- Volume 66, Issue 9, 2016
Volume 66, Issue 9, 2016
- Validation List no. 171
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- Notification List
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- New taxa
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- Actinobacteria
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Kocuria pelophila sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove
A novel spherical actinobacterium, designated RS-2-3T, was isolated from the rhizosphere of a mangrove growing on Rambut Island, Indonesia, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain RS-2-3T was related to the members of the genus Kocuria . The highest 16S rRNA gene sequence similarity value was observed with Kocuria marina KMM 3905T (97.0 %). The peptidoglycan type of strain RS-2-3T was found to be A3α with an interpeptide bridge comprising l-Ala4–5. The predominant menaquinone was MK-7(H2) and the major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content was 71.8 mol%. These characteristics were consistent with those of members of the genus Kocuria . Meanwhile, physiological and biochemical characteristics revealed that strain RS-2-3T differed from the species of the genus Kocuria with validly published names. Therefore, strain RS-2-3T represents a novel species of the genus Kocuria , for which the name Kocuria pelophila sp. nov. is proposed. The type strain is RS-2-3T (=NBRC 110990T=InaCC A704T).
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Actinomadura montaniterrae sp. nov., isolated from mountain soil
More LessThe taxonomic position of the mountain soil actinomycete, strain CYP1-1BT, was clarified by a polyphasic study. The strain produced a single spore, or occasionally a chain of spores, on aerial mycelium. Chemotaxonomic data supported the classification of CYP1-1BT as representing a member of the genus Actinomadura on the basis of the presence of meso-diaminopimelic acid in the peptidoglycan; galactose, glucose, madurose and ribose as whole cell sugars; MK-9(H6), MK-9(H8) and MK-9(H4) as dominant menaquinones; C16 : 0, 10-methylated C18 : 0 and C18 : 1ω9c as the major cellular fatty acids; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol manosides as the predominant phospholipids. The DNA G+C content was 74.3 mol%. On the basis of the combination of morphological and chemotaxonomic characteristics, CYP1-1BT was identified as representing a member of the genus Actinomadura . On the basis of the results of 16S rRNA gene analysis, CYP1-1BT, was shown to be closely related to Actinomadura nitritigenes DSM 44137T (98.9 %). Phenotypic, genotypic and DNA–DNA hybridization data supported the hypothesis that CYP1-1BT represents a novel species of the genus Actinomadura for which the name Actinomadura montaniterrae sp. nov. is proposed. The type strain is CYP1-1BT (=JCM 16995T=KCTC 39784T=PCU 349T=TISTR 2400T).
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Nocardia shinanonensis sp. nov., isolated from a patient with endophthalmitis
A nocardioform strain IFM 11456T was isolated from the aqueous humor from a patient with endophthalmitis and was characterized to its taxonomic position. IFM 11456T contained arabinose, galactose and meso-diaminopimelic acid in whole-cell hydrolysates and mycolic acids that co-migrated with those from the type strain of Nocardia asteroides . The acyl type of muramic acid was N-glycolyl. The diagnostic polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and two unidentified glycolipids and the predominant menaquinone was MK-8(H4, ω-cycl.). These characteristics are typical of members of the genus Nocardia . Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate represented a novel species of the genus Nocardia and was most closely related to the type strains of Nocardia mikamii JCM 15508T (98.1 %) and Nocardia aobensis IFM 0372T (98.1 %). However, analysis of partial gyrB sequences showed that strain IFM 11456T had 90.2 % similarity to Nocardia concava IFM 0354T and 90 % to Nocardia niigatensis IFM 0330T. The DNA–DNA relatedness values for strain IFM 11456T compared with N. mikamii JCM 15508T, N. aobensis IFM 0372T and N. concava IFM 0354T ranged from 24.4 to 39.9 %. Phenotypic characteristics that differentiated IFM 11456T from phylogenetically related species were growth at 45 °C, utilization of citrate and growth with inositol as a sole carbon source. On the basis of this polyphasic study, the isolate represents a novel species within the genus Nocardia , for which the name Nocardia shinanonensis sp. nov. is proposed. The type strain is IFM 11456T (=NBRC 109590T=TBRC 5149T).
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Tsukamurella serpentis sp. nov., isolated from the oral cavity of Chinese cobras (Naja atra)
Two bacterial strains, HKU54T and HKU55, were isolated from the oral cavity of two Chinese cobras (Naja atra) in Hong Kong. 16S rRNA gene sequence analysis revealed 100 % sequence identity between HKU54T and HKU55, and the two strains shared 99.0 % sequence identities with T sukamurella inchonensis ATCC 700082T. The two strains had unique biochemical profiles distinguishable from closely related species of the genus Tsukamurella . DNA–DNA hybridization confirmed that they belonged to the same species (≥92.1±7.9 % DNA–DNA relatedness) but were distinct from all other known species of the genus Tsukamurella (≤52.6±5.3 % DNA–DNA relatedness). Chemotaxonomic and morphological analyses of the two strains also demonstrated results consistent with their classification in the genus Tsukamurella . The DNA G+C contents of strains HKU54T and HKU55 were 69.2±1.5 mol% and 69.2±1.3 mol% (mean±sd; n=3) respectively. A novel species, Tsukamurella serpentis sp. nov., is proposed to accommodate strains HKU54T and HKU55, with HKU54T (=JCM 31017T=DSM 100915T) designated as the type strain.
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Flexivirga endophytica sp. nov., an endophytic actinobacterium isolated from a leaf of Sweet Basil
A Gram-reaction-positive, aerobic, non-motile, irregular coccoid strain, designated YIM 7505T, was isolated from a leaf of Sweet Basil. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparisons revealed that strain YIM 7505T was closely related to Flexivirga alba NBRC 107580T (98.9 % 16S rRNA gene sequence similarity) and formed a robust clade with F. alba NBRC 107580T in the neighbour-joining tree. Optimum growth of strain YIM 7505T was observed at 28–35 °C, pH 7.0 and in the presence of 0–3.0 % NaCl (w/v). The chemotaxonomic profiles of the strain comprised of anteiso-C16 : 0 as the major cellular fatty acid and MK-8(H4) as the respiratory menaquinone. The peptidoglycan of strain YIM 7505T contained serine, alanine, glycine, glutamic acid and lysine. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, six unidentified phospholipids, four unidentified glycolipids, an unidentified aminolipid and an unidentified aminophospholipid. The G+C contents of the genomic DNA of strain YIM 7505T was 66.7 mol%. DNA–DNA hybridizations of strain YIM 7505T with F. alba NBRC 107580T gave relatedness values of 50.6±2.2 %. On the basis of the data recorded from the present study, strain YIM 7505T is considered to represent a novel species of the genus Flexivirga, for which the name Flexivirga endophytica sp. nov. is proposed. The type strain is YIM 7505T (=KCTC 39536T=CGMCC 1.15085T).
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Propionibacterium namnetense sp. nov., isolated from a human bone infection
A polyphasic taxonomic study was performed on two Gram-positive-staining, anaerobic, pleomorphic, rod-shaped strains isolated from human bone and tissue samples. Sequencing of the 16S rRNA genes revealed that the strains belong to a novel species within the genus Propionibacterium , most closely related to Propionibacterium acnes subsp. acnes and Propionibacterium acnes subsp. elongatum with similarity values of 98.4 % and 98.1 %, respectively. In addition, protein-coding genes for rpoB, recA and gyrB clearly separated the novel organism from all species and subspecies of the genus Propionibacterium . However, a DNA–DNA hybridization analysis between the novel organism and the type strain P. acnes ATCC 6919T revealed a value of only 61.1 %. Furthermore, whole genome analysis using the program OrthoANI gave a value of 88.5 %, which is significantly below the cut-off value of 95 % for species delineation. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0. The DNA G+C content of the type strain was 59.7 mol%. When taken collectively, phenotypic, molecular genetic, chemotaxonomic and phylogenetic information demonstrate that the organism represents a distinct, albeit close relative of P. acnes On the basis of the results presented, the organism represents a novel member of the genus Propionibacterium for which the name Propionibacterium namnetense sp. nov. is proposed. The type strain is NTS 31307302T (=DSM 29427T=CCUG 66358T).
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Micromonospora ureilytica sp. nov., Micromonospora noduli sp. nov. and Micromonospora vinacea sp. nov., isolated from Pisum sativum nodules
More LessA diversity study on the presence of strains representing the genus Micromonospora in Pisum sativum nodules collected from Cañizal (Spain) has provided evidence of the high number of isolates that might represent novel species. In the present work, we have characterized three of these isolates: GUI23T, GUI43T and GUI63T. Phenotypic and genotypic analyses confirmed that all strains represent novel species of the genus Micromonospora with the following proposed names: Micromonospora ureilytica sp. nov., type strain GUI23T (=CECT 9022T=DSM 101692T), Micromonospora noduli sp. nov., type strain GUI43T (=CECT 9020T=DSM 101694T), and Micromonospora vinacea sp. nov., type strain GUI63T (=CECT 9019T=DSM 101695T).
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Corynebacterium pollutisoli sp. nov., isolated from hexachlorocyclohexane-contaminated soil
More LessA Gram-stain-positive, alkaliphilic, non-spore-forming, non-motile bacterium, designated VDS11T, was isolated from a soil sample collected from the hexachlorocyclohexane dumpsite, located at Ummari Village, Lucknow, Uttar Pradesh, India. 16S rRNA gene sequence analysis indicated that strain VDS11T occupies a distinct phylogenetic position within the genus Corynebacterium , showing the highest sequence similarity with Corynebacterium humireducens MFC-5T (98.7 %) and Corynebacterium nasicanis 2673/12T (98.4 %). The DNA G+C content was 50.6 mol% and the DNA–DNA hybridization (DDH) relatedness value with C. humireducens MFC-5T and C. nasicanis 2673/12T was 49.7 and 39.6 %, respectively. Strain VDS11T contained C16 : 0 (28.3), C18 : 1ω9c (52.3), C18 : 0 (1.3) and C20 : 0 (3.0) as the major cellular fatty acids. The major isoprenoid quinone was MK-9(H2). Strain VDS11T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, unidentified aminolipids, glycolipids, phospholipids and unidentified lipids as the major polar lipids. The peptidoglycan type was A31 (meso 2, 6-diaminopimelic acid, directly cross-linked). Based on the results of DDH studies and the biochemical and physiological data, strain VDS11T represents a novel species of the genus Corynebacteriumfor which the name Corynebacterium pollutisoli sp. nov., has been proposed. The type strain is VDS11T(=DSM 100104T=MCC 2722T=KCTC 39687T).
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Streptomyces rhizosphaerihabitans sp. nov. and Streptomyces adustus sp. nov., isolated from bamboo forest soil
More LessThree novel isolates belonging to the genus Streptomyces , designated JR-35T, JR-46 and WH-9T, were isolated from bamboo forest soil in Damyang, Korea. The 16S rRNA gene sequences of strains JR-35T and JR-46 showed highest similarities with Streptomyces olivochromogenes NBRC 3178T (99.1 %), Streptomyces siamensis KC-038T (98.9 %), Streptomyces chartreusis NBRC 12753T (98.9 %), Streptomyces resistomycificus NRRL ISP-5133T (98.9 %) and Streptomyces bobili JCM 4627T (98.8 %), and strain WH-9Tshowed highest sequence similarities with Streptomyces . bobili JCM 4627T (99.2 %), Streptomyces phaeoluteigriseus NRRL ISP-5182T (99.2 %), Streptomyces alboniger NBRC 12738T (99.2 %), Streptomyces galilaeus JCM 4757T (99.1 %) and Streptomyces pseudovenezuelae NBRC 12904T (99.1 %). The predominant menaquinones were MK-9 (H6) and MK-9 (H8). The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C14 : 0 and iso-C15 : 0 for strains JR-35T and JR-46 and anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0 for strain WH-9T. The G+C content of the genomic DNA of strains JR-35T, JR-46 and WH-9T were 69.4, 74.4 and 74.1 mol%, respectively. Based on the phenotypic and genotypic data, the three strains are assigned to two novel species of the genus Streptomyces , for which the names Streptomyces rhizosphaerihabitans sp. nov. (type stain JR-35T=KACC 17181T=NBRC 109807T) and Streptomyces adustus sp. nov. (type strain WH-9T=KACC 17197T=NBRC 109810T) are proposed.
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Flexivirga lutea sp. nov., isolated from the faeces of a crested ibis, Nipponia nippon, and emended description of the genus Flexivirga
A novel Gram-staining-positive, aerobic, non-motile and coccus-shaped bacterium, designated strain TBS-100T, was isolated from the faeces of a crested ibis, Nipponia nippon. The phylogenetic analysis based on the 16S rRNA gene sequences showed that the closest relative of TBS-100T was Flexivirga alba DSM 24460T with 97.11 % sequence similarity, and that strain TBS-100T belonged to the genus Flexivirga . The optimum growth conditions for strain TBS-100T were 30 °C, at a pH of 7 and in the presence of 0 % (w/v) NaCl. The primary cellular fatty acids of strain TBS-100T were anteiso-C17 : 0 and iso-C17 : 0. The predominant isoprenoid quinones were MK-8 (H4) (70.2 %) and MK-8 (H6) (29.7 %). The polar lipids were diphosphatidylglycerol, phosphatidylinositol, seven unidentified lipids and an unidentified phospholipid. The whole-cell sugars of strain TBS-100T were ribose, glucose, galactose, rhamnose and mannose. The peptidoglycan contained alanine, lysine, glutamic acid, glycine and aspartic acid. The DNA G+C content was 64.8 mol%. The phenotypic, phylogenetic and genotypic analyses indicated that strain TBS-100T represents a novel species of the genus Flexivirga for which the name Flexivirga lutea sp. nov. is proposed. The type strain is TBS-100T (=KCTC 39625T=JCM 31200T). In addition, an emended description of the genus Flexivirga is proposed.
