- Volume 66, Issue 11, 2016
Volume 66, Issue 11, 2016
- New taxa
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- Firmicutes and related organisms
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Falcatimonas natans gen. nov., sp. nov., a strictly anaerobic, amino-acid-decomposing bacterium isolated from a methanogenic reactor of cattle waste
More LessA strictly anaerobic bacterial strain (WN011T) was isolated from a methanogenic reactor treating waste from cattle farms. Cells of the strain were Gram-stain-negative curved rods with a polar flagellum. Spores were not produced. The optimum temperature for growth was 35–37 °C and the optimum pH was 6.7. The strain did not utilize carbohydrates as growth substrates. The strain grew in PY medium and produced acetate, butyrate, isovalerate and H2 as well as propionate and isobutyrate as minor products. Amino acids (l-isoleucine, l-leucine, l-lysine, l-serine, l-threonine and l-valine) added to PY medium enhanced growth of the strain and increased the amounts of fermentation products. Oxidase, catalase and nitrate-reducing activities were negative. Hydrogen sulfide was produced. The genomic DNA G+C content was 38.8 mol%. Compounds related to iso-C15 : 0 (fatty acid, dimethylacetal and aldehyde) were detected as predominant components by the cellular fatty acids analysis. The diagnostic diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequences, three clones from wastewater were very closely related to strain WN011T (up to 99.9 % sequence similarity). The most closely related described species were those in cluster XIVa of the class Clostridia such as Ruminococcus gauvreauii (93.8 % 16S rRNA gene sequence similarity), Clostridium fimetarium (93.5 %) and Clostridium bolteae (93.5 %). Based on the distinct differences in phylogenetic and phenotypic characteristics of strain WN011T from those of related species, it is concluded that strain WN011T represents a novel species of a new genus in the family Lachnospiraceae, for which the name Falcatimonas natans gen. nov., sp. nov. is proposed. The type strain of the type species is WN011T (=JCM 16476T=DSM 22923T).
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Saccharibacillus qingshengii sp. nov., isolated from a lead-cadmium tailing
More LessA Gram-stain-positive, strictly aerobic strain, H6T, was isolated from a soil sample of lead-cadmium tailing in Qixia district, Nanjing (China). Cells of the strain are rod-shaped and colonies on LB agar are red. Strain H6T has subpolar and polar flagella and the optimal condition for growth is 30 °C, with 1 % (w/v) NaCl and at pH 7.0. Based on the 16S rRNA gene sequences, phylogenetic analysis showed that strain H6T was closely related to the genus Saccharibacillus , and the closest relatives were Saccharibacillus deserti WLJ055T (99.0 % 16S rRNA gene sequence similarity), Saccharibacillus kuerlensis HR1T (97.0 %) and Saccharibacillus sacchari GR21T (96.4 %). The DNA–DNA relatedness value between strain H6T and S. deserti WLJ055T was 55.0 %. The major polar lipids of strain H6T were diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid and three unknown glycolipids. The DNA G+C content was 58.4 mol% and MK-7 was the major isoprenoid quinone. The major fatty acids were anteiso-C15 : 0 and C16 : 0. meso-Diaminopimelic acid was detected in the peptidoglycan. Based on the phylogenetic, biochemical and chemotaxonomic data, strain H6T represents a novel species of the genus Saccharibacillus , for which the name Saccharibacillus qingshengii sp. nov., is proposed. The type strain is H6T (=CCTCC AB 2016001T=JCM 31172T).
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Polygonibacillus indicireducens gen. nov., sp. nov., an indigo-reducing and obligate alkaliphile isolated from indigo fermentation liquor for dyeing
More LessObligately alkaliphilic and halophilic strains, designated In2-9T and D2-7, were isolated from a fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample obtained from a craft centre in Date City, Hokkaido, Japan. The 16S rRNA gene sequence phylogeny suggested that strain In2-9T is a member of the genus Bacillus with the closest relatives being the alkaliphilic species of the genus Bacillus , Bacillus hemicellulosilyticusJCM 9152T (96.4 % 16S rRNA gene sequence similarity) and Bacillus alcalophilus DSM 485T (96.5 %). Cells of the isolate stained Gram-positive and were facultatively anaerobic straight rods that were motile by peritrichous flagella. Strain In2-9T grew between 13 and 45 °C with optimum growth at approximately 35–37 °C. The isolates grew in the pH range of 8–12 with optimum growth at pH 10. The isoprenoid quinone detected was menaquinone-6 (MK-6) and the DNA G+C content was 39.4 mol%. The whole-cell fatty acid profile mainly (>10 %) consisted of iso-C15 : 0, anteiso-C15 : 0 and C16 : 0. Spore shape and location and chemotaxonomic characteristics revealed that the isolates were distinctly different from phylogenetic neighbouring alkaliphilic species of the genus Bacillus . On the basis of phenotypic and chemotaxonomic characteristics and phylogenetic data, the isolates represent a novel species of a new genus, for which the name Polygonibacillus indicireducens gen. nov., sp. nov. is proposed. The type strain of the type species is In2-9T (=JCM 30831T=NCIMB 14982T), and strain D2-7 is an additional strain of the species.
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Scopulibacillus daqui sp. nov., a thermophilic bacterium isolated from high temperature daqu
More LessA Gram-stain-positive, facultatively anaerobic, thermophilic bacterium, designated ZQ18-1T, was isolated from a high temperature daqu sample collected from the sesame-flavour liquor-making process. Oval endospores were formed at the centre of cells with swollen sporangia. The isolate was able to grow at temperatures of 20–60 °C (optimum growth at 50 °C), at pH 4–9 (optimum growth at pH 8) and in the presence of 0–10 % (w/v) NaCl (optimum growth with 2 % NaCl). Glucose and galactose were major cell-wall sugars, and meso-diaminopimelic acid was the diagnostic amino acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and three glycolipids. The major cellular fatty acids were anteiso-C17 : 0 and iso-C16 : 0, and the predominant menaquinone was MK-7. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZQ18-1T was most closely related to Scopulibacillus darangshiensis DLS-06T, Pullulanibacillus pueri YN3T, Tuberibacillus calidus 607T, Pullulanibacillus naganoensis ATCC 53909T, Pullulanibacillus uraniitolerans UG-2T, Sporolactobacillus terrae DSM 11697T and Sporolactobacillus inulinus NRIC 1133T. Strain ZQ18-1T showed low DNA–DNA relatedness (40.7, 23.1, 46.5, 27.2, 45.6, 33.7 and 55.1 %) with the strains mentioned above. Based on morphological characteristics, chemotaxonomic characteristics, DNA–DNA hybridization data and physiological properties, strain ZQ18-1T represents a novel species of the genus Scopulibacillus , for which the name Scopulibacillus daqui sp. nov. is proposed. The type strain is Scopulibacillus daqui ZQ18-1T (=DSM 28236T=CICC 10824T). An emended description of the genus Scopulibacillus is provided.
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Bacillus wiedmannii sp. nov., a psychrotolerant and cytotoxic Bacillus cereus group species isolated from dairy foods and dairy environments
A facultatively anaerobic, spore-forming Bacillus strain, FSL W8-0169T, collected from raw milk stored in a silo at a dairy powder processing plant in the north-eastern USA was initially identified as a Bacillus cereus group species based on a partial sequence of the rpoB gene and 16S rRNA gene sequence. Analysis of core genome single nucleotide polymorphisms clustered this strain separately from known B. cereus group species. Pairwise average nucleotide identity blast values obtained for FSL W8-0169T compared to the type strains of existing B. cereus group species were <95 % and predicted DNA–DNA hybridization values were <70 %, suggesting that this strain represents a novel B. cereus group species. We characterized 10 additional strains with the same or closely related rpoB allelic type, by whole genome sequencing and phenotypic analyses. Phenotypic characterization identified a higher content of iso-C16 : 0 fatty acid and the combined inability to ferment sucrose or to hydrolyse arginine as the key characteristics differentiating FSL W8-0169T from other B. cereus group species. FSL W8-0169T is psychrotolerant, produces haemolysin BL and non-haemolytic enterotoxin, and is cytotoxic in a HeLa cell model. The name Bacillus wiedmannii sp. nov. is proposed for the novel species represented by the type strain FSL W8-0169T (=DSM 102050T=LMG 29269T).
