- Volume 66, Issue 10, 2016
Volume 66, Issue 10, 2016
- Notification List
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- New taxa
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- Actinobacteria
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Geodermatophilus pulveris sp. nov., a gamma-radiation-resistant actinobacterium isolated from the Sahara desert
A black-pigmented, aerobic actinobacterium, tolerant to ionizing radiation, designated BMG 825T, was isolated from desert limestone dust in Tunisia. The strain grew within the temperature range 10–40 °C, at pH 5.5–11.0 and in the presence of 2 % NaCl. The DNA G+C content was 75.7 mol%, and its cell-wall peptidoglycan contained meso-diaminopimelic acid. Sugars of whole-cell hydrolysates were galactose, glucose, and trace amounts of ribose and mannose. The predominant menaquinone was MK-9(H4), and the major fatty acids were iso-C16 : 0 and C16 : 1 ω7c. The polar lipid profile comprised phosphatidylcholine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine and an unspecified glycolipid. 16S rRNA gene sequence analysis revealed that the strain fell into the genus Geodermatophilus , showing the highest similarity with Geodermatophilus poikilotrophus DSM 44209T (99.1 %). DNA–DNA hybridization results, phylogenetic distinctiveness and phenotypic properties supported the classification of this strain as a representative of a novel species of the genus Geodermatophilus , for which the name Geodermatophilus pulveris sp. nov. is proposed. The type strain is BMG 825T (=CECT 9003T=DSM 46839T).
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Nocardiopsis sediminis sp. nov., isolated from mangrove sediment
A filamentous actinomycete, designated strain 1SS5-02T, was isolated from mangrove sediment collected from Ranong province, Thailand. The strain formed aerial and substrate mycelia composed of long, branched hyphae. Aerial mycelia differentiated into non-motile, rod-shaped spores. The organism contained meso-diaminopimelic acid and no diagnostic sugars in whole-cell hydrolysates. The predominant menaquinones were MK-11(H4), MK-11(H6) and MK-11(H8). Polar lipids comprised phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids and four unidentified lipids. The major fatty acids were iso-C16 : 0, C18 : 1 ω9c, 10-methyl C18 : 0 and anteiso-C17 : 0. The G+C content of the genomic DNA was 73.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1SS5-02T belonged to the genus Nocardiopsis . The strain showed the highest degree of 16S rRNA gene sequence similarity with ‘ Nocardiopsis mangrovei ’ HA11166 (97.9 %) and Nocardiopsis trehalosi VKM Ac-942T (97.8 %). However, strain 1SS5-02T could be distinguished from its nearest phylogenetic relatives in the genus Nocardiopsis on the basis of DNA–DNA relatedness values and the combination of phenotypic properties. On the basis of polyphasic taxonomy, strain 1SS5-02T is considered to represent a novel species of the genus Nocardiopsis , for which the name Nocardiopsis sediminis sp. nov. is proposed. The type strain is 1SS5-02T (=BCC 75410T=NBRC 110934T).
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Nocardioides intraradicalis sp. nov., isolated from the roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu
A Gram-stain-positive, non-spore-forming and non-motile strain, designated YIM DR1091T, was isolated from the roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu collected from Gejiu, Yunnan, China. The taxonomic position of strain YIM DR1091T was investigated by a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YIM DR1091T is a member of the genus Nocardioides . Strain YIM DR1091T was closely related to Nocardioides pyridinolyticus OS4T, Nocardioides caricicola YC6903T, Nocardioides hankookensis DS-30T and Nocardioides aquiterrae GW-9T, with which it shared pairwise 16S rRNA gene sequence similarities of 97.6, 97.5, 97.2 and 97.2 %, respectively. Mean DNA–DNA relatedness values between strain YIM DR1091T and related type strains N. pyridinolyticus JCM 10369T, N. caricicola JCM 17686T, N. hankookensis JCM 15302T and N. aquiterrae JCM 11813T were 44.9±1.7, 50.2±1.3, 46.8±0.9 and 43.0±0.2 %, respectively. The respiratory menaquinone for strain YIM DR1091T was MK-8(H4) while the major fatty acids (>5 %) were iso-C16 : 0, C17 : 1 ω8c, C17 : 0, iso-C15 : 0 and iso-C14 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and three unidentified phospholipids. Whole-cell hydrolysates contained mannose, ribose, glucose and galactose, along with ll-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan. The DNA G+C content was 74.6 mol%. Phenotypic, phylogenetic and chemotaxonomic data indicated that strain YIM DR1091T represents a novel species of the genus Nocardioides , for which the name Nocardioides intraradicalis sp. nov. is proposed. The type strain is YIM DR1091T (=JCM 30632T=CGMCC4.7251T).
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Streptomyces camponoticapitis sp. nov., an actinomycete isolated from the head of an ant (Camponotus japonicus Mayr)
More LessA novel single-spore-producing actinomycete, designated strain 2H-TWYE14T, was isolated from the head of an ant (Camponotus japonicus Mayr) and characterized using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain 2H-TWYE14T belongs to the genus Streptomyces , with highest sequence similarity to Streptomyces niveus NRRL 2466T (98.84 %). Analysis based on the gyrB gene also indicated that strain 2H-TWYE14T should be assigned to the genus Streptomyces . The chemotaxonomic properties of strain 2H-TWYE14T were consistent with those of members of the genus Streptomyces . The cell wall contained ll-diaminopimelic acid. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were iso-C16 : 0 and iso-C15 : 0. DNA–DNA hybridization experiments and phenotypic tests were carried out between strain 2H-TWYE14T and its phylogenetically closely related strain S. niveus JCM 4251T, which further clarified their relatedness and demonstrated that 2H-TWYE14T could be distinguished from S. niveus. Therefore, it is concluded that strain 2H-TWYE14T can be classified as representing a novel species of the genus Streptomyces , for which the name Streptomyces camponoticapitis sp. nov. is proposed. The type strain is 2H-TWYE14T (=DSM 100523T=CGMCC 4.7275T).
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Amycolatopsis albispora sp. nov., isolated from deep-sea sediment
More LessA novel Gram-stain-positive, aerobic, non-motile actinobacterium, designated strain WP1T, was isolated from a deep-sea sediment sample collected from the Indian Ocean, and examined in a taxonomic study using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain WP1T formed a distinct phyletic lineage in the genus Amycolatopsis and was closely related to A. magusensis KT2025T (97.8 % 16S rRNA gene sequence similarity), A. palatopharyngis 1BDZT (97.3 %) and A. marina Ms392AT (97.2 %). The isolate grew at 4–45 °C, pH 5–11 and in the presence of 0–8 % (w/v) NaCl. The cell wall of the novel strain contained meso-diaminopimelic acid and arabinose and galactose as the diagnostic sugars. Major fatty acids identified were iso-C16 : 0, C17 : 1ω8c and C17 : 1ω6c. The predominant menaquinones were MK-9(H4) and MK-7. The polar lipids detected were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylmethylethanolamine, four unknown phospholipids and one unknown glycolipid. The genomic DNA G+C content was 72.2 mol%. Strain WP1T displayed low DNA–DNA reassociation with A. magusensis DSM 45510T (mean value 36.2 %), A. palatopharyngis JCM 12460T (31.5 %) and A. marina JCM 16121T (29.7 %). Based on the data reported here, strain WP1T represents a novel species within the genus Amycolatopsis , for which the name Amycolatopsis albisporasp. nov. is proposed. The type strain is WP1T (=KCTC 39642T=MCCC 1A10745T).
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Streptomyces phyllanthi sp. nov., isolated from the stem of Phyllanthus amarus
The novel endophytic actinomycete strain PA1-07T was isolated from the stem of Phyllanthus amarus. The strain displayed the consistent characteristics of members of the genus Streptomyces . The strain produced short spiral spore chains on aerial mycelia. It grew at pH 5–9, at 40 °C and with a maximum of 5 % (w/v) NaCl. It contained ll-diaminopimelic acid, glucose and ribose in the whole-cell hydrolysate. The major cellular menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8), while the major cellular fatty acids were C16 : 0, iso-C14 : 0, iso-C16 : 0 and anteiso-C15 : 0. The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and four unknown lipids. The DNA G+C content of the strain was 71 mol%. The strain showed the highest 16S rRNA gene sequence similarity with Streptomyces curacoi JCM 4219T (98.77 %). The DNA–DNA relatedness values between strain PA1-07T and S. curacoi JCM 4219T were lower than 70 %, the cut-off level for assigning strains to the same species. On the basis of these phenotypic and genotypic characteristics, the strain could be distinguished from closely related species of the genus Streptomyces and thus represents a novel species of the genus Streptomyces, for which the name Streptomyces phyllanthi sp. nov. is proposed. The type strain is PA1-07T (=JCM 30865T=KCTC 39785T=TISTR 2346T).
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Gordonia hongkongensis sp. nov., isolated from blood culture and peritoneal dialysis effluent of patients in Hong Kong
Two bacterial strains, HKU50T and HKU46, were isolated in Hong Kong from the blood culture and the peritoneal dialysis effluent of two patients. The strains are Gram-stain-positive, acid-fast, non-motile, non-sporulating bacilli. They grow on Columbia agar with 5 % defibrinated sheep blood and brain–heart infusion agar under aerobic conditions with 5 % CO2 at 37 °C as pink-to-orange, non-haemolytic colonies. The strains are catalase-positive and oxidase-negative, and have a unique biochemical profile distinguishable from other closely related species. DNA sequencing revealed that both isolates possessed multiple intra-genomic 16S rRNA gene copies (99.8–100 % sequence identities to Gordonia lacunae NRRL B-24551T and Gordonia terrae NRRL B-16283T). Phylogenetic analysis of the 16S rRNA gene, secA1 and gyrB showed that the two isolates formed a distinct branch within the genus Gordonia and were most closely related to G. lacunae and G. terrae . DNA–DNA hybridization demonstrated ≤53.7 % and ≤49.4 % DNA relatedness between the two isolates and G. lacunae , and between the two isolates and G. terrae , respectively. Hierarchical cluster analysis of MALDI–TOF MS main spectrum profiles showed that strains HKU50T and HKU46 were closely related to each other, but were distinct from G. lacunae , G. terrae , or any other species of the genus Gordonia in the Bruker database. The chemotaxonomic traits of the two strains were highly similar, and the major fatty acids were summed feature 4 (iso-C15 : 0 2-OH/C16 : 1 trans-9), C16 : 0, C18 : 1 cis-9, and tuberculostearic acid. A novel species named Gordonia hongkongensis sp. nov. is proposed to accommodate strains HKU50T and HKU46, with strain HKU50T (=CCOS 955T=CIP 111027T=NBRC 111234T=NCCP 16210T) as the type strain.
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Jatrophihabitans huperziae sp. nov., an endophytic actinobacterium isolated from surface-sterilized tissue of the medicinal plant Huperzia serrata (Thunb.)
More LessA novel endophytic actinobacterium, designated strain CPCC 204076T, was isolated from surface-sterilized tissue of the medicinal plant Huperzia serrata (Thunb.) collected from Sichuan Province, south-west China. The taxonomic position of the isolate was investigated by a polyphasic approach. The strainwas aerobic, Gram-stain-positive, non-motile, non-spore-forming and rod-shaped. Growth was observed at 10–37 °C, at pH 5.0–10.0 and with 0–3.0 % (w/v) NaCl. The polar lipid fraction consisted of diphosphatidylglycerol, a phospholipid, an aminolipid, a glycolipid, an aminophospholipid and phosphatidylinositol. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the peptidoglycan was of type A4γ. The menaquinone system consisted of MK-9(H4) and MK-8(H4). The major cellular fatty acids (>10 %) were iso-C16 : 0 and anteiso-C17 : 0. The genomic DNA G+C content of strain CPCC 204076T was found to be 71.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that CPCC 204076T belongs to the genus Jatrophihabitans with highest sequence similarity to Jatrophihabitans endophyticus DSM 45627T (96.5 %), Jatrophihabitans soli DSM 45908T (96.5 %) and Jatrophihabitans fulvus JCM 30448T (96.1 %), and much lower similarities (<95.0 %) to other available 16S rRNA gene sequences from validly described pure cultures. However, DNA–DNA hybridyzation values between strain CPCC 204076T and the three recognized Jatrophihabitans species were 31±3.1 % ( J. endophyticus DSM 45627T), 33±2.9 % ( J. soli DSM 45908T) and 37±1.7 % ( J. fulvus JCM 30448T), which were all far below the recommended cut-off value of 70 %. The phenotypic and genomic characteristics distinctly indicated that strain CPCC 204076T represents a novel species of the genus Jatrophihabitans , for which the name Jatrophihabitans huperziae sp. nov. is proposed. The type strain is CPCC 204076T (I13A-01604) (=DSM 46866T=NBRC 110718T).
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Streptomyces palmae sp. nov., isolated from oil palm (Elaeis guineensis) rhizosphere soil
More LessActinomycete strain CMU-AB204T was isolated from oil palm rhizosphere soil collected in Chiang Mai University (Chiang Mai, Thailand). Based on morphological and chemotaxonomic characteristics, the organism was considered to belong to the genus Streptomyces . Whole cell-wall hydrolysates consisted of ll-diaminopimelic acid, glucose, ribose and galactose. The predominant menaquinones were MK-9(H4), MK-9(H6), MK-9(H2) and MK-8(H4). The fatty acid profile contained iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0 as major components. The principal phospholipids detected were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content of strain CMU-AB204T was 70.9 mol%. Based on 16S rRNA gene sequence similarity, strain CMU-AB204T was closely related to Streptomyces orinoci JCM 4546T (98.7 %), Streptomyces lilacinus NBRC 12884T (98.5 %), Streptomyces abikoensis CGMCC 4.1662T (98.5 %), Streptomyces griseocarneus JCM 4905T (98.4 %) and Streptomyces xinghaiensis JCM 16958T (98.3 %). Phylogenetic trees revealed that the new strain had a distinct taxonomic position from closely related type strains of the genus Streptomyces . Spiny to hairy spores clearly differentiated strain CMU-AB204T from the five most closely related Streptomyces species, which produced smooth spores. On the basis of evidence from this polyphasic study, it is proposed that strain CMU-AB204T represents a novel species of the genus Streptomyces , namely Streptomyces palmae sp. nov. The type strain is CMU-AB204T (=JCM 31289T=TBRC 1999T).