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Streptomyces verrucosisporus sp. nov., isolated from marine sediments
Five actinomycete isolates, CPB1-1T, CPB2-10, BM1-4, CPB3-1 and CPB1-18, belonging to the genus Streptomyces were isolated from marine sediments collected from Chumphon Province, Thailand. They produced open loops of warty spore chains on aerial mycelia. ll-Diaminopimelic acid, glucose and ribose were found in their whole-cell hydrolysates. Polar lipids found were diphosphatidylglycerol, phosphatidylethanolamine, lysophosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. Menaquinones were MK-9(H6), MK-9(H8), MK-10(H6) and MK-10(H8). Major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The taxonomic position of the strains was described using a polyphasic approach. blastn analysis of the 16S rRNA gene sequence revealed that these five strains exhibited the highest similarities with ‘ Streptomyces mangrovicola ' GY1 (99.0 %), Streptomyces fenghuangensis GIMN4.003T (98.6 %), Streptomyces barkulensis RC 1831T (98.5 %) and Streptomyces radiopugnans R97T (98.3 %). However, their phenotypic characteristics and 16S rRNA gene sequences as well as DNA–DNA relatedness differentiated these five strains from the other species of the genus Streptomyces . Here, we propose the novel actinomycetes all being representatives of the same novel species, Streptomyces verrucosisporus , with type strain CPB1-1T (=JCM 18519T=PCU 343T=TISTR 2344T).
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Microlunatus nigridraconis sp. nov., an actinobacterium from rhizosphere soil
More LessAn actinobacterium, designated strain CPCC 203993T, was isolated from a rhizosphere soil sample collected from Heilongjiang Province, northeast China, and was characterized using a polyphasic taxonomy approach. Cells of the strain were Gram-stain-positive, non-motile and non-endospore-forming cocci. The 16S rRNA gene sequence comparison of strain CPCC 203993T with members of the genus Microlunatu s yielded 93.9 % to 97.8 % similarities. In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 203993T was affiliated to the clade of the genus Microlunatus next to Microlunatus parietis DSM 22083T, while the DNA–DNA hybridization value of 31.5 % (±1.8 %) between strain CPCC 203993T and Microlunatus. parietis DSM 22083T was far below 70 %. This result indicated that strain CPCC 203993T represented a different genomic species from M. parietis . Chemotaxonomically, the strain contained ll-2,6-diaminopimelic acid as the diagnostic diamino acid, MK-9(H4) as the only menaquinone, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, three unidentified glycolipids and one unidentified phospholipid in the polar lipids extracts, and anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids, without mycolic acids. The genomic DNA G+C content was 64.04 mol%. The above evidence from the polyphasic study merit the recognition of strain CPCC 203993T as a representative of a novel species of the genus Microlunatus , for which Microlunatus nigridraconis sp. nov. is proposed. The type strain is CPCC 203993T (=DSM 29529T=NBRC 110715T=KCTC 29689T).
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Mycobacterium lutetiense sp. nov., Mycobacterium montmartrense sp. nov. and Mycobacterium arcueilense sp. nov., members of a novel group of non-pigmented rapidly growing mycobacteria recovered from a water distribution system
From our recent survey of non-pigmented rapidly growing mycobacteria in the Parisian water system, three groups of isolates (taxons 1–3) corresponding to possible novel species were selected for taxonomic study. The three taxa each formed creamy white, rough colonies, had an optimal growth temperature of 30 °C, hydrolyzed Tween 80, were catalase-positive at 22 °C and expressed arylsulfatase activity. All three were susceptible to amikacin, ciprofloxacin and tigecycline. The three taxa produced specific sets of mycolic acids, including one family that has never previously been described, as determined by thin layer chromatography and nuclear magnetic resonance. The partial rpoB sequences (723 bp) showed 4–6 % divergence from each other and more than 5 % differences from the most similar species. Partial 16S rRNA gene sequences showed 99 % identity within each species. The most similar sequences for 16S rRNA genes (98–99 % identity over 1444–1461 bp) were found in the Mycobacterium fortuitum group, Mycobacterium septicum and Mycobacterium farcinogenes . The three taxa formed a new clade (bootstrap value, 99 %) on trees reconstructed from concatenated partial 16S rRNA, hsp65 and rpoB sequences. The above results led us to propose three novel species for the three groups of isolates, namely Mycobacterium lutetiense sp. nov. [type strain 071T=ParisRGMnew_1T (CIP 110656T=DSM 46713T)], Mycobacterium montmartrense sp. nov. [type strain 196T=ParisRGMnew_2T (CIP 110655T=DSM 46714T)] and Mycobacteriu marcueilense sp. nov. [type strain of 269T=ParisRGMnew_3T (CIP 110654T=DSM 46715T)].
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Populibacterium corticicola gen. nov., sp. nov., a member of the family Jonesiaceae, isolated from symptomatic bark of Populus × euramericana canker
More LessFour Gram-stain-positive, aerobic, motile bacterial strains were isolated from the bark tissue of Populus × euramericana canker. Growth occurred between 10 and 37 °C and at pH 6–10, with optimal growth at 28–30 °C and pH 7.0–8.0. Growth occurred at 0–3 % (w/v) salinity. The strains were positive for oxidase and catalase activity. The major fatty acids were anteiso-C15 : 0 and C16 : 0. The phospholipid profiles contained diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, two phospholipids and five glycolipids. The peptidoglycan type was A4α, which is based on l-Lys–d-Ser–d-Asp. The DNA G+C content was 58.5 mol%. Based on 16S rRNA gene sequence analysis, as well as physiological and biochemical characteristics, the strains are considered to represent a novel species of a new genus in the family Jonesiaceae . The name proposed is Populibacterium corticicola gen. nov., sp. nov. The type strain of Populibacterium corticicola is 2D-4T (=CFCC 11886T=KCTC 33576T).
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Agromyces aureus sp. nov., isolated from the rhizosphere of Salix caprea L. grown in a heavy-metal-contaminated soil
A Gram-reaction-positive, motile, yellow-pigmented and rod-shaped bacterial strain, designated AR33T, was isolated from the rhizosphere of Salix caprea L. growing in a former zinc/lead mining and processing site in Austria. A polyphasic approach was applied to determine its taxonomic position. 16S rRNA gene sequence analysis, and morphological and chemotaxonomic properties showed that strain AR33T belongs to the genus Agromyces . Strain AR33T had peptidoglycan type B2γ and the major menaquinones were MK-11, MK-10 and MK-12. The main branched-chain fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. Strain AR33T showed catalase and oxidase activity and multiple heavy metal resistances to zinc, lead and cadmium. The DNA G+C content was 70.1 mol%. Levels of 16S rRNA gene sequence similarity with closely related recognized species of the genus Agromyces ranged between 98 and 99 %. However, DNA–DNA hybridization between strain AR33T and the type strains of three Agromyces species showed values lower than 42 % relatedness. Therefore, differential phenotypic characteristics together with DNA–DNA relatedness suggested that strain AR33T can be recognized as representing a distinct Agromyces species, for which the name Agromyces aureus sp. nov. is proposed. The type strain is AR33T (=DSM 101731T=LMG 29235T).
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- Archaea
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Pyrodictium delaneyi sp. nov., a hyperthermophilic autotrophic archaeon that reduces Fe(III) oxide and nitrate
A hyperthermophilic, autotrophic iron and nitrate reducer, strain Su06T, was isolated from an active deep-sea hydrothermal vent chimney on the Endeavour Segment in the north-eastern Pacific Ocean. It was obligately anaerobic, hydrogenotrophic and reduced Fe(III) oxide to magnetite and NO3 − to N2. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was more than 97 % similar to other species of the genera Pyrodictium and Hyperthermus . Therefore, overall genome relatedness index analyses were performed to establish whether strain Su06T represents a novel species. For each analysis, strain Su06T was most similar to Pyrodictium occultum PL-19T. Relative to this strain, the average nucleotide identity score for strain Su06T was 72 %, the genome-to-genome direct comparison score was 13–19 % and the species identification score at the protein level was 89 %. For each analysis, strain Su06T was below the species delineation cutoff. Based on its whole genome sequence and its unique phenotypic characteristics, strain Su06T is suggested to represent a novel species of the genus Pyrodictium , for which the name Pyrodictium delaneyi is proposed. The type strain is Su06T (=DSM 28599T=ATCC BAA-2559T).
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- Bacteroidetes
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Rubrivirga profundi sp. nov., isolated from deep-sea water, and emended description of the genus Rubrivirga
More LessA Gram-staining-negative, rod-shaped, facultatively anaerobic, non-motile and pale-red-pigmented bacterium, designated SAORIC-476T, was isolated from deep-sea water from the Pacific Ocean. 16S rRNA gene sequence analyses showed that strain SAORIC-476T was most closely related to Rubrivirga marina SAORIC-28T (96.8 % similarity) and formed a robust phylogenetic clade with Rubrivirga marina of the family Rhodothermaceae . Optimal growth of strain SAORIC-476T was observed at 25 °C, pH 7.5 and in the presence of 3.0 % (w/v) NaCl. The DNA G+C content of strain SAORIC-476T was 66.2 mol%, and the sole isoprenoid quinone was MK-7. The predominant cellular fatty acids were summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0), iso-C17 : 0, C17 : 1ω8c and iso-C15 : 0. The major polar lipids constituted phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unknown phospholipids and four unknown polar lipids. On the basis of taxonomic data obtained in this study, it was concluded that strain SAORIC-476T represents a novel species of the genus Rubrivirga , for which the name Rubrivirga profundi sp. nov. is proposed. The type strain of Rubrivirga profundi is SAORIC-476T (=NBRC 110607T=KACC 18401T).
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Zeaxanthinibacter aestuarii sp. nov., isolated from estuary sediment and emended description of the genus Zeaxanthinibacter Asker et al. 2007
More LessA Gram-staining-negative, strictly aerobic and yellow-pigmented bacterium, designated strain S2-22T, was isolated from estuary sediment in South Korea. Cells of strain S2-22T were oxidase- and catalase-positive rods without gliding motility. Growth was observed at 15–43 °C (optimum, 35–37 °C), at pH 5.5–9.0 (optimum, pH 6.5–7.5) and in the presence of 0.0–10.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S2-22T formed a tight phyletic lineage with Zeaxanthinibacter enoshimensis TD-ZE3T with a high bootstrap value and their 16S rRNA gene sequence similarity was 94.6 %. The respiratory quinone detected was menaquinone 6 (MK-6) only and iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) and iso-C15 : 1G were the major fatty acids. Phosphatidylethanolamine was identified as the major polar lipid and five unidentified aminolipids, two unidentified phospholipids and three unidentified lipids were also detected as minor polar lipids. The G+C content of the genomic DNA was 45.5 mol%. Based on the phenotypic, chemotaxonomic and molecular features, strain S2-22T clearly represents a novel species of the genus Zeaxanthinibacter , for which the name Zeaxanthinibacter aestuarii sp. nov. is proposed. The type strain is S2-22T (=KACC 18503T=JCM 31155T). An emended description of the genus Zeaxanthinibacter is also proposed.
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Wenyingzhuangia fucanilytica sp. nov., a sulfated fucan utilizing bacterium isolated from shallow coastal seawater
More LessA Gram-staining-negative, rod-shaped, strictly aerobic, non-flagellated, non-gliding and yellow-pigmented bacterial strain, designated as strain CZ1127T, capable of utilizing sulfated fucan, was isolated from shallow coastal seawater of Jiaozhou Bay, Qingdao, PR China. Its taxonomic position was investigated by a polyphasic approach. CZ1127T grew at 15–37 °C (optimum, 25 °C), pH 5.5–9.0 (optimum, pH 6.5–7.5) and in the presence of 0–4 % (w/v) NaCl [optimum, 0–3 % (w/v)]. CZ1127T contained MK-6 as the sole menaquinone, and iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c/C16 : 1ω6c and iso-C15 : 0 3-OH as its major fatty acids. The DNA G+C content of strain CZ1127T was 32.2 mol%. Phylogenetic analysis based on the 16S rRNA gene indicated that strain CZ1127T clustered with members of the genus Wenyingzhuangia and was closely related to Wenyingzhuangia marina CGMCC 1.12162T (97.4 % 16S rRNA gene sequence similarity) and Wenyingzhuangia gracilariae KCTC 42246T (96.1 %). The DNA–DNA relatedness between strain CZ1127T and W. marina CGMCC 1.12162T was 41.9±1.5 %. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, CZ1127T represents a novel species of the genus Wenyingzhuangia, for which the name Wenyingzhuangia fucanilytica sp. nov. is proposed. The type strain is CZ1127T (=CCTCC AB 2015089T=KCTC 42864T).
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Longibacter salinarum gen. nov., sp. nov., isolated from a marine solar saltern
A bacterial strain, designated WDS2C18T, was isolated from a marine solar saltern from the coast of Weihai, Shandong Province, China. Cells of strain WDS2C18T were long rod-shaped, red, and approximately 6.0–12.0 µm in length and 0.3–0.4 µm in width. The strain was Gram-stain-negative, facultatively anaerobic, heterotrophic, catalase-positive and oxidase-negative. Optimal growth was observed at 40 °C, at pH 7.5–8.0 with 8–12 % (w/v) NaCl. Nitrate was not reduced. Glycerol, sucrose, starch and d-mannitol stimulated growth, but not glucose, d-fructose, d-galactose, d-lactose, maltose, d-mannose, d-xylose, d-ribose, d-arabinose, l-rhamnose or cellobiose. The G+C content of the genomic DNA was 58.1 mol% (HPLC). The sole methyl naphthoquinone was MK-7 and the predominant cellular fatty acids (>10 %) were iso-C15 : 0 2-OH/C16 : 1 ω7c, iso-C17 : 1 ω9c, iso-C15 : 0 and iso-C17 : 0. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, glycolipid, three unidentified phospholipids and two unidentified lipids. Phylogenetic analysis, based on 16S rRNA gene sequences, demonstrated that strain WDS2C18T was affiliated with the family Rhodothermaceae . The closest related neighbours were species of the genera Salisaeta andLongimonas; strain WDS2C18T shared highest 16S rRNA gene sequence similarities with Salisaeta longa DSM 21114T (91.7 %) and Longimonas halophila SYD6T (90.8 %) and less than 90.0 % to other species of the family Rhodothermaceae . On the basis of these phenotypic and phylogenetic data, strain WDS2C18T should be classified as representing a novel species of a new genus within the family Rhodothermacea e, for which the name Longibacter salinarum gen. nov., sp. nov. is proposed. The type strain of Longibacter salinarum is WDS2C18T (=MCCC 1H00132T=KCTC 52045T).
