- Volume 69, Issue 10, 2019
Volume 69, Issue 10, 2019
- New Taxa
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- Proteobacteria
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Sphingomonas aracearum sp. nov., isolated from rhizospheric soil of Araceae plants
More LessA Gram-stain-negative, single polar flagellum bacterium, WZY27T, was isolated from rhizospheric soil of Araceae plants. The results of phylogenetic analysis based on 16S rRNA gene sequences showed that this strain is closely related to Sphingomonas adhaesiva DSM 7418T (97.2 % similarity), Sphingomonas koreensis KCTC 2883 (97.1 %) and Sphingomonas ginsenosidimutans JCM 17074T (97.0 %). The genomic average nucleotide identity values between strain WZY27T and the above three strains were 75.3, 73.2 and 75.4 %, and the in silico DNA–DNA hybridization values were 19.1 , 20.1 and 20.9 %, respectively. The major fatty acids (>5 %) of strain WZY27T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C16 : 0, C14 : 0 2-OH and C18 : 1 ω7c 11-methyl. The predominant respiratory quinone and polyamine were ubiquinone Q-10 and homospermidine, respectively. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipids, glycolipids, phosphatidylcholine and sphingoglycolipid. The G+C content of the genomic DNA was 68.4 mol%. Based on the results of genotypic, chemotaxonomic and phenotypic characterization, strain WZY27T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas aracearum sp. nov. is proposed. The type strain is WZY27T (=KCTC 62523T=CCTCC AB 2018056T).
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Roseomonas wenyumeiae sp. nov., isolated from faeces of Tibetan antelopes (Pantholops hodgsonii) on the Qinghai–Tibet Plateau
Two Gram-stain-negative, catalase- and oxidase-positive, non-spore-forming, aerobic, motile, flagellated, and coccus-shaped strains (Z23T and Z24) were isolated from faeces of Tibetan antelopes (Pantholops hodgsonii) on the Qinghai–Tibet Plateau, PR China. Results of the morphological, biochemical, and phylogenetic studies indicated that they were similar to each other, but distinct from existing species of the genus Roseomonas . The proposed type strain, Z23T, had 97.8, 97.1 and 96.8 % 16S rRNA similarity to Roseomonas ludipueritiae DSM 14915T, Roseomonas aerofrigidensis JCM 31878T and Roseomonas aerophila KACC 16529T. Results from further phylogenetic analyses based on the 16S rRNA gene and 857 core genes indicated that the two strains were members of Roseomonas , but clearly separated from the currently recognized species. Strains Z23T had 43.8 %, 25.0 % DNA–DNA relatedness and 91.2, 81.3 % ANI values with R. ludipueritiae DSM 14915T and R. aerophila KACC 16529T. The genomic DNA G+C content of strain Z23T was 68.6 mol%. The major cellular fatty acids of strain Z23T were C18 : 1ω7c and/or C18 : 1ω6c and C19 : 0cyclo ω8c. The cell-wall sugars included glucose, rhamnose and ribose. Q-10 was the sole respiratory quinone, and spermidine was the major polyamine component. Polar lipids present in strain Z23T were phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, three aminolipids, two phospholipids and two unidentified lipids. Based on the distinct differences from other Roseomonas species judged from the genotypic and phenotypic data, a novel species represented by Z23T and Z24, Roseomonas wenyumeiae sp. nov., is proposed. The type strain is Z23T (=CGMCC 1.16540T=DSM 106207T).
