Dickeya aquatica sp. nov., isolated from waterways

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2264-2266 ◽  
Author(s):  
Neil Parkinson ◽  
Paul DeVos ◽  
Minna Pirhonen ◽  
John Elphinstone
Keyword(s):  
Dna Hybridization ◽  
Profile Analysis ◽  
Sequence Similarity ◽  
Branch Length ◽  
Rrna Gene ◽  
New Taxon ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Uk

Pectinolytic Gram-negative bacteria were isolated from different waterways in the UK and Finland. Three strains (174/2T, 181/2 and Dw054) had the same 16S rRNA gene sequences which shared 99 % sequence similarity to species of the genus Dickeya , and a phylogeny of related genera confirmed attribution to this genus. Fatty acid profile analysis of all three strains found a high proportion of C16 : 1ω7c/C16 : 1ω7c and C16 : 0 fatty acids, and library profile searches found closest matches to Dickeya chrysanthemi . Production of a concatenated phylogeny using six loci, recA, gapA, atpD, gyrB, infB and rpoB, provided a high-resolution phylogeny which placed strains 174/2T and 181/2 as a distinct clade, separated from the other species of the genus Dickeya by a relatively long branch-length. DNA–DNA hybridization analysis with a limited number of reference species also supported the distinctiveness of strains 174/2T and 181/2 within the genus Dickeya . All three strains could be phenotypically distinguished from other species of the genus by fermentation of melibiose and raffinose but not d-arabinose or mannitol. The name Dickeya aquatica sp. nov. is proposed for the new taxon; the type strain is 174/2T ( = NCPPB 4580T = LMG 27354T).

scholarly journals Pseudovibrio axinellae sp. nov., isolated from an Irish marine sponge

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 141-145 ◽  
Author(s):  
John A. O’Halloran ◽  
Teresa M. Barbosa ◽  
John P. Morrissey ◽  
Jonathan Kennedy ◽  
Alan D. W. Dobson ◽  
...  
Keyword(s):  
Marine Sponge ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-negative, motile, rod-shaped bacterial strain, designated Ad2T, was isolated from a marine sponge, Axinella dissimilis, which was collected from a semi-enclosed marine lake in Ireland. Strain Ad2T grew optimally at 24 °C, at pH 7.0 and in the presence of 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Ad2T clustered with members of the genus Pseudovibrio , and showed 97.3–98.2 % sequence similarity to the type strains of recognized Pseudovibrio species. DNA–DNA relatedness values between strain Ad2T and the type strains of other Pseudovibrio species were <27 %. The DNA G+C content of strain Ad2T was 50.5 mol%. The major fatty acid was 18 : 1ω7c. Differences in phenotypic properties, together with phylogenetic and DNA–DNA hybridization analyses, indicated that strain Ad2T represented a novel species of the genus Pseudovibrio . The name Pseudovibrio axinellae sp. nov. is proposed, with Ad2T ( = DSM 24994T = NCIMB 14761T) as the type strain.

scholarly journals Hymenobacter ginkgonis sp. nov., isolated from bark of Ginkgo biloba

2020 ◽  
Vol 70 (8) ◽  
pp. 4760-4766 ◽  
Author(s):  
Inseong Cha ◽  
Heeyoung Kang ◽  
Haneul Kim ◽  
Seokhyeon Bae ◽  
Kiseong Joh
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
16S Rrna Gene Sequences ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type

Strain HMF4947T, isolated from the bark of a ginkgo tree, was a pale-pink coloured, Gram-stain-negative, non-motile, strictly aerobic and rod-shaped bacterium. The isolate grew optimally on Reasoner's 2A agar at 30 °C, pH 7.0 and with 0 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HMF4947T belonged to the genus Hymenobacter and was most closely related to Hymenobacter metalli A2-91T (96.9 % sequence similarity) and Hymenobacter pomorum 9-2-1-1T (96.5 %). The average nucleotide identity and estimated DNA–DNA hybridization values between strain HMF4947T and Hymenobacter arizonensis DSM 17870T were 74.3 and 20.5 %, respectively. The major fatty acids were summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), iso-C15 : 0 and C16 : 1  ω5c. The predominant isoprenoid quinone was menaquinone-7. The polar lipids comprised phosphatidylethanolamine, one unidentified aminoglycolipid, three unidentified aminophospholipids, one unidentified phospholipid, three unidentified aminolipids, two unidentified glycolipids and three unidentified polar lipids. The genomic DNA G+C content was 59.3 mol%. Thus, based on phylogenetic, phenotypic and chemotaxonomic data, strain HMF4947T represents a novel species of the genus Hymenobacter , for which the name Hymenobacter ginkgonis sp. nov. is proposed. The type strain of the species is strain HMF4947T (=KCTC 72780T=NBRC 114271T).