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Clavibacter michiganensis subsp. capsici subsp. nov., causing bacterial canker disease in pepper
Clavibacter michiganensis is a Gram-stain-positive bacterium with eight subspecies. One of these subspecies is C. michiganensis subsp. michiganensis , which causes bacterial canker disease in tomato. Bacterial strains showing very similar canker disease symptoms to those of a strain originally classified as C. michiganensis have been isolated from pepper. In this paper, we reclassified strains isolated from pepper. On the basis of phylogenetic analysis with 16S rRNA gene sequences, the strains isolated from pepper were grouped in a separate clade from other subspecies of C. michiganensis . Biochemical, physiological and genetic characteristics of strain PF008T, which is the representative strain of the isolates from pepper, were examined in this study. Based on multi-locus sequence typing and other biochemical and physiological features including colony color, utilization of carbon sources and enzyme activities, strain PF008T was categorically differentiated from eight subspecies of C. michiganensis . Moreover, genome analysis showed that the DNA G+C content of strain PF008T is 73.2 %. These results indicate that PF008T is distinct from other known subspecies of C. michiganensis . Therefore, we propose a novel subspecies, C. michiganensis subsp. capsici , causing bacterial canker disease in pepper, with a type strain of PF008T (=KACC 18448T=LMG 29047T).
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Lipingzhangella halophila gen. nov., sp. nov., a new member of the family Nocardiopsaceae
An alkaliphilic and halophilic actinomycete strain, designated EGI 80537T, was isolated from a saline-alkali soil sample of Xinjiang, north-west China and subjected to a taxonomic characterization using a polyphasic approach. Strain EGI 80537T formed reticulate long aerial hyphae. Whole-cell hydrolysates of the isolate contained meso-diaminopimelic acid as the cell-wall diamino acid and mannose as the diagnostic sugar. The major fatty acids identified were iso-C16 : 0, anteiso-C17 : 0 and 10-methyl-C18 : 0 (TBSA). The predominant menaquinones detected were MK-10(H8) and MK-10(H6). The G+C content of the genomic DNA of strain EGI 80537T was 67.6 mol%. Strain EGI 80537T showed the highest 16S rRNA gene sequence similarity to Allosalinactinospora lopnorensis CA15-2T (96.7 %). Phylogenetic analysis showed that strain EGI 80537T clustered with the members of the family Nocardiopsaceae . Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain EGI 80537T represents a novel species of a new genus in the family Nocardiopsaceae, for which the name Lipingzhangella halophila gen. nov., sp. nov. is proposed. The type strain of the type species is EGI 80537T(=CGMCC 4.7224T= DSM 102030T).
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Herbihabitans rhizosphaerae gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from rhizosphere soil of the herb Limonium sinense (Girard)
The taxonomic position of an actinobacterium, designated CPCC 204279T, which was isolated from a rhizosphere soil sample of the herb Limonium sinense collected from Xinjiang Province, China, was established using a polyphasic approach. Whole-cell hydrolysates of strain CPCC 204279T contained galactose and arabinose as diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The muramic acid residues in the peptidoglycan were N-acetylated. The predominant menaquinone was MK-9(H4). The phospholipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were iso-C16 : 0, iso-C16 : 0 2-OH, C16 : 1ω9c, iso-C16 : 1 and C16 : 0. The genomic DNA G+C content was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204279T should be placed in the family Pseudonocardiaceae , in which the strain formed a distinct lineage next to the genus Actinophytocola . Signature nucleotides in the 16S rRNA gene sequence showed that the strain contained the Pseudonocardiaceae family-specific 16S rRNA signature nucleotides and a genus-specific diagnostic nucleotide signature pattern. The combination of phylogenetic analysis and phenotypic characteristics supported the conclusion that strain CPCC 204279T represents a novel species of a new genus in the family Pseudonocardiaceae , for which the name Herbihabitans rhizosphaerae gen. nov., sp. nov. is proposed. Strain CPCC 204279T (=NBRC 111774T=DSM 101727T) is the type strain of the type species.
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Yimella radicis sp. nov., an endophytic actinobacterium isolated from the root of Paris polyphylla Smith var. yunnanensis
More LessAn endophytic actinobacterial strain, designated py1292T, was isolated from the root of Paris polyphylla Smith var. yunnanensis collected from Yunnan province, China, and subjected to a polyphasic taxonomic characterization. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolate in the family Dermacoccaceae and clustered with Yimella lutea (showing the highest similarity of 99.1 %). DNA–DNA relatedness between strain py1292T and Y. lutea YIM 45900T was 45.6±3.2 % (reciprocal 47.8±3.6 %). The novel isolate was found to be a Gram-staining-positive rod, catalase- and oxidase-positive. It grew at pH 6.0–8.0, with 0–9 % NaCl and at 20–45 ºC, optimally at pH 7.0, with 0–3 % NaCl and at 28 ºC. The predominant menaquinone was MK-8(H4), while the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, two unknown phospholipids and two unknown polar lipids. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0. The whole-cell hydrolysates contained mannose, ribose, rhamnose, glucose and galactose. The peptidoglycan contained alanine, glycine, serine, aspartic acid, glutamic acid and lysine. The genomic DNA G+C content was determined to be 65.6 mol%. Phylogenetic, phenotypic and chemotaxonomic data (especially the same peptidoglycan type) showed that strain py1292T should be classified as a representative of a novel species of the genus Yimella , for which the name Yimella radicis sp. nov. is proposed. The type strain is py1292T (=KCTC 39612T=LMG 29070T).
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Demequina litorisediminis sp. nov., isolated from a tidal flat, and emended description of the genus Demequina
More LessA Gram-stain-positive, facultatively anaerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, GHD-1T, was isolated from a tidal flat sediment on the Yellow Sea, South Korea. It grew optimally at 30 °C, at pH 6.5–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain GHD-1T fell within the cluster comprising the type strains of species of the genus Demequina . Strain GHD-1T exhibited 16S rRNA gene sequence similarity values of 97.0–98.8 % to the type strains of Demequina globuliformis , D. salsinemoris , D. flava , D. sediminicola and D. activiva , and of 95.5–96.9 % to the type strains of the other species of the genus Demequina . The peptidoglycan type of strain GHD-1T is A4β based on l-Orn−l-Ser−l-Asp. It contained DMK-9(H4) and DMK-8(H4) as the major menaquinones and anteiso-C15 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0 as the major fatty acids. The major polar lipids were phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified glycolipid. The DNA G+C content of strain GHD-1T was 68.7 mol%, and its DNA–DNA relatedness values with the type strains of five phylogenetically related species of the genus Demequina were 13–29 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain GHD-1T is separated from other recognized species of the genus Demequina . On the basis of the data presented, strain GHD-1T is considered to represent a novel species of the genus Demequina , for which the name Demequina litorisediminis sp. nov. is proposed. The type strain is GHD-1T (=KCTC 52260T=NBRC 112299T).
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Streptomyces pini sp. nov., an actinomycete isolated from phylloplane of pine (Pinus sylvestris L.) needle-like leaves
A novel siderophore-producing actinomycete, designated PL19T, was isolated from the Scots-pine needle-like leaves collected from TNAU campus, Coimbatore, India. The isolate was chemoorganotrophic in nutrition and able to grow at 30 °C, and the optimum pH and NaCl facilitated the growth pH 6–11 and 0–8 % (w/v), respectively. The cells are filamentous and the mycelia formed are basically of wide and intricately branched substrate mycelium from which aerial mycelia arises, later gets differentiated into spores that are warty and arranged spirally. The 16S rRNA gene of strain PL19T was sequenced and was highly similar to the type strains of species of the genus Streptomyces , including Streptomyces barkulensis RC1831T (98.8 % pairwise similarity), Streptomyces fenghuangensis GIMN4.003T (98.2 %), Streptomyces nanhaiensis SCSIO 01248T (98.0 %), Streptomyces radiopugnans R97T (97.9 %), Streptomyces atacamensis C60T (97.8 %) and Streptomyces macrosporus NBRC 14749T (97.2 %), all of which were subjected to taxonomical characterization using a polyphasic approach. The strains showed unique carbon utilization patterns, and it possesses iso-C16 : 0 anteiso-C15 : 0 and anteiso-C17 : 0 as a major cellular fatty acids. The cell-wall was dominated with ll-type diaminopimelic acid, and the menaquinone type was MK-9(H6, H8). These chemotaxonomic evidences placed strain PL19T within the genus Streptomyces . The determination of G+C ratio (69.5 mol%) and DNA–DNA hybridization values (13.4–31.8 % with the phylogenetically related species) helped in further hierarchical classification of strain PL19T. Based on morphological, physiological and chemotaxonomic data as well as DNA–DNA hybridization values, strain PL19T could be distinguished from the evolutionarily closest species currently available. All these collective data show that strain PL19T represents a novel species of the genus Streptomyces, for which the name Streptomyces pini sp. nov. is proposed. The type strain is PL19T (=NRRL B-24728T=ICMP 17783T).
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Nocardioides baekrokdamisoli sp. nov., isolated from soil of a crater lake
A novel actinobacterial strain, B2-12T, was isolated from soil of a crater lake, Baekrokdam, Hallasan, Jeju, Republic of Korea. Cells of strain B2-12T were Gram-stain-positive, non-motile, non-spore-forming and coccoid to short-rod-shaped. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that strain B2-12T belonged to the genus Nocardioides and shared highest sequence similarity with ‘Nocardioidespaucivorans’ KIS31-44 (98.4 %). The predominant isoprenoid quinone was MK-8(H4). The major fatty acids of strain B2-12T were C16 : 1 (ω7c and/or ω6c), summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl), C17 : 0 10-methyl, iso-C16 : 0, C16 : 0 and C17 : 1 ω6c. The diagnostic diamino acid in the cell-wall peptidoglycan was ll-diaminopimelic acid. It contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the polar lipids. The DNA G+C content was 67.0 mol%. Based on phylogenetic, chemotaxonomic and phenotypic data, 16S rRNA gene sequence comparisons and DNA–DNA hybridization data, strain B2-12T represents a novel species in the genus Nocardioides , for which the name Nocardioidesbaekrokdamisolisp. nov. is proposed. The type strain is B2-12T (=KCTC 39748T=NRRL B-65313T=DSM 100725T).
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- Archaea
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Halobium palmae gen. nov., sp. nov., an extremely halophilic archaeon isolated from a solar saltern
More LessA novel and extremely halophilic archaeon, designated strain 2a_47_2T, was isolated from a solar saltern sample collected in Indonesia. Cells of the strain were Gram-stain-negative, non-motile and pleomorphic and formed orange–red pigmented colonies. Strain 2a_47_2T grew at 20–48 °C (optimum 38–41 °C), pH 6.0–8.5 (optimum pH 7.5), >1.7 M NaCl (optimum 2.6 M) and <0.5 M MgCl2 (optimum 0.3 M). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two phospholipids and sulfated diglycosyl diether. The cells mainly contained menaquinone-8. The G+C content in the genomic DNA of the strain was 67.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 2a_47_2T represents a member of the family Halorubraceae and is different from any other known halophilic archaea. This finding was also demonstrated by phylogenetic analyses based on deduced RpoB′ amino acid sequences. Collectively, these results show that strain 2a_47_2T represents a novel genus and species in the family Halorubraceae , and the name Halobium palmae gen. nov., sp. nov. is proposed. The type strain is 2a_47_2T (=NBRC 111368T=InaCC Ar34T).
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- Bacteroidetes
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Porphyromonas loveana sp. nov., isolated from the oral cavity of Australian marsupials
An obligatory anaerobic, Gram-stain-negative coccobacillus with black-pigmented colonies was isolated from the oral cavity of selected Australian marsupial species. Phenotypic and molecular criteria showed that this bacterium was a distinct species within the genus Porphyromonas , and was closely related to Porphyromonas gingivalis and Porphyromonas gulae . This putative novel species and P. gulae could be differentiated from P. gingivalis by catalase activity. Further characterization by multi-locus enzyme electrophoresis of glutamate dehydrogenase and malate dehydrogenase enzyme mobility and matrix-assisted laser desorption ionization time-of-flight MS showed that this putative novel species could be differentiated phenotypically from P. gingivalis and P. gulae . Definitive identification by 16S rRNA gene sequencing showed that this bacterium belonged to a unique monophyletic lineage, phylogenetically distinct from P. gingivalis (94.9 % similarity) and P. gulae (95.5 %). This also was supported by 16S–23S rRNA intergenic spacer region and glutamate dehydrogenase gene sequencing. A new species epithet, Porphyromonas loveana sp. nov., is proposed for this bacterium, with DSM 28520T (=NCTC 13658T=UQD444T=MRK101T), isolated from a musky rat kangaroo, as the type strain.
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Hymenobacter glacieicola sp. nov., isolated from glacier ice
A Gram-stain-negative, rod-shaped, non-motile and red–pink-pigmented bacterial strain, designated B1909T, was isolated from an ice core drilled from Muztagh Glacier on the Tibetan Plateau, China. A phylogenetic tree based on 16S rRNA gene sequences showed that strain B1909T formed a lineage within the genus Hymenobacter and was closely related to Hymenobacter xinjiangensis X2-1gT (96.16 % similarity) and Hymenobacter psychrotolerans Tibet-IIU11T (95.99 %). The predominant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 4 (iso-C17 : 1 ω6c I/anteiso B), C16 : 1 ω5c, anteiso-C15 : 0 and iso-C17 : 0 3-OH. The major menaquinone was MK-7. The major polar lipid was phosphatidylethanolamine. The DNA G+C content was 59 mol%. On the basis of the phenotypic, phylogenetic and chemotaxonomic data presented, strain B1909T is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter glacieicola sp. nov. is proposed; the type strain is B1909T (=JCM 30596T=CGMCC 1.12990T).
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Lewinella aquimaris sp. nov., isolated from seawater
More LessA Gram-staining-negative, oval- or rod-shaped, non-motile bacterial strain, designated HDW-36T, was isolated from seawater off the Korean peninsula. Strain HDW-36T was found to grow optimally at pH 7.0–8.0, at 25 °C and in the presence of 2–3 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain HDW-36T falls within the clade comprising thespecies of the genus Lewinella , clustering with the type strains of Lewinella xylanilytica and Lewinella marina , with which it exhibited 95.9 % and 95.2 % sequence similarity values, respectively. The 16S rRNA gene sequence similarity values between strain HDW-36T and type strains of other species of the genus Lewinella were 88.4–92.8 %. Strain HDW-36T was found to contain MK-7 as the predominant menaquinone and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), iso-C15 : 0 and C16 : 0 as the major fatty acids. The major polar lipids were identified as phosphatidylethanolamine and an unidentified lipid. The DNA G+C content of strain HDW-36T was determined to be 60.9 mol%. Differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrate that strain HDW-36T is distinguishable from other species of the genus Lewinella . On the basis of the data presented, strain HDW-36T is considered to represent a novel species, for which the name Lewinella aquimaris sp. nov. is proposed. The type strain of Lewinella aquimaris is HDW-36T (=KCTC 42719T=CECT 8901T).