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Corticimicrobacter populi gen. nov., sp. nov., a member of the family Alcaligenaceae, isolated from symptomatic bark of Populus × euramericana canker
More LessOne Gram-negative aerobic bacterial strain was isolated from the bark tissue of Populus × euramericana and investigated using a polyphasic approach including 16S rRNA gene sequencing and both phenotypic and chemotaxonomic assays. The 16S rRNA gene and housekeeping gene phylogenies suggest that the novel isolate is different from the other genera of the family Alcaligenaceae . The G+C content, major fatty acids, physiological and biochemical data supported the distinctiveness of the novel strain from reference species. The major fatty acids detected in the novel isolate were C16 : 1ω7c and/or C16 : 1ω6c, C16 : 0, C14 : 0 3OH and/or C16 : 1isoI and C18 : 1ω7c. The phospholipid profile of strain d3-2-2T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminolipid, aminophospholipid and an unidentified lipid. The quinone of the novel isolate was Q-8. Therefore, based on the data, the strain constitutes a novel species of a novel genus within the family Alcaligenaceae , for which the name Corticimicrobacter populi gen. nov., sp. nov. is proposed. The type strain is 3d-2-2T (=CFCC 11891T=KCTC 52807T).
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Paenimaribius caenipelagi gen. nov., sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, strictly aerobic, non-motile and ovoid- or rod-shaped bacterial strain, JBTF-M29T, was isolated from tidal flat sediment sampled from the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain JBTF-M29T clustered with the type strains of Maribius species and this cluster joined the clade comprising Pseudomaribius and Palleronia species. Strain JBTF-M29T exhibited 16S rRNA gene sequence similarity values of 96.2–96.6 % to the type strains of three Maribius species, of 96.4 % to the type strain of Pseudomaribius aestuariivivens and of 93.9–94.7 % to the type strains of three Palleronia species. In the UPGMA dendrogram based on the ANI values of genomic sequences, strain JBTF-M29T formed an evolutionary lineage independent of the genera Maribius and Palleronia and some other taxa. Strain JBTF-M29T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C18 : 0 as the major fatty acids. The major polar lipids of strain JBTF-M29T were phosphatidylglycerol and one unidentified aminolipid. The DNA G+C content of strain JBTF-M29T was 64.5 mol%. The differences in fatty acid and polar lipid profiles and other differential phenotypic properties including nitrate reduction and casein hydrolysis made it reasonable to distinguish strain JBTF-M29T from the genera Maribius , Pseudomaribius and Palleronia . Therefore, on the basis of the polyphasic taxonomic data presented here, strain JBTF-M29T constitutes a new genus and species within the class Alphaproteobacteria , for which the name Paenimaribius caenipelagi gen. nov., sp. nov. is proposed. The type strain is JBTF-M29T (=KACC 19867T=NBRC 113548T).
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Ferruginivarius sediminum gen. nov., sp. nov., isolated from a marine solar saltern
More LessA novel Gram-stain-negative, facultatively anaerobic, oxidase-negative, catalase-positive bacillus, designated WD2A32T, was isolated from a marine solar saltern in the coast of Weihai, Shandong Province, PR China. Strain WD2A32T grew optimally at 37–40 °C (range, 20–45 °C) and pH 7.0–7.5 (range, 6.5–8.0) and was tolerant to 6–8 % (w/v) NaCl (range, 2–12 %). The 16S rDNA of strain WD2A32T was most similar (93.5 %) to that of Rhodovibrio salinarum DSM 9154T (the type species of the genus Rhodovibrio ), followed by Limimonas halophila DSM 25584T (92.4 %; the type species of the genus Limimonas ). The similarities to the type strains of the genera Pelagibius and Limibacillus were less than 91.0 %. The draft genome sequence of strain WD2A32T contained 72 contigs (>507 bp) of 4 237 996 bp with a DNA G+C content of 65.5 mol%. The major polar lipids of strain WD2A32T were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and unidentified aminolipids; major cellular fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) and C19 : 0 cyclo ω8c; the major respiratory quinone was Q-10. On the basis of the results from chemotaxonomic, physiological and biochemical analyses, strain WD2A32T represents a novel species of a novel genus in the family Rhodospirillaceae , for which the name Ferruginivarius sediminum gen. nov., sp. nov. has been proposed. The type strain is WD2A32T (=KCTC 52888T=MCCC 1H00201T).