scholarly journals Arachidicoccus soli sp. nov., a bacterium isolated from soil

2020 ◽  
Author(s):  
Shin Ae Lee ◽  
Tae-Wan Kim ◽  
Mee-Kyung Sang ◽  
Jaekyeong Song ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated KIS59-12T, was isolated from a soil sample collected on Hodo island, Boryeong, Republic of Korea. The strain grew at 10–33 °C, pH 6.0–7.5 and with 0–4 % NaCl (w/v). Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain KIS59-12T was in the same clade as Arachidicoccus rhizosphaerae Vu-144T and Arachidicoccus ginsenosidivorans Gsoil809T with 97.5 and 97.2 % sequence similarity, respectively. Comparative genome analysis between strain KIS59-12T and A. rhizosphaerae Vu-144T showed that average nucleotide identity value was 69.4 % and the digital DNA–DNA hybridization value was 19.1 %. The major respiratory quinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine and an unknown polar lipid. The predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH, which supported the affiliation of strain KIS59-12T with the genus Arachidicoccus . The major polyamines were homospermidine and putrescine. The genomic DNA G+C content was 36.4 mol%. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, strain KIS59-12T represents a novel species of the genus Arachidicoccus , for which the name Arachidicoccus soli sp. nov. is proposed. The type strain of Arachidicoccus soli is KIS59-12T (=KACC 17340T=NBRC 113161T).

scholarly journals Brenneria populi sp. nov., isolated from symptomatic bark of Populus×euramericana canker

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 432-437 ◽  
Author(s):  
Yong Li ◽  
Wei Fang ◽  
Han Xue ◽  
Wen-xing Liang ◽  
Lai-fa Wang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Populus Euramericana ◽  
Link Type ◽  
Bark Tissue ◽  
Single Cluster

Five Gran-stain-negative, facultatively anaerobic, motile, bacterial strains were isolated from symptomatic bark tissue of Populus×euramericana canker. Strains grew at 4–41 °C, pH 4–10 and 0–6 % (w/v) salinity. They were positive with respect to catalase activity and negative for oxidase activity, nitrate reduction and the Voges–Proskauer reaction. Analysis of 16S rRNA gene sequences indicated that these five poplar isolates belong to the genus Brenneria , having highest sequence similarity of 95.98 % with Brenneria goodwinii LMG 26270T. These five isolates formed a single cluster based on multilocus sequence analysis, indicating that they all belong to a single taxon within the genus Brenneria , which was confirmed by DNA–DNA hybridization. The DNA G+C content was 54.9–55.7 mol%, and the main fatty acids were C16 : 0, C18 : 1ω7c, C17 : 0 cyclo and C16 : 1ω7c/iso-C15 : 0 2-OH. Based on these results, we describe a novel species of the genus Brenneria with the proposed name Brenneria populi sp. nov. The type strain is D9-5T ( = CFCC 11963T = KCTC 42088T).

Faecalibacter rhinopitheci sp. nov., a bacterium isolated from the faeces of Rhinopithecus bieti

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Qiong Wang ◽  
Xiu-Lin Han ◽  
Zhi-Pang Huang ◽  
Song Huang ◽  
De-Feng An ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
National Park ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Rhinopithecus Bieti ◽  
Content Type ◽  
Link Type ◽  
Pr China

A novel Gram-stain-negative strain, WQ 117T, isolated from the faeces of Rhinopithecus bieti collected at Yunnan Snub-nosed Monkey National Park, Yunnan province, PR China, was subjected to a polyphasic taxonomic study. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate represented a member of the genus Faecalibacter , sharing 97.64 % sequence similarity with the type strain Faecalibacter macacae YIM 102668T. The G+C content of the genomic DNA of WQ117T was 30.5 mol%. The predominant isoprenoid quinone was MK-6. The major cellular fatty acids was iso-C15 : 0. The whole genome average nucleotide identity (gANI) values and the digital DNA–DNA hybridization values between WQ 117T and YIM 102668T were 79.66 % and 22.20 %, respectively. Growth occurred at 0–50 °C (optimally at 28–35 °C), pH 7.0–9.0 (optimally at pH 8.0) and with 0–2 % (w/v) NaCl (optimally without NaCl). On the basis of the taxonomic evidence, a novel species, Faecalibacter rhinopitheci sp. nov., is proposed. The type strain is WQ 117T (=KCTC 82394T=CCTCC AA 2020027T).