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Pullulanibacillus camelliae sp. nov., isolated from Pu’er tea
More LessA novel Gram-stain-positive, strictly aerobic, endospore-forming, rod-shaped bacterial strain 7578-24T was isolated from ripened Pu’er tea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 7578-24T clustered with species of the genus Pullulanibacillus in the family Sporolactobacillaceae with 97.8–95.2 % sequence similarities, and was most closely related to Pullulanibacillus pueri YN3T with 97.8 % 16S rRNA gene sequence similarity. The DNA–DNA relatedness value between strain 7578-24T and P. pueri YN3T was 35 %. Strain 7578-24T had a cell-wall type A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The major menaquinone was menaquinone 7 (MK-7). C18 : 1 ω7c (45.4 %), anteiso-C17 : 0 (30.6 %) and anteiso-C15 : 0 (10.1 %) were the predominant fatty acids, and diphosphatidylglycerol, phosphatidylglycerol, five unknown phospholipids and one unknown aminolipid were the major polar lipids. The DNA G+C content of strain 7578-24T was 45.2 mol%. Strain 7578-24T could be differentiated from other related species of the genus Pullulanibacillus based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA–DNA hybridization data. On the basis of polyphasic evidence from this study, a novel species of the genus Pullulanibacillus named Pullulanibacillus camelliae sp. nov. is proposed, with strain 7578-24T (=CGMCC 1.15371T=JCM 31236T) as the type strain.
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Description of Alteribacillus alkaliphilus sp. nov., reassignment of Bacillus iranensis (Bagheri et al. 2012) as Alteribacillus iranensis comb. nov. and emended description of the genus Alteribacillus
More LessA novel Gram-stain-positive, aerobic, endospore-forming, non-motile, rod-shaped bacterium (strain JC229T) was isolated from a water sample collected from waterlogged alkaline soil. Strain JC229T was oxidase- and catalase-positive. Based on 16S rRNA gene sequence analysis, strain JC229T was identified as belonging to the genus Alteribacillus of the phylum Firmicutes and was found to be most closely related to Alteribacillus bidgolensis P4BT (97.9 % similarity), Bacillus iranensis X5BT (97.2 %) and Alteribacillus persepolensis HS136T (96.6 %), and more distantly related to other members of the genus Bacillus (<95.2 %). Strain JC229T was further identified to be distinctly related to the type strains of A. bidgolensis and B. iranensis (<26 % based on DNA–DNA hybridization and ΔT m of >5 °C). Strain JC229T grew optimally at pH 8 (range 5–11), at 35–40 °C (range 20–50 °C) and at a salinity of 3–5 % (range 0.5–24 %). The DNA G+C content was 40.2 mol%. Major cellular fatty acids of strain JC229T were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant quinone system was menaquinone 7. Polar lipids of strain JC229T included diphosphatidylglycerol, phosphatidylglycerol and two unidentified lipids. On the basis of morphological, physiological, genetic, phylogenetic and chemotaxonomic analyses, strain JC229T should be assigned to a novel species of the genus Alteribacillus , for which the name Alteribacillus alkaliphilus sp. nov. is proposed. The type strain is JC229T (=LMG 28999T=KCTC 33726T). It is also suggested to transfer B. iranensis to the genus Alteribacillus as Alteribacillus iranensis comb. nov.
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- Other bacteria
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Detection and identification of the heterogeneous novel subgroup 16SrXIII-(A/I)I phytoplasma associated with strawberry green petal disease and Mexican periwinkle virescence
More LessPhytoplasmas (species of the genus ‘Candidatus Phytoplasma ’) are insect-vectored phytopathogenic bacteria associated with economically and ecologically important crop diseases. Strawberry production represents an important part of agricultural activity in Mexico and elsewhere, and infection of plants with phytoplasma renders the fruit inedible by altering plant development, resulting in virescence and phyllody. In this study we examined samples taken from four strawberry plants showing symptoms associated with strawberry green petal disease and from two periwinkle plants showing virescence, sampled in different areas of Mexico. Analysis of the 16S rRNA-encoding sequences showed that the plants were infected with a phytoplasma previously identified as Mexican periwinkle virescence (MPV; 16SrXIII). Examination of bacterial sequences from these samples revealed that two distinct 16S rRNA gene sequences were present in each sample along with a single chaperonin-60 (cpn60) sequence and a single rpoB sequence, suggesting that this strain displays 16S rRNA gene sequence heterogeneity. Two distinct rrn operons, identified with subgroup 16SrXIII-A and the newly described subgroup 16SrXIII-I, were identified from the six samples analyzed, delineating the novel subgroup 16SrXIII-(A/I)I, following the nomenclature proposed for heterogeneous subgroups.
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Akkermansia glycaniphila sp. nov., an anaerobic mucin-degrading bacterium isolated from reticulated python faeces
More LessA Gram-stain-negative, non-motile, strictly anaerobic, oval-shaped, non-spore-forming bacterium (strain PytT) was isolated from reticulated python faeces. Strain PytT was capable of using mucin as sole carbon, energy and nitrogen source. Cells could grow singly, in pairs, and were also found to aggregate. Scanning electron microscopy revealed the presence of filamentous structures connecting individual bacterial cells. Strain PytT could grow on a limited number of single sugars, including N-acetylglucosamine, N-acetylgalactosamine, glucose, lactose and galactose, but only when a plentiful protein source was provided. Phylogenetic analysis based on 16S rRNA gene sequencing showed strain PytT to belong to the Verrucomicrobiae class I, family Akkermansiaceae , genus Akkermansia , with Akkermansia muciniphila MucT as the closest relative (94.4 % sequence similarity). DNA–DNA hybridization revealed low relatedness of 28.3 % with A. muciniphila MucT. The G+C content of DNA from strain PytT was 58.2 mol%. The average nucleotide identity (ANI) of the genome of strain PytT compared to the genome of strain MucT was 79.7 %. Chemotaxonomic data supported the affiliation of strain PytT to the genus Akkermansia . Based on phenotypic, phylogenetic and genetic characteristics, strain PytT represents a novel species of the genus Akkermansia , for which the name Akkermansia glycaniphila sp. nov. is proposed. The type strain is PytT (=DSM 100705T=CIP 110913T).
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Borrelia mayonii sp. nov., a member of the Borrelia burgdorferi sensu lato complex, detected in patients and ticks in the upper midwestern United States
Bobbi S. Pritt, Laurel B. Respicio-Kingry, Lynne M. Sloan, Martin E. Schriefer, Adam J. Replogle, Jenna Bjork, Gongping Liu, Luke C. Kingry, Paul S. Mead, David F. Neitzel, Elizabeth Schiffman, Diep K. Hoang Johnson, Jeffrey P. Davis, Susan M. Paskewitz, David Boxrud, Alecia Deedon, Xia Lee, Tracy K. Miller, Michelle A. Feist, Christopher R. Steward, Elitza S. Theel, Robin Patel, Cole L. Irish and Jeannine M. PetersenLyme borreliosis (LB) is a multisystem disease caused by spirochetes in the Borrelia burgdorferi sensu lato (Bbsl) genospecies complex. We previously described a novel Bbsl genospecies (type strain MN14-1420T) that causes LB among patients with exposures to ticks in the upper midwestern USA. Patients infected with the novel Bbsl genospecies demonstrated higher levels of spirochetemia and somewhat differing clinical symptoms as compared with those infected with other Bbsl genospecies. The organism was detected from human specimens using PCR, microscopy, serology and culture. The taxonomic status was determined using an eight-housekeeping-gene (uvrA, rplB, recG, pyrG, pepX, clpX, clpA and nifS) multi-locus sequence analysis (MLSA) and comparison of 16S rRNA gene, flaB, rrf–rrl, ospC and oppA2 nucleotide sequences. Using a system threshold of 98.3 % similarity for delineation of Bbsl genospecies by MLSA, we demonstrated that the novel species is a member of the Bbsl genospecies complex, most closely related to B. burgdorferi sensu stricto (94.7–94.9 % similarity). This same species was identified in Ixodes scapularis ticks collected in Minnesota and Wisconsin. This novel species, Borrelia mayonii sp. nov, is formally described here. The type strain, MN14-1420, is available through the Deutsche Sammlung von Mikroorganismen und Zelkulturen GmbH (DSM 102811) and the American Type Culture Collection (ATCC BAA-2743).