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Colwellia ponticola sp. nov., isolated from seawater
More LessA Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated OISW-25T, was isolated from seawater in Republic of Korea. Strain OISW-25T grew optimally at 25 °C and in the presence of 2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain OISW-25T fell within the clade comprising the type strains of Colwellia species. Strain OISW-25T exhibited 16S rRNA gene sequence similarity values of 97.5, 97.2 and 97.1 % to the type strains of C. piezophila , C. maris and C. psychrerythraea , respectively, and of 93.6–96.6 % to the type strains of the other Colwellia species. The average nucleotide identity values between strain OISW-25T and C. piezophila ATCC BAA-637T and two non-type strains of C. psychrerythraea were 78.16–79.35 % and DNA–DNA relatedness value of strain OISW-25T with the type strain of C. maris was 17 %. The DNA G+C content of strain OISW-25T was 39.2 mol% (HPLC) or 38.7 mol% (genome data). Strain OISW-25T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 as the major fatty acids. The major polar lipids of strain OISW-25T were phosphatidylethanolamine and phosphatidylglycerol. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain OISW-25T is distinct from Colwellia species. On the basis of the data presented, strain OISW-25T is considered to represent a novel species of the genus Colwellia , for which the name Colwellia ponticola sp. nov. is proposed. The type strain is OISW-25T (=KCTC 62426T=NBRC 113187T).
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Roseovarius amoyensis sp. nov. and Muricauda amoyensis sp. nov., isolated from the Xiamen coast
More LessStrain GCL-8T and GCL-11T were isolated from Guanyinshan, a sandy beach on the Xiamen coast. Cells of the two strains were Gram-stain-negative, catalase-positive, oxidase-positive, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains GCL-8T and GCL-11T belonged to the genera Roseovarius and Muricauda , with the highest sequence similarities to Roseovarius indicus B108T (96.5%) and Muricauda antarctica CGMCC 1.12174T (97.3%), respectively. The major fatty acids of strain GCL-8T were summed feature 8 (C18:1ω7c/ω6c), C19:0cyclo ω8c, C16:0 and C17:0, while the major fatty acids of strain GCL-11T were iso-C15:1 G, iso-C15:0 and iso-C17:0 3-OH. The G+C contents of the chromosomal DNA of strains GCL-8Tand GCL-11T were 64.1 mol% and 45.67 mol%, respectively. The respiratory quinones of strains GCL-8T and GCL-11T were Q-10 and MK-6, respectively. The polar lipids of strain GCL-8T were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, one unidentified aminolipid, three unidentified phospholipids and three unidentified polar lipids. The polar lipids of strain GCL-11Twere phosphatidylethanolamine, seven unidentified phospholipids and four unidentified polar lipids. The combined genotypic and phenotypic data show that strains GCL-8T and GCL-11T represent two novel species within genera Roseovarius and Muricauda , for which the names Roseovariu samoyensis sp. nov. and Muricauda amoyensis sp. nov. are proposed, with type strains GCL-8T (=MCCC 1A11651T = KCTC 52430T) and GCL-11T (=MCCC 1A11649T=KCTC 52432T).
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Aliishimia ponticola gen. nov., sp. nov., isolated from seawater
A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated MYP11T, was isolated from seawater around Jeju island, Republic of Korea and identified by polyphasic taxonomic study. A neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain MYP11T joined the cluster comprising the type strains of Shimiaabyssi, Shimiaaestuarii and Shimiaaquaeponti, showing 16S rRNA gene sequence similarities of 96.3–96.8 %. Strain MYP11T exhibited 16S rRNA gene sequence similarity values of 94.2–94.9 % to the type strains of other Shimia species. In the upgma dendrogram based on the average nucleotide identity values of genomic sequences, strain MYP11T formed an evolutionary lineage independent of those of Shimia species and other taxa. Strain MYP11T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and cyclo C19 : 0 ω8c as the major fatty acids. The major polar lipids of strain MYP11T were phosphatidylcholine, phosphatidylglycerol, two unidentified lipids and one unidentified aminolipid. The DNA G+C content of strain MYP11T was 63.1 or 61.5 mol%. The differences in the fatty acid and polar lipid profiles and DNA G+C contents made it reasonable to distinguish strain MYP11T from the type strains of S. abyssi , S. aestuarii and S. aquaeponti and those of other Shimia species. On the basis of the polyphasic data presented here, strain MYP11T is considered to constitute a new genus and species within the class Alphaproteobacteria , for which the name Aliishimia ponticola gen. nov., sp. nov. is proposed. The type strain is MYP11T (=KCTC 62899T=NBRC 113544T).