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Echinicola rosea sp. nov., a marine bacterium isolated from surface seawater
More LessA novel Gram-stain-negative, rod-shaped, gliding, halotolerant, aerobic, light-pink-pigmented bacterium, strain JL3085T, was isolated from surface water of the South China Sea (16° 49′ 4″ N 112° 20′ 24″ E; temperature: 28.3 °C, salinity: 34.5%). The major respiratory quinone was menaquinone 7 (MK-7). The polar lipids of strain JL3085T comprised phosphatidylethanolamine, four unidentified phospholipids and three unidentified lipids. The major fatty acids were iso-C15 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c), iso-C17 : 0 3-OH, iso-C17 : 1 ω9c, C17 : 1 ω6c, anteiso-C15 : 0 and C16 : 1 ω5c. The DNA G+C content of strain JL3085T was 43.8 mol%. 16S rRNA gene sequence analysis indicated that strain JL3085T was affiliated with the genus Echinicola , a member of the phylum Bacteroidetes , and was related most closely to Echinicola vietnamensis KMM 6221T (96.8 % similarity). DNA–DNA relatedness between strain JL3085T and E. vietnamensis KMM 6221T was 27.5 %. Based on the evidence presented here, strain JL3085T is regarded as representing a novel species of the genus Echinicola , for which the name Echinicola rosea sp. nov. is proposed. The type strain is JL3085T (=NBRC 111782T=CGMCC 1.15407T).
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Flavobacterium verecundum sp. nov., isolated from a freshwater river
More LessStrain TTM-46T, isolated from a water sample taken from the Caohu River in Taiwan, was characterized using a polyphasic taxonomy approach. Cells of TTM-46T were Gram-staining-negative, strictly aerobic, motile by gliding, rod-shaped, surrounded by a thick capsule and formedyellowish-green colored colonies. Growth occurred at 20–30 °C (optimum, 30 °C), at pH 6–8 (optimum, pH 7) and with 0–0.3 % NaCl (optimum, 0 % w/v). Phylogenetic analyses based on 16 S rRNA gene sequences showed that TTM-46T represented a member of the genus Flavobacterium and was most closely related to Flavobacterium columnare IFO 15943T and Flavobacterium brevivitae TTM-43T with a sequence similarity of 96.9 % for both. TTM-46T contained iso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0), iso-C17 : 0 3-OH, iso-C15 : 1 G, iso-C15 : 0 3-OH and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) as the predominant fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids and five uncharacterized phospholipids. The major polyamine was homospermidine. The genomic DNA G+C content of TTM-46T was 39 mol%. On the basis of the phylogenetic inference and phenotypic data, TTM-46T was recognized as a representative of a novel species within the genus Flavobacterium . The name Flavobacterium verecundum sp. nov. is proposed, with TTM-46T (=BCRC 80914T=LMG 29005T=KCTC 42745T) as the type strain.
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Emticicia paludis sp. nov., isolated from wetland freshwater
More LessA novel bacterium, designated HMF3850T, was isolated from freshwater collected from the Gyeong-an wetland, Republic of Korea. Cells were Gram-stain-negative, aerobic, straight rods, non-motile, and oxidase- and catalase-positive. Growth was observed at pH 6.0–8.0 and at 10–30 °C on R2A agar. Comparative analysis of 16S rRNA gene sequences revealed that strain HMF3850T is a member of the genus Emticicia , sharing highest sequence similarities with Emticicia aquatica HMF2925T (96.7 % 16S rRNA gene sequence similarity), Emticicia sediminis JBR12T (95.0 %), Emticicia ginsengisoli Gsoil 085T (94.9 %) and Emticicia oligotrophica DSM 17448T (94.7 %). The major fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0. The predominant respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine, phosphatidylinositol, one unidentified aminophospholipid, two unidentified aminolipids and eight unidentified polar lipids. The DNA G+C content was 38.5 mol %. On the basis of the evidence presented in this study, strain HMF3850T represents a novel species of the genus Emticicia , for which the name Emticicia paludis sp. nov. is proposed. The type strain is HMF3850T (=KCTC 42851T=CECT 9087T).
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Oceanihabitans sediminis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the Yellow Sea
More LessA Gram-stain-negative, rod-shaped bacterial strain, designated S9-10T, was isolated from a sediment sample from the Yellow Sea near China. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain S9-10T was a member of the family Flavobacteriaceae and formed a distinct lineage. The genomic DNA G+C content of strain S9-10T was 34.2 mol%. The major respiratory quinone was MK-6. The predominant cellular fatty acids were iso-C15 : 0 (21.1 %), iso-C15 : 1G (16.3 %) and iso-C17 : 0 3-OH (12.0 %). The polar lipid profile contained phosphatidylethanolamine, aminophospholipid, aminoglycolipid, two unidentified aminolipids and five unidentified polar lipids. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, strain S9-10T represents a novel species of a novel genus of the family Flavobacteriaceae , for which the name Oceanihabitans sediminis gen. nov., sp. nov. is proposed. The type strain of Oceanihabitans sediminis is S9-10T (=DSM 28133T =LMG 28074T).
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Aquimarina aggregata sp. nov., isolated from seawater
More LessA novel Gram-stain-negative, agarolytic, rod-shaped, non-flagellated, strictly aerobic strain with gliding motility, designated RZW4-3-2T, was isolated from coastal seawater of the Yellow Sea in China (119.625° E 35.517° N). The organism grew optimally at 28 °C, at pH 7.0 and in the presence of 2.0–3.0 % (w/v) NaCl. The strain required seawater or artificial seawater for growth, and NaCl alone did not support growth. Strain RZW4-3-2T contained MK-6 as the major respiratory quinone and iso-C17 : 0 3-OH, iso-C15 : 0, iso-C15 : 1 G and iso-C15 : 0 3-OH as the dominant fatty acids. The polar lipids of strain RZW4-3-2T comprised phosphatidylethanolamine, five unknown phospholipids and one unknown lipid. The DNA G+C content of strain RZW4-3-2T was 32.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was related most closely to Aquimarina pacifica SW150T, Aquimarina macrocephali JCM 15542T and Aquimarina muelleri LMG 22569T with 98.1, 97.4 and 97.1 % sequence similarities, respectively. The estimated DNA–DNA hybridization values were 20.00±2.31 %, 20.70±2.33 % and 20.70±2.32 % between strain RZW4-3-2T and A. pacifica SW150T, A. macrocephali JCM 15542T and A. muelleri LMG 22569T, respectively. On the basis of results of polyphasic analyses, strain RZW4-3-2T represents a novel species of the genus Aquimarina , for which the name Aquimarina aggregata sp. nov. is proposed. The type strain is RZW4-3-2T (=JCM 30824T=MCCC 1K00698T).
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Flavisolibacter tropicus sp. nov., isolated from tropical soil
A Gram-stain-negative, non-motile, deep yellow, rod-shaped bacterium, designated strain LCS9T, was isolated from a soil sample at the tropical zone within the Ecorium of the National Institute of Ecology in Seocheon, central-western Korea. 16S rRNA gene sequence analysis showed that strain LCS9T clustered with members of the genus Flavisolibacter of the family Chitinophagaceae , phylum Bacteroidetes . Sequence similarities between strain LCS9T and the type strains of the genus Flavisolibacter ranged from 94.6 to 94.9 %. Strain LCS9T grew at 10–37 °C (optimum, 25 °C) and at pH 6.0–10.0 (optimum, pH 7); was positive for catalase and oxidase; and negative for nitrate reduction and production of indole. Cells showed pigment absorbance peaks at 451 and 479 nm, and had 0.03 % survival following exposure to 3 kGy gamma radiation. Strain LCS9T had the following chemotaxonomic characteristics: the major quinone was menaquinone-7 (MK-7); the major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH; polar lipids included phosphoatidylethanolamine, an unidentified aminophospholipid, unidentified aminolipidsand unidentified lipids. The DNA G+C content was 39.4 mol%. Based on polyphasic analysis, the type strain LCS9T (=KCTC 42070T=JCM 19972T) represents a novel species for which the name Flavisolibacter tropicus sp. nov. is proposed. Radiation resistance in the genus Flavisolibacter has not been reported to date, and so this is the first report of low-level radiation resistance of a member of the genus.
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Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil
More LessA Gram-stain-negative, pseudo-rod, non-spore-forming, oxidase- and catalase-positive, strictly aerobic bacterium, designated Gsoil 221T, was isolated from soil of a ginseng field and subjected to a taxonomic analysis using a polyphasic approach. Strain Gsoil 221T grew at 10–37 °C and at pH 5.0–8.0 on R2A medium. Strain Gsoil 221T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1 and Rc (two dominant active components of ginseng) to ginsenoside F2. Phylogenetic study based on the 16S rRNA gene sequence positioned strain Gsoil 221T in a distinct lineage in the family Chitinophagaceae , sharing less than 94.4 % 16S rRNA gene sequence similarity with all taxa with validly published names. The strain showed the highest sequence similarities with members of the genera Parasegetibacter , Flavitalea , Niastella and Terrimonas . Strain Gsoil 221T contained MK-7 as predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G as major fatty acids. The DNA G+C content was 47.1 mol%. Strain Gsoil 221T could be distinguished from the other members of the family Chitinophagaceae by a number of chemotaxonomic and phenotypic characteristics. The major polar lipids of strain Gsoil 221T were diphosphatidylglycerol, phosphatidylethanolamine and one unidentified polar lipid. Based on these combined data, strain Gsoil 221T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Pseudobacter ginsenosidimutans gen. nov., sp. nov. is proposed. The type strain of the type species is Gsoil 221T (=KACC 14278T=DSM 18116T).
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Sphingobacterium populi sp. nov., isolated from bark of Populus × euramericana
More LessA Gram-stain-negative, aerobic, non-motile bacterial strain, 7Y-4T, was isolated from bark tissue of Populus × euramericana. The isolate was able to grow between 10 and 37 °C, with optimal growth occurring at 28–30 °C. Strain 7Y-4T was positive for oxidase and catalase activities, but did not reduce nitrite from nitrate. Positive reactions were observed for the activities of β-galactosidase, urease and β-glucosidase, but negative reactions for the activities of gelatinase and the production of indole, acetoin and H2S. Citrate was not utilized. The major fatty acids of strain 7Y-4T are iso-C15 : 0 (28.6 %), C16 : 1ω7c/C16 : 1ω6c (31.8 %) and iso-C17 : 0 3-OH (23.3 %).The major polar lipids of the novel isolate include phosphatidylethanolamine, three unknown phospholipids (PL1–3) and six unknown lipids (L1–6), and the predominant menaquinone is MK-7. The DNA G+C content is 41.7 mol%. Analysis of 16S rRNA gene sequences revealed that the novel isolate shared the greatest sequence similarity with Sphingobacterium hotanense XH4T (93.50 %). On the basis of phenotypic and genotypic characteristics, strain 7Y-4T represents a novel species of the genus Sphingobacterium , for which the name Sphingobacterium populi is proposed. The type strain is 7Y-4T (=CFCC 11742T=KCTC 42247T).
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Hymenobacter coalescens sp. nov., isolated from wetland freshwater
More LessA non-motile and rod-shaped bacterium, designated strain WW84T, was isolated from freshwater collected from the Woopo wetland (Republic of Korea). Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were C16 : 0, C18 : 0, iso-C15 : 0 and iso-C17 : 1I and/or anteiso-C17 : 1B. The strain contained MK-7 as the major isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine. The DNA G+C content was 59 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain WW84T forms an evolutionary lineage within the radiation including the members of the genus Hymenobacter with Hymenobacter o cellatus Myx 2105T (96.96 % sequence similarity) as its nearest neighbor. A number of phenotypic characteristics distinguished strain WW84T from the related members of the genus Hymenobacter . On the basis of the evidence presented in this study, a novel species, Hymenobacter coalescens sp. nov. is proposed with strain WW84T (=KCTC 32530T=JCM 19493T) as the type strain.
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Taeania maliponensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater
More LessA Gram-strain-negative, rod-shaped, non-motile bacterial strain, designated MM-8T, was isolated from seawater in the Korean peninsula. Strain MM-8T was found to grow optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain MM-8T falls within the clade comprising members of the genera Actibacter , Lutimonas and Namhaeicolain the family Flavobacteriaceae . Strain MM-8T exhibited 16S rRNA gene sequence similarity values of 94.4–96.9 % with respect to the type strains of members of the genera Actibacter , Lutimonas and Namhaeicola . Strain MM-8T was found to contain MK-6 (90.0 %) and MK-7 (10.0 %) as the predominant menaquinones and iso-C15 : 0 (32.4 % ), iso-C15 : 1 G (11.4 %) and iso-C15 : 0 3-OH (10.1 %) as the major fatty acids. The major polar lipids were identified as phosphatidylethanolamine and an unidentified lipid. The DNA G+C content of strain MM-8T was determined to be 40.7 mol%. Differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrate that strain MM-8T is distinguishable from the type strains of type species of the genera Actibacter , Lutimonas and Namhaeicola . On the basis of the data presented, strain MM-8T is considered to represent a novel genus and species, for which the name Taeania maliponensis gen. nov., sp. nov. is proposed. The type strain is MM-8T (=KCTC 52209T=NBRC 112238T).
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Algoriphagus roseus sp. nov., isolated from a hexachlorocyclohexane-contaminated dumpsite
More LessA Gram-staining negative, reddish-pink, non-motile, rod-shaped bacterial strain designated W29T, was isolated from a hexachlorocyclohexane-contaminated dumpsite located in the northern part of India at Ummari Village, Lucknow. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain W29T formed a lineage within the genus Algoriphagus and exhibited highest sequence similarity to Algoriphagus trabzonensis MS7T (98.8 %), followed by Algoriphagus alkaliphilus AC-74T (97.1 %). The 16S rRNA gene sequence similarity between strain W29T and other species of the genus Algoriphagus ranged from 93.3–98.8 %. The DNA–DNA relatedness between strain W29T and A. trabzonensis MS7T was 47 % and with other related strains was found to be less than 45 %, confirming strain W29T represents a novel species. The DNA G+C content of strain W29T was 46.2 mol%. Strain W29T was oxidase- and catalase-positive. The major fatty acids (>10 %) of strain W29T were iso-C15 : 0, summed feature 9 (comprising 10-methyl C16 : 0 and/or iso-C17 : 1ω9c) and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). The respiratory quinone was MK-7. The polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, two unidentified aminolipids, an unidentified aminophospholipid, an unidentified phospholipid and unidentified lipids. On the basis of the results obtained from DNA–DNA hybridization, and biochemical and physiological tests in this study, strain W29T represents a novel species of the genus Algoriphagus for which the name Algoriphagus roseus sp. nov. is proposed. The type strain is W29T (=KCTC 42940T=MCC 2876T=DSM 100160T).