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- Proteobacteria
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Legionella saoudiensis sp. nov., isolated from a sewage water sample
A Gram-stain-negative, bacilli-shaped bacterial strain, LS-1T, was isolated from a sewage water sample collected in Jeddah, Saudi Arabia. The taxonomic position of strain LS-1T was investigated using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences and those of four other genes indicated that strain LS-1T belongs to the genus Legionella in the family Legionellaceae . Regarding the 16S rRNA gene, the most closely related species are Legionella rowbothamii LLAP-6T (98.6 %) and Legionella lytica L2T (98.5 %). The mip gene sequence of strain LS-1T showed 94 % sequence similarity with that of L. lytica L2T and 93 % similarity with that of L. rowbothamii LLAP-6T. Strain LS-1T grew optimally at a temperature of 32 °C on a buffered charcoal yeast extract (BCYE) agar plate in a 5 % CO2 atmosphere and had a flagellum. The combined phylogenetic, phenotypic and genomic sequence data suggest that strain LS-1T represents a novel species of the genus Legionella , for which the name Legionella saoudiensis sp. nov. is proposed. The type strain is LS-1T (=DSM 101682T=CSUR P2101T).
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Dyella humi sp. nov., isolated from forest soil
More LessA Gram-stain-negative, aerobic, motile, rod-shaped, yellow-pigmented bacterium, designated as DHG40T, was isolated from a soil sample collected from the forest of Dinghushan Biosphere Reserve, Guangdong Province, China. Strain DHG40T grew at pH 4.0–8.0 and 10–37 °C (optimum at pH 6.0–7.0 and 25–28 °C). NaCl inhibited growth at concentrations above 2.5 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate fell within the cluster of the genus Dyella . Strain DHG40T was closely related to Dyella ginsengisoli Gsoil 3046T (97.6 % 16S rRNA gene sequence similarity), Dyella marensis CS5-B2T (97.5 %), Dyella koreensis BB4T (97.4 %) and Dyella jejuensis JP1T (97.4 %). The DNA–DNA relatedness values between strain DHG40T and its phylogenetically closest relatives were all below 40 %. The DNA G+C content was 60.3 mol%. In addition, iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and iso-C17 : 1 ω9c were the major fatty acids (>10 %) and ubiquinone-8 was the respiratory quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unidentified aminolipid and an unidentified phospholipid. On the basis of phylogenetic, phenotypic, physiological and chemotaxonomic distinctiveness, strain DHG40T should be placed in the genus Dyella as a representative of a novel species, for which the name Dyella humi sp. nov. is proposed. The type strain is DHG40T (=KCTC 42629T=LMG 28842T).
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Pseudoalteromonas profundi sp. nov., isolated from a deep-sea seamount
More LessA Gram-stain-negative, rod-shaped, strictly aerobic, motile bacterial strain, designated TP162T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP162T was related to the genus Pseudoalteromonas and had highest 16S rRNA gene sequence similarities with the type strains Pseudoalteromonas shioyasakiensis SE3T (98.2 %), Pseudoalteromonas lipolytica LMEB 39T (97.7 %), P seudoalteromonas arabiensis k53T (97.4 %) and Pseudoalteromonas aliena KMM 3562T (97.2 %). The predominant cellular fatty acids were summed feature 3 (composed of iso-C1 5 : 0 2-OH and/or C1 6 : 1ω7c), C1 7 : 1ω8c and C1 6 : 0. The quinone system for strain TP162T comprised predominantly ubiquinone-8, and the polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and four unidentified lipids. The genomic DNA G+C content of strain TP162T was 46.7 mol%. Strain TP162T shared 28 % DNA–DNA relatedness with P . shioyasakiensis JCM 18891T, 21 % with P. lipolytica JCM 15903T, 35 % with P . arabiensis JCM 17292T and 18 % with P . aliena LMG 22059T. Combined data from phenotypic, chemotaxonomic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain TP162T is a representative of a novel species of the genus Pseudoalteromonas , for which we propose the name Pseudoalteromonas profund i sp. nov. (type strain TP162T=KACC 18554T=CGMCC 1.15394T).
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Rhizobium favelukesii sp. nov., isolated from the root nodules of alfalfa (Medicago sativa L)
Strains LPU83T and Or191 of the genus Rhizobium were isolated from the root nodules of alfalfa, grown in acid soils from Argentina and the USA. These two strains, which shared the same plasmid pattern, lipopolysaccharide profile, insertion-sequence fingerprint, 16S rRNA gene sequence and PCR-fingerprinting pattern, were different from reference strains representing species of the genus Rhizobium with validly published names. On the basis of previously reported data and from new DNA-DNA hybridization results, phenotypic characterization and phylogenetic analyses, strains LPU83T and Or191 can be considered to be representatives of a novel species of the genus Rhizobium , for which the name Rhizobium favelukesii sp. nov. is proposed. The type strain of this species is LPU83T (=CECT 9014T=LMG 29160T), for which an improved draft-genome sequence is available.
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Croceicoccus pelagius sp. nov. and Croceicoccus mobilis sp. nov., isolated from marine environments
Strain Ery9T, isolated from surface seawater of the Atlantic Ocean, and strain Ery22T, isolated from deep-sea sediment of the Indian Ocean, were subjected to a taxonomic study using a polyphasic approach. Cells of the two strains were Gram-stain-negative, aerobic and rod-shaped. They produced yellow pigments and lacked bacteriochlorophyll a. On the basis of 16S rRNA gene sequence analysis, strain Ery9T was closely related to Croceicoccus naphthovorans PQ-2T (with 16S rRNA gene sequence similarity of 97.7 %), and strain Ery22T was closely related to Croceicoccus marinus E4A9T (98.3 %). The 16S rRNA gene sequence similarity between strain Ery9T and strain Ery22T was 96.6 %. Phylogenetic analyses revealed that strains Ery9T and Ery22T fell within the cluster of the genus Croceicoccus and represented two independent lineages. The average nucleotide identity (ANI) values and the genome-to-genome distances between strains Ery9T and Ery22T and the type strains of species of the genus C roceicoccus with validly published names were 73.7–78.4 % and 20.1–22.3 %, respectively. The major respiratory quinone of the two isolates was ubiquinone-10 (Q-10). The DNA G+C contents of strains Ery9T and Ery22T were 62.8 and 62.5 mol%, respectively. Differential phylogenetic distinctiveness and chemotaxonomic differences, together with phenotypic properties, revealed that strains Ery9T and Ery22T could be differentiated from their closely related species. Therefore, it is concluded that strains Ery9T and Ery22T represent two novel species of the genus Croceicoccus , for which the names Croceicoccus pelagius sp. nov. (type strain Ery9T=CGMCC 1.15358T=DSM 101479T) and Croceicoccus mobilis sp. nov. (type strain Ery22T=CGMCC 1.15360T=DSM 101481T), are proposed.
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Isolation and characterization of a novel Rickettsia species (Rickettsia asembonensis sp. nov.) obtained from cat fleas (Ctenocephalides felis)
A novel rickettsial agent, ‘Candidatus Rickettsia asembonensis’ strain NMRCiiT, was isolated from cat fleas, Ctenocephalides felis, from Kenya. Genotypic characterization of the new isolate based on sequence analysis of five rickettsial genes, rrs, gltA, ompA, ompB and sca4, indicated that this isolate clustered with Rickettsia felis URRWXCal2. The degree of nucleotide similarity demonstrated that isolate NMRCiiT belongs within the genus Rickettsia and fulfils the criteria for classification as a representative of a novel species. The name Rickettsia asembonensis sp. nov. is proposed, with NMRCiiT (=DSM 100172T=CDC CRIRC RAS001T=ATCC VR-1827T) as the type strain.
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Campylobacter hepaticus sp. nov., isolated from chickens with spotty liver disease
More LessTen strains of an unknown Campylobacter species were isolated from the livers of chickens with spotty liver disease in Australia. The strains were Gram-stain-negative, microaerobic, catalase- and oxidase-positive and urease-negative. Unlike most other species of the genus Campylobacter , most of the tested strains of this novel species hydrolysed hippurate and half of them could not reduce nitrate. All strains showed resistance, or intermediate resistance, to nalidixic acid and most of them were resistant to cephalothin. Examination of negatively stained cells under transmission electron microscopy revealed that they were S-shaped, with bipolar unsheathed flagella. Phylogenetic analyses based on the 16S rRNA gene and the heat shock protein 60 (hsp60) gene sequences indicated that the strains formed a robust clade that was clearly distinct from recognized Campylobacter species. Unusually, they had a DNA G+C content of 27.9 mol%, lower than any previously described Campylobacter species, and they showed less than 84 % average nucleotide identity to the nearest sequenced species. Taken together, these data indicate that the strains belong to a novel Campylobacter species, for which the name Campylobacter hepaticus sp. nov. is proposed. The type strain is HV10T (=NCTC 13823T=CIP 111092T).