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Rhodoferax lacus sp. nov., isolated from a large freshwater lake
More LessA Gram-staining-negative, aerobic, motile with a single polar flagellum and rod-shaped bacterium as a bacterial host of podovirus P26218, designated IMCC26218T, was isolated from Lake Soyang, South Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC26218T belonged to the genus Rhodoferax of the family Comamonadaceae and shared 97.7–99.0 % sequence similarities with Rhodoferax species. The draft whole genome sequence of strain IMCC26218T was ca. 4.9 Mbp in size with the DNA G+C content of 62.3 mol%. Average nucleotide identity (ANI) and digital DNA–DNA hybridisation (dDDH) values between strain IMCC26218T and other Rhodoferax were 74.0–77.3 % and 19.5–21.0 %, respectively, showing that the strain represents a new Rhodoferax species. The strain contained summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and C16 : 0 as the major fatty acids and phosphatidylethanolamine, three unidentified phospholipids, two unidentified aminolipids and two unidentified lipids as major polar lipids. The predominant isoprenoid quinone of the strain was ubiquinone-8 (Q-8). On the basis of the phylogenetic and phenotypic characteristics, strain IMCC26218T is considered to represent a novel species of the genus Rhodoferax , for which the name Rhodoferax lacus sp. nov. is proposed. The type strain is IMCC26218T (=KACC 18983T=NBRC 112709T).
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Pseudomonas edaphica sp. nov., isolated from rhizospheric soil of Cistus ladanifer L. in Spain
During a study on biodiversity of bacteria inhabiting rhizospheric soil of rockrose (Cistus ladanifer L.), we isolated a strain coded RD25T in a soil from Northern Spain. The 16S rRNA gene sequence showed 99.5 % identity with respect to the closest related species Pseudomonas brenneri DSM15294T, and 99.4 % with respect to P. paralactis WS4672T. The following related Pseudomonas species showed 99.3 % or less identity, and therefore RD25T was classified within genus Pseudomonas . The phylogenetic analysis of 16S rRNA and the housekeeping genes rpoB, rpoD and gyrB suggested that this strain could be a novel species. The strain RD25T has several polar-subpolar flagella. It can grow at 36 °C, at 0–6 % NaCl concentration and a range of pH 5–9. Positive for arginine dihydrolase and urease production, and negative for reduction of nitrate. The strain is catalase and oxidase positive. Major fatty acids are C16 : 1 ω7c / C16 : 1 ω6c in summed feature 3, C16 : 0, and C18 : 1 ω7c / C18 : 1 ω6c in summed feature 8. The respiratory ubiquinone is Q9. The DNA G+C content was 59.9 mol%. The digital DNA–DNA hybridisation average values (dDDH) ranged between 30–61.2 % relatedness and the ANIb values ranged between 93.9–80.5 % with respect to the type strains of the closely related species. Therefore, the genotypic, genomic, phenotypic and chemotaxonomic data support the classification of strain RD25 as a novel species of genus Pseudomonas , for which the name P. edaphica sp. nov. is proposed. The type strain is RD25T (=LMG 30152T=CECT 9373T).
