175T from its closest species with validly published names. Strain PIP175T showed good activity against methicillin-resistant Staphylococcus aureus 03120385. Genome mining of strain PIP175T revealed biosynthetic genes encoding proteins relating to antibiotic production, plant growth promotion and biodegradation enzymes. The name proposed for the new species is Streptomyces phytophilus sp. nov. The type strain is PIP175T (=DSM 103379T=TBRC 6026T).
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Streptomyces beihaiensis sp. nov., a chitin-degrading actinobacterium, isolated from shrimp pond soil
More LessA Gram-stain-positive actinobacterium, designated strain GXMU-J5T, was isolated from a sample of shrimp pond soil collected in Tieshangang Saltern, Beihai, PR China. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Streptomyces . The organism formed an extensively branched substrate mycelium, with abundant aerial hyphae that differentiated into spores. Phylogenetic analysis of 16S rRNA gene sequences showed that strain GXMU-J5T was most related to Streptomyces kunmingensis DSM 41681T (similarity 97.74 %) and Streptomyces endophyticus YIM 65594T (similarity 96.80 %). However, the values of digital DNA–DNA hybridization, average nucleotide identity and evolutionary distance of multilocus sequence analysis between strain GXMU-J5T and its closest relatives indicated that it represented a distinct species. Strain GXMU-J5T contained ll-diaminopimelic acid and the major whole-cell hydrolysates were xylose and galactose. The predominant menaquinones of strain GXMU-J5T were revealed as MK-9(H4), MK-9(H6) and MK-9(H8). The polar lipids consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannosides and phospholipids of unknown structure containing glucosamine. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0. The whole genome size of strain GXMU-J5T was 6.79 Mbp with a 71.39 mol% G+C content. Genomic analysis indicated that strain GXMU-J5T had the potential to degrade chitin. On the basis of these genotypic and phenotypic data, it is supported that strain GXMU-J5T represents a novel species of the genus Streptomyces , for which the name Streptomyces beihaiensis sp. nov. is proposed. The type strain is strain GXMU-J5T (=MCCC 1K08064T=JCM 35629T).
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Streptomyces salinarius sp. nov., an actinomycete isolated from solar saltern soil
An actinobacterium, designated strain SS06011T, was isolated from solar saltern soil collected from Samut Sakhon province, Thailand. The taxonomic position of this strain was established using the polyphasic taxonomic approach. The strain produced grey aerial spore mass on International Streptomyces Project 2 seawater agar that differentiated into spiral spore chains with rugose-surfaced spores. Strain SS06011T was found to have ll -diaminopimelic acid in the cell peptidoglycan. Whole-cell hydrolysates contained galactose, glucose and ribose. MK-9(H6) and MK-9(H4) were major menaquinones. The major cellular fatty acids comprised iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were detected in cells. These characteristics were coincident with the typical morphological and chemotaxonomic properties of the genus Streptomyces . The taxonomic affiliation at the genus level of this strain could also be confirmed by its 16S rRNA gene sequence data. Strain SS06011T showed the highest 16S rRNA gene sequence similarity to Streptomyces ardesiacus NRRL B-1773T (99.1 %), Streptomyces coelicoflavus NBRC 15399T (99.1 %) and Streptomyces hyderabadensis OU-40T (99.1 %). Digital DNA–DNA hybridization (dDDH), average nucleotide identity-blast (ANIb) and average amino acid identity (AAI) values between strain SS06011T and its closely related type strains, S. ardesiacus NBRC 15402T, S. coelicoflavus NBRC 15399T and S. hyderabadensis JCM 17657T, were in the range of 45.4–48.4 % (for dDDH), 90.8–91.9 % (for ANIb) and 90.8–91.7 % (for AAI), respectively, which are lower than the cut-off criteria for species delineation. The DNA G+C content of genomic DNA was 71.9 mol%. With the differences in physiological, biochemical and genotypic data, strain SS06011T could be discriminated from its closest neighbours. Thus, strain SS06011T should be recognized as representing a novel species of the genus Streptomyces , for which the name Streptomyces salinarius sp. nov. is proposed. The type strain is SS06011T (=TBRC 9951T=NBRC 113998T).
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- Archaea
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Thermococcus argininiproducens sp. nov., an arginine biosynthesis archaeal species isolated from the Central Indian Ocean ridge
A strictly anaerobic hyperthermophilic archaeon, designated strain IOH2T, was isolated from a deep-sea hydrothermal vent (Onnuri vent field) area on the Central Indian Ocean Ridge. Strain IOH2T showed high 16S rRNA gene sequence similarity to Thermococcus sibiricus MM 739T (99.42 %), Thermococcus alcaliphilus DSM 10322T (99.28 %), Thermococcus aegaeus P5T (99.21 %), Thermococcus litoralis DSM 5473T (99.13 %), ‘Thermococcus bergensis’ T7324T (99.13 %), Thermococcus aggregans TYT (98.92 %) and Thermococcus prieurii Bio-pl-0405IT2T (98.01 %), with all other strains showing lower than 98 % similarity. The average nucleotide identity and in silico DNA–DNA hybridization values were highest between strain IOH2T and T. sibiricus MM 739T (79.33 and 15.00 %, respectively); these values are much lower than the species delineation cut-offs. Cells of strain IOH2T were coccoid, 1.0–1.2 µm in diameter and had no flagella. Growth ranges were 60–85 °C (optimum at 80 °C), pH 4.5–8.5 (optimum at pH 6.3) and 2.0–6.0 % (optimum at 4.0 %) NaCl. Growth of strain IOH2T was enhanced by starch, glucose, maltodextrin and pyruvate as a carbon source, and elemental sulphur as an electron acceptor. Through genome analysis of strain IOH2T, arginine biosynthesis related genes were predicted, and growth of strain IOH2T without arginine was confirmed. The genome of strain IOH2T was assembled as a circular chromosome of 1 946 249 bp and predicted 2096 genes. The DNA G+C content was 39.44 mol%. Based on the results of physiological and phylogenetic analyses, Thermococcus argininiproducens sp. nov. is proposed with type strain IOH2T (=MCCC 4K00089T=KCTC 25190T).
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- Bacteroidota
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Sphingobium nicotianae sp. nov., isolated from tobacco soil
More LessBacterial strain H33T was isolated from tobacco plant soil and was characterized using a polyphasic taxonomy approach. Strain H33T was a Gram-stain-negative, rod-shaped, non-motile and strictly aerobic bacterium. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of the up-to-date bacterial core gene set (92 protein clusters) indicated that H33T belongs to the genus Sphingobium . Strain H33T showed the highest 16S rRNA gene sequence similarity to Sphingobium xanthum NL9T (97.2%) and showed 72.3–80.6 % average nucleotide identity and 19.7–29.2 % digital DNA–DNA hybridization identity with the strains of other species of the genus Sphingobium . Strain H33T grew optimally at 30°C, pH 7 and could tolerate 0.5 % (w/v) NaCl. The isoprenoid quinones were ubiquinone-9 (64.1%) and ubiquinone-10 (35.9%). Spermidine was the major polyamine. The major fatty acids of H33T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The polar lipid profile consisted of a mixture of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, sphingoglycolipid, two unidentified lipids, two unidentified glycolipids, two unidentified aminoglycolipids and an unidentified phospholipid. The genomic DNA G+C content of H33T was 64.9 mol%. Based on the phylogenetic and phenotypic data, H33T was considered a representative of a novel species in the genus Sphingobium . We propose the name Sphingobium nicotianae sp. nov., with H33T (=CCTCC AB 2022073T=LMG 32569T) as the type strain.