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Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root
A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain, designated 65T, was isolated from surface-sterilized root tissue of maize, collected from Fangshan District of Beijing, People’s Republic of China, and was subjected to a taxonomic study by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 65T belonged to the genus Dyadobacter and had highest 16S rRNA gene sequence similarity to Dyadobacter jiangsuensis CGMCC 1.12969T (99.1 %), Dyadobacter beijingensis CGMCC 1.6375T (98.8 %), Dyadobacter fermentans DSM 18053T (98.6 %) and Dyadobacter soli KCTC 22481T (98.6 %). However, the new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to D. jiangsuensis CGMCC 1.12969T (18.2±1.3 %), D. beijingensis CGMCC 1.6375T (14.2±2.0 %), D. fermentans DSM 18053T (14.1±2.0 %) and D. soli KCTC 22481T (13.8±0.6 %). The predominant respiratory quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1 ω5c, iso-C15 : 0 3-OH, C16 : 0 3-OH and C16 : 0. The polar lipid profile of strain 65T revealed the presence of phosphatidylethanolamine, four aminolipids and two unidentified phospholipids. The DNA G+C content was 46.6 mol%. The results of physiological and biochemical tests and the differences in the fatty acid profiles allowed the clear phenotypic differentiation of strain 65T from closely related species of the genus Dyadobacter . Strain 65T thus represents a novel species within the genus Dyadobacter , for which the name Dyadobacter endophyticus sp. nov. is proposed. The type strain is 65T (=CGMCC 1.15288T=DSM 100786T).
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Filimonas aurantiibacter sp. nov., an orange-pigmented bacterium isolated from lake water and emended description of the genus Filimonas
A Gram-stain-negative bacterium was isolated from Lake Michigan water. 16S rRNA gene sequence analysis revealed that strain 1458T had a sequence similarity to Filimonas lacunae YT21T, Sediminibacterium goheungense HME7863T, Parasegetibacter terrae SGM2-10T, Sediminibacterium ginsengisoli DCY13T, Terrimonas ferruginea DSM 30193T, Lacibacter cauensis NJ-8T, Flavihumibacter solisilvae 3-3T, Parasegetibacter luojieneis RHYL-37T, Vibrionimonas magnilacihabitans MU-2T and Parafilimonas terrae 5GHs7-2T with values of 93.4, 92.3, 91.9, 91.9, 91.8, 91.6, 91.6, 91.6, 91.5 and 90.4 %, respectively. The primary cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1G and summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c). The primary polar lipids were phosphatidylethanolamine and an unidentified polar lipid only detectable after total polar lipid staining. The quinone system was menaquinone MK-7, and in the polyamine pattern, sym-homospermidine was predominant. Additional phenotypic characteristics included growth at 15 to 40 °C and pH 5.0 to 8.0, a salt tolerance range of 0 to 2.0 % (w/v), production of orange cell-bound pigment flexirubin, and gliding motility. After phenotypic, chemotaxonomic and molecular analyses, strain 1458T was identified as a novel species of the genus Filimonas, for which the name Filimonas aurantiibacter sp. nov. is proposed. The type strain is 1458T (=NRRL B-65305T=LMG 29039T). An emended description of the genus Filimonas is also provided.
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Mucilaginibacter pedocola sp. nov., isolated from a heavy-metal-contaminated paddy field
More LessStrain TBZ30T was isolated from soil of a heavy-metal-contaminated paddy field. Cells of strain TBZ30T were Gram-staining-negative, rod-shaped, non-motile and non-spore-forming. The isolate was strictly aerobic, pink-pigmented, catalase- and oxidase-positive and produced exopolysaccharides. On the basis of 16S rRNA gene phylogeny, strain TBZ30T belonged to the genus Mucilaginibacter and appeared most closely related to Mucilaginibacter gynuensis YC7003T (95.8 %), Mucilaginibacter litoreus BR-18T (95.4 %) and Mucilaginibacter mallensis MP1X4T (95.4 %). Strain TBZ30T contained menaquinone-7 as the only ubiquinone. The main cellular fatty acids included summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH and C16 : 1 ω5c. The polar lipids were phosphatidylethanolamine, an unidentified phospholipid, two unidentified aminophospholipids, four unidentified aminolipids, three unidentified lipids and two unidentified glycolipids. The genomic DNA G+C content was 49.0 mol%. On the basis of polyphasic taxonomy analyses, strain TBZ30T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter pedocola sp. nov. is proposed. The type strain is TBZ30T (=KCTC 42833T=CCTCC AB 2015301T).
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Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field
More LessA ginsenoside-transforming bacterium, designated Gsoil 1550T, was isolated from soil of a ginseng field and subjected to a polyphasic taxonomic analysis. Colonies of strain Gsoil 1550T were yellow, of low convexity and with regular margin. Cells were long rods, 0.5–1.2 µm wide and 1.6–3 µm long. The isolate grew at 10–37 °C and at pH 5–9 on R2A agar medium; maximum growth occurred at 30 °C and pH 6–7. Phylogenetic study based on the 16S rRNA gene sequence positioned Gsoil 1550T in a distinct lineage in the family Chitinophagaceae , sharing 92.5–92.8 % sequence similarity with members of the closely related genera Terrimonas , Parafilimonas , Sediminibacterium and Parasegetibacter . Strain Gsoil 1550T contained menaquinone MK-7 as the predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and iso-C15 : 1 G as major fatty acids. The DNA G+C content was 44.6 mol%. Strain Gsoil 1550T could be distinguished from other members of the family Chitinophagaceae by a number of chemotaxonomic and phenotypic characteristics. The major polar lipid of strain Gsoil 1550T was phosphatidylethanolamine. Based on this polyphasic taxonomic analysis, strain Gsoil 1150T represents a novel species within a new genus, for which the name Panacibacter ginsenosidivorans gen. nov., sp. nov. is proposed. The type strain of Panacibacter ginsenosidivorans is Gsoil 1550T (=KCTC 12658T=JCM 31452T).
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Chryseobacterium montanum sp. nov. isolated from mountain soil
More LessA Gram-staining-negative, strictly aerobic, non-spore-forming, rod-shaped bacterium, designated WG4T, was isolated from soil of the Tianmen Mountain located in Hunan province, PR China. 16S rRNA gene sequence analysis showed that the strain belongs to the genus Chryseobacterium in the family Flavobacteriaceae , with 97.4 % and 97.1 % sequence identities to Chryseobacterium anthropi NF 1366T and Chryseobacterium haifense H38T, respectively. In comparison with the other strains representing the genus Chryseobacterium , the 16S rRNA gene sequence identities were less than 97.0 %. The DNA–DNA relatedness values were 63.3 % (±1) between C. anthropi NF 1366T and strain WG4T and 62.7 % (±2) between C. haifense DSM 19056T and strain WG4T. The DNA G+C content of strain WG4T was 37.7 mol%. The predominant fatty acids of strain WG4T were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, three unidentified lipids and two unidentified aminolipids. The major menaquinone of strain WG4T was menaquinone 6. Strain WG4T showed some unique physiological and biochemical characteristics, such as being negative for gelatin hydrolysis, and valine arylamidase and α-glucosidase activity, and positive for acid production from cellobiose. Based on the differentiating phylogenetic inference and biochemical data, strain WG4T represents a novel species, for which the name Chryseobacterium montanum sp. nov. is proposed, with the type strain WG4T (=KCTC 52204T=CCTCC AB 2016058T).
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Proposal of Mucilaginibacter phyllosphaerae sp. nov. isolated from the phyllosphere of Galium album
A pink-pigmented, Gram-stain-negative, rod-shaped, non-spore-forming bacterial strain, PP-F2F-G21T, was isolated from the phyllosphere of Galium album. Phylogenetic analysis of the nearly full-length 16S rRNA gene sequence of strain PP-F2F-G21T showed the closest relationship to type strains of the species Mucilaginibacter lutimaris (97.7 %), Mucilaginibacter soli (97.3 %) and Mucilaginibacter rigui (97.1 %). Sequence similarities to all other type strains were below 97 %. The predominant cellular fatty acids of strain PP-F2F-G21T are C16 : 1 ω7c/iso-C15 : 0 2-OH (measured as summed feature 3 fatty acids) and iso-C15 : 0 followed by iso-C17 : 0 3-OH, C16 : 1 ω5c and C16 : 0. The major compound in the polyamine pattern was sym-homospermidine and the diamino acid of the peptidoglycan was meso-diaminopimelic acid. The quinone system was exclusively composed of menaquinone MK-7. The polar lipid profile contained the major lipid phosphatidylethanolamine and in addition 18 unidentified lipids. Based on phylogenetic, chemotaxonomic and phenotypic analyses, we propose a novel species of the genus Mucilaginibacter named Mucilaginibacter phyllosphaerae sp. nov. The type strain is PP-F2F-G21T (=CCM 8625T=CIP 110921T=LMG 29118T).
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Pseudoflavitalea rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere of tomato, and proposal to reclassify Flavitalea soli as Pseudoflavitalea soli comb. nov.
A bacterial strain, designated T16R-265T, was isolated from rhizosphere of tomato in Buyeo-gun, Chungcheongnam-do, South Korea. The strain was Gram-stain-negative, aerobic, non-flagellated and rod- or long-rod-shaped. It grew at the range of 10–40 °C (optimum 28–30 °C), pH 6.0–9.0 (optimum pH 7.0) and with 0–3 % (w/v) NaCl (optimum 0 %). 16S rRNA gene sequence analysis showed that strain T16R-265T had the highest sequence similarity (98.0 %) with Flavitalea soli KIS20-3T and low sequence similarities of below 95 % with all other taxa. The phylogenetic tree revealed that the strain formed a robust monophyletic line with Flavitalea soli KIS20-3T separable from other clades. The predominant quinone of strain T16R-265T was MK-7, the polar lipids consisted of large amounts of phosphatidylethanolamine and an unknown lipid, and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. DNA–DNA hybridization values with Flavitalea soli KACC 17319T were below 70 %. The DNA G+C content of strain T16R-265T is 46.2 mol%. Based on phylogenetic evidence and the results of phenotypic, genotypic and chemotaxonomic analyses, strain T16R-265T represents a novel species of a new genus, for which the name Pseudoflavitalea rhizosphaerae gen. nov., sp. nov. is proposed. The type strain of the type species is T16R-265T (=KACC 18655T=NBRC 111880T). We also propose the reclassification of Flavitalea soli as Pseudoflavitalea soli comb. nov. (type strain KIS20-3T=KACC 17319T=JCM 19937T).
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Pontibacter litorisediminis sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, aerobic, non-flagellated, motile by gliding and ovoid or rod-shaped bacterial strain, designated YKTF-7T, was isolated from a tidal flat sediment on the Yellow Sea, South Korea. Strain YKTF-7T grew optimally at pH 7.0–8.0, at 30–37 °C and in the presence of 0.5–2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain YKTF-7T fell within the clade comprising the type strains of species of the genus Pontibacter , clustering with the type strains of Pontibacter odishensis and Pontibacter korlensis with which it exhibited 98.0–98.7 % sequence similarity. Strain YKTF-7T exhibited 16S rRNA gene sequence similarities of 94.7–96.8 % to the type strains of the other species of the genus Pontibacter and of less than 91.7 % to those of other recognized species. Strain YKTF-7T contained MK-7 as the predominant menaquinone and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) and iso-C15 : 0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain YKTF-7T was 54.0 mol%, and its mean DNA–DNA relatedness values with the type strains of P . odishensis and P . korlensis were 25 and 14 %, respectively. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain YKTF-7T is separated from recognized species of the genus Pontibacter . On the basis of the data presented, strain YKTF-7T is considered to represent a novel species of the genus Pontibacter , for which the name Pontibacter litorisediminis sp. nov. is proposed. The type strain is YKTF-7T(=KCTC 52252T=NBRC 112298T).
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Maribacter litorisediminis sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, aerobic, non-spore-forming, non-flagellated, non-gliding and rod-shaped bacterial strain, HPTF-2T, was isolated from a tidal flat in the Yellow Sea in South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain HPTF-2T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain HPTF-2T fell within the clade comprising the type strains of species of the genus Maribacter . Strain HPTF-2T exhibited 16S rRNA gene sequence similarity values of 97.1–98.0 % to the type strains of Maribacter stanieri , M. orientalis, M. arcticus, M. dokdonensis , M. confluentis, M. aquivivus, M. sedimenticola and M. caenipelagi , and of 95.1–96.7 % to the type strains of the other species of the genus Maribacter . Strain HPTF-2T contained MK-6 as the predominant menaquinone and iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 1 G as the major fatty acids. The major polar lipids of strain HPTF-2T were phosphatidylethanolamine and two unidentified lipids. Mean DNA–DNA relatedness values of strain HPTF-2T with the type strains of the nine phylogenetically related species of the genus Maribacter were 10–26 %. The DNA G+C content of strain HPTF-2T was 38.4 mol%. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain HPTF-2T is separated from other species of the genus Maribacter . On the basis of the data presented, strain HPTF-2T represents a novel species of the genus Maribacter , for which the name Maribacter litorisediminis sp. nov. is proposed. The type strain is HPTF-2T (=KCTC 52251T=NBRC 112297T).
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Description of Ancylomarina subtilis gen. nov., sp. nov., isolated from coastal sediment, proposal of Marinilabiliales ord. nov. and transfer of Marinilabiliaceae, Prolixibacteraceae and Marinifilaceae to the order Marinilabiliales
More LessA Gram-stain-negative, facultatively anaerobic, moderately halophilic, filamentous, non-motile bacterium, designated FA102T, was isolated from marine sediment from the coast of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FA102T formed a distinct evolutionary lineage within the family Marinifilaceae and its closest relative was Marinifilum fragile JCM 15579T (93.2 % sequence similarity). The DNA G+C content of the novel strain was 36.5 mol%. The predominant cellular fatty acids and respiratory quinone were iso-C15 : 0 and iso-C15 : 0 3-OH, and MK-7, respectively. On the basis of the phylogenetic, phenotypic and physiological data, strain FA102T represents a novel genus and species, for which the name Ancylomarina subtilis gen. nov., sp. nov. is proposed. The type strain of Ancylomarina subtilis is FA102T (=KCTC 42257T=DSM 28825T=CICC 10902T). Furthermore, a new order named Marinilabiliales is proposed to accommodate three families previously classified in the order Bacteroidales . Marinilabiliales ord. nov. encompasses the families Marinilabiliaceae , Prolixibacteraceae and Marinifilaceae.
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Flavobacterium terriphilum sp. nov., isolated from soil
A novel aerobic, yellow-pigmented, Gram-stain-negative, rod-shaped bacterial strain, CUG00004T, was isolated from a soil sample. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CUG00004T was a member of the genus Flavobacterium and showed high sequence similarity with Flavobacterium soli DSM 19725T (96.9 %) and Flavobacterium glaciei CGMCC 0499T (95.6 %). The level of DNA–DNA relatedness between strain CUG00004T and F . soli DSM 19725T and F . glaciei CGMCC 1.5380T was 42.5 and 43.4 %, respectively. Strain CUG00004T was moderately alkaliphilic and grew optimally at pH 8.0, at 28 °C and in the presence of 0–1 % (w/v) NaCl. This organism contained menaquinone-6 (MK-6) as the only isoprenoid quinone and iso-C15 : 0, iso-C17 : 0 3-OH, anteiso-C15 : 0 and summed feature 9 (comprising iso-C17 : 1 ω9c and/or C16 : 0 10-methyl) as the major fatty acids. The DNA G+C content of strain CUG00004T was 36.3 mol%. On the basis of phylogenetic, physiological and chemotaxonomic analyses, strain CUG00004T represents a novel species, for which the name Flavobacterium terriphilum sp. nov. is proposed. The type strain is CUG00004T (=CCTCC AB 2014151T=KCTC 42876T).