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Chelatococcus reniformis sp. nov., isolated from a glacier
A Gram-stain-negative, non-motile, reniform bacterial strain, B2974T, was isolated from an ice core of the Muztagh Glacier, on the Tibetan Plateau, China. Strain B2974T grew optimally at pH 7.0–7.5 and 25–30 °C in the presence of 0–2.0 % (w/v) NaCl. 16S rRNA gene sequence similarity analysis indicated that strain B2974T was closely related to Chelatococcus asaccharovorans LMG 25503T at a level of 97.1 %. The major quinone of strain B2974T was ubiquinone Q10. The predominant fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C19 : 0 cyclo ω8c. sym-Homospermidine was the major polyamine. The genomic DNA G+C content of the strain was 64 mol%. In DNA–DNA hybridization tests, strain B2974T shared 49.32 % DNA–DNA relatedness with the type strain of Chelatococcus asaccharovorans LMG 25503T. Based on the results of phenotypic and chemotaxonomic characteristics, strain B2974T was considered as a novel species of the genus Chelatococcus , for which the name Chelatococcus reniformis sp. nov. is proposed. The type strain is B2974T (=JCM 30308T=CGMCC 1.12919T).
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Paraburkholderia pallidirosea sp. nov., isolated from a monsoon evergreen broad-leaved forest soil
More LessA Gram-stain-negative, rod-shaped, aerobic and motile bacterial strain, DHOK13T, was isolated from the forest soils of Dinghushan Biosphere Reserve, Guangdong Province, PR China (112° 31′ E, 23° 10′ N). It grew optimally at 28–33 °C and pH 7.0–7.5. The main fatty acids were C16 : 0, C17 : 0 cyclo, C19 : 0 cycloω8c, summed feature 2 (C12 : 0 aldehyde and/or unknown 10.9525) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The organism contained ubiquinone Q-8 as the predominant isoprenoid quinone. The total DNA G+C content of strain DHOK13T was 62.0 mol%. Phylogenetic analysis of the 16S rRNA gene, as well as the sequence of the partial housekeeping genes, gyrB and recA, showed consistently that strain DHOK13T formed an independent cluster with Paraburkholderia phenazinium LMG 2247T. DNA-DNA hybridization studies showed relatively low relatedness values (39 %) of strain DHOK13T with P. phenazinium LMG 2247T. The phenotypic, chemotaxonomic and phylogenetic data showed that strain DHOK13T represents a novel species of the genus Paraburkholderia for which the name Paraburkholderia pallidirosea sp. nov. is proposed. The type strain is DHOK13T (=KCTC 42626T=LMG 28846T).
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Description of Altererythrobacter aerius sp. nov., isolated from air, and emended description of the genus Altererythrobacter
More LessA Gram-stain-negative, yellow-pigmented, ovoid to rod-shaped, strictly aerobic bacterial strain, designated 100921-2T, was isolated from air at the foot of Xiangshan Mountain. Phylogenetic and phenotypic analysis of the organism revealed that the isolate belongs to the genus Altererythrobacter . Strain 100921-2T showed high 16S rRNA gene sequence similarity (96.01–94.70 %) to other type strains of the genus Altererythrobacter , with the highest similarity to Altererythrobacter marensis MSW-14T. Growth of strain 100921-2T was observed at 4–50 °C (optimum, 30 °C), at pH 4.5–10.0 (optimum, pH 7.0) and at salinities of 0–10 % (w/v) NaCl (optimum 0–0.5 %). The major fatty acids were C18 : 1 ω7c (27.8 %), C17 : 1 ω6c (23.1 %), 11-methyl C18 : 1 ω7c(11.9 %), summed feature 3 (9.1 %) and C15 : 0 2-OH (7.9 %). The predominant respiratory quinone was ubiquinone-10 (Q-10). Polar lipid analysis indicated the presence of diphosphatidylglycerol, sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unknown phospholipids, five unknown polar lipids and two unknown glycolipids. The DNA G+C content of the type strain was 67.5 mol%. On the basis of the data from the polyphasic characterization, strain 100921-2T represents a novel species, for which the name Altererythrobacter aerius sp. nov. is proposed. The type strain is 100921-2T (=CFCC 14287T=KCTC 42844T).
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Wenzhouxiangella sediminis sp. nov., isolated from coastal sediment
More LessA novel Gram-stain-negative, non-spore-forming, non-motile, facultatively anaerobic, rod-shaped strain, designated XDB06T, was isolated from coastal sediment of Xiaoshi Island, Weihai, China. Optimal growth occurred at 37 °C, pH 7.5 and with 4.0 % (w/v) NaCl. Q-8 was the sole respiratory quinone. The major cellular fatty acids in strain XDB06T were iso-C15 : 0 and iso-C16 : 0. The polar lipids of strain XDB06T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified glycolipids and four unidentified phospholipids. The genomic DNA G+C content of the strain was 65.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XDB06T clusters within the genus Wenzhouxiangella and is most closely related to Wenzhouxiangella . marina MCCC 1K00261T, with a 16S rRNA gene sequence similarity of 96.50 %. Based on data from the current polyphasic study, strain XDB06T represents a novel species of the genus Wenzhouxiangella , for which the name Wenzhouxiangella sediminis sp. nov. is proposed. The type strain is XDB06T (=KCTC 52041T=MCCC 1K02285T).
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Silicimonas algicola gen. nov., sp. nov., a member of the Roseobacter clade isolated from the cell surface of the marine diatom Thalassiosira delicatula
More LessA Gram-negative, aerobic, non-motile bacterium, designated strain KC90BT, was isolated from the surface of a cell of the marine diatom Thalassiosira delicatula. The bacterial cells were pleomorphic and formed very small, beige colonies on marine agar. Optimal growth was obtained at 25 °C, at pH 6.5–7.5 and in the presence of 1.5–2.0 % (w/v) NaCl. Phylogenetic analyses based on its 16S rRNA gene sequence revealed that strain KC90BT belonged to the Roseobacter clade and formed a monophyletic cluster with the sequences of Boseongicola aestuarii , Profundibacterium mesophilum , Hwanghaeicola aestuarii , Maribius pelagius and M. salinus, showing 91.4–95.7 % sequence similarities. Ubiquinone Q-10 was the predominant lipoquinone but a significant amount of ubiquinone Q-9 was also detected. The major cellular fatty acids were C18 : 1 ω7c, 11-methyl C18 : 1 ω7c and C18 : 0. Strain KC90BT also contained specific fatty acids (C17 : 0, anteiso-C15 : 0 and anteiso-C17 : 0) that were not detected in its closest described relatives. The major polar lipids of strain KC90BT comprised phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and an unidentified aminolipid. The DNA G+C content of strain KC90BT was 65.2 mol%. The phylogenetic analysis of strain KC90BT, together with the differential phenotypic and chemotaxonomic properties demonstrate that strain KC90BT is distinct from type strains of B. aestuarii , P. mesophilum , H. aestuarii , M. pelagius and M. salinus . Based on the data presented in this study, strain KC90BT represents a novel genus and species within the family Rhodobacteraceae , for which the name Silicimonas algicola gen. nov., sp. nov. is proposed. The type strain is KC90BT (=DSM 103371T=RCC 4681T).
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Sphingomonas naphthae sp. nov., isolated from oil-contaminated soil
More LessDuring the study of hydrocarbon-degrading bacteria in the oil-contaminated soil of Gunsan, North Jeolla Province, South Korea, a yellow, Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated strain DKC-5-1T, was isolated. This strain was non-sporulating, catalase-negative and oxidase-positive. It was able to grow at 10–33 °C, pH 6.0–8.5 and at an NaCl concentration of 0–1.5 % (w/v). This strain was characterized taxonomically using a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain DKC-5-1T belongs to the genus Sphingomonas and is closely related to Sphingomonas laterariae LNB2T (96.65 % sequence similarity), Sphingomonas haloaromaticamans A175T (96.63 % sequence similarity), Sphingomonas histidinilytica UM2T (96.63 % sequence similarity), and Sphingomonas wittichii RW1T (96.43 % sequence similarity). The only respiratory quinone was ubiquinone-10 and the major polyamine was homospermidine. The polar lipid profile revealed the presence of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and phosphatidyldimethylethanolamine. The predominant fatty acids of strain DKC-5-1T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, C14 : 0 2-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C17 : 1ω6c and C14 : 0. The genomic DNA G+C content of this novel strain was 65.9 mol%. Morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain DKC-5-1T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas naphthae sp. nov. is proposed. The type strain is DKC-5-1T (=KEMB 9005-380T=KACC 18716T=JCM 31294T).