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Vitellibacter aquimaris sp. nov., a marine bacterium isolated from seawater
A Gram-staining-negative, aerobic, yellow–orange-pigmented, rod-shaped bacterium designated D-24T was isolated from seawater from sandy shoreline in Johor, Malaysia. The 16S rRNA gene sequence analysis revealed that strain D-24T is affiliated with the genus Vitellibacter . It shared more than 96 % sequence similarity with the types of some of the validly published species of the genus: Vitellibacter vladivostokensis KMM 3516T (99.5 %), Vitellibacter soesokkakensis RSSK-12T (97.3 %), Vitellibacter echinoideorum CC-CZW007T (96.9 %), Vitellibacter nionensis VBW088T (96.7 %) and Vitellibacter aestuarii JCM 15496T (96.3 %). DNA–DNA hybridization and genome-based analysis of average nucleotide identity (ANI) of strain D-24T versus V. vladivostokensis KMM 3516T exhibited values of 35.9±0.14 % and 89.26 %, respectively. Strain D-24T showed an even lower ANI value of 80.88 % with V. soesokkakensis RSSK-12T. The major menaquinone of strain D-24T was MK-6, and the predominant fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. Strain D-24T contained major amounts of phosphatidylethanolamine, two lipids and two aminolipids, and a phosphoglycolipid that was different to that of other species of the genus Vitellibacter . The genomic DNA G+C content was 40.6 mol%. On the basis of phenotypic properties, DNA–DNA relatedness, ANI value and chemotaxonomic analyses, strain D-24T represents a novel species of the genus Vitellibacter , for which the name Vitellibacter aquimaris sp. nov. is proposed. The type strain is D-24T (=KCTC 42708T=DSM 101732T).
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Compostibacter hankyongensis gen. nov., sp. nov., isolated from compost
More LessA novel bacterial strain, designated strain BS27T, was isolated from mushroom compost and subjected to a taxonomic study using a polyphasic approach. Colonies of BS27T were milky-white, circular with regular fringes and opaque. Cells were short rods, 0.3–0.5 µm wide and 1.2–2.0 µm long. Phylogenetic study based on the 16S rRNA gene sequence placed BS27T in a distinct lineage in the family Chitinophagaceae , sharing 90.1–90.9 % sequence similarity with members of the closely related genera Chitinophaga , Flavitalea , Flavihumibacter , Lacibacter and Flavisolibacter . The novel isolate showed the highest sequence similarities with the members of the genus Chitinophaga . BS27T contained MK-7 as predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) and iso-C17 : 1I and/or anteiso-C17 : 1B (summed feature 4) as major fatty acids. The DNA G+C content was 53.0 mol%. The major polar lipids of BS27T were phosphatidylethanolamine (PE) and five unidentified polar lipids (L1, L2, L5, L6 and L7). The results of physiological and biochemical tests allowed phenotypic differentiation of BS27T from its closest phylogenetic neighbours. On the basis of the evidence of this polyphasic study, isolate BS27T represents a novel genus and species in the family Chitinophagaceae for which the name Compostibacter hankyongensisgen. nov., sp. nov. is proposed. The type strain is BS27T (=KACC 18745T=JCM 17664T).
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Pseudotenacibaculum haliotis gen. nov., sp. nov., a new member within the Tenacibaculum-Polaribacter clade of the family Flavobacteriaceae, isolated from the intestine of adult abalones, Haliotis diversicolor and H. discus hannai
More LessTwo rod-shaped marine bacterial strains named FDZSB0410T and FDZWPB0420, were isolated from the intestine of two adult abalone species, Haliotis diversicolor and Haliotis discus hannai, respectively. The strains were non-flagellated, motile by gliding, oxidase-positive but catalase-negative, and agar-degrading. The two strains had identical 16S rRNA gene sequences with the highest sequence similarity less than 96.0 % with species of the genera Tenacibaculum and Polaribacter within the family Flavobacteriaceae . Phylogenetic analysis indicated the strains represented an independent cluster neighbouring with the species of the genera Tenacibaculum and Polaribacter . Strain FDZSB0410T can grow under conditions at 15 to 37 °C with optimum of 30 °C, salinity range from 3 to 4 % (NaCl, w/v) with optimum of 3 %, and pH range from 7 to 8 with optimum of pH 7. The predominant fatty acids of strain FDZSB0410T consisted of iso-C15 : 0, iso-C15 :1 G, summed feature 3 (comprising C16 : 1 ω7c/C16 : 1 ω6c), iso-C13 : 0, iso-C17 : 0 3-OH, and iso-C15 : 0 3-OH. The ubiquinone system detected was MK-6. The flexirubin pigment was absent, but the carotenoid was present. The polar lipids were identified as aminolipid, glycolipid, phosphatidylglycerol, an unknown phospholipid and four unknown lipids. The DNA G+C content was 35.3 mol%. On the basis of the genotypic and phenotypic characterizations, strain FDZSB0410T and strain FDZWPB0420 represent a novel species of a new genus in the family Flavobacteriaceae, for which the name Pseudotenacibaculum haliotis gen. nov., sp. nov. is proposed. The type strain of the type species is FDZSB0410T (=KCTC 52127T=MCCC 1A01897T).
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- Firmicutes and related organisms
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Streptococcus pantholopis sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii)
Two bacterial strains were isolated from faecal samples of Tibetan antelopes. The isolates were Gram-stain-positive, catalase-negative, coccus-shaped organisms that were tentatively identified as representing a novel streptococcal species based on their morphological features, biochemical test results and phylogenomic findings. Comparative 16S rRNA gene sequencing studies confirmed that the organisms were members of the genus Streptococcus , but they did not correspond to any recognized species of the genus. The nearest phylogenetic relative of the unknown coccus was Streptococcus ursoris NUM 1615T (93.4 % 16S rRNA gene sequence similarity). Analysis of groEL and rpoB gene sequences of the novel isolates showed interspecies divergence of 27.0 and 22.2 %, respectively, from the type strain of its closest 16S rRNA gene phylogenetic relative, S. ursoris. The complete genome of strain TA 26T has been sequenced. Digital DNA–DNA hybridization studies between strain TA 26T and other species of the genus Streptococcus deposited in the GenBank database showed less than 70 % DNA–DNA relatedness, supporting a novel species status of the strain. On the basis of their genotypic and phenotypic differences from recognized Streptococcus species, the two isolates represent a novel species of the genus Streptococcus , for which the nameStreptococcus pantholopis sp. nov. (type strain TA 26T=CGMCC 1.15667T=DSM 102135T) is proposed.
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Paenibacillus aceti sp. nov., isolated from the traditional solid-state acetic acid fermentation culture of Chinese cereal vinegar
Pan Li, Weifeng Lin, Xiong Liu, Sha Li, Lixin Luo and Wei-Tie LinA Gram-stain-negative, rod-shaped, motile, endospore-forming, facultatively anaerobic bacterium, designated strain L14T, was isolated from the traditional acetic acid fermentation culture of Chinese cereal vinegars. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain L14T was affiliated to the genus Paenibacillus , most closely related to Paenibacillus motobuensis MC10T with 97.8 % similarity. Chemotaxonomic characterization supported the allocation of the strain to the genus Paenibacillus . The polar lipid profile of strain L14T contained the major compounds diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The predominant menaquinone was MK-7, and the major fatty acid components were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. The DNA G+C content of strain L14T was 49.9 mol%. The DNA–DNA relatedness value between strain L14T and P. motobuensis MC10T was 51.2 %. The results of physiological and biochemical tests allowed phenotypic differentiation of strain L14T from closely related species. On the basis of phenotypic and chemotaxonomic analyses, phylogenetic analysis and DNA–DNA relatedness values, strain L14T is considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus aceti sp. nov. is proposed. The type strain is L14T (=CGMCC 1.15420T=JCM 31170T).
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Bacillus oryzisoli sp. nov., isolated from rice rhizosphere
More LessThe taxonomy of strain 1DS3-10T, a Gram-staining-positive, endospore-forming bacterium isolated from rice rhizosphere, was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the novel strain was grouped with established members of the genus Bacillus and appeared to be closely related to the type strains Bacillus benzoevorans DSM 5391T (97.9 %), Bacillus circulans DSM 11T (97.7 %), Bacillus novalis JCM 21709T (97.3 %), Bacillus soli JCM 21710T (97.3 %), Bacillus oceanisediminis CGMCC 1.10115T (97.3 %) and Bacillusnealsonii FO-92T (97.1 %). The fatty acid profile of strain 1DS3-10T, which showed a predominance of iso-C15 : 0 and anteiso-C15 : 0, supported the allocation of the strain to the genus Bacillus . The predominant menaquinone was MK-7 (100 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unknown aminolipids. Cell-wall peptidoglycan contained meso-diaminopimelic acid. DNA–DNA hybridization values between strain 1DS3-10T and the type strains of closely related species were 25–33 %, which supported that 1DS3-10T represented a novel species in the genus Bacillus . The results of some physiological and biochemical tests also allowed the phenotypic differentiation of strain 1DS3-10T from the most closely related recognized species. On the basis of the phylogenetic and phenotypic evidence, strain 1DS3-10T represents a novel species of the genus Bacillus , for which the name Bacillus oryzisoli sp. nov. is proposed. The type strain of the novel species is 1DS3-10T (=ACCC 19781T=DSM 29761T).
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Pseudogracilibacillus marinus sp. nov., isolated from a biofilm formed in coastal seawater
A Gram-staining-positive, aerobic, motile, rod-shaped (0.4–0.5×2.0–4.0 µm), endospore-forming bacterium, designated strain NIOT.bflm.S4T, was isolated from biofilm formed on high-density polyethylene test coupons in coastal seawater. The strain required seawater for growth. It grew with 1.0–8.0 % (w/v) NaCl, at 4–45 °C and at pH 6.5–9.0, with optimum growth with 4.0–5.0 % (w/v) NaCl, at 30 °C and at pH 7.0–8.0. Phylogenetic analyses based on 16S rRNA and partial dnaK gene sequences showed that strain NIOT.bflm.S4T formed a phylogenetic lineage with Pseudogracilibacillus auburnensis P-207T, the only known species of the genus Pseudogracilibacillus and shared sequence identities of 96.9 and 83 %, respectively, with this strain. The identities of 16S rRNA and partial dnaK gene sequences with members of other related genera such as Gracilibacillus , Paraliobacillus , Ornithinibacillus , Oceanobacillus , Virgibacillus and Lentibacillus were ≤95 and ≤78 %, respectively. The DNA G+C content of strain NIOT.bflm.S4T was 39.1 mol%. MK-7 was found as the sole isoprenoid quinone. The major polar lipids of strain NIOT.bflm.S4T were diphosphatidylglycerol, phosphatidylethanolamine and an unknown lipid. The diagnostic diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. Major cellular fatty acids were anteiso-C15 : 0 (27.9 %), anteiso-C17 : 0 (18.6 %), C12 : 0 (8.7 %) and iso-C15 : 0 (6.6 %). On the basis of phenotypic, phylogenetic and chemotaxonomic results, we propose that the isolate represents a novel species of the genus Pseudogracilibacillus , for which the name Pseudogracilibacillus marinus sp. nov. is proposed. The type strain is NIOT.bflm.S4T (=KACC 18456T=MTCC 12376T=TBRC 5831T).
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Jeotgalicoccus schoeneichii sp. nov. isolated from exhaust air of a pig barn
More LessA Gram-staining-positive, non-motile, non-spore-forming, coccus (strain 140805-STR-02T) was isolated from exhaust air of a pig barn on Columbia Blood Agar Base (Oxoid) supplemented with 5 % defibrinated horse blood, Streptococcus selective supplement and 0.5 mg erythromycin l−1. The strains shared high 16S rRNA gene sequence similarity to Jeotgalicoccus pinnipedialis (98.6 %) but only a maximum of 94 % sequence similarity to all other species of the genus Jeotgalicoccus . DNA–DNA hybridisation values between strain 140805-STR-02T and J. pinnipedialis CIP 107946T were 60.3 % (reciprocal, 51.2 %). The quinone system of 140805-STR-02T contained predominantly menaquinone MK-7 and minor amounts of MK-6. The polar lipid profile of strain 140805-STR-02T contained the major compounds diphosphatidylglycerol and phosphatidylglycerol and four unidentified lipids present in minor to moderate amounts. In the polyamine pattern spermidine and spermine were predominant. The fatty acid profile comprising iso-C15 : 0 and anteiso-C15 : 0 as major fatty acids, and was in congruence with those reported for other species of the genus Jeotgalicoccus and thus supported the affiliation of strain 140805-STR-02T to this genus. The results of physiological and biochemical tests allowed a clear phenotypic differentiation of strain 140805-STR-02T from the most closely related species. Strain 140805-STR-02T represents a novel species, for which the names Jeotgalicoccus schoeneichii sp. nov. is proposed, with the type strain 140805-STR-02T (=LMG 29445T=CCM 8667T).
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Agathobaculum butyriciproducens gen. nov. sp. nov., a strict anaerobic, butyrate-producing gut bacterium isolated from human faeces and reclassification of Eubacterium desmolans as Agathobaculum desmolans comb. nov.