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Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil
More LessA Gram-stain-negative, yellow-pigmented and facultatively aerobic bacterium, designated strain U1T, was isolated from plastic dumped soil sampled in the Republic of Korea. Cell of strain U1T were non-motile rods showing catalase-negative and oxidase-positive activities. Strain U1T was shown to grow at 10–37 °C (optimum, 25–30 °C) and pH 6.0–9.0 (optimum, pH 8.0), and in the presence of 0–0.5 % (w/v) NaCl (optimum, 0 %). Strain U1T contained iso-C15 : 0, C16 : 0, C16 : 1 ω5c and summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c) as the major cellular fatty acids (>5 %) and menaquinone-7 as the sole respiratory quinone. Phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids were identified as the major polar lipids. The DNA G+C content of strain U1T calculated from the whole-genome sequence was 45.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain U1T formed a distinct phylogenetic lineage within the genus Dyadobacter . Strain U1T has the highest 16S rRNA sequence similarity to Dyadobacter bucti QTA69T (97.9 %). Average nucleotide identity and digital DNA–DNA hybridization values between strain U1T and D. bucti QTA69T were 74.6 % and 18.9 %, respectively. Based on phenotypic, chemotaxonomic and molecular features, strain U1T represents a novel species of the genus Dyadobacter , for which the name Dyadobacter pollutisoli sp. nov. is proposed. The type strain is U1T (= KACC 22210T=JCM 34491T).
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Chryseobacterium oryctis sp. nov., isolated from the gut of the beetle Oryctes rhinoceros, and Chryseobacterium kimseyorum sp. nov., isolated from a stick insect rearing cage
Two strains of Chryseobacterium identified from different experiments are proposed to represent new species. Strain WLa1L2M3T was isolated from the digestive tract of an Oryctes rhinoceros beetle larva. Strain 09-1422T was isolated from a cage housing the stick insect Eurycantha calcarata. Sequence analysis of the 16S rRNA and rpoB genes found both strains to be similar but not identical to other Chryseobacterium species. Whole-genome sequencing suggested the isolates represent new species, with average nucleotide identity values ranging from 74.6 to 80.5 %. Genome-to-genome distance calculations produced values below 25.3 %, and digital DNA–DNA hybridization values were 13.7–29.9 %, all suggesting they are distinct species. The genomic DNA G+C content of WLa1L2M3T is approximately 32.53 %, and of 09-1422T is approximately 35.89 %. The predominant cellular fatty acids of strain WLa1L2M3T are C15 : 0 iso, summed feature 9 (C16 : 0 10OH or C17 : 1 iso ω6c), C17 : 0 iso 3OH, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C15 : 0 iso 3OH, C15 : 0 anteiso and C13 : 0 iso, and those of strain 09-1422T are C15 : 0 iso, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C17 : 0 iso 3OH, C15 : 0 anteiso, C15 : 0 iso 3OH, C16 : 1 ω7c, C17 : 0 2OH and C18 : 0. In addition, physiological and biochemical tests revealed phenotypic differences from related Chryseobacterium type strains. These cumulative data indicate that the two strains represent novel species of the genus Chryseobacterium for which the names Chryseobacterium oryctis sp. nov. and Chryseobacterium kimseyorum sp. nov. are proposed with WLa1L2M3T (=BCRC 81350T=JCM 35215T=CIP 112035T) and 09-1422T (=UCDFST 09-1422T=BCRC 81359T=CIP 112165T), as type strains, respectively.
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Flavobacterium pygoscelis sp. nov., isolated from a chinstrap penguin chick (Pygoscelis antarcticus)
More LessStrain I-SCBP12nT, a novel Gram-stain-negative, aerobic, non-spore-forming, motile-by-gliding and rod-shaped bacterium, was isolated from a chinstrap penguin chick (Pygoscelis antarcticus) during a 2015 expedition to the Chilean Antarctic territory. Phylogenetic analysis based on 16S rRNA gene sequencing confirmed that strain I-SCBP12nT belonged to the genus Flavobacterium , being closely related to strains Flavobacterium chryseum P3160T (98.52 %), Flavobacterium hercynium WB 4.2-33T (98.47 %) and Flavobacterium chilense LM-19-FpT (98.47 %). The genome size of strain I-SCBP12nT was 3.69 Mb with DNA G+C content 31.95 mol%. Genomic comparisons of strain I-SCBP12nT with type species in the genus Flavobacterium were performed, with obtained average values near 75.17 and 84.33 % for the blast and MUMer analyses of average nucleotide identity, respectively, and 0.86 for the tetranucleotides frequency analysis. These values are far from the accepted species cut-off values. Strain I-SCBP12nT contained MK-6 as the predominant menaquinone and the major polar lipids were aminophospholipid, an unidentified aminolipid and unidentified lipids. The predominant fatty acids (> 5 %) were iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, iso-C16 : 1, iso-C16 : 0 3-OH, C15 : 1 ω6c and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Phenotypic, chemotaxonomic and genomic data supported the assignment of strain I-SCBP12nT (=CECT 30404T=RGM 3223T) to a novel species of Flavobacterium , for which the name Flavobacterium pygoscelis sp. nov.is proposed.
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Aridibaculum aurantiacum gen. nov., sp. nov., isolated from the Kumtag Desert soil
A novel orange-coloured bacterium, designated strain SYSU D00508T, was isolated from a sandy soil sampled from the Kumtag Desert in China. Strain SYSU D00508T was aerobic, Gram-stain-negative, oxidase-positive, catalase-positive and non-motile. Growth occurred at 4–45°C (optimum 28–30°C), pH 6.0–9.0 (optimum pH 7.0–8.0) and with 0–2.5 % NaCl (w/v, optimum 0–1.0 %). The major polar lipids consisted of phosphatidylethanolamine (PE), unidentified aminolipids (AL1-3) and unidentified polar lipids (L1-5) were also detected. The major respiratory quinone was MK-7 and the major fatty acids (>10 %) were iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 1 G. The genomic DNA G+C content was 42.6 %. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SYSU D00508T belonged to the family Chitinophagaceae and showed 93.9 % ( Segetibacter koreensis DSM18137T), 92.9 % ( Segetibacter aerophilus NBRC 106135T), 93.0 % ( Terrimonas soli JCM 32095T) and 92.8 % ( Parasegetibacter terrae JCM 19942T) similarities. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain SYSU D00508T is proposed to represent a novel species of a new genus, named Aridibaculum aurantiacum gen. nov., sp. nov., within the family Chitinophagaceae . The type strain is SYSU D00508T (=KCTC 82286T=CGMCC 1.18648T=MCCC 1K05005T).
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Spirosoma oryzicola sp. nov., isolated from dried rice husk
More LessStrain RHs26T is an aerobic, Gram-stain-negative, non-flagellated and rod- or filamentous-shaped (1.0–1.1×2.3–50 µm) bacterium that was isolated from dried rice husk. It was positive for oxidase and catalase, hydrolysed starch and Tween 80, and weakly hydrolysed CM-cellulose. The strain grew at temperatures between 10 and 37 °C (optimum, 28 °C), in 0–1 % NaCl (optimum, 0 %) and at pH 6.0–9.0 (optimum, pH 7.0–8.0). The predominant membrane fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 1 ω5c, iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid, two unidentified aminophospholipids and two unidentified lipids. The predominant quinone was menaquinone MK-7. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain RHs26T belongs to the genus Spirosoma , presenting the highest sequence similarity to Spirosoma agri S7-3-3T (95.8 %). The genomic DNA G+C content of strain RHs26T was 49.5 %. Strain RHs26T showed the highest orthologous average nucleotide identity (OrthoANI) and digital DNA–DNA hybridization (dDDH) values of 76.4 % and 20.0 % with S. agri KCTC 52727T while sharing OrthoANI and dDDH values of 74.6 % and 19.2 % with Spirosoma terrae KCTC 52035T, the closest relative in the phylogenomic tree. Based on the results of a polyphasic taxonomic study, strain RHs26T represents a novel species in the genus Spirosoma , for which the name Spirosoma oryzicola sp. nov. is proposed. The type strain is RHs26T (=JCM 35224T=KACC 17318T).