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Pseudomonas turukhanskensis sp. nov., isolated from oil-contaminated soils
A bacterial strain named IB1.1T was isolated in a screening of hydrocarbon-degrading bacteria from oil-contaminated soils on the territory of the Turukhansk District of Krasnoyarsk Krai, East Siberia, Russia. The 16S rRNA gene sequence had 98.7 % identity with respect to the closest phylogenetic relative, Pseudomonas granadensis F-278,770T, and the next most closely related species with 98.6 % similarity was Pseudomonas punonensis , suggesting that IB1.1T should be classified within the genus Pseudomonas . The analysis of housekeeping genes rpoB, rpoD and gyrB showed similarities lower than 90 % in all cases with respect to the closest relatives, confirming its phylogenetic affiliation. The strain showed a polar flagellum. The respiratory quinone was Q9. The major fatty acids were 16 : 1ω7c/16 : 1ω6c (summed feature 3), 18 : 1ω7c and 16 : 0. The strain was oxidase- and catalase-positive, but the arginine dihydrolase system was not present. Nitrate reduction, urease and β–galactosidase production, and aesculin hydrolysis were negative. The temperature range for growth was 4–34 °C, and the strain could grow at pH 11. The DNA G+C content was 58.5 mol%. DNA–DNA hybridization results showed values of less than 30 % relatedness with respect to the type strains of the eight most closely related species. Therefore, the dataset of genotypic, phenotypic and chemotaxonomic data support the classification of strain IB1.1T into a novel species of the genus Pseudomonas , for which the name Pseudomonas turukhanskensis sp. nov. is proposed. The type strain is IB1.1T (=VKM B-2935T=CECT 9091T).
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Pseudoduganella danionis sp. nov., isolated from zebrafish (Danio rerio)
One beige-pigmented, Gram-staining-negative, rod-shaped bacterium, strain E3/2T, was isolated from a zebrafish, Daniorerio. Phylogenetic analysis based on nearly full-length 16S rRNA gene sequences showed that the isolate shared 97.7 % 16S rRNA gene sequence similarity to the species Pseudoduganella violaceinigra and between 97.4 to 97.0 % to some species of the genera Duganella and Massilia , including Duganella radicis , Duganella phyllosphaerae , Massilia dura , Massilia lutea , Duganella sacchari , Duganella zoogloeoides , Massilia albidiflava and Massilia umbonata . Sequence similarities to all other species were below 97 %. The main cellular fatty acids of the strain were summed feature 3 fatty acids (C16 : 1 ω7c/iso-C15 : 0 2-OH), C10 : 0 3-OH, C16 : 0 and C12 : 0. The polyamine pattern of strain E3/2T contained predominantly putrescine and 2-hydroxyputrescine. The major quinone was ubiquinone Q-8. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on phylogenetic, chemotaxonomic, genomic and phenotypic analyses we propose a novel species of the genus Pseudoduganella named Pseudoduganella danionis sp. nov., with strain E3/2T (=LMG 29678T=CCM 8698T) as the type strain.
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Litorisediminivivens gilvus gen. nov., sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, non-flagellated, aerobic and coccoid, ovoid or rod-shaped bacterium, designated YSM-17T, was isolated from tidal flat sediment collected from the South Sea, South Korea, and subjected to a polyphasic taxonomic study. The novel strain grew optimally at 30 °C, at pH 6.5–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain YSM-17T forms a distinct evolutionary lineage independent of other taxa in the family Rhodobacteraceae . Strain YSM-17T exhibited 16S rRNA gene sequence similarity values of 96.8 and 96.6 % to the type strains of Pseudopelagicola gijangensis and Pelagicola litoralis , respectively, and of less than 96.5 % to the type strains of other recognized taxa. Strain YSM-17T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids detected in strain YSM-17T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and one unidentified aminolipid. The fatty acid and polar lipid profiles of strain YSM-17T were distinguished from those of the genera Pseudopelagicola and Pelagicola . The DNA G+C content of strain YSM-17T was 64.6±0.04 mol%. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain YSM-17T is considered to represent a novel species of a new genus within the family Rhodobacteraceae , for which the name Litorisediminivivens gilvus gen. nov., sp. nov., is proposed. The type strain of Litorisediminivivens gilvus is YSM-17T (=KCTC 52249T=NBRC 112330T).
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Halomonas lutescens sp. nov., a halophilic bacterium isolated from a lake sediment
More LessA novel, Gram-stain-negative, facultatively anaerobic, halophilic bacterium, designated strain Q1UT, was isolated from a sediment sample collected from Qinghai Lake, PR China. The cells of the strain were short rod-shaped (0.2–0.3×0.6–2.5 µm) and non-motile. Strain Q1UT formed yellowish colonies and grew at temperatures of 2–37 °C (optimum 30–33 °C), at pH 6.0–9.0 (optimum pH 7.0) and in the presence of 0–20 % (w/v) NaCl (optimum 7.5 %). The major cellular fatty acids were C18 : 1ω7c (58.6 %), C16 : 1ω7c and/or C16 : 1ω6c (14.8 %) and C16 : 0 (10.1 %). The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown phospholipid and unknown lipids. The genomic DNA G+C content was 61.5 mol%, and the predominant respiratory ubiquinone Q-9. Based on phylogenetic analysis of the 16S rRNA gene sequences and concatenated 16S rRNA, gyrB and rpoD gene sequences, the isolate was found to belong to the genus Halomonas in the class Gammaproteobacteria . The most closely related species were Halomonas venusta DSM 4743T (98.3 % 16S rRNA sequence similarity), Halomonas songnenensis DSM 25870T (98.2 %) and Halomonas hydrothermalis DSM 15725T (98.2 %). DNA–DNA relatedness values between strain Q1UT and the type strains of eight other species of the genus Halomonas ranged from 21.3 % to 10.1 %. On the basis of phenotypic, phylogenetic and chemotaxonomic analyses, and DNA–DNA hybridization relatedness values, strain Q1UT is considered to represent a novel species of the genus Halomonas; the name Halomonas lutescens sp. nov. is proposed. The type strain is Q1UT (=CGMCC 1.15122T=KCTC 42517T).
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Novosphingobium lotistagni sp. nov., isolated from a lotus pond
A Gram-staining-negative, aerobic, non-motile, rod-shaped and yellow-pigmented bacterium, designated strain THG-DN6.20T, was isolated from a lotus pond near Donghaksa temple in Daejeon, Republic of Korea. According to 16S rRNA gene sequence comparisons, strain THG-DN6.20T was found to be most closely related to Novosphingobium rosa IFO 15208T (97.6 % sequence similarity), Novosphingobium sediminicola HU1-AH51T (97.5 %) and Novosphingobium barchaimii LL02T (96.9 %). The DNA–DNA relatedness between strain THG-DN6.20T and its phylogenetically closest neighbours was below 60.0 %. The respiratory quinone and polyamine detected in strain THG-DN6.20T were ubiquinone Q-10 and spermidine, respectively. The DNA G+C content was 63.1 mol%. The major polar lipids were found to be phosphatidylethanolamine, diphosphatidylglycerol, sphingoglycolipid and phosphatidylcholine. The major fatty acids were identified as C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C14 : 0 2-OH. These data supported the affiliation of strain THG-DN6.20T to the genus Novosphingobium . Strain THG-DN6.20T could be distinguished from related species of the genus Novosphingobium by physiological and biochemical characteristics. Therefore, the novel isolate represents a novel species, for which the name Novosphingobium lotistagni sp. nov. is proposed, with THG-DN6.20T as the type strain (=KACC 18541T=CCTCC AB 2015354T).