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Undibacterium piscinae sp. nov., isolated from Korean shiner intestine
A novel Gram-stain-negative, non-spore-forming, obligate aerobic, motile, rod-shaped, and flagellated bacterium, designated S11R28T, was isolated from the intestinal tract of a Korean shiner, Coreoleuciscus splendidus. Based on 16S rRNA gene sequences, strain S11R28T was identified as member of the genus Undibacterium in class Betaproteobacteria , and was closely related to Undibacterium parvum DSM 23061T (98.49 %). The isolate grew at 4–25 °C, pH 6–9, with 0 % (w/v) NaCl, and grew optimally at 20 °C, pH 8, in the absence of NaCl. The main cellular fatty acids were C16 : 0 and summed features 3 (C16 : 1ω7c and/or C16 : 1ω6c). The strain possessed diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine as predominant polar lipids, and ubiquinone Q-8 as a respiratory quinone. The polyamine profile composed of 2-hydroxyputrescine, spermidine, putrescine, and benzoic acid. A genomic DNA G+C content was 51.4 mol%. The average nucleotide identity between strains S11R28T and U. parvum DSM 23061T was 78.66 %. Thus, Undibacterium piscinae can be considered a novel species within the genus Undibacterium with the type strain S11R28T (=KCTC 62668T=JCM 33224T).
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Kosakonia quasisacchari sp. nov. recovered from human wound secretion in China
More LessA novel Kosakonia strain WCHEs120001T was recovered from the wound secretion of a patient at West China Hospital, Chengdu, PR China, in 2017. The strain was Gram-stain-negative, facultatively anaerobic, motile, and non-spore-forming. A preliminary analysis based on the 16S rRNA gene sequence revealed that this strain was closely related to members of the genus Kosakonia . The strain was subjected to whole genome sequencing. Phylogenetic analysis based on core gene sequences of type strains of all Enterobacteriaceae species revealed that this strain belonged to the genus Kosakonia but were distinct from any previously known Kosakonia species. Both average nucleotide identity (ANI) and in silico DNA–DNA hybridisation (isDDH) values between strain WCHEs120001T and type strains of all known Kosakonia species were 82.02 to 92.37% and 25.6 to 50.9 %, respectively, which are lower than the 95 % (ANI) and 70 % (isDDH) cutoff for species delineation. The major fatty acids of the strain WCHEs120001T are C16 : 0, sum of C16:1ω7c/C16:1ω6c and C18:1ω7c, which are similar to other Kosakonia species. Genomic DNA G+C content of strain WCHEs120001T was 53.33 mol%. Strain WCHEs120001T is positive for methyl-d-glucopyranoside but does not ferment adonitol, d-arabitol, dulcitol and melibiose, which distinguishes it from all other Kosakonia species. Genotypic and phenotypic characteristics indicate that strain WCHEs120001T represents a novel species of the genus Kosakonia , for which the name Kosakonia quasisacchari sp. nov. is proposed. The type strain of K. quasisacchari sp. nov. is WCHEs120001T (=GDMCC1.1570T=NCTC 14272T).
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Actinobacillus vicugnae sp. nov., isolated from alpaca (Vicugna pacos)
Ten strains of an Actinobacillus -like organism were isolated from alpaca (Vicugna pacos) in the UK over a period of 5 years, with no known epidemiological linkages. The isolates are distinct, based on both phenotype and genotype, from any previously described Actinobacillus species. Molecular analysis, based on 16S rRNA, rpoB and infB gene sequences, placed the isolates as a novel, early branching, lineage within the currently recognised Actinobacillus sensu stricto. In agreement with the results of the single-gene analysis, average nucleotide identity values, based on whole genome sequences, showed very similar identities to a number of members of the Actinobacillus sensu stricto notably Actinobacillus equuli, Actinobacillus suis and Actinobacillus ureae . At least two phenotypic characteristics differentiate the alpaca isolates from other Actinobacillus sensu stricto species, and from taxa likely falling within this group but awaiting formal species description, with Actinobacillus anseriformium and A. equuli subsp. haemolyticus being the most closely related phenotypically. The alpaca isolates can be differentiated from A. anseriformium by production of β-galactosidase (ONPG) and acid from raffinose, and from A. equuli subsp. haemolyticus by production of acid from d-sorbitol and failure to produce acid from d-xylose. Isolates were obtained from multiple sites in alpaca including respiratory tract, alimentary tract and internal organs although further evidence is required to understand any pathogenic significance. Based on the results of characterization described here, it is proposed that the isolates constitute a novel species, Actinobacillus vicugnae sp. nov. The type strain is W1618T (LMG30745T NCTC14090T) isolated in the UK in 2012 from oesophageal ulceration in an alpaca (Vicugna pacos).