A novel bacterial strain, SR79T, was isolated from a Korean faecal sample and characterized using a polyphasic approach. SR79T was found to be a strictly anaerobic, Gram-stain-positive, non-spore-forming, non-motile, catalase- and oxidase-negative short rod with no flagella. SR79T grew optimally at 37 °C in the presence of 0.5 % (w/v) NaCl at pH 7. The NaCl range for growth was 0–1 % (w/v). The isolate produced butyric acid (>18 mM) as a major end product. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the most closely related type strains were Eubacterium desmolans ATCC 43058T and Butyricicoccus pullicaecorum 25-3T (96.4 and 96.0 % similarity, respectively). The DNA G+C content was determined to be 52.9 mol%. The major cellular fatty acids (>10 %) were C16 : 0, C18 : 1 cis-9, C19 : 1 cyc 9,10 and C14 : 0. Meso-diaminopimelic acid was present in the cell wall peptidoglycan and the cell wall hydrolysates contained ribose, glucose and galactose. The 16S rRNA gene sequence similarity, phylogenetic analysis, chemotaxonomic and phenotypic characteristics allowed differentiation of SR79T, which represents a novel species of a new genus within the family Ruminococcaceae , for which the name Agathobaculum butyriciproducens gen. nov. sp. nov. is proposed. The type strain is SR79T (=KCTC 15532T=DSM 100391T). Based on the results of this study, it is also proposed to transfer Eubacterium desmolans to this new genus, as Agathobaculum desmolans comb. nov. The type strain of Agathobaculum desmolans is ATCC 43058T (=CCUG 27818T).
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Paenibacillus segetis sp. nov., isolated from soil of a tropical rainforest
More LessA Gram-stain-positive, facultatively anaerobic, endospore-forming, irregular rod-shaped bacterium, designated DB13260T, was isolated from tropical rainforest soil in Jianfengling Nature Reserve in Hainan, China. The isolate was found to grow with 0–4 % (w/v) NaCl, at 5–40 °C and pH 6.0–10.5, with an optimum of 0 % NaCl, 30–37 °C and pH 8.5–9.0, respectively. The predominant isoprenoid quinone was menaquinone 7 (MK-7), and the major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. The G+C content of the genomic DNA was 53.7 mol%. Analysis of the 16S rRNA gene sequence of strain DB13260T showed an affiliation of the strain with the genus P aenibacillus , sharing 98.3 % and 97.8 % 16S rRNA gene sequence similarities with the closest relatives P aenibacillus anaericanus MH21T and Paenibacillus selenii W126T, respectively. The DNA–DNA hybridization values between strain DB13260T and the two type strains were 60.4 % and 42.6 %, respectively. The combined phenotypic and DNA–DNA hybridization data supported the conclusion that strain DB13260T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus segetis sp. nov. is proposed. The type strain is DB13260T (=CGMCC 1.12769T=DSM 28014T).
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Marinicrinis sediminis gen. nov., sp. nov., isolated from marine sediment
More LessNovel Gram-stain-variable, bent rods or long filaments that were endospore-forming, facultatively anaerobic, oxidase- and catalase-negative, and designated strain NC2-42T, were isolated from sediment on the coast of Weihai, China. Optimal growth occurred at 37 °C, pH 7.5 and with 2–3 % (w/v) NaCl. MK-7 was the sole respiratory quinone and meso-diaminopimelic acid was a diagnostic diamino acid in the peptidoglycan. The polar lipid profile of this novel isolate consisted of phosphatidylglycerol, phosphatidylethanolamine, an unknown phospholipid, an unknown phosphoaminolipid, two unknown glycolipids and an unknown lipid. The major cellular fatty acids in strain NC2-42T were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. The G+C content of the genomic DNA of strain NC2-42T was 58.11 mol% (HPLC). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NC2-42T showed the highest similarity (92.32 %) to Paenibacillus profundus within the family Paenibacillaceae . Based on data from this taxonomic study using a polyphasic approach, the isolate is proposed to represent a novel species of a new genus within the family Paenibacillaceae, with the name Marinicrinis sediminis gen. nov., sp. nov. The type strain of the type species is NC2-42T (=KCTC 33676T=MCCC 1K01238T).
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Chryseomicrobium palamuruense sp. nov., a haloalkalitolerant bacterium isolated from a sediment sample
More LessA novel Gram-stain-positive, rod shaped, motile bacterium, designated strain PU1T, was isolated from a sediment sample collected from a drainage near hostel of Palamuru University, Mahabubnagar district, T.S, India (16°43′23″N 77°58′49″E). Cells of strain PU1T are positive for catalase, oxidase, phosphatase, lipase and urease, and negative for gelatinase, amylase, protease, cellulase, lysine decarboxylase and ornithine decarboxylase. The fatty acids were dominated by saturated fatty acids (82.7 %), with a high abundance of iso-C15 : 0 (48.8 %), anteiso-C15 : 0 (7.3 %), iso-C16 : 0 (11.9 %), C16 : 1ω7c alcohol (11.8 %) and iso-C17 : 0 (5.3 %). Strain PU1T contained MK-8 as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine make up the phospholipid composition. The cell-wall peptidoglycan contains meso-diaminopimelic acid as the diamino acid and cell-wall sugars are d-glucose and d-galactose. 16S rRNA gene sequence analysis indicated Chryseomicrobium imtechense and Chryseomicrobium amylolyticum , members of family Planococcaceae within the phylum Firmicutes , are the closest related species with 16S rRNA gene sequence similarities of 99 %. Other members of the family Planococcaceae had sequence similarities of 99 %, and DNA–DNA relatedness values between strain PU1T and Chryseomicrobium imtechense MW 10T, Chryseomicrobium amylolyticum JC16T were 38 and 32 % respectively. The G+C content of DNA of strain PU1T is 48.5 mol%. Based on the above-mentioned phenotypic and phylogenetic characteristics, strain PU1T represents a novel species of the genus Chryseomicrobium for which the name Chryseomicrobium palamuruense sp. nov. is proposed. The type strain is PU1T(=CCUG 59101T=JCM 16712T=KCTC 13722T=NBRC106750T).
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- Other bacteria
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Brevitalea aridisoli, B. deliciosa and Arenimicrobium luteum, three novel species of Acidobacteria subdivision 4 (class Blastocatellia) isolated from savanna soil and description of the novel family Pyrinomonadaceae
Three novel strains of the phylum Acidobacteria (Ac_11_E3T, Ac_12_G8T and Ac_16_C4T) were isolated from Namibian semiarid savanna soils by a high-throughput cultivation approach using low-nutrient growth media. 16S rRNA gene sequence analysis placed all three strains in the order Blastocatellales of the class Blastocatellia ( Acidobacteria subdivision 4). However, 16S rRNA gene sequence similarities to their closest relative Pyrinomonas methylaliphatogenes K22T were ≤90 %. Cells of strains Ac_11_E3T, Ac_12_G8T and Ac_16_C4T were Gram-staining-negative and non-motile and divided by binary fission. Ac_11_E3T and Ac_16_C4T formed white colonies, while those of Ac_12_G8T were orange-yellowish. All three strains were aerobic chemoorganoheterotrophic mesophiles with a broad pH range for growth. All strains used a very limited spectrum of carbon and energy sources for growth, with a preference for complex proteinaceous substrates. The major respiratory quinone was MK-8. The major shared fatty acid was iso-C15 : 0. The DNA G+C contents of strains Ac_11_E3T, Ac_12_G8T and Ac_16_C4T were 55.9 mol%, 66.9 mol% and 54.7 mol%, respectively. Based on these characteristics, the two novel genera Brevitalea gen. nov. and Arenimicrobium gen. nov. are proposed, harboring the novel species Brevitalea aridisoli sp. nov. (Ac_11_E3T=DSM 27934T=LMG 28618T), Brevitalea deliciosa sp. nov. (Ac_16_C4T=DSM 29892T=LMG 28995T) and Arenimicrobium luteum sp. nov. (Ac_12_G8T=DSM 26556T=LMG 29166T), respectively. Since these novel genera are only distantly related to established families, we propose the novel family Pyrinomonadaceae fam. nov. that accommodates the proposed genera and the genus Pyrinomonas ( Crowe et al., 2014 ).
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‘Candidatus Phytoplasma hispanicum’, a novel taxon associated with Mexican periwinkle virescence disease of Catharanthus roseus
More LessMexican periwinkle virescence (MPV) phytoplasma was originally discovered in diseased plants of Madagascar periwinkle (Catharanthus roseus) in Yucatán, Mexico. On the basis of results from RFLP analysis of PCR-amplified 16S rRNA gene sequences, strain MPV was previously classified as the first known member of phytoplasma group 16SrXIII, and a new subgroup (16SrXIII-A) was established to accommodate MPV phytoplasma. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain MPV represents a lineage distinct from previously described ‘Candidatus Phytoplasma ’ species. Nucleotide sequence alignments revealed that strain MPV shared less than 97.5 % 16S rRNA gene sequence similarity with all previously described ‘Ca. Phytoplasma ’ species. Based on unique properties of the DNA, we propose recognition of Mexican periwinkle virescence phytoplasma strain MPV as representative of a novel taxon, ‘Candidatus Phytoplasma hispanicum’.
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Description and prevalence of Mycoplasma ciconiae sp. nov. isolated from white stork nestlings (Ciconia ciconia)
The mycoplasma strain ST 57T was isolated from the trachea of a clinically healthy, free-ranging white stork nestling in Nielitz, Mecklenburg-Western Pomerania, Germany. Strain ST 57T grew in fried-egg-shaped colonies on mycoplasma (SP4) agar plates and was dependent on sterol for growth. The organism fermented glucose and did not hydrolyse arginine or urea. The optimal growth temperature was 37 °C, with a temperature range from 23 to 44 °C. Strain ST 57Tcould not be identified as a representative of any of the currently described mycoplasma species by alignment of the 16S rRNA gene sequence or 16S–23S intergenic transcribed spacer region, or by immunobinding assays. Thus, this organism appears to be a representative of a novel species, for which the name Mycoplasma ciconiae sp. nov. is proposed. The type strain is ST 57T (=ATCC BAA-2401T=DSM 25251T). Four further strains of this species are included in this description (ST 24=DSM 29908, ST 56 Clone 1=DSM 29054, ST 99=DSM 29909, ST 102=DSM 29010). The prevalence of this mycoplasma species in clinically healthy, white stork nestlings in northern Germany was determined. Our species-specific PCR detected 57.8 % (48/83) of the samples positive for M. ciconiae sp. nov. As this species appears to be widespread in the healthy free-ranging white stork population, we conclude that this species is either apathogenic or an opportunistic pathogen in white storks.
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Potamolinea gen. nov. (Oscillatoriales, Cyanobacteria): a phylogenetically and ecologically coherent cyanobacterial genus
More LessPhormidium Kützing ex Gomont, a common genus of the Cyanobacteria , is widely known as a problematic group. Its simple morphology is not congruent with its genetic heterogeneity and several new generic entities have been described based on 16S rRNA gene sequence analyses from populations with similar morphology. During a study of the diversity of Phormidioideae (Phormidiaceae, Oscillatoriales) in Brazil, ten Phormidium-like strains from south-eastern and mid-western regions were isolated in monospecific cultures and submitted to polyphasic evaluation (morphological, ecological and molecular studies). The populations studied presented homogeneous morphology (trichomes straight, not attenuated and apical cell rounded or obtuse), differing mainly in cell length from the type species of the genus Phormidium (Phormidium lucidum Agardh ex Gomont) and occurring as three morphotypes. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the populations studied, with European Phormidium aerugineo-caeruleum (Gomont) Anagnostidis & Komárek strains, were placed together in a very distinctive and highly supported clade. Thus, the set of characteristics of the strains resulted in the recognition of the new genus Potamolinea Martins et Branco with two species: Potamolinea magna as the type species (strains 47PC and 48PC) and Potamolinea aerugineo-caerulea (Gomont) Martins et Branco (strains 1PC, 2PC and 38PC). These two species plus one still undetermined lineage,Potamolinea sp., are morphologically and genetically distinguishable, whereas the secondary structures of the D1-D1′, box-B and V3 regions were conserved within each one. The generic name and specific epithets of the new taxa are proposed under the provisions of the International Code of Nomenclature for algae, fungi and plants.
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- Proteobacteria
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Colwellia sediminilitoris sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, aerobic, motile and rod-shaped or ovoid bacterial strain, designated YSM-23T, was isolated from a tidal flat on the South Sea in South Korea, and subjected to a polyphasic taxonomic study. Strain YSM-23T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain YSM-23T represented a member of the genus Colwellia . Strain YSM-23T exhibited 16S rRNA gene sequence similarity values of 98.0, 97.4 and 97.3 % to the type strains of Colwellia aestuarii , Colwellia polaris and Colwellia chukchiensis , respectively, and of 94.5–96.8 % to the type strains of the other species of the genus Colwellia . Strain YSM-23T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acid. The major polar lipids detected in strain YSM-23T were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain YSM-23T was 43.8±0.08 mol% and its DNA–DNA relatedness values with the type strain of C . aestuarii , C . polaris and C . chukchiensis were 10±3.5–22±4.9 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain YSM-23T is separated from species of the genus Colwellia with validly published names. On the basis of the data presented, strain YSM-23T is considered to represent a novel species of the genus Colwellia , for which the name Colwellia sediminilitoris sp. nov. is proposed. The type strain is YSM-23T (=KCTC 52213T=NBRC 111994T).
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Sedimentitalea todarodis sp. nov., isolated from the intestinal tract of a Japanese flying squid
A novel Gram-stain-negative, motile, aerobic and rod-shaped alphaproteobacterium, designated strain KHS03T, was isolated from the intestinal tract of a Japanese flying squid, Todarodes pacificus, which was collected from the East Sea, Korea. The new isolate shared 97.4 % 16S rRNA gene sequence similarity with Sedimentitalea nanhaiensis NH52FT. The isolate grew optimally at 25 °C and pH 7 in the presence of 1–2 % (w/v) NaCl, and had an absolute requirement of sodium ions for growth. The major cellular fatty acid was C18 : 1 ω7c. The primary isoprenoid quinone was ubiquinone-10. Polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. Genotypic analyses indicated that the whole genomic DNA of the isolate had a G+C content of 59.9 mol%. DNA–DNA hybridization showed that the isolate shared 17.1±2.3 % (reciprocal 17.0±1.9 %) genomic relatedness with the closest related type strain, S. nanhaiensis NH52FT. Strain KHS03T is thus suggested to represent a novel species of the genus Sedimentitalea , for which the name Sedimentitalea todarodis sp. nov. is proposed. The type strain is KHS03T (=KCTC 42412T=JCM 31160T).