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Paraflavisolibacter caeni gen. nov., sp. nov., a novel taxon within the family Chitinophagaceae isolated from sludge
More LessA Gram-stain-negative bacterium, designated strain LB-8T, was isolated from an activated sludge sample collected from a factory in Binzhou city, Shandong province, PR China. Cells of strain LB-8T were strictly aerobic, non-motile and rod-shaped. Growth occurred at 15–40 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 7.0) and at 0–7.5 % (w/v) NaCl (optimum, 0.5 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LB-8T formed a distinct phyletic branch within the family Chitinophagaceae and was most closely related to members of the genera Flavisolibacter , Cnuella and Paracnuella with 92.7–93.3 % 16S rRNA gene sequence similarities. The average amino acid identity values between strain LB-8T and its closed phylogenetic neighbours Flavisolibacter , Cnuella and Paracnuella were below 70 % supporting that strain LB-8T was a member of a novel genus. The predominant cellular fatty acids of LB-8T were iso-C15 : 0, anteiso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C17 : 0 3-OH, and the only isoprenoid quinone was menaquinone-7 (MK-7). The major polar lipids of strain LB-8T were phosphatidylethanolamine, four unidentified aminolipids and two unidentified lipids. The genome size of strain LB-8T was 7.01 Mbp with 41.2 mol% G+C content. On the basis of the evidence presented in this study, strain LB-8T represents a novel species of a new genus in the family Chitinophagaceae , for which the name Paraflavisolibacter caeni gen. nov., sp. nov. (type strain LB-8T=GDMCC 1.3631T=KCTC 92688T) is proposed.
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Solitalea agri sp. nov., a new member of the genus Solitalea isolated from rhizospheric soil of a jujube tree
More LessA Gram-stain negative, aerobic, rod-shaped and creamy pink-coloured bacterium, designated MAHUQ-68T, was isolated from rhizospheric soil of a jujube tree. Colonies grew at 10–40 °C (optimum, 28 °C), pH 6.0–9.0 (optimum pH, 7.0) and in the presence of 0–1.5 % NaCl (optimum 0–0.5 %). Positive for both catalase and oxidase activity. Strain MAHUQ-68T hydrolysed casein, starch, aesculin and l-tyrosine. Based on the results of phylogenetic analysis using 16S rRNA gene and genome sequences, strain MAHUQ-68T clustered together within the genus Solitalea . The closest members were Solitalea longa HR-AVT (98.8 % sequence similarity), Solitalea canadensis DSM 3403T (96.9 %) and Solitalea koreensis R2A36-4T (94.0 %). The genome of strain MAHUQ-68 T was 4 250 173 bp long with 68 scaffolds and 3 570 protein-coding genes. The genomic DNA G+C content of the type strain was 38.0 mol%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain MAHUQ-68T and its closest relatives were 72.0–81.4% and 19.8–24.3 %, respectively. The major cellular fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The main respiratory quinone was menaquinone-7. The polar lipids comprised phosphatidylethanolamine, an unidentified aminolipid and four unidentified lipids. Based on these data, strain MAHUQ-68T represents a novel species in the genus Solitalea , for which the name Solitalea agri sp. nov. is proposed. The type strain is MAHUQ-68T (=KACC 22249T=CGMCC 1.19062T).
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Salinimicrobium profundisediminis sp. nov., isolated from deep-sea sediment of the Mariana Trench
A Gram-stain-negative, aerobic, rod-shaped, non-gliding bacterial strain, designated as MT39T, was isolated from a deep-sea sediment sample collected from the Mariana Trench. Strain MT39T grew optimally at 35°C and pH 7.0, and could tolerate up to 10% (w/v) NaCl. The strain was positive for catalase and negative for oxidase. The genome of strain MT39T was 4 033 307 bp, with a 41.1 mol % genomic G+C content and 3514 coding sequences. Phylogenetic analysis based on 16S rRNA gene sequences placed strain MT39T within the genus Salinimicrobium , showing the highest 16S rRNA gene sequence similarity to Salinimicrobium terrea CGMCC 1.6308T (98.1%). The average nucleotide identity and in silico DNA–DNA hybridization values between strain MT39T and the type strains of seven Salinimicrobium species were all less than the threshold values to discriminate bacterial species, indicating that strain MT39T is affiliated with a novel species within the genus. The major cellular fatty acids of strain MT39T were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH. Polar lipids of strain MT39T included phosphatidylethanolamine, one unidentified aminolipid and four unidentified lipids. Menaquinone-6 was the only respiratory quinone in strain MT39T. On the basis of the polyphasic data present in this study, strain MT39T represents a novel species of the genus Salinimicrobium , for which the name Salinimicrobium profundisediminis sp. nov. is proposed, with type strain being MT39T (=MCCC 1K07832T=KCTC 92381T).
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- Bacillota
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Paenibacillus soyae sp. nov., isolated from the rhizosphere of soya bean
More LessA Gram-positive, facultatively anaerobic, agar-hydrolytic and rod-shaped bacterium with peritrichous flagellation, designated strain SCIV0701T, was isolated from soya bean rhizosphere soil collected from Bazhong, Sichuan Province, PR China and characterized by using polyphasic taxonomy. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SCIV0701T belonged to the genus Paenibacillus , and showed highest similarity to Paenibacillus nanensis MX2-3T (97.59 %), Paenibacillus paeoniae M4BSY-1T (97.45 %) and Paenibacillus pinisoli NB5T (97.45 %). The average nucleotide identity values and in silico DNA–DNA hybridization scores between strain SCIV0701T and P. nanensis MX2-3T, P. paeoniae M4BSY-1T and P. pinisoli NB5T were lower than recommended thresholds of 95% and 70 %, respectively, for species delineation. Menaquinone-7 was the predominant respiratory quinone. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified phospholipids and one unidentified aminophospholipid. The major fatty acids were anteiso-C15 : 0, C16 : 00 and iso-C16 : 0. Physiological and biochemical features differentiated strain SCIV0701T from the closely related Paenibacillus species. Based on the results of polyphasic taxonomic analysis, strain SCIV0701T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus soyae sp. nov. is proposed. The type strain is SCIV0701T (=GDMCC 1.2482T=JCM 34672T).
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Bacillus cabrialesii subsp. cabrialesii subsp. nov. and Bacillus cabrialesii subsp. tritici subsp. nov., plant growth-promoting bacteria and biological control agents isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico
Strain TSO2T, a plant growth-promoting rhizobacteria and biological control agent, was isolated from wheat rhizosphere sampled from the Yaqui Valley in Mexico. The strain was identified using a polyphasic approach. Based on its analysis of the full-length 16S rRNA gene, strain TSO2T was assigned to the genus Bacillus , which was supported by morphological and metabolic traits, such as Gram-positive staining, rod shape, spore formation, strictly aerobic metabolism, catalase-positive activity, starch, and casein hydrolysis, reduction of nitrate to nitrite, growth in presence of lysozyme and 2 % NaCl, citrate utilization, growth at pH 6.0, acid production from glucose and indole production from tryptophan. Additionally, strain TSO2T possesses swarming motility, presenting a featureless mat pattern that can cover the whole petri dish. The whole-genome phylogenetic relationship analysis elucidated that strain TSO2T is closely related to Bacillus cabrialesii TE3T. The maximum values for average nucleotide identity (ANI) and in silico DNA–DNA hybridization from the genome-to-genome distance calculator (GGDC) were 97 and 73.4 %, respectively, related to Bacillus cabrialesii TE3T, where both ANI and GGDC values were barely above the species delimitation threshold, but below the subspecies limit. Also, strain TSO2T showed the ability to produce a fatty acid (C18 : 0) that is not present in closely related Bacillus species. These results provide evidence that strain TSO2T is a novel subspecies of the species Bacillus cabrialesii , for which the name Bacillus cabrialesii subsp. tritici subsp. nov. is proposed. The type strain of Bacillus cabrialesii subsp. tritici subsp. nov. is TSO2T (CM-CNRG TB52T=LBPCV TSO2T). The description of this novel subspecies automatically creates the subspecies Bacillus cabrialesii subsp. cabrialesii subsp. nov. for which the type strain is TE3T (CM-CNRG TB54T=CCStamb A1T).