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Lysobacter rhizophilus sp. nov., isolated from rhizosphere soil of mugunghwa, the national flower of South Korea
More LessA Gram-staining-negative, aerobic, motile, rod-shaped, catalase- and oxidase-negative strain with one polar flagellum, designated THG-YS3.6T, was isolated from rhizosphere soil of a mugunghwa flower collected from Kyung Hee University, Yongin, South Korea. Growth occurred at 10–37 °C (optimum 25–30 °C), at pH 6–8 (optimum 7.0) and with 0–2.0 % NaCl (optimum 1 %). The isoprenoid quinone was ubiquinone-8 (Q–8). The major cellular fatty acids were iso-C11 : 0, iso-C11 : 0 3-OH, iso-C15 : 0, iso-C16 : 0, C16 : 1ω7c alcohol, C16 : 0, iso-C17 : 0 and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, one unknown phospholipid, one unknown lipid and three unknown aminolipids. The DNA G+C content of strain THG-YS3.6T was 65.3 mol%. Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-YS3.6T were identified as Lysobacter yangpyeongensis KACC 11407T (98.7 %), Lysobacter oryzae KCTC 22249T (98.0 %), Lysobacter niabensis KACC 11587T (97.6 %) and Lysobacter terrae KACC 17646T (97.1 %). The DNA–DNA relatedness values between strain THG-YS3.6T and L. yangpyeongensis KACC 11407T, L. oryzae KCTC 22249T, L. niabensis KACC 11587T and L. terrae KACC 17646T were 53.8±1.0 %, 12.9±1.2 %, 10.9±0.6 % and 7.0±1.9 %, respectively. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA–DNA hybridization data, strain THG-YS3.6T represents a novel species of the genus Lysobacter , for which the name Lysobacter rhizophilus sp. nov. is proposed. The type strain is THG-YS3.6T (=KCTC 52082T=CCTCC AB 2015358T).
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Xylella taiwanensis sp. nov., causing pear leaf scorch disease
More LessA Gram-stain-negative, nutritionally fastidious bacterium (PLS229T) causing pear leaf scorch was identified in Taiwan and previously grouped into Xylella fastidiosa . Yet, significant variations between PLS229T and Xylella fastidiosa were noted. In this study, PLS229T was evaluated phenotypically and genotypically against representative strains of Xylella fastidiosa , including strains of the currently known subspecies of Xylella fastidiosa , Xylella fastidiosa subsp. multiplex and ‘ Xylella fastidiosa subsp. pauca ’. Because of the difficulty of in vitro culture characterization, emphases were made to utilize the available whole-genome sequence information. The average nucleotide identity (ANI) values, an alternative for DNA–DNA hybridization relatedness, between PLS229T and Xylella fastidiosa were 83.4–83.9 %, significantly lower than the bacterial species threshold of 95 %. In contrast, sequence similarity of 16S rRNA genes was greater than 98 %, higher than the 97 % threshold to justify if two bacterial strains belong to different species. The uniqueness of PLS229T was also evident by observing only about 87 % similarity in the sequence of the 16S-23S internal transcribed spacer (ITS) between PLS229T and strains of Xylella fastidiosa , discovering significant single nucleotide polymorphisms at 18 randomly selected housekeeping gene loci, observing a distinct fatty acid profile for PLS229T compared with Xylella fastidiosa , and PLS229T having different observable phenotypes, such as different susceptibility to antibiotics. A phylogenetic tree derived from 16S rRNA gene sequences showed a distinct PLS229T phyletic lineage positioning it between Xylella fastidiosa and members of the genus Xanthomonas . On the basis of these data, a novel species, Xylella taiwanensis sp. nov. is proposed. The type strain is PLS229T (=BCRC 80915T=JCM 31187T).
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Reclassification of the larval pathogen for marine bivalves Vibrio tubiashii subsp. europaeus as Vibrio europaeus sp. nov.
The Orientalis clade has a relevant significance for bivalve aquaculture since it includes the pathogens Vibrio bivalvicida , Vibrio tubiashii subsp. tubiashii and Vibrio tubiashii subsp. europaeus . However, the previous taxonomic description of the subspecies of V. tubiashii shows some incongruities that should be emended. In the genomic age, the comparison between genome assemblies is the key to clarify the taxonomic position of both subspecies. With this purpose, we have tested the ability of multilocus sequence analysis based on eight housekeeping gene sequences (gap A, gyr B, fts Z, mre B, pyr H, rec A, rpo A and top A), different in silico genome-to-genome comparisons, chemotaxonomic features and phenotypic traits to reclassify the subspecies V. tubiashii subsp. europaeus within the Orientalis clade. This polyphasic approach clearly demonstrated that this subspecies is phylogenetically and phenotypically distinct from V. tubiashii and should be elevated to the rank of species as Vibrio europaeus sp. nov. This reclassification allows us to update the Orientalis clade ( V. bivalvicida , V. brasiliensis , V. crosai , V. hepatarius , V. orientalis , V. sinaloensis , V. tubiashii and V. europaeus sp. nov.) and reconstruct a better phylogeny of the genus Vibrio . An emended description of V. tubiashii is provided. Finally, the proposed novel species is represented by emergent bivalve pathogens [type strain PP-638T (=CECT 8136T=DSM 27349T), PP2-843 and 07/118 T2] responsible for high mortalities in Spanish and French hatcheries.
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Mesorhizobium sediminum sp. nov., isolated from deep-sea sediment
A novel Gram-staining-negative, short rod, non-motile, non-spore-forming, aerobic bacterium, designated strain YIM M12096T, was isolated from deep-sea sediment collected from the Indian Ocean. Optimal growth conditions of the strain were observed at 25–30 °C, pH 6.0 and in the presence of 3–5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM M12096T was closely related to Nitratireductor indicus C115T (97.4 % 16S rRNA gene sequence similarity) and Mesorhizobium thiogangeticum SJTT (97.3 %). The strain, however, formed a robust clade with members of the genus Mesorhizobium in phylogenetic dendrograms generated with neighbour-joining, maximum-likelihood and maximum-parsimony trees. Analysis based on the sequence of housekeeping gene recA also gave a similar phylogenetic relationship, indicating that strain YIM M12096T is a member of the genus Mesorhizobium . DNA–DNA relatedness values between strain YIM M12096T and related type strains N. indicus CCTCC AB209298T and M. thiogangeticum DSM 17097T were 40.5 % and 36.7 %, respectively. Chemotaxonomic features of the isolate included phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminophospholipid and an unidentified phospholipid as its characteristic polar lipids and Q-10 as respiratory ubiquinone. Major fatty acids (>10 %) detected were C18 : 1 ω7c and/or C18 : 1 ω6c, 11-methyl-C18 : 1 ω7c and cyclo-C19 : 0 ω8c. Based on the chemotaxonomic properties and phylogenetic analyses, strain YIM M12096T is determined to be a member of the genus Mesorhizobium . The strain could be differentiated from the closely related species by the differences in physiological and biochemical properties supported by low DNA–DNA relatedness values. It is therefore concluded that strain YIM M12096T represents a novel species of the genus Mesorhizobium , for which the name Mesorhizobium sediminum sp. nov. is proposed. The type strain is YIM M12096T (=CCTCC AB 2014219T=KCTC 42205T).
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Allofrancisella inopinata gen. nov., sp. nov. and Allofrancisella frigidaquae sp. nov., isolated from water-cooling systems, and transfer of Francisella guangzhouensis Qu et al. 2013 to the new genus as Allofrancisella guangzhouensis comb. nov.
Five bacterial strains (SYSU YG23T, SYSU 10HL1970T, 10HP82-10, 10HL1938, 10HP457) isolated from water reservoirs of cooling systems were characterized using a polyphasic taxonomic approach. The isolates were Gram-stain-negative, strictly aerobic and non-motile. Growth was enhanced in the presence of l-cysteine. The major fatty acids (>5 %) for the five strains were C10 : 0, C16 : 0, C16 : 0 3-OH, C18 : 0 3-OH and C18 : 1 ω9c. Ubiquinone-8 was detected as the respiratory quinone while the polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, three unidentified phospholipids, two unidentified aminophospholipids and three unidentified glycolipids. The strains shared 16S rRNA gene sequence similarities of 99.0–99.2 % with Francisella guangzhouensis 08HL01032T but less than 95.2 % with other members of the family Francisellaceae . The phylogenetic dendrogram based on 16S rRNA gene sequences showed that these strains form a separate cluster along with Francisella guangzhouensis . This cluster was also confirmed from multilocus-sequence typing based on sequences of the mdhA, rpoB and sdhA genes. Matrix-assisted laser desorption ionization time-of-flight MS analyses of the strains along with closely and distantly related Francisella strains also showed a distinct cluster for these strains. Based on the findings from the polyphasic taxonomy studies, the strains were considered to represent two novel species of a new genus for which the names Allofrancisella inopinata gen. nov., sp. nov. (type strain SYSU YG23T=KCTC 42968T=DSM 101834T) and Allofrancisella frigidaquae sp. nov. (type strain SYSU 10HL1970T=KCTC 42969T=DSM 101835T) are proposed. In addition, Francisella guangzhouensis Qu et al. 2013 is proposed to be transferred to this new genus as Allofrancisella guangzhouensis comb. nov.