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- Firmicutes and related organisms
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Enterococcus saigonensis sp. nov., isolated from retail chicken meat and liver
Two Gram-stain-positive strains, VE80T and VE116, which were resistant to vancomycin, were isolated from retail chicken meat and liver in Ho Chi Minh, Vietnam, respectively. These strains were characterized by sequence analyses of 16S rRNA, RNA polymerase α-subunit (rpoA), ATP synthase α-subunit (atpA), and phenylalanyl-tRNA synthase α-subunit (pheS) genes, determination of DNA G+C content, cellular fatty acid methyl ester analysis, DNA–DNA hybridization, and conventional morphological and biochemical tests. Strains VE80T and VE116 had 99.6 % 16S rRNA gene sequence similarity with Enterococcus canintestini LMG 13590T, and 99.1 % 16S rRNA gene sequence similarity with Enterococcus dispar ATCC 51266T. However, the two isolates could be clearly differentiated from these reference strains by the low sequence similarities (86.1–86.8 %) of the atpA gene, low DNA–DNA relatedness (<22.8 %), and differences in the production of acid from melezitose and methyl α-d-glucoside. Based on the results obtained in the present study, these two isolates are considered to represent a novel species of the genus Enterococcus , for which the name Enterococcus saigonensis sp. nov., is proposed. The type strain is VE80T (=JCM 31193T=CCUG 68827T).
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Lactococcus garvieae subsp. bovis subsp. nov., lactic acid bacteria isolated from wild gaur (Bos gaurus) dung, and description of Lactococcus garvieae subsp. garvieae subsp. nov.
More LessA taxonomic investigation was performed on a Gram-stain-positive coccus, designated strain BSN307T, isolated from gaur (Indian bison, Bos gaurus) dung based on phenotypic and molecular approaches. Based on the biochemical tests, cellular morphology and 16S rRNA gene sequence similarity, this strain was found to be a member of the genus Lactococcus and closely related to Lactococcus garvieae ATCC 49156T (99.6 % 16S rRNA gene sequence similarity) and L.actococcus formosensis 516T (99.0 %). However, DNA–DNA hybridization studies showed that the level of relatedness between strain BSN307T and L. garvieae ATCC 49156T was 75.8 %, suggesting that it represented a novel subspecies of L. garvieae . The inability to grow in brain heart infusion (BHI) medium at pH 9.6, in tryptic soy agar (TSA) with 4 % (w/v) NaCl and at 42 °C (MRS agar) clearly differentiated BSN307T from L. garvieae ATCC 49156T. Rep-PCR fingerprint patterns, substantial differences in summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C19 : 0 cyclo ω8c and C16 : 0 also differentiated strain BSN307T from the reference strain of L. garvieae. Moreover, analysis of the housekeeping genes pheS and rpoA revealed sequence similarities that were at the limit for species differentiation (92.2 and 97.8 %, respectively). Combined genotypic and phenotypic data indicate that strain BSN307T represents a subspecies of L. garvieae for which the name Lactococcus garvieae subsp. bovis subsp. nov. is proposed. The type strain is BSN307T (=DSM 100577 T=MCC 2824T=KCTC 21083T).
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Salinicoccus amylolyticus sp. nov., isolated from a saltern
More LessA Gram-stain-positive coccus, strain JC304T, was isolated from a saltern of Nari along the Bhavnagar Coast, Gujarat, India. The 16S rRNA gene sequence analysis and sequence comparison data indicated that JC304T represented a member of the genus Salinicoccus and was most closely related to Salinicoccus roseus 9T (99.6 %), Salinicoccus luteus YIM 70202T (97.0 %), Salinicoccus hispanicus J-82T (97.0 %) and the remaining species of the genus Salinicoccus (<97 %). Genome relatedness based on DNA–DNA hybridization of JC304T with the type strains of the most closely related species was less than 46 % and the ΔTm was >5 °C indicating that the strain represents a novel species of the genus Salinicoccus . Independent and concatenated phylogenetic analysis of recA/fusA gene translated product showed a clear distinction of JC304T from its phylogenetic neighbors. Diphosphotidylglycerol, phosphatidylglycerol, an unidentified glycolipid and three unidentified lipids (L1, L2 and L3) were the polar lipids of JC304T. Iso-C15 : 0 and anteiso-C15 : 0 were the major (>10 %) fatty acids in strain JC304T. The cell-wall amino acids were l-lysine and d-glycine. Hopanoids were not detected. The major isoprenoid quinone was menaquinone (MK-6). The DNA G+C content of JC304T was 48 mol%. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic analyses, strain JC304T is considered to represent a novel species of the genus Salinicoccus , for which the name Salinicoccus amylolyticus sp. nov. is proposed. The type strain is JC304T (=KCTC 33661T=LMG 28757T).
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Anaerosporomusa subterranea gen. nov., sp. nov., a spore-forming anaerobe belonging to the class Negativicutes isolated from saprolite
More LessA Gram-stain-negative, spore-forming, anaerobic bacterium designated strain RU4T was isolated from a saprolite core collected from Oak Ridge, Tennessee, USA. Cells were slightly curved rods and exhibited an outer membrane exterior to a thin cell wall. Strain RU4T formed heat-resistant endospores in late-log phase and stationary phase cultures. Under anaerobic conditions, strain RU4T grew by fermenting fumarate and maleate, but did not grow on glucose, glycerol, pyruvate, lactate, succinate, citrate, formate, acetate, propionate, butyrate or valerate. Strain RU4T did not reduce sulfate or ferric iron. The main cellular fatty acids were C17 : 0 cyclo, C16 : 0 and C15 : 0. The DNA G+C content was 52 mol%. Analysis of the 16S rRNA, rpoB, recA, infB, gyrB and atpD gene sequences indicated that the isolate is related to members of the family Sporomusaceae . Based on 92 % sequence similarity of the 16S rRNA gene to its closest relatives in the family Sporomusaceae and divergent physiological traits, the newly-cultivated isolate was assigned to a novel species of a new genus, Anaerosporomusa subterranea gen. nov., sp. nov. The type strain of Anaerosporomusa subterranea is RU4T (=DSM 29728T=ATCC BAA-2723T).
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Paenibacillus silagei sp. nov. isolated from corn silage
More LessA Gram-stain-negative, rod-shaped, endospore-forming bacterium, strain LOOC204T, was isolated from corn silage that had been prepared and stored in Hokkaido, Japan. The isolate grew well at 4–37 °C and at pH 6.0–8.5. The major cellular fatty acids were anteiso-C15 : 0, C16 : 0, iso-C14 : 0 and iso-C16 : 0. The major menaquinone was MK-7. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, one unidentified phospholipid, two unidentified aminolipids and three unidentified lipids were detected as the cellular polar lipids. The genomic DNA G+C content of LOOC204T was 52.2±0.7 mol%. A comparative 16S rRNA gene sequence analysis showed that LOOC204T represented a member of the genus Paenibacillus , and high levels of sequence similarity of LOOC204T with Paenibacillus borealis KK19T (97.5 %) and Paenibacillus jilunlii Be17T (97.4 %) were found. Based on sequence analysis of the RNA polymerase β subunit (rpoB) gene, LOOC204T was clearly separated from its phylogenetic neighbors in the genus Paenibacillus . DNA–DNA hybridisation experiments showed that LOOC204T displayed less than 40 % reassociation values toward its nearest phylogenetic neighbours of the genus Paenibacillus , indicating the unique taxonomic status of LOOC204T. Based on these data, we conclude that strain LOOC204T represents a novel species of the genus Paenibacillus , named Paenibacillus silagei sp. nov. The type strain is LOOC204T (=JCM 30974T=DSM 101953T).
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Streptococcus dentiloxodontae sp. nov., isolated from the oral cavity of elephants
More LessA Gram-stain-positive, catalase-negative, coccus-shaped organism was isolated from oral cavity samples collected from healthy elephants. The isolated strain, NUM 2404T, was tentatively identified as a streptococcal species based on the results of biochemical tests. Although a comparative 16S rRNA gene sequence analysis suggested the classification of this organism into the genus Streptococcus , it did not correspond to any recognized species of the genus. Strain NUM 2404T was related most closely to Streptococcus saliviloxodontae NUM 6306T with 95.8 % 16S rRNA gene sequence similarity, but the phylogenetic tree reconstructed based on the 16S rRNA gene sequence showed that NUM 2404T clustered with Streptococcus mutans NCTC 10449T and Streptococcus troglodytae TKU 31T. Comparative sequence analysis based on two housekeeping genes, groEL, which encodes the 60 kDa heat-shock protein, and rpoB, encoding the β subunit of RNA polymerase, of NUM 2404T indicated that it was most closely related to those of Streptococcus orisratti A63T and Streptococcus sobrinus ATCC 33478T with 82.7 and 85.1 % sequence similarities, respectively. On the basis of genotypic and phenotypic differences, it is proposed that the novel isolate be classified in the genus Streptococcus as representative of a novel species, Streptococcus dentiloxodontae sp. nov. The type strain is NUM 2404T (=JCM 19284T=DSM 27381T).
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Pontibacillus salipaludis sp. nov., a slightly halophilic bacterium isolated from a salt pan
Two novel Gram-stain-positive, facultatively anerobic, rod-shaped, motile, endospore-forming bacterial strains, 9DMT and 6DM, were isolated from Tuticorn, India. The high 16S rRNA gene sequence similarity (99.9 %) and DNA–DNA relatedness (88±2 %) indicated that strains 9DMT and 6DM were members of a single species. Based on 16S rRNA gene sequence analysis these strains were identified as belonging to the genus Pontibacillus and were related most closely to the type strains of Pontibacillus chungwhensis (99.7 % sequence similarity) and Pontibacillus marinus (97.9 %). The DNA G+C content of strains 9DMT and 6DM was 41.6 and 41.4 mol%, respectively. However, the level of DNA–DNA relatedness of these strains with P. chungwhensis KCTC 3890T and P. marinus KCTC 3917T was only 40.9 + 0.8 and 39.8 + 0.9 %, respectively. Strains 9DMT and 6DM were facultative anaerobes with optimal growth at 37 °C, at pH 7.0–8.0 and with 2–3 % (w/v) NaCl. The cell-wall peptidoglycan of strain 9DMT contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and three unknown lipids. The isoprenoid quinone was MK-7. Major fatty acids of strain 9DMT were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed the clear differentiation of strains 9DMT and 6DM, which are considered to represent a novel member of the genus Pontibacillus , for which the name Pontibacillus salipaludis sp. nov. is proposed. The type strain is 9DMT (= KCTC 33742T=LMG 29102T= CGMCC 1.15353T).
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Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses
Species of the genus Trichococcus share high similarity of their 16S rRNA gene sequences (>99 %). Digital DNA–DNA hybridization values (dDDH) among type strains of all described species of the genus Trichococcus ( T. flocculiformis DSM 2094T , T. pasteurii DSM 2381T , T. collinsii DSM 14526T , T. palustris DSM 9172T, and T. patagoniensis DSM 18806T) indicated that Trichococcus sp. strain R210T represents a novel species of the genus Trichococcus . The dDDH values showed a low DNA relatedness between strain R210T and all other species of the genus Trichococcus (23–32%). Cells of strain R210T were motile, slightly curved rods, 0.63–1.40×0.48–0.90 µm and stained Gram-positive. Growth was optimal at pH 7.8 and at temperature of 30 °C. Strain R210T could utilize several carbohydrates, and the main products from glucose fermentation were lactate, acetate, formate and ethanol. The genomic DNA G+C content of strain R210T was 47.9 mol%. Based on morphological, physiological and biochemical characteristics along with measured dDDH values for all species of the genus Trichococcus , it is suggested that strain R210T represents a novel species within the genus Trichococcus , for which the name Trichococcus ilyis sp. nov. is proposed. The type strain is R210T (=DSM 22150T=JCM 31247T).
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Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater
A Gram-stain-negative, microaerophilic rod-shaped organism designated as strain Z9T was isolated from groundwater of 1.7 km depth from the Mt. Simon Sandstone of the Illinois Basin, Illinois, USA. Cells of strain Z9T were rod shaped with dimensions of 0.3×(1–10) µm and stained Gram-negative. Strain Z9T grew within the temperature range 20–60 °C (optimum at 30–40 °C), between pH 5 and 8 (optimum 5.2–5.8) and under salt concentrations of 1–5 % (w/v) NaCl (optimum 2.5 % NaCl). In addition to growth by fermentation and nitrate reduction, this strain was able to reduce Fe(III), Mn(IV), Co(III) and Cr(VI) when H2 or organic carbon was available as the electron donor, but did not actively reduce oxidized sulfur compounds (e.g. sulfate, thiosulfate or S0). The G+C content of the DNA from strain Z9T was 36.1 mol%. Phylogenetic analysis of the 16S rRNA gene from strain Z9T showed that it belongs to the class Bacilli and shares 97 % sequence similarity with the only currently characterized member of the genus Tepidibacillus , T. fermentans. Based on the physiological distinctness and phylogenetic information, strain Z9T represents a novel species within the genus Tepidibacillus , for which the name Tepidibacillus decaturensis sp. nov. is proposed. The type strain is Z9T (=ATCC BAA-2644T=DSM 103037T).
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Harryflintia acetispora gen. nov., sp. nov., isolated from chicken caecum
More LessMore than 100 isolates of a Gram-stain-negative, curved rod-shaped, so far uncultured bacterium were isolated from chicken caecal content. The strains were obligate anaerobes which formed endospores. They were catalase-positive, cytochrome-oxidase-negative and did not hydrolyse aesculin. The detected predominant metabolic end product in reinforced clostridial bedium broth was acetate. The DNA G+C content was 62.2 mol%. The cell fatty acid composition was dominated by C15 : 0 iso, C15 : 0 anteiso, C16 : 0, C13 : 0 iso, C14 : 0 iso and C16 : 0 DMA. Analysis of the 16S rRNA gene sequences of the novel isolates showed 99 % similarity to each other. Phylogenetically they are placed in Clostridium cluster IV. They exhibited 99 % 16S rRNA gene sequence similarity to uncultured bacterial clone SJTU_C_03_83 (GenBank accession no. EF404038.1) and to three other so far uncultured strains. The closest related type strains, Hydrogenoanaerobacterium saccharovorans SW51T and Anaerotruncus colihominis WAL 14565T, exhibited a 16S rRNA gene sequence divergence of at least 8 % to the newly described isolates. In addition, morphological and biochemical characteristics allowed differentiation of the novel isolates from these and other related and validly published species, including Clostridium methylpentosum and Acetanaerobacterium elongatum . Therefore, a new genus, Harryflintia gen. nov., is proposed for the isolated hitherto unknown strains with V20-281aT (=DSM 100433T =CECT 8892T) as the type strain of its type species, Harryflintia acetispora gen. nov., sp. nov.