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Paenibacillus auburnensis sp. nov. and Paenibacillus pseudetheri sp. nov., isolated from the rhizosphere of Zea mays
Two Gram-stain-positive, aerobic, endospore-forming bacterial strains, isolated from the rhizosphere of Zea mays were studied for their detailed taxonomic allocation. Based on 16S rRNA gene sequence similarity comparisons, both strains JJ-7T and JJ-60T were shown to be members of the genus Paenibacillus . Strain JJ-7T was most closely related to the type strains of Paenibacillus tianjinensis (99.6 %) and P. typhae (98.7 %), and strain JJ-60T to Paenibacillus etheri (99.5 %). The 16S rRNA gene sequence similarities to all other Paenibacillus species were ≤98.4 %. Both strains JJ-7T and JJ-60T showed 97.6 % 16S rRNA gene sequence similarity between each other. Genomic comparisons showed that the average nucleotide identity and digital DNA–DNA hybridization values to next related type strain genomes were always <94 and <56 %, respectively. The polar lipid profiles of both strains contain a number of phospholipids including diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, which is in accord with the genus Paenibacillus . The major quinone was MK-7 in both strains. Major fatty acids were iso- and anteiso-branched. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strains JJ-7T and JJ-60T from the most closely related species. Thus, each strain represents a novel species of the genus Paenibacillus , for which the names Paenibacillus auburnensis sp. nov. and Paenibacillus pseudetheri sp. nov. are proposed, with JJ-7T (=CIP 111892T=DSM 111785T=LMG 32088T=CCM 9087T) and JJ-60T (=CIP 111894T=DSM 111787T=LMG 32090T=CCM 9086T) as the type strains, respectively.
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Paenibacillus dendrobii sp. nov., an indole-3-acetic acid-producing endophytic bacterium isolated from Dendrobium nobile
More LessA novel rod-shaped, Gram-stain-positive, spore-forming and motile by peritrichous flagella strain, designated HJL G12T, was isolated from the root of Chinese herb Dendrobium nobile. Strain HJL G12T grew optimally at pH 7.0, 30 °C and in the presence of 1.0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene and genomic sequences showed that HJL G12T clustered with Paenibacillus chibensis NBRC 15958T and Paenibacillus dokdonensis YH-JAE5T with 98.3 and 98.2 % sequence similarity. The DNA–DNA hybridization values between strain HJL G12T and the two reference strains were 23.6 % and 24.9 %, respectively. Menaquinone-7 was the only respiratory quinone and meso-diaminopimelic acid was present in the cell-wall peptidoglycan. Antesio-C15 : 0 and iso-C16 : 0 were detected to be the major cellular fatty acids. The cellular polar lipid profile contained diphosphatidyglycerol, phosphatidylglycerol, phosphatidylethanolamine, lysyl-phospatidylglycerol and three unidentified aminophospholipids. Based on these results, strain HJL G12T is considered to represent a novel species within the genus Paenibacillus , for which the name Paenibacillus dendrobii sp. nov. is proposed, with HJL G12T (=NBRC 115617T=CGMCC 1.18520T) as the type strain.
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Paenibacillus melissococcoides sp. nov., isolated from a honey bee colony affected by European foulbrood disease
A novel, facultatively anaerobic, Gram-stain-positive, motile, endospore-forming bacterium of the genus Paenibacillus , designated strain 2.1T, was isolated from a colony of Apis mellifera affected by European foulbrood disease in Switzerland. The rod-shaped cells of strain 2.1T were 2.2–6.5 µm long and 0.7–1.1 µm wide. Colonies of strain 2.1T were orange-pigmented under oxic growth conditions on solid basal medium at 35–37 °C. Strain 2.1T showed catalase and cytochrome c oxidase activity. Its polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and phospholipid. The only respiratory quinone was menaquinone 7, and the major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, iso-C17 : 0 and palmitic acid (C16 : 0), which is consistent with other members of the genus Paenibacillus . The G+C content of the genomic DNA of strain 2.1T was 53.3 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence similarity showed that strain 2.1T was closely related to Paenibacillus dendritiformis LMG 21716T (99.7 % similarity) and Paenibacillus thiaminolyticus DSM 7262T (98.8 %). The whole-genome average nucleotide identity between strain 2.1T and the type strains of P. dendritiformis and P. thiaminolyticus was 92 and 91 %, respectively, and thus lower than the 95 % threshold value for delineation of genomic prokaryotic species. Based on the results of phylogenetic, genomic, phenotypic and chemotaxonomic analyses we propose the name Paenibacillus melissococcoides sp. nov. for this novel Paenibacillus species. The type strain is 2.1T (=CCOS 2000T=DSM 113619T=LMG 32539T).
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Ectobacillus ponti sp. nov., a novel bacterium isolated from Pearl River Estuary
A Gram-staining-positive, aerobic, motile, and rod-shaped strain, designated SYSU M60031T, was isolated from a Pearl River Estuary sediment sample, Guangzhou, Guangdong, China. The isolate could grow at pH 5.0–8.0 (optimum, pH 7.0), 25–37 °C (optimum, 28 °C) and in the presence of 0–1 % (w/v) NaCl (optimum, 0 %). The predominant respiratory menaquinone of SYSU M60031T was MK-7. The cellular polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, and one unidentified aminolipid. The major fatty acids (>10 % of total) were iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, and C16 : 0. The genomic DNA G+C content was 51.2 %. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M60031T belonged to the genus Ectobacillus and showed the highest sequence similarity to Ectobacillus funiculus NAF001T (96.16%), followed by Ectobacillus antri SYSU K30001T (95.08 %). Based on the phenotypic, genotypic, and phylogenetic data, strain SYSU M60031T should be considered to represent a novel species of the genus Ectobacillus , for which the name Ectobacillus ponti sp. nov. is proposed. The type strain of the proposed novel isolate is SYSU M60031T (=CGMCC 1.19243T =NBRC 115614T).
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Sellimonas catena sp. nov., isolated from human faeces
More LessObligately anaerobic, Gram-stain-positive, small-chain coccobacilli, strains 12EGH17T and 18CBH55, were isolated from faecal samples of healthy Japanese humans. Strain 12EGH17T showed the highest 16S rRNA gene sequence similarity to Sellimonas intestinalis BR72T (95.5 %), Coprococcus comes ATCC 27758T (94.4 %) and Clostridium nexile DSM 1787T (93.7 %). The percentage of conserved proteins values between the genome of strain 12EGH17T and that of the members of the genus Sellimonas were >54 %, suggesting that strain 12EGH17T belongs to the genus Sellimonas . The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains 12EGH17T and 18CBH55 were higher than the cut-off values of species demarcation (90 % dDDH and 99 % ANI), indicating these two strains are the same species. However, the dDDH and ANI values of these strains were lower than the cut-off values of species demarcation against other strains (<30 % dDDH and <79 % ANI). These results indicate that the isolates should be considered to represent a new species of the genus Sellimonas . The isolates were differentiated from the type species, S. intestinalis , by the ability of aesculin hydrolysis. Based on the collected data, strains 12EGH17T and 18CBH55 represent a novel species in the genus Sellimonas , for which the name Sellimonas catena sp. nov. is proposed. The type strain of S. catena is 12EGH17T (=JCM 35622T=DSM 114916T).
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Comparative genomic analysis of the genus Weissella and taxonomic study of Weissella fangxianensis sp. nov., isolated from Chinese rice wine starter
More LessIn this study, three lactic acid bacteria, namely, HBUAS51963T, HBUAS51964 and HBUAS51965, were isolated from Chinese rice wine starter sampled in Fangxian County, PR China. All were non-motile, non-spore-forming and Gram-positive spherical cells. Their taxonomic status was characterized using a polyphasic approach. Genome-based analysis revealed that all three strains were phylogenomically related to Weissella thailandensis KCTC 3751T and Weissella paramesenteroides ATCC 33313T. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the three strains and the phylogenetically related type strains were less than 54.8 and 93.8 %, respectively, and thus, they were below the thresholds of dDDH and ANI for species definition. The genomic DNA G+C content was 38.6 mol %. The predominant fatty acid methyl esters (>10 %) were C16 : 0, C19 : 0 cyc11 and summed feature 10 (C18 : 1 cyc11 and/or ECL 17.834). The polar lipids in the cells of strain HBUAS51963T were mainly phosphatidylglycerol, diphosphatidylglycerol, unidentified glycolipids, phospholipids and lipids. Finally, the three strains were capable of producing d-lactic acid (4.29 g l–1) and various organic acids such as tartaric, acetic, lactic and succinic acids. Overall, the results of genotypic, phenotypic and genomic analyses suggest that the three strains represent a new species of the genus Weissella , for which the name Weissella fangxianis sp. nov. is proposed. The type strain is HBUAS51963T (=GDMCC 1.3506T= JCM 35803T).