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Piscinibacter defluvii sp. nov., isolated from a sewage treatment plant, and emended description of the genus Piscinibacter Stackebrandt et al. 2009
More LessA Gram-staining-negative, strictly aerobic bacterium, designated SH-1T, was isolated from activated sludge in Korea. Cells were motile rods with a single polar flagellum, showing oxidase-positive and catalase-negative activities. Growth was observed at 25–40 °C (optimum, 37 °C), pH 6.0–9.5 (optimum, pH 7.0) and with 0–0.5 % (w/v) NaCl (optimum, 0 %). Strain SH-1T contained summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, C12 : 0, summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c) and C10 : 0 3-OH as the major fatty acids and ubiquinone-8 as the sole isoprenoid quinone. Phosphatidylethanolamine was the major polar lipid, and diphosphatidylglycerol, phosphatidylglycerol, one aminophospholipid, one phospholipid, five unidentified aminolipids and two unidentified lipids were also detected as the minor polar lipids. The predominant polyamines were 2-hydroxyputrescine, cadaverine and putrescine. The DNA G+C content was 69.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SH-1T formed a tight phyletic lineage with Piscinibacter aquaticus IMCC1728T with a 98.3 % sequence similarity. However, the DNA–DNA relatedness value between strain SH-1T and the type strain of P. aquaticus was 38.0±1.8 %. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that strain SH-1T represents a novel species of the genus Piscinibacter , for which the name Piscinibacter defluvii sp. nov. is proposed. The type strain is SH-1T (=KACC 18594T=JCM 31230T). An emended description of the genus Piscinibacter is also proposed.
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Marinibaculum pumilum gen. nov., sp. nov., isolated from seawater
More LessA Gram-stain-negative, facultatively anaerobic, motile and rod-shaped strain, designed H2T, was isolated from the Western Pacific Ocean, and subjected to a taxonomic investigation using a polyphasic approach. Strain H2T grew at 15–40 °C and pH 6.0–9.0 (optimum 37 °C and pH 6.5), and with 1–10 % (w/v) NaCl (optimum 2 %). The predominant respiratory quinone was ubiquinone-10 (Q-10) and the major fatty acids identified were C19 : 0 cyclo ω8c, C18 : 1 ω7c, C18 : 0 and 11-methyl-C18 : 1 ω7c. The polar lipids of strain H2T consisted of phosphatidylglycerol, one unknown phospholipid, one unknown glycolipid and three unidentified aminolipids. The DNA G+C content was 75.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H2T formed a distinct clade belong to the family Rhodospirillaceae within the Alphaproteobacteria . On the basis of morphological, physiological and chemotaxonomic characteristics, together with the results of phylogenetic analysis, strain H2T represents a novel species in a new genus in the family Rhodospirillaceae, for which the name Marinibaculum pumilum gen. nov., sp. nov. is proposed. The type strain of the type species is H2T(=MCCC 1K02279T=KCTC 42964T).
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- Eukaryotic micro-organisms
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Pseudochaetosphaeronema ginkgonis sp. nov., an endophyte isolated from Ginkgo biloba
More LessAn endophytic strain (designated as SYPF 7195T) was isolated from a branch of a ginkgo tree in Liaoning province of China. Strain SYPF 7195T was characterized by its grey to greyish-green aerial mycelium, velvety to floccose surface and swelling near the septa. Phylogenetic analyses, which were inferred from the internal transcribed spacer (ITS) and partial sequences of the LSU and SSU of the rDNA and translation elongation factor 1-alpha (TEF1), showed that strain SYPF 7195T belonged to the genus Pseudochaetosphaeronema, and was distinct from all other species with high bootstrap-supported values (92 %). Strain SYPF 7195T constitutes a separate evolutionary clade with Pseudochaetosphaeronema larense and Pseudochaetosphaeronema martinelli, with P. martinelli as its closest phylogenetic neighbour. The nucleotide differences between strain SYPF 7195T and P. martinelli were 71 substitutions in the ITS region. Strain SYPF 7195Tcould also be distinguished from P. martinelli by a number of physiological characteristics. Combined with morphology and molecular analyses, strain SYPF 7195T merits recognition as a representative of a novel species of the genus Pseudochaetosphaeronema, for which the name Pseudochaetosphaeronema ginkgonis sp. nov. is proposed. The type strain is CBS 140953T (=CGMCC 3.17865T=SYPF 7195T). The Mycobank number is MB 816567.
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Penicillium pedernalense sp. nov., isolated from whiteleg shrimp heads waste compost
More LessNovel Penicillium-like strains were isolated during the characterization of the mycobiota community dynamics associated with shrimp waste composting. Phylogenetic analysis of the partial β-tubulin (BenA) gene and the ribosomal DNA internal transcribed spacer region (ITS1–5.8S–ITS2) sequences revealed that the novel strains were members of section Lanata-Divaricata and were closely related to Penicillium infrabuccalum DAOMC 250537T. On the basis of morphological and physiological characterization, and phylogenetic analysis, a novel Penicillium species, Penicillium pedernalense sp. nov., is proposed. The type strain is F01-11T (=CBS 140770T=CECT 20949T), which was isolated from whiteleg shrimp (Litopenaeus vannamei) heads waste compost in the Pedernales region (Manabí province, Ecuador).
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Sugiyamaella mastotermitis sp. nov. and Papiliotrema odontotermitis f.a., sp. nov. from the gut of the termites Mastotermes darwiniensis and Odontotermes obesus
More LessTwo novel yeast species were isolated from the guts of two different termite species. A new member of the genus Sugiyamaella was isolated from the hindgut and nest material of the lower Australian termite Mastotermes darwiniensis. The second novel yeast species, isolated from the higher termite Odontotermes obesus, was identified as a member of the genus Papiliotrema. Both yeast species were able to hydrolyse xylan, methylumbelliferyl β-xylobiose and methylumbelliferyl β-xylotriose. The ability to debranch different hemicellulose side chains and growth without the addition of external vitamins was observed. A symbiotic role of the novel yeast species is indicated, especially in respect to xylan degradation and the production of vitamins. Here, we describe these species as Sugiyamaella mastotermitis sp. nov., MycoBank 816574 (type strain MD39VT=DSM 100793T=CBS 14182T), and Papiliotrema odontotermitis f.a., sp. nov., MycoBank 816575 (type strain OO5T=DSM 100791T=CBS 14181T). Additionally, we transfer Candida qingdaonensis to the genus Sugiyamaella and propose the following combination: Sugiyamaella qingdaonensis f.a., comb. nov., MycoBank 816576.
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Five novel species in the Lodderomyces clade associated with insects
More LessDuring a survey of yeasts associated with insects in Central China's natural ecosystems, 116 yeast strains were isolated from the gut of adult insects in two families and from one beetle larva. Among the yeasts isolated in this study, 102 strains were identified as 20 known species in the class Saccharomycetes. The remaining 14 strains were identified as representing five novel species in the Lodderomyces clade based on the combined sequences of the D1/D2 domains of the LSU rRNA gene and the internal transcribed spacer (ITS) regions, as well as other taxonomic characteristics. Lodderomyces beijingensis sp. nov. (type strain CBS 14171T=CICC 33087T=NYNU 15764T) formed a clade with Lodderomyces elongisporus and Candida oxycetoniae. The other four novel species, namely Candida margitis sp. nov. (type strain CBS 14175T=CICC 33091T=NYNU 15857T), Candida xiaguanensis sp. nov. (type strain CBS 13923T=CICC 33056T=NYNU 1488T), Candida parachauliodis sp. nov. (type strain CBS 13928T=CICC 33058T=NYNU 14959T) and Candida coleopterorum sp. nov. (type strain CBS 14180T=CICC 33084T=NYNU 1582T), showed close relationships to the species near Candida parapsilosis, Candida sakaeoensis, Candida chauliodes and Candida corydalis. Descriptions of these novel yeast species are provided as well as discussions of their ecology in relation to their insect hosts.