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Cohaesibacter intestini sp. nov., isolated from the intestine of abalone, Haliotis discus hannai
More LessA Gram-stain-negative, rod-shaped and facultative anaerobic strain named YE-B6T was isolated from the intestine of abalone, Haliotis discus hannai. The reactions of oxidase and catalase were both positive. Strain YE-B6T could grow at 10–37 °C (optimum, 28–33 °C), at pH 7–9 (optimum, pH 7) and in salinity of 0–8 % NaCl (w/v; optimum, 2 %). The 16S rRNA gene sequence of strain YE-B6T had maximum sequence similarities to Cohaesibacter celericrescens H1304T (98.0 %), Cohaesibacter marisflavi DQHS21T (97.4 %), Cohaesibacter haloalkalitolerans JC131T (97.4 %) and Cohaesibacter gelatinilyticus CL-GR15T (97.3 %). Results of phylogenetic analysis showed that it was affiliated to the genus Cohaesibacter within the order Rhizobiales in the Alphaproteobacteria . The respiratory quinone of strain YE-B6T was Q-10. The cellular fatty acids mainly comprised C18 : 1 ω7c and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, two unidentified aminolipids, two unidentified polar lipids and one unidentified phospholipid. The G+C content of strain YE-B6T was 55.6 mol%. Based on its genotypic, physiological and biochemical characteristics, strain YE-B6T represented a novel species within the genus Cohaesibacter , for which the name Cohaesibacter intestini sp. nov. is proposed. The type strain of the new species is YE-B6T (=MCCC 1A13131T=KCTC 62716T).
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Elevation of Pectobacterium carotovorum subsp. odoriferum to species level as Pectobacterium odoriferum sp. nov., proposal of Pectobacterium brasiliense sp. nov. and Pectobacterium actinidiae sp. nov., emended description of Pectobacterium carotovorum and description of Pectobacterium versatile sp. nov., isolated from streams and symptoms on diverse plants
The Pectobacterium carotovorum species corresponds to a complex, including two subspecies with validly published names, two proposed subspecies and two new species, Pectobacterium polaris and Pectobacterium aquaticum . Recent studies suggested that this complex needed revision. We examined the taxonomic status of 144 Pectobacterium strains isolated from a wide range of plant species, various geographical origins and waterways. Sequences of the leuS, dnaX and recA housekeeping genes clustered 114 of these Pectobacterium strains together within a not yet described clade. We sequenced eight strains of this clade and analysed them together with the 102 Pectobacterium genomes available in the NCBI database. Phylogenetic analysis, average nucleotide identity calculation and in silico DNA–DNA hybridization allowed us to differentiate seven clades. This led us to propose the elevation of Pectobacterium carotovorum subsp. odoriferum to species level as Pectobacterium odoriferum sp. nov. (type strain CFBP 1878T=LMG 5863T=NCPPB 3839T=ICMP 11533T), the proposal of Pectobacterium actinidiae sp. nov. (type strain KKH3=LMG 26003 T=KCTC 23131T) and Pectobacterium brasiliense sp. nov. (type strain CFBP 6617T= LMG 21371T=NCPPB 4609T), to emend the description of Pectobacterium carotovorum (type strain CFBP 2046T=LMG 2404T=NCPPB 312T=ICMP 5702T), and to propose a novel species, Pectobacterium versatile sp. nov (type strain CFBP6051T= NCPPB 3387T=ICMP 9168T) which includes the strains previously described as ‘Candidatus Pectobacterium maceratum’. Phenotypic analysis performed using Biolog GENIII plates on eight strains of P. versatile sp. nov. and related strains completed our analysis.