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Clostridium folliculivorans sp. nov., isolated from soil samples of an organic paddy in Japan
Two Gram-stain-negative, terminal endospore-forming, rod-shaped and aerotolerant bacterial strains designated D1-1T and B3 were isolated from soil samples of an organic paddy in Japan. Strain D1-1T grew at 15–37 °C, pH 5.0–7.3, and with up to 0.5 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene revealed that strain D1-1T belonged to the genus Clostridium and was closely related to Clostridium zeae CSC2T (99.7 % sequence similarity), Clostridium fungisolvens TW1T (99.7 %) and Clostridium manihotivorum CT4T (99.3 %). Strains D1-1T and B3 were whole-genome sequenced and indistinguishable, with an average nucleotide identity value of 99.7 %. The average nucleotide identity (below 91.1 %) and digital DNA–DNA hybridization (below 43.6 %) values between the two novel isolates and their corresponding relatives showed that strains D1-1T and B3 could be readily distinguished from their closely related species. A novel Clostridium species, Clostridium folliculivorans sp. nov., with type strain D1-1T (=MAFF 212477T=DSM 113523T), is proposed based on genotypic and phenotypic data.
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- Other Bacteria
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Aeoliella straminimaris sp. nov., a novel member of the phylum Planctomycetota with an unusual filamentous structure
More LessOrganisms with distinctive biological features and cellular organization constitute the bacterial phylum Planctomycetota . In this study, we formally describe a novel isolate, strain ICT_H6.2T, isolated from sediment samples collected in the brackish environment of the Tagus River estuary (Portugal) using an iChip-based culturing technique. The 16S rRNA gene analysis placed this strain into the phylum Planctomycetota and family Lacipirellulaceae , with a similarity value of 98.0 % to its closest relative Aeoliella mucimassa Pan181T, the currently only known member of the genus. Strain ICT_H6.2T has a genome size of 7.8 Mbp and a DNA G+C content of 59.6 mol %. Strain ICT_H6.2T is heterotrophic, aerobic and capable of microaerobic growth. This strain grows from 10 to 37 °C and from pH 6.5 to 10.0, requires salt to grow, and can tolerate up to 4 % (w/v) NaCl. Diverse nitrogen and carbon sources are utilized for growth. Morphologically, strain ICT_H6.2T is white to beige pigmented, spherical to ovoid in shape and around 1.4×1.1 µm in size. The strain clusters mainly in aggregates and younger cells show motility. Ultrastructural studies showed a cell plan with cytoplasmatic membrane invaginations and unusual filamentous structures with hexagonal organization in transversal section. Morphological, physiological and genomic comparison between strain ICT_H6.2T and its closest relatives strongly suggests it represents a novel species within the genus Aeoliella , for which we propose the name Aeoliella straminimaris sp. nov., represented by strain ICT_H6.2T as the type strain (=CECT 30574T=DSM 114064T).
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- Pseudomonadota
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Alcanivorax quisquiliarum sp. nov., isolated from anaerobic fermentation liquid of food waste by high-throughput cultivation
More LessStrain CY1518T was isolated from an anaerobic fermentation liquid of food waste treatment plant in Beijing, PR China, and characterized to assess its taxonomy. Cells of CY1518T were Gram-stain-negative, oxidase-negative, catalase-positive and ellipsoidal. Growth occurred at 20–42 °C (optimum, 37 °C), pH 6.0–10.0 (optimum, pH 8) and with 0–6.0 % (w/v) NaCl (optimum, 1.5%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CY1518T belongs to the genus Alcanivorax , with the highest sequence similarity to Alcanivorax pacificus W11-5T (95.97 %), followed by Alcanivorax indicus SW127T (95.08%). The similarity between strain CY1518T and other strains of Alcanivorax was less than 95 %. The genomic DNA G+C content of strain CY1518T was 60.88 mol%. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between strain CY1518T and the closely related taxa A. pacificus W11-5T and A. indicus SW127T were 77.61, 78.03 and 21.2 % and 74.15, 70.02 and 19.3%, respectively. The strain was able to use d-serine, Tween 40 and some organic acid compounds for growth. The polar lipids comprised aminophospholipid, diphosphatidylglycerol, glycolipid, an unknown polar lipid, phosphatidylethanolamine, phosphatidylglycerol and phospholipid. The principal fatty acids (>5 %) were C19 : 0 cyclo ω8c (36.3%), C16 : 0 (32.3%), C12 : 0 3-OH (8.3%) and C12 : 0 (7.6%). Based on its phenotypic, genotypic and genomic characteristics, strain CY1518T represents a novel species in the genus Alcanivorax , for which the name Alcanivorax quisquiliarum sp. nov. is proposed. The type strain is CY1518T (=GDMCC 1.2918T=JCM 35120T).
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Shewanella septentrionalis sp. nov. and Shewanella holmiensis sp. nov., isolated from Baltic Sea water and sediments
Two bacterial strains, SP1W3T and SP1S2-7T, were isolated from samples of water and sediments collected in Vaxholm, a town located on the Stockholm archipelago in the Baltic Sea, in November 2021. The strains were identified as novel genomic species within the genus Shewanella , based upon comparative analysis of whole genome sequence data. Strain SP1W3T (genome size, 5.20 Mbp; G+C content, 46.0 mol%), isolated from water, was determined to be most closely related to S. hafniensis ATCC-BAA 1207T and S. baltica NCTC 10735T, with digital DNA–DNA hybridization (dDDH) values of 61.7% and 60.4 %, respectively. Strain SP1S2-7T (genome size, 4.26 Mbp; G+C content, 41.5 mol%), isolated from sediments, was observed to be most closely related to S. aestuarii JCM17801T, with a pairwise dDDH value of 33.8 %. Polyphasic analyses of physiological and phenotypic characteristics, in addition to genomic analyses, confirmed that each of these two strains represent distinct, novel species within the genus Shewanella , for which the names Shewanella septentrionalis sp. nov. (type strain SP1W3T=CCUG 76164T=CECT 30651T) and Shewanella holmiensis sp. nov. (type strain SP1S2-7T=CCUG 76165T=CECT 30652T) are proposed.
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Dasania phycosphaerae sp. nov., isolated from phytoplankton sample from the south coast of the Republic of Korea
More LessA novel bacterial strain, designated as GY-18T, was isolated from particulate material sampled from the Korean south coast. The bacterium was Gram-stain-negative, aerobic and rod-shaped. Oxidase and catalase were positive. Optimal growth was observed at 30 °C, pH 7.0, in the presence of 1 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene and whole-genome sequences suggested that strain GY-18T was a member of the genus Dasania , but represented a separate lineage. The 16S rRNA gene sequence of strain GY-18T showed high similarities to Dasania marina KCTC 12566T (98.4 %), Halioglobus japonicus KCTC 23429T (92.2 %), Marimicrobium arenosum KCTC 42300T (92.4 %) and Seongchinamella unica KCTC 62383T (92.2 %), respectively. The genome length of strain GY-18T was 3 808 450 bp with a DNA G+C content of 47.8 mol %. The major cellular fatty acids of strain GY-18T were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C10 : 0 3-OH (>10 %). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospholipids were shown to be the major polar lipids. The predominant isoprenoid quinone was Q-8. Based on phylogenetic, phenotypic, chemotaxonomic and genomic features, we propose that strain GY-18T represents a novel species in the genus Dasania of the family Spongiibacteraceae , with the proposed name Dasania phycosphaerae sp. nov. The type strain is GY-18T (=KCTC 92290T=GDMCC 1.3586T).