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Reclassification of Eubacterium desmolans as Butyricicoccus desmolans comb. nov., and description of Butyricicoccus faecihominis sp. nov., a butyrate-producing bacterium from human faeces
More LessA Gram-positive-staining, coccoid-shaped, non-motile, asporogenous, obligately anaerobic and butyrate-producing bacterium was recovered from a healthy human’s faeces. The organism was isolated by the enrichment culture technique using yeast extract-casein hydrolysate-fatty acids broth supplemented with 0.5 % mucin. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the novel strain should be classified as a member of the Eubacterium desmolans -related cluster in the family Ruminococcaceae . Furthermore, this analysis demonstrated that the type strains of Butyricicoccus pullicaecorum (95.6 %) and Eubacterium desmolans (94.7 %) were the closest phylogenetic neighbours to strain YIT 12789T. However, DNA‒DNA reassociation values with these closest strains were less than 20 %. On the basis of the phenotypic, genotypic and chemotaxonomic features, the novel coccoid-shaped bacterium should be designated as a representative of a novel species of the genus Butyricicoccus , for which the name Butyricicoccus faecihominis sp. nov. is proposed. The type strain is YIT 12789T (=JCM 31056T=DSM 100989T). It is also proposed that Eubacterium desmolans be reclassified in the genus Butyricicoccus as Butyricicoccus desmolans comb. nov.
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Herbinix luporum sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor
More LessPhylogenetic studies were performed on a group of novel Gram-stain-positive, anaerobic, non-sporulating rod-shaped bacteria isolated from a thermophilic biogas plant. The novel organisms were able to degrade crystalline cellulose. 16S rRNA gene sequence comparison indicated that the isolates SD1DT, SD1G, SD1I and RK1P share 100 % sequence identity, and are most closely related to Herbinix hemicellulosilytica T3/55T with which they share a 16S rRNA gene sequence similarity of 96.4 %. As a representative of the whole group of isolates, strain SD1DT was further characterized. Strain SD1DT was catalase-negative, indole-negative, and produced acetate, ethanol, butyric acid and hydrogen as major end-products during fermentative cellobiose utilization. Cells are rod-shaped, growing optimally at 40–65 °C and pH 6.5–8.5. The major cellular fatty acids (>10 %) were C19 : 0 cyc 9,10 dimethyl acetal, C16 : 0 and C14 : 0. The DNA G+C content was 35.1 mol%. Due to the genetic and phenotypic differences to the most closely affiliated species, the isolates represent a novel species of the genus Herbinix within the family Lachnospiraceae , for which the name Herbinix luporum sp. nov. is proposed. The type strain is SD1DT(=DSM 100831T=CECT 8959T).
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Streptococcus halotolerans sp. nov. isolated from the respiratory tract of Marmota himalayana in Qinghai-Tibet Plateau of China
Two Gramstaining-positive, catalase-negative, α-hemolytic, coccus-shaped organisms were isolated separately from the respiratory tracts of two Marmota himalayana animals from the Qinghai-Tibet Plateau, PR China. Morphological, biological, biochemical, and molecular genetic studies were performed on these two isolates (HTS9T and HTS12). Their biochemical characteristics, such as acid production from different sugars and enzymatic activities, indicated that they represented a member of the genus Streptococcus . They are most closely related to Streptococcus thoraltensis CIP 105518T based on sequence analysis of their 16S rRNA, groEL, sodA and rpoB genes, with similarities of 97.6, 89.9, 92.6 and 91.1 % the four genes respectively. The whole genome phylogenetic tree reconstructed using 372 core genes from 65 genomes of members of the genus Streptococcus validates that HTS9T forms a distinct subline and exhibits specific phylogenetic affinity with S. thoraltensis . In silico DNA–DNA hybridization of HTS9T showed a DNA reassociation value of 32.1 %, closest to that of S. thoraltensis CIP 105518T. Based on their phenotypic characteristics and in particular the phylogenetic findings (DNA–DNA hybridization, three phylogenetic trees built from the partial 16S rRNA/housekeeping genes, and from 372 core genes of 65 genomes of members of the genus Streptococcus ), we propose with confidence that strains HTS9T and HTS12 should be classified as representing a novel species of the genus Streptococcus , Streptococcus halotolerans sp. nov. The type strain is HTS9T (=DSM 101996T=CGMCC1.15532T). Genome analysis of Streptococcus halotolerans sp. nov. shows that its genome is 1 823 556 bp long with a DNA G+C content of 39.9 mol% and contains 2068 genes.
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Oceanobacillus longus sp. nov., a moderately halophilic bacterium isolated from a salt lake
A Gram-stain-positive, endospore-forming, long rod-shaped, strictly aerobic, moderately halophilic bacterium, designated strain T9BT, was isolated from a brine sample of the hypersaline lake Aran-Bidgol in Iran. Cells of strain T9BT were motile and produced colonies with a brown pigment. Growth occurred between 1.0 and 20 % (w/v) NaCl and the isolate grew optimally at 5.0 % (v/w) NaCl. The optimum pH and temperature for growth of the strain were pH 7.0 and 35 °C, while it was able to grow over pH and temperature ranges of pH 6.0–9.0 and 25–45 °C. Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain T9BT is a member of the genus Oceanobacillus . The closest relative to this strain was Oceanobacillus rekensis PT-11T with a similarity of 97.4 %, followed by Oceanobacillus profundus CL-MP28T and Oceanobacillus polygoni SA9T with 97.3 and 97.1 % similarity, respectively. The major cellular fatty acids of the isolate were anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The polar lipids of strain T9BT consisted of phosphatidylglycerol, diphosphatidylglycerol, three phospholipids and one aminoglycolipid. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The G+C content of the genomic DNA of this strain was 42.9 mol%. Phylogenetic analysis, DNA–DNA hybridization data and phenotypic characteristics allowed strain T9BT to be differentiated from other members of the genus Oceanobacillus . A novel species, Oceanobacillus longus sp. nov., is therefore proposed to accommodate this strain. The type strain is T9BT (=IBRC-M 10703T=LMG 29250T).
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- Other bacteria
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Thermodesulfatator autotrophicus sp. nov., a thermophilic sulfate-reducing bacterium from the Indian Ocean
More LessA novel sulfate-reducing bacterium, strain S606T, was isolated from a sulfide sample collected at a depth of 2764 m from a deep-sea vent chimney wall in the Indian Ocean. Phylogenetic 16S rRNA gene sequence analyses placed strain S606T within the genus Thermodesulfatator , with highest sequence similarity of 98.2 % to Thermodesulfatator indicus DSM 15286T, followed by Thermodesulfatator atlanticus AT1325T (97.4 %). The average nucleotide identity (ANI) values between S606T and the two other type strains (T. indicus DSM 15286T and T. atlanticus AT1325T) were 79.2 % and 71.5 %, respectively. The digital DNA–DNA hybridization estimate values between S606T and these two type strains were 22.7±2.4 % and 18.1±2.3 %, respectively. Cells were Gram-stain-negative, anaerobic, motile rods (1–1.8×0.5–0.7 µm). The novel isolate grew at NaCl concentrations ranging from 1.5 to 4.5 % (optimum 2.5–3 %), from pH 5.5 to 8 (optimum 6.5–7.0) and at temperatures between 50 and 80 °C (optimum 65–70 °C). S606T grew chemolithoautotrophically in an H2/CO2 atmosphere (80 : 20, v/v; 200 kPa), used sulfate as a terminal electron acceptor, but not sulfur, sulfite nor thiosulfate. The predominant fatty acids were C16 : 0 (24.2 %), summed feature 8 (C18 : 1ω6c and/or C18 : 1 ω7c, 26.3 %), C18 : 0 (22.2 %) and C18 : 1ω9c (9.2 %). The DNA G+C content of the chromosomal DNA was 43.1 mol%. The combined genotypic, chemotaxonomic and phenotypic traits show that S606T should be described as representing a novel species of the genus Thermodesulfatator , for which the name Thermodesulfatator autotrophicus sp. nov. is proposed. The type strain is S606T (=DSM 101864T=MCCC 1A01871T).
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- Proteobacteria
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Sulfitobacter faviae sp. nov., isolated from the coral Favia veroni
More LessThree closely related, non-sporulating, aerobic, Gram-stain-negative, motile, rod-shaped isolates (S5-53T, S6-62 and S6-64) were obtained from mucus of corals Favia veroni from the Andaman Sea, India. Colonies grown on marine agar were small, circular and cream-coloured. Heterotrophic growth was observed at 10–40 °C and pH 6–10; optimum growth occurred at 25–30 °C and pH 7–8. 16S rRNA gene sequence analysis confirmed the isolates belonged to the genus Sulfitobacter and the three isolates shared more than 99 % pairwise sequence similarity. Strain S5-53T shared highest 16S rRNA gene sequence similarity of 98.43 % with Sulfitobacter dubius KMM 3554T. DNA–DNA relatedness among the three isolates was above 70 % whereas strain S5-53T showed less than 70 % relatedness with the type strains of closely related species. The DNA G+C content of strain S5-53T was 61 mol%. It contained phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol as major polar lipids. Predominant fatty acids included C18 : 1 ω7c, C18 : 1 ω7c 11-methyl, C16 : 0 and C10 : 0 3-OH. Q10 was the major respiratory quinone. Based on this polyphasic analysis, the new isolates (S5-53T, S6-62 and S6-64) are considered to represent a novel species of the genus Sulfitobacter , for which the name Sulfitobacter faviae sp. nov. is proposed. The type strain is S5-53T(=JCM 31093T=LMG 29156T).
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Roseomonas rubra sp. nov., isolated from lagoon sediments
More LessA novel Gram-stain-negative, coccus to oval-shaped, non-motile bacterium, designated strain S5T, was isolated from lagoon sediments collected from North Carolina, USA. Strain S5T was able to grow at 12–45 °C (optima, 30–37 °C) and at pH 6.3–9.0 (optima, 6.5–7.5). No added NaCl was required for growth of strain S5T. Strain S5T was positive for catalase and oxidase activity. C18 : 1 ω6c/C18 : 1 ω7c, C16 : 1 ω6c/C16 : 1 ω7c and C16 : 0 were predominant fatty acids with minor amounts of C8 : 0 3-OH, C14 : 0, C16 : 0 3-OH, C18 : 1 2-OH, C14 : 1 ω5c, C16 : 1 ω5c and C19 : 0 cyclo ω8c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified glycolipid were major polar lipids. Minor amounts of an unidentified amino lipid and three unidentified lipids were also detected. The G+C content of the genomic DNA was 73.5 mol%. 16S rRNA gene sequence comparisons indicated that strain S5T represents a member of the genus Roseomonas within the family Acetobacteraceae of the class Alphaproteobacteria . Strain S5T had a sequence similarity of 97.80 % with Roseomonas rhizosphaerae YW11T, 97.69 % with Roseomonas aestuarii JC17T and <97 % with other members of the genus Roseomonas . However, strain S5T showed only 45.2±2 and 17±2 % relatedness (based on DNA–DNA hybridization) with R . rhizosphaerae KACC 17225T (=YW11T) and R . aestuarii KCTC 22692T (=JC17T), respectively. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain S5T as a representative of a novel species in the genus Roseomonas , for which the name Roseomonas rubra sp. nov. is proposed. The type strain is S5T (=KEMB 563-468T=JCM 31177T).
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Halomonas sediminicola sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment
More LessA Gram-stain-negative, moderately halophilic bacterium, designated strain CPS11T, was isolated from the sediment of a solar pond located in Shinan, Korea. Strain CPS11T was a strictly aerobic, motile, straight rod-shaped bacterium that grew at pH 5.0–9.0 (optimum, pH 7.0–8.0), at 10–37 °C (optimum, 28 °C) and at salinities of 1–20 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CPS11T belonged to the genus Halomonas , with sequence similarity of 98.5–94.3 % to existing type strains, showing highest sequence similarity to Halomonas fontilapidosi 5CRT (98.5 %), Halomonas ventosae Al12T (98.5 %), Halomonas campaniensis 5AGT (98.2 %), Halomonas huangheensis BJGMM-B45T (98.0 %), Halomonas alimentaria YKJ-16T (98.0 %), Halomonas mongoliensis Z-7009T (97.8 %), Halomonas shengliensis SL014B-85T (97.5 %) and Halomonas cupida DSM 4740T (97.5 %). The predominant ubiquinone was Q-9. The major fatty acids were C19 : 0 cyclo ω8c, C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C16 : 0, C17 : 0 cyclo, C12 : 0 3-OH and C18 : 1 ω7c. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, an unknown phospholipid and unknown lipids. The DNA G+C content of this novel isolate was 64.3 mol%. Levels of DNA–DNA relatedness between strain CPS11T and the type strains of ten other species of the genus ranged from 50 to 21 %. On the basis of the polyphasic analysis conducted in this study, strain CPS11T represents a novel species of the genus Halomonas , for which the name Halomonas sediminicola sp. nov. is proposed. The type strain is CPS11T(=KACC 18262T=NBRC 110636T).
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Chromobacterium rhizoryzae sp. nov., isolated from rice roots
A novel facultatively anaerobic, rod-shaped bacterium, designated LAM1188T, was isolated from the roots of rice (Oryzasativa) in Hubei Province. Cells of LAM1188T were Gram-stain-negative and motile. The temperature and pH ranges for growth were 15–40 °C (optimum: 30 °C) and pH 5–10 (optimum: pH 7), respectively. The strain did not require NaCl for growth but tolerated up to 3.5 % NaCl (w/v). Analysis of the 16S rRNA gene sequence indicated that the isolate represented a member of the genus Chromobacterium , and was most closely related to Chromobacterium haemolyticum MDA0585T and Chromobacterium aquaticum CC-SEYA-1T with 98.7 % and 97.3 % sequence similarity, respectively. The values of DNA–DNA hybridization between LAM1188T and C. haemolyticum JCM 14163T and C. aquaticum CCUG 55175T were 54.0±2.1 % and 44.0±1.2 %, respectively. The major cellular fatty acids were C16 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids and four unidentified lipids. The respiratory quinone was ubiquinone Q-8. The DNA G+C content was 64.1 mol% as determined by the Tm method. On the basis of its phenotypic, chemotaxonomic and phylogenetic characteristics, strain LAM1188T is suggested to represent a novel species of the genus Chromobacterium, for which the name Chromobacte riumrhizoryzae sp. nov. is proposed. The type strain is LAM1188T (=ACCC 19900T=JCM 31180T).