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Rhizorhabdus dicambivorans sp. nov., a dicamba-degrading bacterium isolated from compost
More LessStrain Ndbn-20T, a Gram-staining-negative, non-spore-forming bacterium, was isolated from compost of plant litter. The strain was able to degrade dicamba. Phylogenetic analysis based on 16S rRNA gene sequences indicated that Ndbn-20Trepresented a member of the family Sphingomonadaceae of the Alphaproteobacteria and showed high sequence similarities to Rhizorhabdusargentea SP1T (98.8 %), Sphingomonaswittichii RW1T (97.9 %), Sphingomonasstarnbergensis 382T (97.7 %) and Sphingomonashistidinilytica UM2T (97.7 %). However, the strain showed low DNA sequence relatedness with R. argentea SP1T (45.6±1.9 %), S. wittichii RW1T (33.5±2.3 %), S. histidinilytica UM2T (39.4±3.6 %) and S. starnbergensis 382T (42.1±4.1 %). Ndbn-20T possessed Q-10 as the predominant ubiquinone, spermidine as the major polyamine, and summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c), C17 : 1ω6c, C16 : 0 and C14 : 02-OH as the major fatty acids (>5 % of the total). The profile of polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, glycolipid, sphingoglycolipid, phosphatidyldimethylethanolamine and phosphatidylglycerol. The DNA G+C content was 65.4 mol%. Based on a polyphasic taxonomic analysis, strain Ndbn-20T is proposed to represent a novel species of the genus Rhizorhabdus , with the proposed name of Rhizorhabdus dicambivorans sp. nov. The type strain is Ndbn-20T (=CCTCC AB 2016143=KACC 18661).
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Aureimonas galii sp. nov. and Aureimonas pseudogalii sp. nov. isolated from the phyllosphere of Galium album
Four yellow-pigmented, Gram-stain-negative, rod-shaped bacteria, strains PP-WC-4G-234T, PP-CE-2G-454T, PP-WC-1G-202 and PP-CC-3G-650, were isolated from the phyllosphere of Galium album. The strains shared 99.7–100 % 16S rRNA gene sequence similarity but could be differentiated by genomic fingerprinting using rep- and random amplification of polymorphic DNA PCRs. Phylogenetic analysis based on the 16S rRNA gene placed the strains within the family Aurantimonadaceae with highest 16S rRNA gene sequence similarity of 97.2–97.3 % to the type strain of Aureimonas phyllosphaerae. Sequence similarities to all other Aurantimonadaceae were below 97 %. The main cellular fatty acids of the strains were C18 : 1 ω7c as the predominant fatty acid followed by C16 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω8c). The polyamine patterns of strains PP-WC-4G-234T and PP-CE-2G-454T contained sym-homospermidine as a major compound, and the major respiratory quinone was ubiquinone Q-10. Predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine, sulfoquinovosyldiacylglycerol, three unidentified phospholipids and one unidentified lipid only detectable after total lipid staining. The DNA G+C content was 66.4, 68.9, 67.4 and 70.5 mol% for strains PP-WC-4G-234T, PP-CE-2G-454T, PP-WC-1G-202 and PP-CC-3G-650, respectively. Based on phylogenetic, chemotaxonomic and phenotypic analyses we propose two novel species of the genus Aureimonas, Aureimonas galii sp. nov. with PP-WC-4G-234T (=LMG 28655T=CIP 110892T) as the type strain and Aureimonas pseudogalii sp. nov. with PP-CE-2G-454T (=LMG 29411T=CCM 8665T) as the type strain and two further strains representing the same species, PP-WC-1G-202 and PP-CC-3G-650.
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Rhodovulum algae sp. nov., isolated from an algal mat
More LessA reddish-brown-pigmented, phototrophic bacterium, designated strain JA877T, was isolated from a brown algae mat sample collected from Jalandhar beach, Gujarat, India. On the basis of the 16S rRNA gene sequence, strain JA877T belongs to the class Alphaproteobacteria and is closely related to the type strains Rhodovulum viride JA756T (99.0 %), Rhodovulum sulfidophilum Hansen W4T (98.9 %), Rhodovulum visakhapatnamense JA181T (98.8 %), Rhodovulum kholense JA297T (97.5 %) and Rhodovulum salis JA746T (97.0). However, strain JA877T showed only 20–45 % relatedness with its phylogenetic neighbours and had a ∆T m between 5.8 and 7.0 °C. The major respiratory quinone was ubiquinone-10 (Q10), and the polar lipid profile was composed of the major components phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, two unidentified sulfolipids and five unidentified lipids. The major fatty acids were C18 : 1ω5c, C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C18 : 0. The DNA G+C content was 64.5 mol%. On the basis of 16S rRNA gene sequence analysis, physiological data, and chemotaxonomic and molecular differences, strain JA877T is significantly different from other species of the genus Rhodovulum and represents a novel species, for which the name Rhodovulum algae sp. nov. is proposed. The type strain is JA877T (=LMG 29228T= KCTC 42963T).
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Pseudoalteromonas neustonica sp. nov., isolated from the sea surface microlayer of the Ross Sea (Antarctica), and emended description of the genus Pseudoalteromonas
More LessA Gram-stain-negative, facultatively anaerobic, rod-shaped and motile strain, designated PAMC 28425T, was isolated from a sea surface microlayer sample from the Ross Sea, Antarctica. Analysis of the 16S rRNA gene sequence of strain PAMC 28425T showed an affiliation with the genus Pseudoalteromonas . Phylogenetic analyses revealed that strain PAMC 28425T formed a clade with Pseudoalteromonas prydzensis MB8-11T and Pseudoalteromonas mariniglutinosa KMM 3635T with 16S rRNA gene sequence similarities of 98.3–98.6 %. Genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strain PAMC 28425T is clearly distinguished from the phylogenetically close relatives. Cells of strain PAMC 28425T grew optimally at 25 °C and pH 7.5–8.5 in the presence of 1.0–3.0 % (w/v) sea salts. The major cellular fatty acids (>10 %) were C16 : 1ω6c and/or C16 : 1ω7c, C16 : 0, and C18 : 1ω6c and/or C18 : 1ω7c. The genomic DNA G+C content was 39.7 mol%. On the basis of the phylogenetic, genomic, chemotaxonomic and phenotypic data presented, we propose the name Pseudoalteromonas neustonica sp. nov. with the type strain PAMC 28425T (=KCCM 43187T=JCM 31286T).
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Marinobacterium zhoushanense sp. nov., isolated from surface seawater
A Gram-stain-negative, facultatively anaerobic bacterium, designated WM3T, was isolated from surface seawater collected from the East China Sea. Cells were catalase- and oxidase-positive, short rods and motile by means of a single polar flagellum. Growth occurred at 15–43 °C (optimum 37–40 C), pH 5.5–9.5 (optimum pH 6.5–7.5) and with 0.25–9.0 % (w/v) NaCl (optimum 1.0–1.5 %). Chemotaxonomic analysis showed that the respiratory quinone was ubiquinone-8, the major fatty acids included C16 : 0 (23.6 %), C18 : 1ω7c (26.2 %) and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH, 22.1 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain WM3T was most closely related to the genus Marinobacterium , sharing the highest 16S rRNA gene sequence similarity of 95.5 % with both Marinobacterium litorale KCTC 12756T and Marinobacterium mangrovicola DSM 27697T. The genomic DNA G+C content of the strain WM3T was 55.8 mol%. On the basis of phenotypic, chemotaxonomic and genotypic characteristics presented in this study, strain WM3T is suggested to represent a novel species of the genus Marinobacterium , for which the name Marinobacterium zhoushanense sp. nov. is proposed. The type strain is WM3T (=KCTC 42782T=CGMCC 1.15341T).
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Campylobacter geochelonis sp. nov. isolated from the western Hermann's tortoise (Testudo hermanni hermanni)
More LessDuring a screening study to determine the presence of species of the genus Campylobacter in reptiles, three putative strains (RC7, RC11 and RC20T) were isolated from different individuals of the western Hermann’s tortoise (Testudo hermanni hermanni). Initially, these isolates were characterized as representing C ampylobacter fetus subsp. fetus by multiplex PCR and partial 16S rRNA gene sequence analysis. Further whole- genome characterization revealed considerable differences compared to other Campylobacter species. A polyphasic study was then undertaken to determine the exact taxonomic position of the isolates. The three strains were characterized by conventional phenotypic tests and whole genome sequencing. We generated robust phylogenies that showed a distinct clade containing only these strains using the 16S rRNA and atpA genes and a set of 40 universal proteins. Our phylogenetic analysis demonstrates their designation as representing a novel species and this was further confirmed using whole- genome average nucleotide identity within the genus Campylobacter (~80 %). Compared to most Campylobacter species, these strains hydrolysed hippurate, and grew well at 25 °C but not at 42 °C. Phenotypic and genetic analyses demonstrate that the three Campylobacter strains isolated from the western Hermann’s tortoise represent a novel species within the genus Campylobacter , for which the name Campylobacter geochelonis sp. nov. is proposed, with RC20T (=DSM 102159T=LMG 29375T) as the type strain.
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Paracoccus a cridae sp. nov., isolated from the insect Acrida cinerea living in deserted cropland
More LessA Gram-stain-negative, aerobic, rod-shaped, non-motile bacterial strain, designated SCU-M53T, was isolated from the insect Acrida cinerea. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain SCU-M53T belonged to the genus Paracoccus , having Paracoccus chinensis NBRC 104937T (97.04 % 16S rRNA gene sequence similarity) and Paracoccus niistensis KCTC 22789T (96.70 %) as the most closely related phylogenetic neighbours. Growth occurred at 10–40 °C (optimum 25–30 °C), pH 5.0–10.0 (optimum pH 6.5–7.5) and with 0–4 % (w/v) NaCl (optimum 0–1 % NaCl). The fatty acids of strain SCU-M53T were C18 : 1 ω7c, C18 : 0, C16 : 0, C14 : 0 3-OH, C14 : 0 and C10 : 0 3-OH. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unknown aminolipid, two unknown phospholipids and two unknown lipids. The isoprenoid quinone was ubiquinone-10. The DNA G+C content was 60.6 mol%. Strain SCU-M53T exhibited 36.5 and 28.6 % DNA–DNA relatedness to P. chinensis NBRC 104937T and P. niistensis KCTC 22789T, respectively. According to these results, strain SCU-M53T represents a novel species of the genus Paracoccus , for which the name Paracoccus acridae sp. nov. is proposed. The type strain is SCU-M53T (=KCTC 42932T=CGMCC 1.15419T).
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Parvularcula flava sp. nov., an alphaproteobacterium isolated from surface seawater of the South China Sea
More LessAn aerobic, coccoid to short rod, yellow-pigmented, non-sporulating and Gram-staining-negative bacterium, designated NH6-79T, was isolated from surface seawater of the South China Sea. The isolate was motile with a polar flagellum. Growth was observed at 4–42 °C (optimum 37 °C), at pH 6.0–8.5 (optimum pH 7.0), and with 0.5–11 % (w/v) NaCl (optimum 4.5 %) and 1.5–17 % (w/v) sea salt (optimum 3.5–5 %). Strain NH6-79T could decompose peptone to produce H2S, but could not hydrolyse skimmed milk. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NH6-79T had the closest affinity to the genus Parvularcula , sharing the highest 16S rRNA gene sequence similarity with ‘ Parvularcula oceanus ’ JLT2013 (94.1 %), Parvularcula lutaonensis CC-MMS-1T (93.4 %), Parvularcula dongshanensis SH25T (92.9 %) and Parvularcula bermudensis HTCC2503T (92.7 %), and lower sequence similarities (<90 %) with all other genera. The dominant fatty acids were C18 : 1 ω7c and C16 : 0. The polar lipid profile was mainly composed of three unidentified glycolipids. The predominant isoprenoid quinone was ubiquinone-10. The DNA G+C content was 60.7 mol%. Based on the polyphasic taxonomic characterization, strain NH6-79T is considered to represent a novel species of the genus Parvularcula , for which the name Parvularcula flava sp. nov. is proposed. The type strain is NH6-79T (=CGMCC 1.14984T=JCM 30557T=MCCC 1K00277T).
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Sulfuriflexus mobilis gen. nov., sp. nov., a sulfur-oxidizing bacterium isolated from a brackish lake sediment
More LessA chemolithotrophic sulfur-oxidizing bacterium, strain aks1T, was isolated from sediment of a brackish lake in Japan. The cells were curved rod-shaped and Gram-stain-negative. The G+C content of the genomic DNA was 53 mol%. The major components in the cellular fatty acid profile were C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). As electron donor for chemolithoautotrophic growth, strain aks1T oxidized thiosulfate, sulfide, and elemental sulfur. The strain could utilize oxygen and nitrate as an electron acceptor for thiosulfate oxidation. Growth was observed at a temperature range of 5–34 °C, with optimum growth at 30–32 °C. Growth of the strain was observed at a pH range of 6.4–8.7. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain is related to members of the family Granulosicoccaceae within the order Chromatiales , with sequence similarities around 92 %. On the basis of phylogenetic and phenotypic properties, strain aks1T represents a novel species of a new genus, for which the name Sulfuriflexus mobilis gen. nov., sp. nov. is proposed. The type strain of the type species is aks1T (=DSM 102939T=NBRC 111889T).
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Phenylobacterium aquaticum sp. nov., isolated from the reservoir of a water purifier
More LessA Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming, rod-shaped bacterial strain designated W2-3-4T was isolated from the reservoir of a water purifier. This bacterium was characterized to determine its taxonomic position by using a polyphasic approach. Strain W2-3-4T grew well at 25–30 °C on nutrient and R2A agars. On the basis of 16S rRNA gene sequence similarity, strain W2-3-4T was shown to belong to the family Caulobacteraceaeand to be related to Phenylobacterium conjunctum FWC21T (98.0 % sequence similarity) and Phenylobacterium haematophilum CCUG 26751T (97.2 %). Lower sequence similarities were found with the type strains of all other recognized members of the genus Phenylobacterium (95.7–97.1 %). The G+C content of the genomic DNA was 68.7 mol%. The major respiratory quinone was Q-10 and the major fatty acids were summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0, C18 : 1 ω7c 11-methyl and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c). The polar lipids were phosphatidylglycerol, an unknown phospholipid, four unknown glycolipids and three unidentified polar lipids. DNA–DNA relatedness values between strain W2-3-4Tand its closest phylogenetically neighbours were below 7 %. Strain W2-3-4T could be differentiated genotypically and phenotypically from recognized species of the genus Phenylobacterium . The isolate therefore represents a novel species, for which the name Phenylobacterium aquaticum sp. nov. is proposed, with the type strain W2-3-4T (=KACC 18306T=LMG 28593T).