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Limimaricola litoreus sp. nov., isolated from intertidal sand of the Yellow Sea
More LessA novel species of the genus Limimaricola , designated ASW11-118T, was isolated from an intertidal sand sample of the Yellow Sea, PR China. Growth of strain ASW11-118T occurred at 10–40 °C (optimum, 28 °C), pH 5.5–8.5 (optimum, pH 7.5) and with 0.5–8.0 % (w/v) NaCl (optimum, 1.5%). Strain ASW11-118T has the highest 16S rRNA gene sequence similarity to Limimaricola cinnabarinus LL-001T (98.8%) and 98.6 % to Limimaricola hongkongensis DSM 17492T. Phylogenetic analysis based on genomic sequences indicated that strain ASW11-118T belongs to the genus Limimaricola . The genome size of strain ASW11-118T was 3.8 Mb and DNA G+C content was 67.8 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain ASW11-118T and other members of the genus Limimaricola were below 86.6 and 31.3 %, respectively. The predominant respiratory quinone was ubiquinone-10. The predominant cellular fatty acid was C18 : 1 ω7c. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and one unknown aminolipid. On the basis of the data presented, strain ASW11-118T is considered to represent a novel species of the genus Limimaricola , for which the name Limimaricola litoreus sp. nov. is proposed. The type strain is ASW11-118T (=MCCC 1K05581T=KCTC 82494T).
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Ferranicluibacter rubi gen. nov., sp. nov., a new member of family Rhizobiaceae isolated from stems of elmleaf blackberry (Rubus ulmifolius Schott) in Northwest Spain
Strain CRRU44T was isolated from the stems of Rubus ulmifolius plants growing in Salamanca (Spain). The phylogenetic analysis of the 16S rRNA gene sequence places this strain within the family Rhizobiaceae showing that it is equidistant to the type species of several genera from this family with similarity values ranging from 91.0 to 96.3 %. Strain CRRU44T formed a divergent lineage which clustered with Endobacterium cereale RZME27T, Neorhizobium galegae HAMBI540T and Pseudorhizobium pelagicum R1-200B4T. The phylogenomic analysis showed that strain CRRU44T was equal to or more distant from the remaining genera of the family Rhizobiaceae than other genera among them. The calculated average nucleotide identity based on blast and average amino acid identity values with respect to the type species of all genera from the family Rhizobiaceae were lower than 78.5 and 76.5 %, respectively, which are the currently cut-off values proposed to differentiate genera within this family. All these results together with those from phenotypic and chemotaxonomic analyses support that strain CRRU44T represents a novel species of a novel genus within the family Rhizobiaceae , for which the name Ferranicluibacter rubi gen. nov., sp. nov. is proposed (type strain CRRU44T=CECT 30117T=LMG 31822T).
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Aquitalea palustris sp. nov., isolated from a wild cranberry bog in the Cape Cod National Seashore
More LessA novel species in the genus Aquitalea was isolated from soil and plant surfaces in wild cranberry bogs of the Cape Cod National Seashore. Aquitalea is a little-known genus in the family Chromobacteriaceae (betaproteobacteria) that is associated with freshwater habitats. As part of a culture-dependent comparative survey of bacteria in wild and cultivated cranberry bogs in Massachusetts, strains MWU14-2217T and MWU14-2470 were characterized for taxonomic placement by phenotypic and genotypic testing, and confirmed by genome comparison with a third isolate, MWU14-2238. Genome analysis methods placed the isolates in the genus Aquitalea with >98.54 % 16S rRNA gene sequence similarity each to the four recognized Aquitalea species, but with a DNA–DNA relatedness of 46 % by digital DNA–DNA hybridization (formula d4) and 91.92 % by orthologous average nucleotide identity with usearch with its closest relative. DNA G+C content of the three isolates ranged from 60.11 to 60.28 mol%. The strains are facultatively anaerobic, motile and reduce NO3. They are non-pigmented, non-haemolytic on sheep blood agar, grow on mannitol but not on citrate, and do not produce urease or HCN. The predominant fatty acids of both isolates were C16 : 0 and summed C16 : 1ω7c/C16 : 1ω6c. Using a combination of phylogenetic, physiological and phenotypic characterization, isolates MWU14-2217T, MWU14-2470 and MWU14-2238 represent a novel species within the genus Aquitalea , for which the name Aquitalea palustris sp. nov. is proposed. The type strain is MWU14-2217T (=CCOS 1980T=ATCC TSD-261T).
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Xenorhabdus bovienii subsp. africana subsp. nov., isolated from Steinernema africanum entomopathogenic nematodes
Four Gram-negative bacterial strains isolated from Steinernema africanum entomopathogenic nematodes were biochemically and molecularly characterized to determine their taxonomic position. Results of 16S rRNA gene sequencing indicated that they belong to the class Gammaproteobacteria , family Morganellaceae , genus Xenorhabdus , and that they are conspecific. The average 16S rRNA gene sequence similarity between the newly isolated strains and the type strain of its more closely related species, Xenorhabdus bovienii T228T, is 99.4 %. We therefore selected only one of them, XENO-1T, for further molecular characterization using whole genome-based phylogenetic reconstructions and sequence comparisons. Phylogenetic reconstructions show that XENO-1T is closely related to the type strain of X. bovienii , T228T, and to several other strains that are thought to belong to this species. To clarify their taxonomic identities, we calculated average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values. We observed that the ANI and dDDH values between XENO-1T and X. bovienii T228T are 96.3 and 71.2 %, respectively, suggesting that XENO-1T represents a novel subspecies within the X. bovienii species. Noteworthy, the dDDH values between XENO-1T and several other X. bovienii strains are between 68.7 and 70.9 % and ANI values are between 95.8 and 96.4 %, which could be interpreted, in some instances, as that XENO-1T represents a new species. Considering that for taxonomic description the genomic sequences of the type strains are compared, and to avoid future taxonomic conflicts, we therefore propose to assign XENO-1T to a new subspecies within X. bovienii . ANI and dDDH values between XENO-1T and any other of the species with validly published names of the genus are lower than 96 and 70 %, respectively, supporting its novel status. Biochemical tests and in silico genomic comparisons show that XENO-1T exhibit a unique physiological profile that differs from all the Xenorhabdus species with validly published names and from their more closely related taxa. Based on this, we propose that strain XENO-1T represents a new subspecies within the X. bovienii species, for which we propose the name X. bovienii subsp. africana subsp. nov, with XENO-1T (=CCM 9244T=CCOS 2015T) as the type strain.
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Antarcticirhabdus aurantiaca gen. nov., sp. nov., isolated from Antarctic gravel soil
Jie Du, Ying Zhang, Di Xin, Yuhua Xin and Jianli ZhangStrain R10T was isolated from a gravel soil sample obtained from Deception Island, Antarctica. The isolate was a Gram-stain-negative, strictly aerobic, motile, short-rod-shaped bacterium, and its colonies were orange yellow in colour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R10T belonged to the family Aurantimonadaceae and shared highest sequence similarity with Jiella aquimaris LZB041T (96.3 % sequence similarity), Aurantimonas aggregata R14M6T (96.0 %) and Aureimonas frigidaquae JCM 14755T (96.0 %). Phylogenetic analysis showed that strain R10T affiliated with members of the family Aurantimonadaceae and represented an independent lineage. Growth occurred at 10–37 °C (optimum, 28–32 °C), up to 1.0 % (w/v) NaCl (optimum, 0 %) and pH 5.5–9.0 (optimum, pH 7.0). The major respiratory quinone of strain R10T was Q-10. Its major fatty acids were C18 : 1 ω7c and C16 : 0. The polar lipid profile of strain R10T comprised diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, two unknown phospholipids and two unknown aminophospholipids. The genome of strain R10T was 5.92 Mbp with a G+C content of 69.1 % based on total genome calculations. Average nucleotide identity (ANI) values between R10T and other related species of the family Aurantimonadaceae were found to be low (ANIm <87.0 %, ANIb <75.0 % and OrthoANIu <77.0 %). Furthermore, digital DNA–DNA hybridization (dDDH) and average amino acid identity (AAI) values between strain R10T and the closely related species ranged from 19.5–20.6% and from 60.6–64.0 %, respectively. Based on the results of our phylogenetic, phenotypic, genotypic and chemotaxonomic analyses, it is concluded that strain R10T represents a novel genus and species of the family Aurantimonadaceae , for which the name Antarcticirhabdus aurantiaca gen. nov., sp. nov. is proposed. The type strain is R10T (=KCTC 72466T=CGMCC 1.17155T).