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Acinetobacter pragensis sp. nov., found in soil and water ecosystems
More LessThis study aimed to define the taxonomic status of a novel, phenetically distinct group of seven strains belonging to the genus Acinetobacter , which were isolated from environmental soil and water samples collected in Central Bohemia, Czech Republic. Comparative sequence analyses of the 16S rRNA, gyrB and rpoB genes showed that all these strains formed respective tight clusters (intracluster sequence similarities of ≥99.8, ≥98.1 and ≥98.3 %, respectively), which were distant from all known Acinetobacter species (≤98.2, ≤84.0 and ≤88.9 %, respectively). The average nucleotide identity and digital DNA–DNA hybridization values (≤83.5 and ≤27.4 %, respectively) between the whole-genome sequence of a group representative (strain ANC 4149T) and those of known taxa were far below the thresholds used to discriminate between bacterial species. The seven 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 MS and could be distinguished from all other members of the genus Acinetobacter by the combination of their ability to assimilate glutarate and l-tartrate and inability to grow at 37 °C and on l-aspartate. It is concluded that the seven strains represent a novel species for which the name Acinetobacter pragensis sp. nov. is proposed. The type strain is ANC 4149T (=CCM 8637T=CCUG 67962T=CNCTC 7530T).
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Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio
More LessA novel sulfate-reducing bacterium, strain J2T, was isolated from a serpentinized peridotite sample from the Indian Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J2T clustered with the genus Desulfovibrio within the family Desulfovibrionaceae , but it showed low similarity (87.95 %) to the type species Desulfovibrio desulfuricans DSM 642T. It was most closely related to Desulfovibrio portus MSL79T (96.96 %), followed by Desulfovibrio aespoeensis Aspo-2T (96.11 %), Desulfovibrio piezophilus C1TLV30T (96.04 %) and Desulfovibrio profundus DSM 11384T (95.17 %). Other available sequences shared less than 93.33 % 16S rRNA gene sequence similarity. Cells were Gram-staining-negative, anaerobic, motile vibrios (2–6×0.4–0.6 µm). Growth was observed at salinities ranging from 0.2 to 6 % (optimum 2.5 %), from pH 5 to 8 (optimum pH 6.5–7) and at temperatures between 9 and 40 °C (optimum 30–35 °C). J2T was piezophilic, growing optimally at 10 MPa (range 0–30 MPa). J2T used lactate, malate, pyruvate, formate and hydrogen as energy sources. Sulfate, thiosulfate, sulfite, fumarate and nitrate were used as terminal electron acceptors. Lactate and pyruvate were fermented. The main fatty acids were iso-C15 : 0, anteiso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and iso-C17 : 0. The DNA G+C content of strain J2T was 63.5 mol%. The combined genotypic and phenotypic data show that strain J2T represents a novel species of a novel genus in the family Desulfovibrionaceae , for which the name Pseudodesulfovibrio indicus gen. nov., sp. nov. is proposed, with the type strain J2T (=MCCC 1A01867T = DSM 101483T). We also propose the reclassification of D. piezophilus as Pseudodesulfovibrio piezophilus comb. nov., D. profundus as Pseudodesulfovibrio profundus comb. nov., D. portus as Pseudodesulfovibrio portus comb. nov. and D. aespoeensis as Pseudodesulfovibrio aespoeensis comb. nov.
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Sphingobium hydrophobicum sp. nov., a hydrophobic bacterium isolated from electronic-waste-contaminated sediment
More LessFour hydrophobic bacteria were isolated from sediment at Guiyu, an electronic-waste recycling site in southeastern China. The isolates had high cell surface hydrophobicity with microbial-adhesion-to-hydrocarbon score of 71.4 %. 16S rRNA gene sequences of the strains all showed highest similarity to the hydrophilic Sphingobium xenophagum DSM 6383T (99.9 % 16S rRNA gene sequence similarity), followed by Sphingobium czechense DSM 25410T (97.1 %). However, DNA–DNA hybridization revealed that the isolates and S. xenophagum DSM 6383T exhibited low DNA–DNA relatedness with a hybridization value of 54.5±0.5 %. The genomic DNA G+C content was 64.2 mol% and the predominant quinone was ubiquinone Q-10. Spermidine was the major polyamine component. The major fatty acids were C18 : 1ω7c, C16 : 1ω7c, C16 : 0, C14 : 0 2-OH and C14 : 0. In contrast to its closest relative S. xenophagum DSM 6383T, the isolates had a much higher proportion of C16 : 0 and C14 : 0 and a much lower proportion of C18 : 1ω9t. Sphingoglycolipid was present and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylmonomethylethanolamine were detected in the polar lipid pattern. Phosphatidyldimethylethanolamine and phosphatidylcholine, which are present in S. xenophagum DSM 6383T, were not detected in the isolates. Results of DNA–DNA relatedness, cell surface hydrophobicity, fatty acids, polar lipids, and biochemical and physiological properties reveal that the isolates represent a novel species of the genus Sphingobium , for which the name Sphingobium hydrophobicum sp. nov. is proposed. The type strain is C1T (=CCTCC AB 2015198T=KCTC 42740T).
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Martelella suaedae sp. nov. and Martelella limonii sp. nov., isolated from the root of halophytes
More LessTwo Gram-stain-negative, aerobic and endophytic bacterial strains, designated YC7033T and YC7034T, were isolated from the roots of halophytes (Suaeda maritime and Limonium tetragonum, respectively) inhabiting tidal flats of the Sacheon area, Korea. The phylogenetic analyses of 16S rRNA gene sequences showed that the two strains were closely related to Martelella endophytica YC6887T, Martelella mangrovi BM9-1T, Martelella radicis BM5-7T and Martelella mediterranea DSM 17316T at 97.6–99.1 % similarity. Sequence similarities with the type strains of another closely related genus, Rhizobium , were lower than 95.0 %. Both strains contained ubiquinone-10 (Q-10) as the major respiratory quinone system. The G+C contents of the genomic DNA of strains YC7033T and YC7034T were 52.8 and 62.2 mol%, respectively. The major fatty acids of both strain YC7033T and strain YC7034T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C19 : 0 cyclo ω8c. On the basis of phylogenetic analysis, and biochemical and phenotypic characteristics, strains YC7033T and YC7034T represent two novel species of the genus Martelella , for which the names Martelella suaedae sp. nov. (type strain: YC7033T=KACC 17175T=NBRC 109440T) and Martelella limonii sp. nov. (type strain: YC7034T=KACC 17176T=NBRC 109441T) are proposed, respectively.
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Shinella curvata sp. nov., isolated from hydrocarbon-contaminated desert sands
More LessThe taxonomic position of a novel bacterial strain, designated C3T, isolated from hydrocarbon-contaminated desert sands was determined. Strain C3T was a Gram-stain-negative, rod- to curved-rod-shaped and non-motile bacterium. It was able to grow at 4–45 °C (optima, 28– 35 °C) and at pH 6.1–8.8 (optima, 6.9–7.7). No added NaCl was required for growth of strain C3T and it tolerated up to 3.5 % (w/v) NaCl with optimal growth with 0.5–1.5 %. Catalase and oxidase were positive. C18 : 1 ω6c/C18 : 1 ω7c, C16 : 0, C12 : 0 aldehyde, C14 : 0 3-OH/iso-C16 : 0 I and C18 : 1 ω7c 11-methyl were predominant fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine were major polar lipids. The genomic DNA G+C content was 65.4 mol%. 16S rRNA gene sequence comparisons indicated that strain C3T represents a member of the genus Shinella within the family Rhizobiaceae of the class Alphaproteobacteria . Strain C3Tshowed a 16S rRNA gene sequence similarity of 98.39 % with Shinella kummerowiae CCBAU 25048T, 98.37 % with Shinella granuli Ch06T, 98.17 % with Shinella zoogloeoides I-16-MT, 97.74 % with Shinella fusca DC-196T, 97.46 % with Shinella yambaruensis MS4T and <96.68 % with other members of the family Rhizobiaceae . DNA–DNA hybridization values between strain C3T and the type strains of the nearest species were clearly below the 70 % threshold for species delineation. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain C3T as a representative of a novel species in the genus Shinella , for which the name Shinella curvata sp. nov. is proposed. The type strain is C3T (=KEMB 2255-446T=JCM 31239T).
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Devosia confluentis sp. nov., isolated from the junction between the ocean and a freshwater lake, and reclassification of two Vasilyevaea species as Devosia enhydra comb. nov. and Devosia mishustinii comb. nov.
More LessA Gram-stain-negative, aerobic, non-flagellated and pleomorphic bacterium, designated HJR-2T, was isolated from a junction between the ocean and a freshwater lake on the East Sea, South Korea. It grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 0–1.5 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain HJR-2T clustered with the type strains of Vasilyevaea enhydra and Vasilyevaea mishustinii and this cluster fell within the clade comprising the type strains of Devosia species. Strain HJR-2T exhibited 16S rRNA gene sequence similarity values of 97.2 and 97.0 % to the type strains of V. enhydra and V. mishustinii , respectively, and 93.9–96.2 % to the type strains of Devosia species. Strain HJR-2T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c, 11-methyl C18 : 1 ω7c and C16 : 0 as major fatty acids. Major polar lipids of strain HJR-2T were phosphatidylglycerol and two unidentified glycolipids. The DNA G+C content was 66.0 mol% and its mean DNA–DNA relatedness values with the type strains of V. enhydra and V. mishustinii were 11–17 %. Differential phenotypic properties, together with its phylo genetic and genetic distinctiveness, revealed that strain HJR-2T is separated from V. enhydra , V. mishustinii and Devosia species. On the basis of the data presented, strain HJR-2T (=KCTC 52211T=NBRC 112271T) is considered to be the type strain of a novel species of the genus Devosia , for which the name Devosia confluentis sp. nov. is proposed. In this study, it is also proposed that V. enhydra and V. mishustinii be reclassified as members of the genus Devosia .
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Skermanella rosea sp. nov., isolated from hydrocarbon-contaminated desert sands
More LessA novel Gram-stain-negative, small rod-shaped, motile strain, designated M1T, was isolated from hydrocarbon-contaminated desert sands collected from Kuwait. M1T grew at 12–45 °C, pH 6.1–8.8 and 0–4.5 % (w/v) NaCl concentration. Casein, Tween-20 and Tween-80 were hydrolyzed while starch, urea, chitin, DNA and carboxymethyl-cellulose were not hydrolyzed by M1T. C18 : 1ω6c/C18 : 1ω7c, C16 : 0 and C12 : 0 aldehyde were predominant fatty acids with minor amounts of iso-C16 : 1I/C14 : 0 3-OH, C16 : 0 3-OH, C18 : 0, C16 : 1ω6c/C16 : 1ω7c, C16 : 1ω11c and C18 : 1ω9c. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and phosphatidylcholine (PC) were the major polar lipids. Minor amounts of unidentified aminolipids (AL1–2), unidentified phospholipids (PL1–2) and unidentified lipids (L1–4) were also detected. Genomic G+C content was 69.5 mol%. Comparisons of 16S rRNA gene sequence indicate that M1T represent a member of the genus Skermanella in the family Rhodospirillaceae of the class Alphaproteobacteria . M1T has a sequence similarity of 97.5 % with Skermanella aerolata 5416T-32T, 96.7 % with Skermanella stibiiresistens SB22T and <95.7 % with the other two species of the genus Skermanella . DNA–DNA hybridization values between M1T and the type strains of the most closely related species were clearly below the 70 % threshold. Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain M1T as a representative of a novel species in the genus Skermanella , for which the name Skermanella rosea sp. nov. is proposed. The type strain is M1T (=KEMB 2255-458T=JCM 31276T).
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Altererythrobacter confluentis sp. nov., isolated from water of an estuary environment
More LessA Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, designated KEM-4T, was isolated from water of an estuary environment on the Yellow Sea, South Korea, and subjected to a polyphasic taxonomic study. Strain KEM-4T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 1.0–2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain KEM-4T fell within the clade comprising the type strains of species of the genus Altererythrobacter , clustering with the type strains of Altererythrobacter aestiaquae, Altererythrobacter gangjinensis and Altererythrobacter luteolus, showing 95.0–96.5 % sequence similarity. Sequences similarities to the type strains of the other species of the genus Altererythrobacter were 93.1–95.1 %. Strain KEM-4T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C17 : 1ω6c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. The DNA G+C content of strain KEM-4T was 59.5 mol%. Differential phenotypic properties, together with the phylogenetic distinctiveness, revealed that strain KEM-4T is separated from species of the genus Altererythrobacter with validly published names. On the basis of the data presented, strain KEM-4T is considered to represent a novel species of the genus Altererythrobacter , for which the name Altererythrobacter confluentissp. nov. is proposed. The type strain is KEM-4T (=KCTC 52259T=NBRC 112305T).
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Lysobacter erysipheiresistens sp. nov., an antagonist of powdery mildew, isolated from tobacco-cultivated soil
More LessA bacterial strain, RS-LYSO-3T, was isolated from tobacco-cultivated soil, collected near Chuxiong, Yunnan province, southwestern China. RS-LYSO-3T could effectively inhibit the invasion of powdery mildew on tobacco. The colonies of RS-LYSO-3T were pale yellow, and its cells were Gram-stain-negative and rod-shaped, with 68 mol% DNA G+C content. Gene sequence analysis for its 16S rRNA gene revealed the highest similarity (97.78 %) with that of Lysobacter spongiicolaKMM 329T. Chemotaxonomic data showed that RS-LYSO-3T possesses a quinone system with Q-8, and iso-C16 : 0, summed feature 9 and iso-C15 : 0 as the predominant fatty acids, all of which support the affiliation of RS-LYSO-3T to the genus Lysobacter . The results of DNA–DNA hybridization, physiological and biochemical tests clearly proved that RS-LYSO-3T is a representative of a novel species of the genus Lysobacter , for which the name Lysobacter erysipheresistens sp. nov. is proposed. The type strain is RS-LYSO-3T (=CCIC 23922T=JCM 31042T).
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Roseomonas arcticisoli sp. nov., isolated from Arctic tundra soil
A pale pink, Gram-reaction-negative, non-motile, aerobic bacterium, designated MC 3624T, was isolated from a tundra soil near Ny-Ålesund, Svalbard Archipelago, Norway (78° N). Growth occurred at 10–37 °C (optimum 25–30 °C) and at pH 6.0–9.0 (optimum pH 8.0). The predominant fatty acids were C16 : 0 (17.7 %), C18 : 1ω7c 11-methyl (13.4 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (10.1 %) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) (38.3 %). The major respiratory quinone was ubiquinone-10, and the main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and an unidentified aminolipids. The DNA G+C content was 68.9 mol%. Carotenoids of the spirilloxanthin series were produced. The nearest neighbour to the novel strain was Roseomonas wooponensis WW53T (94.36 % 16S rRNA gene sequence similarity). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain MC 3624T represents a novel species of the genus Roseomonas , for which the name Roseomonas arcticisoli sp. nov. is proposed. The type strain is MC 3624T (=CCTCC AB 2014278T=LMG 28637T).