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Pandoraea terrae sp. nov., isolated from forest soil, and emended description of the genus Pandoraea Coenye et al. 2000
More LessA Gram-staining-negative, facultatively aerobic, white-colony-forming bacterium, designated strain SE-S21T, was isolated from forest soil of Jeju Island in Korea. Cells were motile rods with a single polar flagellum, showing catalase- and oxidase-positive reactions. Growth was observed at 10–40 °C (optimum, 30 °C), pH 4.0–10.0 (optimum, pH 7.0–7.5) and with 0–4.0 % (w/v) NaCl (optimum, 0–2 %). Only ubiquinone-8 was detected as the isoprenoid quinone, and C16 : 0, C17 : 0 cyclo, C19 : 1ω8c cyclo and summed feature 2 (comprising C12 : 0 aldehyde and/or unknown) were found to be the major fatty acids. Phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid, an unknown aminolipid and an unknown lipid were detected as the major polar lipids. Putrescine and 2-hydroxyputrescine were the predominant polyamines. The DNA G+C content was 61.0 mol%. Phylogenetic analyses based on 16S rRNA and DNA gyrase B gene sequences revealed that strain SE-S21T formed a phyletic lineage within the genus Pandoraea . Strain SE-S21T was most closely related to Pandoraea faecigallinarum KOxT and Pandoraea pnomenusa CCUG 38742T with 98.8 % and 98.7 % 16S rRNA gene sequence similarities, respectively. However, the DNA–DNA relatedness values between strain SE-S21T and the type strains of P. faecigallinarum and P. pnomenusa were 26.6±5.7 % and 20.5±3.7 %, respectively. On the basis of phenotypic, chemotaxonomic and molecular features, strain SE-S21T clearly represents a novel species of the genus Pandoraea , for which the name Pandoraea terrae sp. nov. is proposed. The type strain is SE-S21T (=KACC 18127T=JCM 30137T). An emended description of the genus Pandoraea is also proposed.
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Pseudoalteromonas gelatinilytica sp. nov., isolated from surface seawater
Three Gram-stain-negative, rod-shaped bacteria, designated strains NH153T, F-2-11 and M-1-78, were isolated from surface seawater of the South China Sea and the East China Sea. The three isolates were able to grow at 15–45 °C (optimum 28–37 °C), but no growth occurred at 4 or 50 °C. The pH range for growth was pH 5.5–9.5 (optimum pH 7.5–8.5). The isolates required sea salts for growth and growth occurred in the presence of 0–10 % (w/v) NaCl (optimum 3–5 %); no growth occurred in the presence of 12.0, 15.0 or 20.0 % (w/v) NaCl. They were positive for hydrolysis of gelatin and Tween 80. The sole respiratory quinone was ubiquinone-8 (Q-8). The major cellular fatty acids (>10 %) were C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The major polar lipid components were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid and one unidentified lipid. The genomic DNA G+C content of strain NH153T was 41.4 mol%. Based on 16S rRNA gene sequence analysis, the isolates were closely related to the type strain of Pseudoalteromonas shioyasakiensis (98.0–98.6 % sequence similarity). The 16S rRNA gene sequence similarities between the three isolates were 98.8–99.7 %. Phylogenetic analysis indicated that they formed a distinct lineage and clustered with P. shioyasakiensis and Pseudoalteromonas arabiensis. The level of DNA–DNA relatedness among the three isolates was 78.0–85.5 %. Strain NH153T exhibited average nucleotide identity values of 93.4 and 84.2 % with respect to P. shioyasakiensis JCM 18891T and P. arabiensis JCM 17292T, respectively. The genome-to-genome distance analysis revealed that strain NH153T shared 52.4 % DNA relatedness with P. shioyasakiensis JCM 18891T and 28.1 % with P. arabiensis JCM 17292T. On the basis of the phenotypic, genotypic and chemotaxonomic characterizations, as well as phylogenetic inference obtained in this study, strains NH153T, F-2-11 and M-1-78 represent a novel species within the genus Pseudoalteromonas , for which the name Pseudoalteromonas gelatinilytica sp. nov. is proposed. The type strain is NH153T (=CGMCC 1.15370T=DSM 100951T), and F-2-11 (=CGMCC 1.15364=DSM 100953) and M-1-78 (=CGMCC 1.15365=DSM 100952), are additional strains of the species.
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Acinetobacter lactucae sp. nov., isolated from iceberg lettuce (Asteraceae: Lactuca sativa)
More LessStrain NRRL B-41902T and three closely related strains were isolated from iceberg lettuce. The strain was found to consist of strictly aerobic, Gram-stain-negative rods that formed cocci in late stationary phase. 16S rRNA gene sequence analysis showed that strain NRRL B-41902T was most closely related to species within the genera Acinetobacter , and that a grouping of it and the three other closely related strains was most closely related to the type strain of Acinetobacter pittii, which was also confirmed through a phylogenomic analysis. Moreover, in silico DNA–DNA hybridization analysis revealed a substantial amount of genomic divergence (39.1 %) between strain NRRL B-41902T and the type strain of A. pittii , which is expected if the strains represent distinct species. Further phenotypic analysis revealed that strain NRRL B-41902T was able to utilize a combination of l-serine, citraconic acid and citramalic acid, which differentiated it from other, closely related Acinetobacter species. Therefore, strain NRRL B-41902T (=CCUG 68785T) is proposed as the type strain of a novel species, Acinetobacter lactucae sp. nov.
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Varunaivibrio sulfuroxidans gen. nov., sp. nov., a facultatively chemolithoautotrophic, mesophilic alphaproteobacterium from a shallow-water gas vent at Tor Caldara, Tyrrhenian Sea
More LessA mesophilic, facultatively anaerobic, facultatively chemolithoautotrophic bacterium, designated strain TC8T, was isolated from a sulfidic shallow-water marine gas vent located at Tor Caldara, in the Tyrrhenian Sea, Italy. Cells were Gram-stain-negative curved rods with one or more polar flagella. Cells were approximately 1–1.5 µm in length and 0.6 µm in width. Strain TC8T grew between 20 and 35 °C (optimum 30 °C), with between 5 and 45 g NaCl l−1 (optimum 15–20 g l−1) and between pH 4.5 and 8.5 (optimum pH 6.0–7.0). The generation time under optimal conditions was 8 h. Strain TC8T was a facultative chemolithoautotroph also capable of using organic substrates as electron donors and carbon sources. Chemolithoautotrophic growth occurred with sulfur and thiosulfate as the electron donors, CO2 as the carbon source, and nitrate, oxygen (5 %, v/v) and ferric iron as the electron acceptors. Chemoorganoheterotrophic growth occurred with tryptone, peptone, Casamino acids, pyruvate and glycerol as substrates, while chemolithoherotrophic growth occurred with d(+)-glucose, sucrose, yeast extract, acetate, lactate, citrate and l-glutamine. The G+C content of the genomic DNA was 59.9 mol%. Phylogenetic analysis of the 16S rRNA gene sequence of strain TC8T showed that this organism formed a lineage within the family Rhodospirillaceae , which branched separately from the two closest relatives, Magnetovibrio blakemorei MV1T (91.25 % similarity) and Magnetospira thiophila MMS-1T (90.13 %). Based on phylogenetic, physiological and chemotaxonomic characteristics, it is proposed that the organism represents a novel species of a new genus within the family Rhodospirillaceae,Varunaivibrio sulfuroxidans gen. nov., sp. nov. The type strain of Varunaivibrio sulfuroxidans is TC8T (=DSM 101688T=JCM 31027T).
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Isolation and characterization of Neisseria musculi sp. nov., from the wild house mouse
Members of the genus Neisseria have been isolated from or detected in a wide range of animals, from non-human primates and felids to a rodent, the guinea pig. By means of selective culture, biochemical testing, Gram staining and PCR screening for the Neisseria -specific internal transcribed spacer region of the rRNA operon, we isolated four strains of the genus Neisseria from the oral cavity of the wild house mouse, Mus musculus subsp. domesticus. The isolates are highly related and form a separate clade in the genus, as judged by tree analyses using either multi-locus sequence typing of ribosomal genes or core genes. One isolate, provisionally named Neisseria musculi sp. nov. (type strain AP2031T=DSM 101846T=CCUG 68283T=LMG 29261T), was studied further. Strain AP2031T/ N. musculi grew well in vitro. It was naturally competent, taking up DNA in a DNA uptake sequence and pilT-dependent manner, and was amenable to genetic manipulation. These and other genomic attributes of N. musculi sp. nov. make it an ideal candidate for use in developing a mouse model for studying Neisseria –host interactions.
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Undibacterium danionis sp. nov. isolated from a zebrafish (Danio rerio)
One beige-pigmented, Gram-stain-negative, rod-shaped bacterium, strain E3/4T, was isolated from a zebrafish, Danio rerio. Phylogenetic analysis based on nearly full-length 16S rRNA gene sequences showed that the isolate shared 98.5 % 16S rRNA gene sequence identity to the type strain of Undibacterium macrobrachii and 97.8 % to the type strain of Undibacterium seohonense . Lower 16S rRNA gene sequence similarities (<97.0 %) could be found in comparison with all other species of the genus Undibacterium . DNA–DNA hybridization with Undibacterium macrobrachii LMG 26891T showed a low level of relatedness, <35 %. The main cellular fatty acids of the strain were summed feature 3 fatty acids (C16 : 1ω7c/C16 : 1ω8c), C10 : 0 3-OH and C16 : 0. The polyamine pattern of strain E3/4T contained predominantly putrescine and 2-hydroxyputrescine. The major quinone was ubiquinone Q-8. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of phylogenetic, chemotaxonomic, genomic and phenotypic analyses we propose a novel species of the genus Undibacterium , Undibacterium danionis , with strain E3/4T (=DSM 102221T=CCM 8677T=CIP 111017T) as the type strain.
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Description of Novosphingobium flavum sp. nov., isolated from soil
More LessA novel yellow bacterial strain, designated UCM-28T, was isolated from forest soil in Gyeonggi-Do, South Korea. The isolated strain was Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped, and grew at 10–37 °C, pH 5.5–9 and with 0–1 % NaCl. It could reduce nitrate to nitrite and hydrolyse aesculin. We determined the taxonomic position of strain UCM-28T; based on the 16S rRNA gene sequence, the strain belongs to the genus Novosphingobium . The bacterium showed the highest similarity to Novosphingobium piscinae SLH-16T (98.9 %), Novosphingobium rhizosphaerae JM-1T (97.7 %), Novosphingobium taihuense T3-B9T (97.2 %), Novosphingobium subterraneum DSM 12447T (97.1 %), Novosphingobium aromaticivorans DSM 12444T (97.1 %) and Novosphingobium capsulatum GIFU 11526T (96.7 %). Phylogenic trees also confirmed that strain UCM-28T is most closely related to Novosphingobium piscinae SLH-16T and others, and is positioned within the genus Novosphingobium . The DNA relatedness of strain UCM-28T with its references was in the range of 20.9–35.2 %. The polar lipid profile revealed diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, phosphatidylmonomethylethanolamine, six unidentified polar lipids and two unknown glycolipids. The major quinone was ubiquinone Q-10, and the major polyamine was spermidine. The DNA G+C content was 63.5 mol%. The major fatty acids included (>10 %) summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) (46.3 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (24.9 %) and C14 : 0 2-OH (11.8 %). Based on the phylogenetic and phenotypic data, strain UCM-28T should be classified within the genus Novosphingobium as a representative of a novel species, named Novosphingobium flavum sp. nov. The type strain is UCM-28T (=KACC 18571T=NBRC 111647T).
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Alcanivorax nanhaiticus sp. nov., isolated from deep sea sediment
More LessA taxonomic study was carried out on strain 19-m-6T, which was isolated from deep sea sediment of the South China Sea during the screening of alkane-degrading bacteria. The isolate was Gram-reaction-negative, and oxidase- and catalase- positive. On the basis of 16S rRNA gene sequence similarity, strain 19-m-6T was shown to belong to the genus Alcanivorax , related to Alcanivorax jadensis T9T (97.5 %), Alcanivorax hongdengensis A-11-3T (97.3 %), A. lcanivorax borkumensis SK2T (96.6 %) and seven other species of the genus Alcanivorax (93.9–95.4 %). Average nucleotide identity values between strain 19-m-6T and A. jadensis T9T, A. hongdengensis A-11-3T and A. borkumensis SK2T were 85.12, 85.87 and 84.35 %, respectively. The estimated DNA–DNA hybridization values between strain 19-m-6T and these three type strains were 22.0, 22.6 and 21.2 %, respectively. Four alkane hydroxylase (alkB) genes were obtained from the draft genome sequence. The G+C content of the chromosomal DNA was 56.44 mol%. The major fatty acids were C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, one aminolipid, three phospholipids, two glycolipids and two aminophospholipids. According to its phenotypic features, fatty acid composition and 16S rRNA gene sequence, the novel strain fitted well into the genus Alcanivorax , but could be clearly distinguished from all other known Alcanivorax species described to date. The nameAlcanivorax nanhaiticus sp. nov. is thus proposed, with 19-m-6T (=MCCC 1A05629T=KCTC 52137T) as the type strain.