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Aurantimonas marianensis sp. nov., isolated from deep-sea sediment of the Mariana Trench
More LessA novel strain, designated as LRZ36T, was isolated from deep-sea sediment (from a depth of 5400 m) from the Mariana Trench. Cells of this strain are rod-shaped, Gram-stain-negative, strictly aerobic and non-motile. Phylogenetic analysis of LRZ36T based on 16S rRNA gene sequences revealed a lineage in the family Aurantimonadaceae but distinct from the most closely related species Aurantimonas marina CGMCC 1.17725T, ‘ Aurantimonas litoralis ’ KCTC 12094 and Aurantimonas coralicida DSM 14790T with sequence identities of 99.4 %, 98.0 and 97.9 %, respectively. The genome of LRZ36T was 3.8 Mbp in size with a DNA G+C content of 64.8 %, containing 3623 predicted coding genes. LRZ36T showed average nucleotide identity values of 89.8 %, 78.7 and 78.5 % and digital DNA–DNA hybridization values of 38.9 %, 21.7 and 21.6 % with A. marina CGMCC 1.17725T, ‘ A. litoralis ’ KCTC 12094 and A. coralicida DSM 14790T, respectively. The major respiratory quinone was ubiquinone-10 (Q-10), and the predominant fatty acids were C18 : 1ω7c (74.4 %) and C16 : 0 (12.1 %). The polar lipids in LRZ36T are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine, phosphatidylinositol mannoside, an unidentified aminophospholipid, three unidentified lipids, three unidentified phospholipids and two unidentified aminolipids. On the basis of genotypic and phenotypic evidence, LRZ36T represents a novel species of the genus Aurantimonas , for which the name Aurantimonas marianensis sp. nov. is proposed. The type strain is LRZ36T (= KCTC 92065T = GDMCC 1.2985T=MCCC 1K07227T).
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Vibrio paucivorans sp. nov. and Vibrio qingdaonensis sp. nov., two marine bacteria
Two Gram-stain-negative, facultatively anaerobic, motile, rod-shaped and flagellated marine bacteria, designated strains DBSS07T and ZSDZ65T, were isolated from the surface sediments of the Bohai sea and Qingdao coastal seawater, respectively. Phylogenetic analysis based on 16S rRNA genes, multilocus sequence analysis (MLSA), phylogenomic analysis of single-copy gene families and whole-genome data placed DBSS07T and ZSDZ65T within the genus Vibrio . DBSS07T was most closely related to Vibrio aestivus M22T, with 97.51 % sequence similarity, whereas ZSDZ65T was most closely related to Vibrio variabilis R-40492T with 97.58 % sequence similarity. DBSS07T grew with 1–7 % (w/v) NaCl (optimum 3 %), at 16–37 °C (optimum 28 °C) and at pH 6.0–9.0 (optimum pH 7.0); whereas ZSDZ65T grew with 1–5 % (w/v) NaCl (optimum 2 %), at 16–32 °C (optimum 28 °C) and at pH 6.0–9.0 (optimum pH 8.0). Both strains shared the same major fatty acid components (more than 10 % of total fatty acids) of summed feature 3 (C16 : 1ω7c or/and C16 : 1ω6c), with different proportions. The DNA G+C contents of DBSS07T and ZSDZ65T were 44.7 and 44.3 %, respectively. On the basis of the results of polyphasic analysis, DBSS07T and ZSDZ65T are considered to represent novel species within the genus Vibrio , for which the names V. paucivorans sp. nov. (type strain, DBSS07T = KCTC 82896T= MCCC 1K06284T) and V. qingdaonensis sp. nov. (type strain, ZSDZ65T = KCTC 82893T = MCCC 1K06289T) are proposed, respectively.
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Parvularcula maris sp. nov., an algicidal bacterium isolated from seawater
A taxonomic study was carried out on strain BGMRC 0090T, which was isolated from seawater. The isolate was a Gram-negative, aerobic, flagellated, rod-shaped bacterium with algicidal activity. Optimal growth was observed at 30 °C, pH 6.0 and with 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BGMRC 0090T belonged to the genus Parvularcula , with highest sequence similarity to Parvularcula lutaonensis CC-MMS-1T (98.4 %). Average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values between strain BGMRC 0090T and five strains of the genus Parvularcula with publicly available genomes were below 84.0, 69.2 and 21.4 %, respectively. The genome of strain BGMRC 0090T was 3.2 Mb with 64.8 mol% DNA G+C content and encoded 2905 predicted proteins, three rRNA, 42 tRNA and four ncRNA genes. Some algicidal biosynthesis-associated genes were detected in the genome. Strain BGMRC 0090T contained Q-10 as the major quinone. The predominant fatty acids were identified as summed feature 8 (C18 : 1ω7c/ω6c) and C16 : 0. Based on the polyphasic evidence presented in this paper, strain BGMRC 0090T is concluded to represent a novel species of the genus Parvularcula , for which the name Parvularcula maris sp. nov. is proposed. The type strain is BGMRC 0090T (= KCTC 92591T=MCCC 1K08100T).
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Pseudodesulfovibrio nedwellii sp. nov., a mesophilic sulphate-reducing bacterium isolated from a xenic culture of an anaerobic heterolobosean protist
More LessA novel sulphate-reducing bacterium, strain SYKT, was isolated from a xenic culture of an anaerobic protist obtained from a sulphidogenic sediment of the saline Lake Hiruga in Fukui, Japan. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that SYKT clustered with the members of the genus Pseudodesulfovibrio . The closest relative of strain SYKT was Pseudodesulfovibrio sediminis SF6T, with 16S rRNA gene sequence identity of 97.43 %. Digital DNA–DNA hybridisation and average nucleotide identity values between SYKT and species of the genus Pseudodesulfovibrio fell below the respective thresholds for species delineation, indicating that SYKT represents a novel species of the genus Pseudodesulfovibrio . Cells measured 1.7–3.7×0.2–0.5 µm in size and were Gram-stain-negative, obligately anaerobic, motile by means of a single polar flagellum and had a curved rod or sigmoid shape. Cell growth was observed under saline conditions from pH 6.0 to 9.5 (optimum pH 8.0–9.0) and at a temperature of 10–30 °C (optimum 25 °C). SYKT used lactate, pyruvate, fumarate, formate and H2 as electron donors. It used sulphate, sulphite, thiosulphate and sulphur as terminal electron acceptors. Pyruvate and fumarate were fermented. Major cellular fatty acids were anteiso-C15 : 0, C16 : 0, anteiso-C17 : 1ω9c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of SYKT was 49.4 mol%. On the basis of the the genetic and phenotypic features, SYKT was determined to represent a novel species of the genus Pseudodesulfovibrio for which the name Pseudodesulfovibrio nedwellii sp. nov. is proposed with type strain SYKT (=DSM 114958T=JCM 35746T).
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Whole-genome sequencing of Paracoccus species isolated from the healthy human eye and description of Paracoccus shanxieyensis sp. nov
Currently, the genus Paracoccus comprises 76 recognized species. Members of Paracoccus are mostly isolated from environmental, animal, and plant sources. This report describes and proposes a novel species of Paracoccus isolated from clinical specimens of the human ocular surface. We isolated two aerobic, Gram-stain-negative, non-spore-forming, coccoid or short rod-shaped, and non-motile strains (designated DK398T and DK608) from conjunctival sac swabs of two healthy volunteers. The results showed that the strains grew best under the conditions of 28°C, pH 7.0, and 1.0 % (w/v) NaCl. Sequence analysis based on the 16S rRNA gene showed that strains DK398T and DK608 were members of Paracoccus , most similar to Paracoccus laeviglucosivorans 43PT (98.54 and 98.62 %), Paracoccus litorisediminis GHD-05T (98.34 and 98.41 %), and Paracoccus limmosus NB88T (98.21 and 98.29 %). Phenotypic analysis showed that DK398T and DK608 were positive for catalase and oxidase, negative for producing N-acetyl-β-glucosaminic acid, arginine dihydrolase, and β-glucuronidase but positive for leucine arylamidase. The predominant isoprenoid quinone was Q-10, and the major polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and an unidentified glycolipid. The major fatty acids (>10%) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The meso-diaminopimelic acid was found in the cell wall peptidoglycan of DK398T. The major cell wall sugars were ribose and galactose. Based on the results of phylogenetic analyses, low (<83.22 %) average nucleotide identity, digital DNA–DNA hybridization (<26.0%), chemotaxonomic analysis, and physiological properties, strain DK398T represents a novel species of the genus Paracoccus , for which the name Paracoccus shanxieyensis sp. nov. is proposed. The type strain is DK398T (=CGMCC 1.17227T=JCM 33719T).