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Thalassotalea montiporae sp. nov., isolated from the encrusting pore coral Montipora aequituberculata
More LessA bacterial strain, designated CL-22T, was isolated from an encrusting pore coral, Montipora aequituberculata, collected off the coast of Southern Taiwan. Its taxonomic position was investigated using a polyphasic approach. Cells of strain CL-22T were Gram-stain-negative, aerobic, motile by means of a single polar flagellum, rod-shaped and formed yellow colonies. Optimal growth occurred at 30 °C, pH 6.5−7 and in 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree, based on 16S rRNA gene sequences, showed that strain CL-22T fell into the clade comprising the type strains of species of the genus Thalassotalea . Strain CL-22T exhibited 16S rRNA gene sequence similarity values of 94.7–97.1 % to the type strains of species of the genus Thalassotalea . The major fatty acids (>10 %) of strain CL-22T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The predominant isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content of strain CL-22T was 41.2 mol%. The differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain CL-22T should be classified as a novel species of the genus Thalassotalea ; the name Thalassotalea montiporae sp. nov. is proposed. The type strain is CL-22T (=LMG 24827T=BCRC 17940T).
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Reclassification of Paraburkholderia panaciterrae (Farh et al. 2015) Dobritsa & Samadpour 2016 as a later synonym of Paraburkholderia ginsengiterrae (Farh et al. 2015) Dobritsa & Samadpour 2016
More LessWhole-genome sequencing and PFGE analysis of Paraburkholderia ginsengiterrae DCY85T and Paraburkholderia panaciterrae DCY85-1T showed these strains are highly similar and may even be clones of the same strain. The PFGE patterns of XbaI-, AvaII-, and SpeI-digested genomic DNA of the two strains were indistinguishable. Based on the priority of valid publications of the species basonyms, Burkholderia ginsengiterrae and Burkholderia panaciterrae , it is proposed to reclassify P. panaciterrae as a later synonym of P. ginsengiterrae . The P. ginsengiterrae description was emended by replacing the DNA G+C content value of 66.0 mol%, which is higher than the 65 mol% considered the threshold for species of the genus Paraburkholderia , with the value of 62.4–62.5 mol%, calculated as the mean DNA G+C content of the draft genomes of strains DCY85-1T and DCY85T.
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Massilia psychrophila sp. nov., isolated from an ice core
A Gram-stain-negative, aerobic, rod-shaped, motile bacterium, strain B1555-1T, was isolated from an ice core drilled from Ulugh Muztagh Glacier, China. The optimum growth temperature of strain B1555-1T was 15 °C and optimum pH was 7. The major fatty acids of strain B1555-1T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The predominant respiratory quinone was Q-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain B1555-1T was 66.0 mol%. In 16S rRNA gene sequence comparisons, strain B1555-1T was affiliated to the genus Massilia and shared 98.30 and 97.13 % similarity with Massilia eurypsychrophila B528-3T and Massilia niabensis 5420S-26T, respectively. The results of DNA–DNA hybridization revealed that strain B1555-1T showed 49.8 % relatedness with M. eurypsychrophila B528-3T and 38.5 % with M. niabensis 5420S-26T. Based on the genotypic and phenotypic evidence presented in this study, strain B1555-1T represents a novel species of the genus Massilia , for which the name Massilia psychrophila sp. nov. is proposed. The type strain is B1555-1T (=CGMCC 1.15196T=JCM 30813T).
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Spongiibacter taiwanensis sp. nov., a marine bacterium isolated from aged seawater
More LessA Gram-reaction-negative, heterotrophic, marine bacterium, designated strain SPT1T, was isolated from an aged seawater sample which was collected from the shallow coastal region of Nanya, Keelung, Taiwan and stored at room temperature for more than 7 years. Strain SPT1T was a motile rod which exhibited monotrichous flagellation. It required NaCl for growth and exhibited optimal growth at 30–35 °C, 1–3 % NaCl and pH 7–8. The strain was a strictly aerobic bacterium, incapable of anaerobic growth by nitrate reduction or denitrification, or by fermenting glucose or other carbohydrates. Cellular fatty acids were dominated by C16 : 1ω7c and/or C16 : 1ω6c (23.4 %), C17 : 1ω8c (18.1 %), C16 : 0 (8.5 %), C18 : 1ω7c (8.4 %) and C10 : 0 3-OH (6.3 %). The predominant isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and phosphatidic acid. The DNA G+C content was 57.9 mol%. Phylogeny based on 16S rRNA gene sequences showed that strain SPT1T formed a distinct species-level lineage within the genus Spongiibacter of the class Gammaproteobacteria and shared sequence similarities of 94.4–96.2 % with Spongiibacter marinus and Spongiibacter tropicus, the only two species of the genus Spongiibacter with validly published names. The 16S rRNA gene sequence similarities between strain SPT1T and other species were less than 93.1 %. Polyphasic taxonomic data obtained in this study indicated that strain SPT1T could be classified as a novel species of the genus Spongiibacter , for which the name Spongiibacter taiwanensis sp. nov. is proposed. The type strain is SPT1T (=JCM 31012T=BCRC 80916T).
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Acinetobacter dijkshoorniae sp. nov., a member of the Acinetobacter calcoaceticus–Acinetobacter baumannii complex mainly recovered from clinical samples in different countries
The recent advances in bacterial species identification methods have led to the rapid taxonomic diversification of the genus Acinetobacter . In the present study, phenotypic and molecular methods have been used to determine the taxonomic position of a group of 12 genotypically distinct strains belonging to the Acinetobacter calcoaceticus –Acinetobacter baumannii (ACB) complex, initially described by Gerner-Smidt and Tjernberg in 1993, that are closely related to Acinetobacter pittii . Strains characterized in this study originated mostly from human samples obtained in different countries over a period of 15 years. rpoB gene sequences and multilocus sequence typing were used for comparisons against 94 strains representing all species included in the ACB complex. Cluster analysis based on such sequences showed that all 12 strains grouped together in a distinct clade closest to Acinetobacter pittiithat was supported by bootstrap values of 99 %. Values of average nucleotide identity based on blast between the genome sequence of strain JVAP01T (NCBI accession no. LJPG00000000) and those of other species from the ACB complex were always <91.2 %, supporting the species status of the group. In addition, the metabolic characteristics of the group matched those of the ACB complex and the analysis of their protein signatures by matrix-assisted laser desorption ionization time-of-flight MS identified some specific peaks. Our results support the designation of these strains as representing a novel species, for which the name Acinetobacter dijkshoorniae sp. nov. is proposed. The type strain is JVAP01T (=CECT 9134T=LMG 29605T).
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Aurantimonas endophytica sp. nov., a novel endophytic bacterium isolated from roots of Anabasis elatior (C. A. Mey.) Schischk
An orange-coloured, aerobic, motile, short-rod-shaped bacterial strain, designated EGI 6500337T, was isolated from the surface-sterilized root of a halophyte, Anabasis elatior (C. A. Mey.) Schischk, collected from Urumqi, Xinjiang province, north-west China. Growth occurred at 5–35 °C (optimum 30 °C), at pH 6.0–9.0 (optimum pH 7.0) and in the presence of 0–6 % (w/v) NaCl (optimum 0–1 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain EGI 6500337T formed a distinct lineage in the cluster that comprised the genera Aurantimonas and Aureimonas in the family Aurantimonadaceae . The 16S rRNA gene sequence of strain EGI 6500337T shared highest similarity with those of Aurantimonas coralicida DSM 14790T (97.15 %) and Aurantimonas manganoxydans DSM 21871T (97.15 %). Strain EGI 6500337T contained Q-10 as the dominant isoprenoid quinone. The major cellular fatty acids were C18 : 1 ω7c and C19 : 0 ω8c cyclo. The polar lipid profile of strain EGI 6500337T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine as major components, similarly to members of the genus Aurantimonas . The DNA G+C content of strain EGI 6500337T was 66.8 mol%. The level of DNA–DNA relatedness between strain EGI 6500337T and Aurantimonas coralicida DSM 14790T was 24.7±2.9 %. On the basis of the phylogenetic analysis, chemotaxonomic data and phenotypic characteristics, strain EGI 6500337T represents a novel species of the genus Aurantimonas , for which the name Aurantimonas endophytica sp. nov. is proposed. The type strain is EGI 6500337T (=KCTC 52296T=CPCC 100904T).
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Rhizobium altiplani sp. nov., isolated from effective nodules on Mimosa pudica growing in untypically alkaline soil in central Brazil
Root nodule bacteria were isolated from nodules on Mimosa pudica L. growing in neutral–alkaline soils from the Distrito Federal in central Brazil. The 16S rRNA gene sequence analysis of 10 strains placed them into the genus Rhizobium with the closest neighbouring species (each with 99 % similarity) being R hizobium grahamii , R hizobium cauense , Rhizobium mesoamericanum and R hizobium tibeticum . This high similarity, however, was not confirmed by multi-locus sequence analysis (MLSA) using three housekeeping genes (recA, glnII and rpoB), which revealed R. mesoamericanum CCGE 501T to be the closest type strain (92 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [with majority being C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c)], DNA G+C content (57.6 mol%), and carbon compound utilization patterns supported the placement of the novel strains in the genus Rhizobium . Results of average nucleotide identity (ANI) differentiated the novel strains from the closest species of the genus Rhizobium , R. mesoamericanum , R. grahamii and R. tibeticum with 89.0, 88.1 and 87.8 % similarity, respectively. The symbiotic genes essential for nodulation (nodC) and nitrogen fixation (nifH) were most similar (99–100 %) to those of R. mesoamericanum , another Mimosa-nodulating species. Based on the current data, these 10 strains represent a novel species of the genus Rhizobium for which the name Rhizobium altiplani sp. nov. is proposed. The type strain is BR 10423T (=HAMBI 3664T).
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Characterization of clinical and environmental isolates of Vibrio cidicii sp. nov., a close relative of Vibrio navarrensis
Four Vibrio spp. isolates from the historical culture collection at the Centers for Disease Control and Prevention, obtained from human blood specimens (n=3) and river water (n=1), show characteristics distinct from those of isolates of the most closely related species, Vibrio navarrensis and Vibrio vulnificus , based on phenotypic and genotypic tests. They are specifically adapted to survival in both freshwater and seawater, being able to grow in rich media without added salts as well as salinities above that of seawater. Phenotypically, these isolates resemble V. navarrensis , their closest known relative with a validly published name, but the group of isolates is distinguished from V. navarrensis by the ability to utilize l-rhamnose. Average nucleotide identity and percent DNA–DNA hybridization values obtained from the pairwise comparisons of whole-genome sequences of these isolates to V. navarrensis range from 95.4–95.8 % and 61.9–64.3 %, respectively, suggesting that the group represents a different species. Phylogenetic analysis of the core genome, including four protein-coding housekeeping genes (pyrH, recA, rpoA and rpoB), places these four isolates into their own monophyletic clade, distinct from V. navarrensis and V. vulnificus . Based on these differences, we propose these isolates represent a novel species of the genus Vibrio , for which the name Vibrio cidicii sp. nov. is proposed; strain LMG 29267T (=CIP 111013T=2756-81T), isolated from river water, is the type strain.
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Reclassification of Pseudomonas sp. PB-6250T as Lysobacter firmicutimachus sp. nov.
More LessStrain PB-6250T, isolated from soil in Japan, was first identified in 1992. In contrast to its original taxonomic classification, its 16S rRNA gene sequence showed the highest similarity (99.2 %) to the sequence of Lysobacter enzymogenes DSM 2043T, with Lysobacter antibioticus DSM 2044T being the next most closely related species (98.7 %) with a validly published name. Chemotaxonomic data (fatty acid profile, quinone and polar lipid composition) and the G+C content of strain PB-6250T were compared with those of the closely related type strains L. enzymogenes LMG 8762T, L. antibioticus LMG 8760T, L . capsici DSM 19286T and L. gummosus LMG 8763T; this supported the affiliation of strain PB-6250T to the genus Lysobacter . Phylogenetic analyses, DNA−DNA-hybridization data, biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain PB-6250T from species of Lysobacter with validly published names. Strain PB-6250T, therefore represents a novel species, for which the name Lysobacter firmicutimachus sp. nov. is proposed. The type strain is PB-6250T (=LMG 28994T=DSM 102073T).
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Octadecabacter ponticola sp. nov., isolated from seawater
More LessA Gram-stain-negative, non-spore-forming, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, HDSW-34T, was isolated from seawater of Hwang-do on the Yellow Sea, South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain HDSW-34T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain HDSW-34Tclustered with the type strains of four species of the genus Octadecabacter , showing 96.7–97.6 % sequence similarity. Strain HDSW-34T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids detected in strain HDSW-34T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain HDSW-34T was 62.0 mol% and its DNA–DNA relatedness values with Octadecabacter antarcticus CIP 106731T and Octadecabacter arcticus DSM 13978T were 11–18 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain HDSW-34T is separated from other recognized species of the genus Octadecabacter . On the basis of the data presented, strain HDSW-34T is considered to represent a novel species of the genus Octadecabacter , for which the name Octadecabacter ponticola sp. nov. is proposed. The type strain is HDSW-34T (= KCTC 52250T=NBRC 112296T).
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Paraburkholderia caffeinilytica sp. nov., isolated from the soil of a tea plantation
More LessA novel bacterium, designated strain CF1T, was isolated from a soil sample of a tea plantation and its taxonomic position was determined using a polyphasic approach. Strain CF1T was a Gram-stain-negative, facultatively anaerobic, non-sporulating, non-motile and rod-shaped bacterium. Optimum growth occurred at 25 °C and pH 6.0. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the genus Paraburkholderia , showing highest levels of similarity with respect to Paraburkholderia sediminicola LMG 24238T (98.44 %). Additionally, strain CF1T, P. sediminicola LMG 24238T and Paraburkholderia aspalathi LMG 27731 formed a distinct group in the phylogenetic tree based on 16S rRNA gene sequences. The predominant ubiquinone was Q-8, and the polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid, two unidentified aminolipids and two unidentified polar lipids. The DNA G+C content was 60.2 mol%, and the major fatty acids were C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The DNA–DNA relatedness values between strain CF1T and its close relatives including P. sediminicola LMG 24238T and P. aspalathi LMG 27731 49.3±0.4 % and 38.3±0.5 %, respectively. On the basis of phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate represents a novel species of the genus Paraburkholderia , for which the name Paraburkholderia caffeinilytica sp. nov. is proposed. The type strain is CF1T (=LMG 28690T=CGMCC 1.15103T).