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Massilia pinisoli sp. nov., isolated from forest soil
More LessA Gram-stain-negative, aerobic, motile with a single polar flagellum, non-spore-forming and rod-shaped bacterial strain named T33T was isolated from forest soil collected at Kyonggi University, South Korea. The strain was catalase- and oxidase-positive, colonies grew on R2A agar at 32 °C. Sequencing of the 16S rRNA gene and phylogenetic analysis revealed that T33T represented a member of the genus Massilia and is closely related to Massilia niastensis KACC 12599T (98.7 % sequence similarity), Massilia aerilata KACC 12505T (98.5 %), Massilia tieshanensis KACC 14940T (98.4 %), Massilia kyonggiensis KACC 17471T (98.1 %), Massilia norwichensis LMG 28164T (97.7 %), Massilia haematophila CCUG 38318T (97.4 %), Massilia consociata CCUG 58010T (97.3 %), and Massilia niabensis KACC 12632T (97.0 %). Ubiquinone Q-8 is the predominant respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol are the major polar lipids. The major fatty acids are summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), and C16 : 0. DNA–DNA hybridization revealed <70 % relatedness between strain T33T and the most closely related type strains. The DNA G+C content of strain T33Tis 69.4 mol%. Based on physiological and biochemical test results, Massilia pinisoli T33T is proposed as a novel species of the genus Massilia . The type strain is T33T (=KACC 18748T=KEMB 9005-368T=JCM 31316T).
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Lutimaribacter marinistellae sp. nov., isolated from a starfish
More LessA taxonomic study was carried out on a Gram-staining-negative bacterium, strain SF-12T, isolated from an unidentified starfish living in Sanya, PR China. Cells of SF-12T were non-spore-forming rods, 0.5–0.8 µm wide, 2.2–2.5 µm long and motile by means of flagella. SF-12T was facultatively anaerobic, heterotrophic, oxidase- and catalase-positive. Growth of SF-12T occurred at 15–38 °C (optimum, 30 °C), at pH 6.5–8.5 (optimum, pH 7.0), and in the presence of 2.0–7.0 % (w/v) NaCl (optimum, 3.0–4.0 %). The predominant fatty acids of SF-12T were C18 : 1ω7c and/or C18 : 1ω6c. Ubiquinone 10 was the sole respiratory quinone of SF-12T. The major polar lipids of SF-12T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unknown aminolipids, and seven unknown phospholipids. The DNA G+C content was 61 mol%. SF-12T showed the highest 16S rRNA gene sequence similarity to Lutimaribacter pacificus W11-2BT (96.06 %), followed by Cribrihabitans neustonicus CC-AMHB-3T (96.02 %), Lutimaribacter saemankumensis SMK-117T (96.0 %), Cribrihabitans marinus CZ-AM5T (95.92 %), Lutimaribacter litoralis KU5D5T (95.92 %) and other species of the family Rhodobacteraceae (<95.9 %). However, phylogenetic trees based on 16S rRNA gene sequences showed that SF-12T formed a lineage with members of the genus Lutimaribacter in the trees. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, SF-12T is considered to represent a novel species of the genus Lutimaribacter , for which the name Lutimaribacter marinistellae sp. nov. is proposed. The type strain is SF-12T (=MCCC 1K01154T=KCTC 42911T).
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Thiomicrospira hydrogeniphila sp. nov., an aerobic, hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a seawater tank containing a block of beef tallow
More LessA moderately psychrophilic, aerobic, hydrogen- and sulfur-oxidizing bacterium, designated strain MAS2T, was isolated from a tank containing coastal seawater from Tokyo Bay and a block of beef tallow added as organic material. Growth occurred under aerobic chemolithoautotrophic conditions in the presence of molecular hydrogen, thiosulfate, tetrathionate, elemental sulfur or sulfide as the sole energy source and bicarbonate as a carbon source. The isolate represented a Gram-staining-negative rod with a single polar flagellum and grew in artificial seawater medium with thiosulfate at 2–40 °C (optimum 30 °C). The isolate grew in media with thiosulfate at Na+ concentrations between 30 and 1380 mM (optimum 270 mM). MAS2T possessed C16 : 0, C16 : 1 and C18 : 1 as the major fatty acids. The G+C content of the genomic DNA was 39.6 mol%. The 16S rRNA gene sequence similarity analysis showed that the isolate represented a member of the genus Thiomicrospira within the class Gammaproteobacteria and was most closely related to Thiomicrospira frisia JB-A2T. On the basis of phenotypic and molecular properties, the isolate represents a novel species of the genus Thiomicrospira , for which the name Thiomicrospira hydrogeniphila sp. nov. is proposed (type strain, MAS2T=JCM 30760T=DSM 100274T).
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Taxonomic dissection of Achromobacter denitrificans Coenye et al. 2003 and proposal of Achromobacter agilis sp. nov., nom. rev., Achromobacter pestifer sp. nov., nom. rev., Achromobacter kerstersii sp. nov. and Achromobacter deleyi sp. nov.
The phenotypic and genotypic characteristics of a historical collection of strains identified as Achromobacter denitrificans were examined. Sequence analysis of a 765 bp nrdA gene fragment revealed that eight of these strains belonged to the recently described Achromobacter aegrifaciens, Achromobacter mucicolens , and Achromobacter insolitus , and that one strain belonged to Achromobacter xylosoxidans . The analysis also suggested the presence of four novel species of the genus Achromobacter among the remaining strains. The latter was confirmed by multilocus sequence analysis of concatenated nusA, eno, rpoB, gltB, lepA, nuoL andnrdA gene fragments and extensive genotypic and phenotypic characterization. We propose to name these novel species as Achromobacter agilis sp. nov., nom. rev. (type strain LMG 3411T=CCUG 62454T), Achromobacter pestifer sp. nov., nom. rev. (type strain LMG 3431T=CCUG 61959T) , Achromobacter kerstersii sp. nov. (type strain LMG 3441T=CCUG 62449T) and Achromobacter deleyi sp. nov. (type strain LMG 3458T=CCUG 62433T).
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Reclassification of Alteromonas fuliginea (Romanenko et al. 1995) as Pseudoalteromonas fuliginea comb. nov. and an emended description
More LessA new aerobic marine bacterium, strain S3431, was isolated from swab samples of an unidentified polychaete near Canal Concepción, Chile. This strain was thought to represent a new taxon within the genus Pseudoalteromonas . Although DNA–DNA reassociation values showed less than 70 % genomic DNA relatedness to established Pseudoalteromonas type strains, it shared 78 % DNA–DNA relatedness with Alteromonas fuliginea DSM 15748 (=KMM 216) (Romanenko et al., 1994). A. fuliginea has later been considered a heterotypic synonym of Pseudoalteromonas citrea (Ivanova et al., 1998). Relatedness between strains S3431, A. fuliginea DSM 15748 and the type strain P. citrea LMG 12323T was therefore studied. Physiological traits and genomic information were shared at a high level by strains S3431 and DSM 15748, but not between these and P. citrea LMG 12323T. There was only approximately 20 % DNA–DNA relatedness between P. citrea LMG 12323T and strains S3431 and DSM 15748. Based on the available phylogenetic and phenotypic data, the reclassification of A. fuliginea DSM 15748 (Romanenko et al., 1995) → Pseudoalteromonas citrea (Ivanova et al., 1998) as Pseudoalteromonas fuligineacomb. nov. is proposed, and strain S3431 should be assigned to this new species. The name Pseudoalteromonas fuliginea is proposed with KMM 216T (=DSM 15748T=CIP 105339T) as the type strain.
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Sphingomonas zeicaulis sp. nov., an endophytic bacterium isolated from maize root
A novel Gram-staining-negative, aerobic and rod-shaped strain designated 541T was isolated from surface-sterilized root tissue of maize, collected from the Fangshan District of Beijing, People’s Republic of China, and was subjected to a taxonomic study using a polyphasic approach. According to a phylogenetic tree based on 16S rRNA gene sequences, strain 541T represented a member of the genus Sphingomonas and clustered with Sphingomonas sanxanigenens DSM 19645T, with which it shared the highest 16S rRNA gene sequence similarity (98.8 %). The predominant respiratory quinone was ubiquinone-10 (Q-10), the major polyamine was sym-homospermidine and the major cellular fatty acids were C18 : 1ω7c (50.9 %), C16 : 0 (22.0 %) and C14 : 0 2-OH (11.4 %). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. The DNA G+C content was 64.7 mol%. DNA–DNA relatedness between strain 541T and its closest phylogenetic relative Sphingomonas sanxanigenens DSM 19645T was 50.8 %. The results of physiological and biochemical tests and the differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain 541T from closely related species of the genus Sphingomonas . Strain 541T represents a novel species within the genus Sphingomonas , for which the nameSphingomonas zeicaulis sp. nov. is proposed, with the type strain 541T (=CGMCC 1.15008T=DSM 100587T).
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- Eukaryotic micro-organisms
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Yamadazyma barbieri f.a. sp. nov., an ascomycetous anamorphic yeast isolated from a Mid-Atlantic Ridge hydrothermal site (−2300 m) and marine coastal waters
Two yeast strains that are members of the same species were isolated from different marine habitats, i.e. one from Mid-Atlantic Ridge ocean water samples located in the direct vicinity of black smokers near the Rainbow deep-sea hydrothermal vent and one from Brazilian marine water samples off the Ipanema beach. Strains CLIB 1964T and CLIB 1965 are anamorphic ascomycetous yeasts affiliated to the Yamadazyma clade of Saccharomycetales. Interestingly, these strains were phylogenetically and distinctly positioned into a group of species comprising all species of the genus Yamadazyma isolated from marine habitats including deep-sea hydrothermal vents, i.e.Candida atmosphaerica,C. spencermartinsiae,C. atlantica,C. oceani and C. taylorii. These strains differed significantly in their D1/D2 domain sequences of the LSU rRNA gene from the closely related species mentioned above, by 2.6, 3.0, 3.4, 3.8 and 6.0 %, respectively. Internal transcribed spacer region sequence divergence was also significant and corresponded to 4.6, 4.7, 4.7, 12.0 and 24.7 % with C. atlantica,C. atmosphaerica, C. spencermartinsiae,C. oceani and C. taylorii, respectively. Phenotypically, strains CLIB 1964T and CLIB 1965 could be distinguished from closely related species by their inability to assimilate l-sorbose. CLIB 1964T (=CBS 14301T=UBOCC-A-214001T) is the designated type strain for Yamadazyma barbieri sp. nov. The MycoBank number is MB 815884.
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- Evolution, Phylogeny and Biodiversity
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Possible misidentification of species in the Pseudomonas fluorescens lineage as Burkholderia pseudomallei and Francisella tularensis, and emended descriptions of Pseudomonas brenneri,Pseudomonas gessardii and Pseudomonas proteolytica
More LessBacteria were isolated from an industrial water circuit in the Netherlands. These strains were identified using API 20 NE as possible, or likely, Burkholderia pseudomallei . With VITEK 2 some of these strains scored ‘low discrimination’ for Francisella tularensis , amongst others. A total of twenty-six strains were assigned to the species Pseudomonas brenneri, Pseudomonas gessardii or Pseudomonas proteolytica. Because of the possibility of misidentification of these environmental species as medical- and public-health relevant B. pseudomallei and F. tularensis , an emended description, based on tests results more customarily used in clinical laboratories, was suitable. For this reason, the strains in this study, including the type strains DSM 15294T, DSM 17152T and DSM 15321T, were subjected to a polyphasic identification procedure. This procedure consisted of multiple phenotypic tests, fatty acid analysis, 16S rDNA sequence analysis, matrix-assisted laser desorption ionization time-of-flight mass spectronomy and various species-specific molecular tests. Based on the results of the polyphasic procedures, the species descriptions of P. brenneri, P. gessardii and P. proteolytica have been emended.
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Identification of a novel subgroup 16SrII-U phytoplasma associated with papaya little leaf disease
More LessPapaya is an important fruit crop cultivated in tropical and subtropical regions. Papaya little leaf (PLL) disease was observed in China. The phytoplasma 16S rRNA gene was detected from symptomatic papaya trees via PCR using phytoplasma universal primers P1/P7 followed by R16F2n/R16R2. No amplification products were obtained from templates of asymptomatic papaya trees. These results indicated a direct association between phytoplasma infection and PLL disease. Comparative and phylogenetic analyses of 16S rRNA gene sequences indicated that the papaya-infecting phytoplasmas under study belonged to the peanut witches’ broom phytoplasma group (16SrII). Genotyping through use of computer-simulated RFLP analysis of 16S rRNA genes and coefficients of RFLP pattern similarities (0.97) reveal that the PLL phytoplasma was placed in a new subgroup. In this article, we describe the molecular characterization of a new phytoplasma associated with PLL disease and propose that the PLL phytoplasma be considered as a novel subgroup, 16SrII-U.
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- ICSP Matters
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Limiting the retroactive effects of the note to Rule 61 of the International Code of Nomenclature of Bacteria
More LessAt the plenary session of the Judicial Commission at the 1999 IUMS-BAM International Congress in Sydney changes were made to Rule 61 of the International Code of Nomenclature of Bacteria to prevent extensive grammatical or orthographic corrections to names and epithets that had been included on the Approved Lists, the Validation Lists and the Notification Lists. These changes were implemented by the addition of a note to Rule 61. However, that note appears to be retroactive and has an undesirable effect, appearing to prohibit some of the changes already published. Changes need to be made to Rule 61 to limit the retroactive effects of the note.
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What does Rule 18c of the International Code of Nomenclature of Bacteria really say?
More LessA number of recent Requests for an Opinion have cited Rule 18c of the International Code of Nomenclature of Bacteria as the Rule governing setting a time limit on the search for a neotype strain. This Rule only governs what happens when a neotype is proposed and not what happens when the original type appears to have been lost and a neotype is not found. It is appropriate to emphasize this issue and to examine what other alternatives are available.
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The status of the Notes in the International Code of Nomenclature of Prokaryotes: proposal to emend General Consideration 6
More LessThe International Code of Nomenclature of Prokaryotes contains 48 Notes to the General Considerations, the Principles, the Rules and the Recommendations. However, the formal status of these Notes is not defined in the Code. Therefore, we here propose an emendation of General Consideration 6 stating that the Notes are intended to clarify the preceding text and are an integral part of that text.
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Proposal to modify the Note to Rule 61 of the International Code of Nomenclature of Prokaryotes
More LessIn view of the current difficulty to make minor typographical or orthographic corrections to incorrectly formed names of taxa, we propose a change in the text of the Note to Rule 61 of the International Code of Nomenclature of Prokaryotes, to be applied retroactively from August 2009. The proposed change will enable the List Editors of the International Journal of Systematic and Evolutionary Microbiology and others to correct minor errors without having to refer each case to the Judicial Commission of the International Committee for Systematics of Prokaryotes.
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- Corrigendum
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)