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- Evolution, Phylogeny and Biodiversity
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Re-evaluation of the taxonomy of the Mitis group of the genus Streptococcus based on whole genome phylogenetic analyses, and proposed reclassification of Streptococcus dentisani as Streptococcus oralis subsp. dentisani comb. nov., Streptococcus tigurinus as Streptococcus oralis subsp. tigurinus comb. nov., and Streptococcus oligofermentans as a later synonym of Streptococcus cristatus
More LessThe Mitis group of the genus Streptococcus currently comprises 20 species with validly published names, including the pathogen S. pneumoniae . They have been the subject of much taxonomic confusion, due to phenotypic overlap and genetic heterogeneity, which has hampered a full appreciation of their clinical significance. The purpose of this study was to critically re-examine the taxonomy of the Mitis group using 195 publicly available genomes, including designated type strains for phylogenetic analyses based on core genomes, multilocus sequences and 16S rRNA gene sequences, combined with estimates of average nucleotide identity (ANI) and in silico and in vitro analyses of specific phenotypic characteristics. Our core genomic phylogenetic analyses revealed distinct clades that, to some extent, and from the clustering of type strains represent known species. However, many of the genomes have been incorrectly identified adding to the current confusion. Furthermore, our data show that 16S rRNA gene sequences and ANI are unsuitable for identifying and circumscribing new species of the Mitis group of the genus Streptococci. Based on the clustering patterns resulting from core genome phylogenetic analysis, we conclude that S. oligofermentans is a later synonym of S. cristatus . The recently described strains of the species Streptococcus dentisani includes one previously referred to as ‘ S. mitis biovar 2’. Together with S. oralis , S. dentisani and S. tigurinus form subclusters within a coherent phylogenetic clade. We propose that the species S. oralis consists of three subspecies: S. oralis subsp. oralis subsp. nov., S. oralis subsp. tigurinus comb. nov., and S. oralis subsp. dentisani comb. nov.
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- ICSP Matters
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Priority of the genus name Clostridium Prazmowski 1880 (Approved Lists 1980) vs Sarcina Goodsir 1842 (Approved Lists 1980) and the creation of the illegitimate combinations Clostridium maximum (Lindner 1888) Lawson and Rainey 2016 and Clostridium ventriculi (Goodsir 1842) Lawson and Rainey 2016 that may not be used
More LessIn a recent publication that attempts to deal with the growing problem of taxa being added to the genus Clostridium that are outside of Clostridium (16S rRNA) group I, a solution is proposed that seeks to limit the genus Clostridium Prazmowski 1880 (Approved Lists 1980) to a small number of species ‘related’ to the type species, Clostridium butyricum Prazmowski 1880 (Approved Lists 1980). It has been proposed that this genus should also include members of the genus Sarcina Goodsir 1842 (Approved Lists 1980), Sarcina maxima Lindner 1888 (Approved Lists 1980) and Sarcina ventriculi Goodsir 1842 (Approved Lists 1980), the latter being the nomenclatural type of the genus Sarcina Goodsir 1842 (Approved Lists 1980). In making proposals to treat the genus name Sarcina Goodsir 1842 (Approved Lists 1980) as a synonym of Clostridium Prazmowski 1880 (Approved Lists 1980), reference is made to the wording of the International Code of Nomenclature of Bacteria. However, while that wording is factually correct, other parts of the Code are relevant to this issue and clearly indicate that the proposed course of action is not sanctioned by texts that have not been directly made reference to. Rather than avoiding confusion it has been contributed to, and it is necessary to document where the problems lie.
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The undesirable retroactive changes to Rule 8 of the International Code of Nomenclature of Prokaryotes
More LessChanges have been made to Rule 8 of the International Code of Nomenclature of Prokaryotes that caters for the names and nomenclatural types of classes and subclasses. The changes are retroactive because they are not specifically restricted in time. Consequently, that influences names of classes and subclasses and their nomenclatural types that have previously appeared in print.
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Rule 27 of the International Code of Nomenclature of prokaryotes: the basonym is not enough
More LessProposals to make changes to the wording of Rule 27 of the International Code of Nomenclature of Prokaryotes have been made that include the requirement to make reference to the basonym of a new combination. While this is a step in the right direction, it does not solve problems where new combinations are associated with multiple heterotypic synonyms and the new combination is based on the selection of the genus name or species epithet that is contrary to the Rules.
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The nomenclatural type of the genus Methanocorpusculum Zellner et al. 1988 and the selection of the correct name
More LessA recent Request for an Opinion has raised the issue of the inter-relationship between Methanocorpusculum parvum Zellner et al. 1988, the type species of the genus Methanocorpusculum Zellner et al. 1988 as defined at the time of valid publication of the genus name and the subsequent recognition of Methanocorpusculum aggregans (Ollivier et al., 1985) Xun et al.1989 as an earlier heterotypic synonym. Examination of the relevant literature indicates that there are a number of misunderstandings that have arisen. In particular misinterpretation of Rule 15 of the International Code of Nomenclature of Prokaryotes continues to be a source of confusion. Additional problems centre on whether the nomenclatural type of a taxon continues to be the nomenclatural type even if that name is not treated as the correct name and would not appear in a list of names in a given classification. It would be appropriate to clarify these issues.
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The relationship of validly published names to legitimate and illegitimate names in the International Code of Nomenclature of Prokaryotes
More LessThe International Code of Nomenclature of Prokaryotes defines validly published names, legitimate names and illegitimate names, but does not clearly define the inter-relationship between them. Clarification is required.
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Are Rules 20d and 20e of the International Code of Nomenclature of Prokaryotes superfluous?
More LessThe wording of Rule 20d and 20e of the 1975, 1990 and 2008 revisions of the International Code of Nomenclature of Bacteria/Prokaryotes deals with problems that may arise when the nomenclatural type of a genus was not designated or when there are problems determining what the nomenclatural type should be. However, Rule 16 states that a nomenclatural type must be designated, while Rule 27 clearly states that a requirement of valid publication is the designation of a type for a new taxon and this is reinforced under Rule 29 that deals with the valid publication of a genus or subgenus name. Furthermore, the wording of Rule 18a and Rule 30 strongly suggests that the type of problem envisaged with regards the species included in the genus should no longer occur. The wording of Rule 20d and 20e appears to have originated in earlier revision of the International Code of Nomenclature of Bacteria and may no longer be relevant in the 1975, 1990 and 2008 revisions due to significant changes made in those revisions.
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On the synonymy of Edwardsiella tarda Ewing and McWhorter 1965 (Approved Lists 1980) and Edwardsiella anguillimortifera (Hoshina 1962) Sakazaki and Tamura 1975 (Approved Lists 1980), an old problem in need of a solution
More LessEdwardsiella tarda Ewing and McWhorter 1965 (Approved Lists 1980) and Edwardsiella anguillimortifera (Hoshina 1962) Sakazaki and Tamura 1975 (Approved Lists 1980) are known to be synonyms that share the same nomenclatural type. Edwardsiella tarda Ewing and McWhorter 1965 (Approved Lists 1980) is the nomenclatural type of the genus Edwardsiella Ewing and McWhorter 1965 (Approved Lists 1980). The question of the priority of the epithet anguillimortifera Hoshina 1962 over the epithet tarda Ewing and McWhorter 1965 has been raised in the past, and a Request for an Opinion to conserve the epithet tarda Ewing and McWhorter 1965 in Edwardsiella tarda Ewing and McWhorter 1965 (Approved Lists 1980) was published but later withdrawn. Close examination of the wording of the International Code of Nomenclature of Prokayotes indicates that there may be problems associated with the nomenclatural type of Edwardsiella anguillimortifera (Hoshina 1962) Sakazaki and Tamura 1975 (Approved Lists 1980). Additional issues also arise with the recognition of homonyms under other codes of nomenclature.
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The wording and examples given in Rule 47a of the International Code of Nomenclature of Prokaryotes are misleading
More LessRule 47a of the International Code of Nomenclature of Prokaryotes contains wording that is misleading. The examples given also give the wrong impression with regards the role of genus names in determining the priority of names at a higher taxonomic rank.
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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)