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Spiribacter roseus sp. nov., a moderately halophilic species of the genus Spiribacter from salterns
More LessFour pink-pigmented, non-motile, Gram-staining-negative and moderately halophilic curved rods, designated strains SSL50T, SSL25, SSL97 and SSL4, were isolated from a saltern located in Isla Cristina, Huelva, south-west Spain. Phylogenetic analyses based on 16S rRNA gene sequences showed that they were members of the genus Spiribacter , most closely related to Spiribacter curvatus UAH-SP71T (99.3–99.5 % sequence similarity) and Spiribacter salinus M19-40T (96.5–96.7 %). Other related strains were Alkalilimnicola ehrlichii MLHE-1T (95.1–95.3 %), Arhodomonas recens RS91T (95.1–95.2 %) and Arhodomonas aquaeolei ATCC 49307T (95.0–95.1 %), all members of the family Ectothiorhodospiraceae . The major fatty acids were C18 : 1 ω6c and/or C18 : 1 ω7c, C16 : 0 and C12 : 0. The DNA G+C range was 64.0–66.3 mol%. The DNA–DNA hybridization values between strains SSL50T, SSL25, SSL97, SSL4 and S. piribacter. curvatus UAH-SP71T were 37–49 %. The average nucleotide identity (ANIb) values between the genome of strain SSL50T and those of the two other representatives of the genus Spiribacter , S. curvatus UAH-SP71T and S. salinus M19-40T, were 82.4 % and 79.1 %, respectively, supporting the proposal of a novel species of the genus Spiribacter . On the basis of the polyphasic analysis, the four new isolates are considered to represent a novel species of the genus Spiribacter , for which the name Spiribacter roseus sp. nov. is proposed. The type strain is SSL50T (=CECT 9117T=IBRC-M 11076T).
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Pseudomonas oceani sp. nov., isolated from deep seawater
Ming-qing Wang and Li SunIn this study, we identified a novel Gram-stain-negative, aerobic, motile, and rod-shaped bacterium, strain KX 20T, isolated from the deep seawater in Okinawa Trough, northwestern Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain KX 20T was related to members of the genus Pseudomonas and shares the highest sequence identities with Pseudomonas aestusnigri CECT 8317T (99.4 %) and Pseudomonas pachastrellae JCM 12285T (98.5 %). The 16S rRNA gene sequence identities between strain KX 20T and other members of the genus Pseudomonaswere below 96.6 %. The gyrB and rpoD genes of strain KX 20T shared 82.0 to 89.3 % sequence identity with the gyrB and rpoD genes of the closest phylogenetic neighbours of KX 20T. The predominant cellular fatty acids of strain KX 20T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) (29.2 %), C16 : 0 (24.5 %), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) (21.5 %) and C12 : 0 (8.2 %). The major polar lipids of strain KX 20T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unknown phospholipids. The genomic DNA G+C content of strain KX 20T was 62.9 mol%. On the basis of phylogenetic analysis and phenotypic characteristics, a novel species, Pseudomonas oceani sp. nov. is proposed. The type strain is KX 20T (=CGMCC 1.15195T=DSM 100277T).
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Phylogenetic characterisation of two novel Anaplasmataceae from Australian Ixodes holocyclus ticks: ‘Candidatus Neoehrlichia australis' and ‘Candidatus Neoehrlichia arcana'
More LessRecently, two novel species of Anaplasmataceae were detected in the Australian paralysis tick, Ixodes holocyclus, by 16S rRNA gene metabarcoding. Analysis of these sequences suggested that these novel organisms are closely related to the genus ‘Candidatus Neoehrlichia’. In this study, phylogenetic analysis of 16S rRNA (1264 bp), groESL (1047 bp) and gltA (561 bp) gene sequences, and concatenated (2872 bp) sequences, all concur that these novel species belong in the genus 'Candidatus Neoehrlichia' and are most closely related to, but distinct from the only other recognised members of this genus, ‘Candidatus Neoehrlichia mikurensis’ and ‘Candidatus Neoehrlichia lotoris’. Based on their unique molecular signature, we propose to designate these species ‘Candidatus Neoehrlichia australis’ (reference strain HT41R) and ‘Candidatus Neoehrlichia arcana’ (reference strain HT94R). Identical ‘Candidatus Neoehrlichia australis’ 16S rRNA, groESL and gltA sequences were detected in 34/391 (8.7 %) individual Ixodes holocyclus ticks, and sequences were most similar to ‘Candidatus Neoehrlichia lotoris’ (96.2 %, 83.1 % and 67.2 %, respectively) and ‘Candidatus Neoehrlichia mikurensis’ (96.2 %, 84 % and 68.4 % respectively). Likewise, identical ‘Candidatus Neoehrlichia arcana’ 16S rRNA, groESL and gltA sequences were detected in 12/391 (3.1 %) Ixodes holocyclus ticks, and sequences were most similar to ‘Candidatus Neoehrlichia lotoris’ (98.5 %, 88.7 % and 79.3 %, respectively) and ‘Candidatus Neoehrlichia mikurensis’ (96.3 %, 84 % and 67.4 % respectively). These new species are the first Anaplasmataceae (except Wolbachia spp.) to be found to be endemic to Australia. The pathogenic consequences of these organisms are yet to be determined.
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Chitinibacter fontanus sp. nov., isolated from a spring
More LessA bacterial strain, designated STM-7T, was isolated from a spring in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain STM-7T were Gram-staining-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile by a single polar flagellum, rod-shaped, surrounded by a thick capsule and formed milky-white colonies. Growth occurred at 15–37 °C (optimum, 25–30 °C), at pH 6–8 (optimum, pH 6–7) and with 0–2 % NaCl (optimum, 0–1 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain STM-7T belonged to the genus Chitinibacter and was most closely related to Chitinibacter tainanensis S1T with a sequence similarity of 97.3 %. Strain STM-7T contained summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 as the predominant fatty acids. The major hydroxyl fatty acids were C12 : 0 3-OH and C16 : 0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized phospholipid. The major isoprenoid quinone was Q-8. The DNA G+C content of the genomic DNA was 52.4 mol%. The DNA–DNA hybridization value for strain STM-7T with Chitinibacter tainanensis BCRC 17254T was less than 47 %. On the basis of the phylogenetic inference and phenotypic data, strain STM-7T should be classified as a representative of a novel species, for which the name Chitinibacter fontanus sp. nov. is proposed. The type strain is STM-7T (=BCRC 80923T=LMG 29289T=KCTC 42982T).
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Sphingomonas prati sp. nov., isolated from alpine meadow soil
More LessA Gram-staining-negative, non-motile, orange-coloured and rod-shaped aerobic bacterium, designated W18RDT, was isolated from the alpine meadow soil of the Tibetan plateau. Phylogenetic analysis based on 16S rRNA gene sequences positioned strain W18RDT as a representative of a novel species under the genus Sphingomonas which was most closely related to Sphingomonas fennica DSM 13665T with a sequence similarity level of 97.14 %. Meanwhile, it also had a high level of sequence similarity with Sphingomonas laterariae DSM 25432T (96.51 %), Sphingomonas haloaromaticamans CGMCC 1.10206T (96.43 %) and Sphingomonas formosensis DSM 24164T (96.26 %). The G+C content of the genomic DNA of the type strain W18RDT was 66.4mol%. DNA–DNA relatedness for the type strain W18RDT with respect to its closest phylogenetic relative Sphingomonas. fennica DSM 13665Twas 21.54±1.2 %. Major cellular fatty acids in strain W18RDT were C16 : 1 ω7c and/or C16 : 1 ω6c (48.12 %), C18 : 1 ω7c and/or C18 : 1 ω6c (21.98 %) and C14 : 0 2-OH (14.93 %), with ubiquinone-10 (Q-10) as the predominant respiratory quinone. The polar lipid profile of the strain consisted of phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, diphosphatidylglycerol and two unknown lipids. Based on the evidence from a combination of phenotypic, taxonomic and phylogenetic analyses, strain W18RDT represents a novel species of the genus Sphingomonas , for which the name Sphingomonas prati sp. nov. is proposed. The type strain is W18RDT (=CGMCC 1.15645T=DSM 103336T).
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Rhizobium gei sp. nov., a bacterial endophyte of Geum aleppicum
A bacterial strain, designated as ZFJT-2T, was isolated from the stem of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi Province, north-west China. Cells of strain ZFJT-2T were Gram-stain-negative, strictly aerobic, rod-shaped and motile by means of a single polar flagellum. The major fatty acids were summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0, 11-methyl C18 : 1 ω7c and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), and the DNA G+C content was 58.3 mol% (HPLC). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZFJT-2T was a member of the genus Rhizobium and was most closely related to Rhizobium giardinii KACC 10720T (98.6 % similarity) and Rhizobium herbae CCBAU 83011T (98.5 %). The low levels of sequence similarity found between the atpD, recA and glnII gene sequences of strain ZFJT-2T and those of recognized species of the genus Rhizobium (no more than 94.4, 87.2 and 89.5 %, respectively) indicated that it may represent a separate species of the genus Rhizobium . The DNA–DNA relatedness values for strain ZFJT-2T with respect to R. giardinii KACC 10720T and R. herbae CCBAU 83011T were 17.6 and 41.9 %, respectively. On the basis of phenotypic, phylogenetic and genotypic data, strain ZFJT-2T is considered to represent a novel species of the genus Rhizobium , for which the name Rhizobium gei sp. nov. is proposed. The type strain is ZFJT-2T (=CCTCC AB 2013015T=KCTC 32301T=LMG 27603T).
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- Eukaryotic micro-organisms
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Saturnispora bothae sp. nov., isolated from rotting wood
Two strains representing a novel species of the genus Saturnispora were isolated from rotting wood samples collected in an Atlantic Rainforest site in Brazil. Analyses of the sequences of the D1/D2 domains of the rRNA gene showed that this novel species belongs to a subclade in the Saturnispora clade formed by Saturnispora sanitii, Saturnispora sekii, Saturnispora silvae and Saturnispora suwanaritii. The novel species differed in D1/D2 sequences by 60 or more nucleotide substitutions from these species. The strains produced asci with one to four hemispherical ascospores. A novel species named Saturnispora bothae sp. nov. is proposed to accommodate these isolates. The type strain is UFMG-CM-Y292T (=CBS 13484T). The MycoBank number is MB 817127.
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Wickerhamiella brachini f.a., sp. nov., Wickerhamiella pterostichi f.a., sp. nov. and Wickerhamiella qilinensis f.a., sp. nov., three yeast species isolated from insects
More LessEight strains representing three novel yeast species were isolated from insects distributed in three localities in Nanyang, Henan Province, Central China during 2014 and 2015. Sequence analysis of the D1/D2 domains of the large subunit (LSU) rRNA gene revealed that these species are members of the Wickerhamiella clade. These three novel species have a greater than 2.5 % difference from each other or their closest known species in the D1/D2 sequences. The three yeast species can also be separated from their closest known species in terms of physiological characteristics. Moreover, a sexual state could not be found in these three novel yeast species on various sporulation media. Therefore, the three novel species are described as Wickerhamiella brachini f.a., sp. nov. (type strain, NYNU 15885T=CICC 33092T=CBS 14176T), Wickerhamiella pterostichi f.a., sp. nov. (type strain, NYNU 15896T=CICC 33093T=CBS 14177T) and Wickerhamiella qilinensis f.a., sp. nov. (type strain, NYNU 146103T=CICC 33062T=CBS 13929T). The MycoBank numbers of Wickerhamiella brachini f.a., sp. nov., Wickerhamiella pterostichi f.a., sp. nov. and Wickerhamiella qilinensis f.a., sp. nov. are MB 816962, MB 816963 and MB 816964, respectively.
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Candida vulturna pro tempore sp. nov., a dimorphic yeast species related to the Candida haemulonis species complex isolated from flowers and clinical sample
More LessIn a taxonomic study of yeasts isolated from flowers in Cagayan de Oro, Mindenao Island, The Philippines, strains were identified as representing Kabatiella microsticta, Metschnikowia koreensis and a hitherto undescribed dimorphic species. Sequences of the D1/D2 domains of the LSU 26S rRNA genes, the internal transcribed spacer (ITS) regions and the SSU 18S rRNA genes were identical in the strains of the last-named group and differed from the corresponding sequences of the type strain of the closest related species, Candida duobushaemulonii, by 4 % (D1/D2), 7 % (ITS) and 1 % (SSU). In an independent study, a strain with D1/D2 and ITS sequences very similar to those of the Philippine strains was isolated in Malaysia from the blood of a patient dying of aspiration pneumonia. Both groups of isolates were moderately sensitive to anidulafungin, caspofungin, fluconazole, itraconazole and voriconazole but resistant to amphotericin B. Molecular phylogenetic analysis of the sequences placed the Philippine and Malaysian isolates close to the Candida haemulonis complex of Candida species. To reflect the geographical location of the sites of sample collection, the novel species name Candida vulturna pro tempore sp. nov. is proposed to accommodate these strains. The type strain is 11-1170T (=CBS 14366T=CCY 094-001-001T=NCAIM-Y02177T) isolated in Cagayan de Oro, The Philippines. Mycobank: MB 817222.
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Nematodospora anomalae sp. nov., a novel and D-xylose-fermenting yeast species in the Lodderomyces clade
More LessThree strains of a novel species of ascomycetous yeast were isolated from the beetle species Anomala corpulenta (Scarabaeoidea) collected from the Baotianman and Funiu Mountains of China. These strains produced conjugated asci with a single coiled ascospore. Phylogenetic analysis of the combined sequences of the D1/D2 domains of the large subunit rRNA gene and internal transcribed spacer regions demonstrated that the three strains were closely related to Nematodospora valgi and an undescribed yeast strain, 13Y231. The novel strains could be differentiated from N. valgi CBS 12562T by a 1.6 % sequence divergence (9 substitutions) and from the undescribed yeast strain, 13Y231, by a 1.1 % sequence divergence (6 substitutions) in the D1/D2 sequences. The ITS sequences of these strains displayed more than 4.1 % sequence divergence (12–22 substitutions and 7–8 gaps) from their two closest relatives. Interestingly, all the three strains could ferment d-xylose to ethanol effectively, a rare property among members of the Lodderomyces clade. Therefore, a novel yeast species, Nematodospora anomalae sp. nov., is proposed to accommodate these strains. The type strain of N. anomalae sp. nov. is NYNU 14914T (=CICC 33059T=CBS 13927T). The MycoBank number is MB 816795.
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- ICSP Matters
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Implementation of Rule 8 of the International Code of Nomenclature of Prokaryotes for the renaming of classes. Request for an Opinion
More LessThe new version of Rule 8 of the International Code of Nomenclature of Prokaryotes as approved in Istanbul in 2008 has the clear advantage of establishing a uniform way to name classes of prokaryotes, similar to the way other higher taxa are named. However, retroactive implementation of the modified Rule is problematic as it destabilizes the nomenclature and requires the replacement of a large number of names of classes that have been validly published, which would be in violation of Principle 1 of the Code. Therefore, we call upon the International Committee on Systematics of Prokaryotes and its Judicial Commission to reconsider the retroactivity of Rule 8.
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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)