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Tahibacter soli sp. nov., isolated from soil and Tahibacter amnicola sp. nov., isolated from freshwater
More LessTwo Gram-stain-negative, facultative aerobic, catalase- and oxidase-positive, and non-motile rod bacteria, strains BLT and W38T, that were isolated from soil and freshwater, respectively, were taxonomically characterized. Both strains optimally grew at 30 °C and pH 7.0 in Reasoner's 2A medium and contained ubiquinone-8 as the sole respiratory quinone. As major fatty acids (>10 %), strain BLT contained iso-C15 : 0 and summed features 3 and 9 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c/ω6c and iso-C17 : 1 ω9c and/or C16 : 0 10-methyl, respectively), whereas strain W38T contained iso-C15 : 0, iso-C16 : 0 and summed feature 9. Diphosphatidylglycerol and phosphatidylmonomethylethanolamine as major polar lipids and phosphatidylethanolamine and phosphatidylglycerol as minor polar lipids were detected in both strains. The DNA G+C contents of strains BLT and W38T were 68.3 and 65.3 %, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that strains BLT and W38T formed a tight phylogenetic lineage with Tahibacter species, and they shared 98.8 % 16S rRNA gene sequence similarity and 75.5 % average nucleotide identity (ANI) and 16.6 % digital DNA–DNA hybridization (dDDH) values, indicating that they are different species. Strains BLT and W38T were most closely related to Tahibacter caeni BUT-6T and Tahibacter aquaticus PYM5-11T with 97.7 and 98.0 % 16S rRNA gene sequence similarities, respectively. ANI and dDDH values between strain BLT and T. caeni BUT-6T and between strain W38T and T. aquaticus DSM 21667T were 78.5 and 21.6% and 75.3 and 21.0 %, respectively. Based on their phenotypic, chemotaxonomic and genomic properties, strains BLT and W38T represent two different novel species of the genus Tahibacter , for which the names Tahibacter soli sp. nov. and Tahibacter amnicola sp. nov. are proposed. The type strains of T. soli and T. amnicola are BLT (=KACC 22831T=JCM 35402T) and W38T (=KACC 22832T=JCM 35749T), respectively.
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Microbulbifer zhoushanensis sp. nov., Microbulbifer sediminum sp. nov. and Microbulbifer guangxiensis sp. nov., three marine bacteria isolated from a tidal flat
More LessThree strains, TT30T, TT37T and L3T, were isolated from tidal flat samples. Cells were Gram-stain-negative, non-motile and rod shaped. Cells of strains TT30T and TT37T were able to grow in a medium containing 1.0–15.0 % (w/v) NaCl (optimum, 3.0 and 4.0 %, respectively), and cells of strain L3T was able to grow in a medium containing 1.0–10.0 % (w/v) NaCl (optimum, 1.0 %). Growth of the three strains was observed at pH 6.0–10.0 and at 10–40 °C. Strains TT30T, TT37T and L3T showed the highest similarity to Microbulbifer hydrolyticus DSM 11525T (97.7 %), M . yueqingensis CGMCC 1.10658T (98.0 %) and M. elongatus DSM 6810T (97.9 %), respectively. Results of phylogenetic analyses indicated that the three isolates represented two distinct lineages within the genus Microbulbifer . The DNA G+C contents of strains TT30T, TT37T and L3T were 61.3, 60.9 and 60.2%, respectively. The average nucleotide identity and in silico DNA–DNA hybridization values among strains TT30T, TT37T and L3T and the reference strains were 84.4–87.4 and 19.6–28.9 %, respectively. Differential phenotypic properties, chemotaxonomic differences, phylogenetic distinctiveness, together with the genomic data, demonstrated that strains TT30T, TT37 T and L3T represent novel species of the genus Microbulbifer , which are named Microbulbifer zhoushanensis sp. nov. (TT30T=KCTC 92167T=MCCC 1K07276T), Microbulbifer sediminum sp. nov. (TT37T=KCTC 92168T=MCCC 1K07277T) and Microbulbifer guangxiensis sp. nov. (L3T=KCTC 92165T=MCCC 1K07278T).
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Novosphingobium album sp. nov., Novosphingobium organovorum sp. nov. and Novosphingobium mangrovi sp. nov. with the organophosphorus pesticides degrading ability isolated from mangrove sediments
Members of the genus Novosphingobium were frequently isolated from polluted environments and possess great bioremediation potential. Here, three species, designated B2637T, B2580T and B1949T, were isolated from mangrove sediments and might represent novel species in the genus Novosphingobium based on a polyphasic taxonomy study. Phylogenomic analysis revealed that strains B2580T, B1949T and B2637T clustered with Novosphingobium naphthalenivorans NBRC 102051T, ‘ N. profundi ’ F72 and N. decolorationis 502str22T, respectively. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between isolates and their closely related species were less than 94 and 54 %, respectively, all below the threshold of species discrimination. The sizes of the genomes of isolates B2580T, B2637T and B1949T ranged from 4.4 to 4.6 Mb, containing 63.3–66.4 % G+C content. Analysis of their genomic sequences identified genes related to pesticide degradation, heavy-metal resistance, nitrogen fixation, antibiotic resistance and sulphur metabolism, revealing the biotechnology potential of these isolates. Except for B2637T, B1949T and B2580T were able to grow in the presence of quinalphos. Results from these polyphasic taxonomic analyses support the affiliation of these strains to three novel species within the genus Novosphingobium , for which we propose the name Novosphingobium album sp. nov. B2580T (=KCTC 72967T=MCCC 1K04555T), Novosphingobium organovorum sp. nov. B1949T (=KCTC 92158T=MCCC 1K03763T) and Novosphingobium mangrovi sp. nov. B2637T (KCTC 72969T=MCCC 1K04460T).
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Sphingomicrobium sediminis sp. nov., isolated from marine sediment in the Republic of Korea
More LessA Gram-stain-negative, rod-shaped, bright-orange coloured bacterium without flagellum, designated as strain GRR-S6-50T, was isolated from a tidal flat of Garorim bay, Taean-gun, Chungcheongbuk-do, Republic of Korea. Cells grew aerobically at 20–37 °C (optimum, 30 °C), pH 7.0–10.0 (optimum, pH 7.0) and with 1–5 % (w/v) NaCl (optimum, 3 %). The 16S rRNA gene sequence analysis demonstrated that strain GRR-S6-50T was closely related to Sphingomicrobium aestuariivivum AH-M8T with a sequence similarity of 97.80 % followed by Sphingomicrobium astaxanthinifaciens CC-AMO-30BT (97.44 %), Sphingomicrobium marinum CC- AMZ-30MT (97.16 %), Sphingomicrobium arenosum CAU 1457T (96.37 %), Sphingomicrobium flavum CC-AMZ-30NT (95.31 %) and Sphingomicrobium lutaoense CC-TBT-3T (95.23 %). The average nucleotide identity and digital DNA–DNA hybridization values with related strains ranged from 74.5 to 77.3% and 21.1 to 35.0 %, respectively. The G+C content of strain GRR-S6-50T was 63.30 mol%. The strain has ubiquinone-10 as the predominant respiratory quinone and the major fatty acids were C18 : 3 ω6c (54.57 %) and C17 : 1 ω6c (10.58 %). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, three unidentified lipids and one glycolipid. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic studies, strain GRR-S6-50T is regarded to represent a novel species within the genus Sphingomicrobium , for which the name Sphingomicrobium sediminis sp. nov. (KACC 22562T=KCTC 92123T=JCM 35084T) is proposed.
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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 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)