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Sphingomonas ginkgonis sp. nov., isolated from phyllosphere of Ginkgo biloba
More LessStrain HMF7854T, isolated from a ginkgo tree, was an orange-pigmented, Gram-stain-negative, motile by means of a single flagellum, strictly aerobic, rod-shaped bacterium. The isolate grew optimally on Reasoner's 2A agar at 30 °C, pH 7.0–8.0 and 0 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HMF7854T belonged to the genus Sphingomonas and was most closely related to Sphingomonasagri HKS-06T (96.8 % sequence similarity). The major fatty acids were C17 : 1 ω6c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The predominant isoprenoid quinone was ubiquinone-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified lipids and two unidentified glycolipids. The genomic DNA G+C content was 68.4 mol%. Thus, based on its phylogenetic, phenotypic and chemotaxonomic data, strain HMF7854T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas ginkgonis sp. nov. is proposed. The type strain of the species is strain HMF7854T (=KCTC 62461T=NBRC 113337T).
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Sulfitobacter sabulilitoris sp. nov., isolated from marine sand
More LessA Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, HSMS-29T, was isolated from a marine sand sample collected from the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain HSMS-29T fell within the clade comprising the type strains of Sulfitobacter species. Strain HSMS-29T exhibited 16S rRNA gene sequence similarities of 97.2–98.4 % to the type strains of Sulfitobacter mediterraneus , Sulfitobacter porphyrae , Sulfitobacter marinus , Sulfitobacter pontiacus , Sulfitobacter litoralis , Sulfitobacter brevis , Sulfitobacter noctilucicola and Sulfitobacter dubius and 96.3–96.9 % to the type strains of the other Sulfitobacter species. The genomic ANI values of strain HSMS-29T with the type strains of S. mediterraneus , S. marinus , S. pontiacus , S. litoralis , S. brevis , S. noctilucicola and S. dubius were 72.66–74.99 %. The DNA–DNA relatedness value between strain HSMS-29T and the type strain of S. porphyrae was 17 %. Strain HSMS-29T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids of strain HSMS-29T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain HSMS-29T was 65.0 mol% (HPLC) or 64.4 % (genome analysis). Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain HSMS-29T is separated from recognized Sulfitobacter species. On the basis of the data presented here, strain HSMS-29T is considered to represent a novel species of the genus Sulfitobacter , for which the name Sulfitobacter sabulilitoris sp. nov. is proposed. The type strain is HSMS-29T (=KACC 19870T=NBRC 113549T).
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Acidibrevibacterium fodinaquatile gen. nov., sp. nov., isolated from acidic mine drainage
More LessA heterotrophic and acidophilic bacterial strain, G45-3T, was isolated from acidic mine drainage sampled in Fujian Province, PR China. Cells of strain G45-3T were Gram-stain-negative, non-spore-forming, non-motile and rod-shaped. Catalase and oxidase activities were positive. Strain G45-3T grew aerobically at 20–45 °C (optimum, 37 °C) and at pH 2.5–5.0 (optimum, pH 4.0). Photosynthetic pigments were not produced. Analysis of 16S rRNA gene sequences showed that strain G45-3T was phylogenetically related to different members of the family Acetobacteraceae , and the sequence identities to Acidisphaera rubrifaciens JCM 10600T, Rhodovastum atsumiense G2-11T and Rhodopila globiformis ATCC 35887T were 95.9 , 95.3 and 95.3 %, respectively. Strain G45-3T contained ubiquinone-10 as its respiratory quinone. The major polar lipids were determined to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminophospholipid and an unidentified aminolipid. The predominant fatty acids were cyclo-C19 : 0ω8c, C18 : 1ω7c, C16 : 0 and C18 : 0. The genome of G45-3T consists of one chromosome (3 907 406 bp) and three plasmids (68 344, 45 771 and 16 090 bp), with an average G+C content of 65.9 mol%. Based on the results of phenotypic and genomic analyses, it is concluded that strain G45-3T represents a novel species of a new genus, for which the name Acidibrevibacterium fodinaquatile gen. nov., sp. nov. is proposed. A. fodinaquatile is nominated as type species and its type strain is G45-3T (=CGMCC 1.16069T=KCTC 62275T).
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Parashewanella tropica sp. nov., a mesophilic bacterium isolated from a marine sponge from Chuuk lagoon, Federated States of Micronesia, and emended description of the genus Parashewanella
More LessA mesophilic, straight-rod-shaped, non-flagellated bacterium, designated MEBiC05444T, was isolated from a marine sponge collected from Chuuk lagoon, Federated States of Micronesia. The strain was Gram-negative, catalase- and oxidase-positive, and facultative anaerobic. The isolate aerobically grew at 8–38 °C (optimum, 24–32 °C), pH 4.0–10.0 (pH 7.0–7.5) with an absolute requirement for Na+ up to 6 % (w/v) NaCl (2 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that MEBiC05444T belonged to the family Shewanellaceae , within the class Gammaproteobacteria. Strain MEBiC05444T showed highest 16S rRNA gene sequence similarity to Parashewanella curva C51T, followed by [ Shewanella ] irciniae UST040317-058T and Parashewanella spongiae HJ039T (98.9 %, 97.2 and 95.7 %, respectively). In the phylogenetic tree based on the 16S rRNA gene sequences, MEBiC05444T formed a cluster with P. curva C51T, but the average nucleotide identity value between the two strains was 82 %, thus confirming their separation at species level. The major fatty acids were iso-C15 : 0 (19.7 %), summed feature 3 (composed of C16 : 1 ω7c and/or C16 : 1ω6c; 16.1 %) and C17 : 1ω8c (10.2 %). The only detected respiratory quinone was ubiquinone Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified aminoglycolipids, two unidentified glycolipids, an unidentified aminoglycophospholipid and an unidentified lipid. The genomic DNA G+C content of strain MEBiC05444T was 40.8 mol%. Based on the results of polyphasic analysis, the strain represents a novel species of the genus Parashewanella , distinct from P. curva C51T, [ Shewanella ] irciniae UST040317-058T and P. spongiae HJ039T for which the name Parashewanella tropica sp. nov. is proposed with type strain MEBiC05444T (=KCCM 43304T=JCM 16653T).
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Pseudomonas huaxiensis sp. nov., isolated from hospital sewage
More LessA novel Gram-negative, obligate aerobic, rod-shaped, motile by one or two polar flagella, non-spore-forming bacterial strain, WCHPs060044T, was isolated from the wastewater treatment plant at West China Hospital in Chengdu, PR China. Analysis of its 16S rRNA gene sequence showed that strain WCHPs060044T belonged to the genus Pseudomonas with the highest similarity to Pseudomonas alkylphenolica KL28T (99.73 %), Pseudomonas donghuensis HYST (99.52 %) and Pseudomonas wadenswilerensis CCOS 846T (99.38 %). Phylogenomic analysis based on 107 core gene sequences demonstrated that WCHPs060044T was a member of the Pseudomonas putida group but was distant from all closely related species. Whole-genome comparisons, using average nucleotide identity based on blast (ANIb) and in silico DNA–DNA hybridization (isDDH), confirmed low genome relatedness to its close phylogenetic neighbours [below the recommended thresholds of 95 % (ANIb) and 70 % (isDDH) for species delineation]. Phenotypic characterization tests showed that the utilization of l-arginine, l-fucose, d-galacturonic, d-glucuronic acid, inositol and sorbitol in combination could distinguish this strain from other related species of the genus Pseudomonas . Therefore, based on genetic and phenotypic evidence, strain WCHPs060044T represents a novel species, for which the name Pseudomonas huaxiensis sp. nov. is proposed. The type strain is WCHPs060044T (GDMCC 1.1396T=JCM 32907T=CCTCC AB 2018120T=CNCTC 7663T).
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