‘Candidatus Phytoplasma convolvuli’, a new phytoplasma taxon associated with bindweed yellows in four European countries

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2910-2915 ◽  
Author(s):  
Marta Martini ◽  
Carmine Marcone ◽  
Jelena Mitrović ◽  
Michael Maixner ◽  
Duška Delić ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
New Taxon ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

Plants of Convolvulus arvensis exhibiting symptoms of undersized leaves, shoot proliferation and yellowing, collectively defined as bindweed yellows, were sampled in different regions of Europe and assessed for phytoplasma infection by PCR amplification using phytoplasma universal rRNA operon primer pairs. Positive results were obtained for all diseased plants. RFLP analysis of amplicons comprising the16S rRNA gene alone or the16S rRNA gene and 16-23S intergenic spacer region indicated that the detected phytoplasmas were distinguishable from all other previously described rRNA gene sequences. Analysis of 16S rRNA gene sequences derived from seven selected phytoplasma strains (BY-S57/11, BY-S62/11, BY-I1015, BY-I1016, BY-BH1, BY-BH2 and BY-G) showed that they were nearly identical (99.9–100 % gene sequence similarity) but shared less than 97.5 % similarity with comparable sequences of other phytoplasmas. Thus, BY phytoplasmas represent a new taxon whose closest relatives are stolbur phytoplasma strains and ‘ Candidatus Phytoplasma fragariae ’ with which they share 97.2 % and 97.1 % 16S rRNA gene sequence similarity, respectively. Phylogenetic analysis of 16S rRNA gene sequences confirmed that bindweed yellows phytoplasma strains collectively represent a distinct lineage within the phytoplasma clade and share a common ancestor with previously published or proposed ‘Candidatus Phytoplasma’ taxa within a major branch including aster yellows and stolbur phytoplasmas. On the basis of unique 16S rRNA gene sequences and biological properties that include a single host plant species and a geographical distribution limited to parts of Europe, the bindweed yellows (BY) phytoplasmas represent a coherent but discrete taxon, ‘Candidatus Phytoplasma convolvuli’, with strain BY-S57/11 (GenBank accession no. JN833705) as the reference strain.

Faecalibacter bovis sp. nov., isolated from cow faeces

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Fuxiang Li ◽  
Wenhua Zhao ◽  
Qionghua Hong ◽  
Qingyong Shao ◽  
Jianling Song ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
West China ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-stain-negative, non-spore-forming, yellow-pigmented, aerobic, pleomorphic rod-shaped bacterium, designated ZY171143T, was isolated from faeces of a cow with diarrhoea in Wenshan, Yunnan Province, south-west China and its taxonomic position was studied. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZY171143T belonged to the family Weeksellaceae and was most closely related to the only species of the genus Faecalibacter , Faecalibacter macacae CCTCC AB 2016016T with a sequence similarity of 97.8 %. The genomic OrthoANI and digital DNA–DNA hybridization values between the strain and F. macacae CCTCC AB 2016016T were 86.2 and 30.5 %, respectively. The genomic G+C content was 31.1 mol%. The predominant fatty acids (>5 %) were C15 : 0 iso, C17 : 0 iso 3OH, C16 : 0, C16 : 1 ω5c and summed feature 3 (C16 : 1 ω7c and/or 16 : 1 ω6c). The major polar lipids were phosphatidylethanolamine, triacylglycerol and sulfonolipid. The sole respiratory quinone was MK-6. These chemotaxonomic characterizations also revealed that strain ZY171143T was a member of the genus Faecalibacter . Based on the phenotypic, chemotaxonomic and genotypic data, strain ZY171143T represents a novel species within the genus Faecalibacter , for which the name Faecalibacter bovis sp. nov. is proposed. The type strain is ZY171143T (=CGMCC 1.13663T=KCTC 62642T).

Jeongeupia chitinilytica sp. nov., a chitinolytic bacterium isolated from soil

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 934-938 ◽  
Author(s):  
Wen-Ming Chen ◽  
Rey-Chang Chang ◽  
Chih-Yu Cheng ◽  
Yu-Wen Shiau ◽  
Shih-Yi Sheu
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Novel Bacterium

A novel bacterium, designated strain JchiT, was isolated from soil in Taiwan and characterized using a polyphasic approach. Cells of strain JchiT were aerobic, Gram-stain-negative, motile and rod-shaped. They contained poly-β-hydroxybutyrate granules and formed dark-yellow colonies. Growth occurred at 20–37 °C (optimum between 25 and 30 °C), at pH 6.0–8.0 (optimum between pH 7.0 and pH 8.0) and with 0–2 % NaCl (optimum between 0 and 1 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain JchiT belonged to the genus Jeongeupia and that its closest neighbour was Jeongeupia naejangsanensis BIO-TAS4-2T (98.0 % sequence similarity). The major fatty acids (>10 %) of strain JchiT were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C12 : 0 3-OH. The isoprenoid quinone was Q-8 and the genomic DNA G+C content was 66.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine and two unidentified phospholipids. The DNA–DNA relatedness value between strain JchiT and J. naejangsanensis BIO-TAS4-2T was about 41.0 %. On the basis of the genotypic and phenotypic data, strain JchiT represents a novel species in the genus Jeongeupia , for which the name Jeongeupia chitinilytica sp. nov. is proposed. The type strain is JchiT ( = BCRC 80367T  = KCTC 23701T).

Muriicola soli sp. nov., isolated from soil

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Hye Jeong Kang ◽  
Min-Kyeong Kim ◽  
Su Gwon Roh ◽  
Seung Bum Kim
Keyword(s):  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Optimum Ph ◽  
Genomic Characterization

A Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, orange-pigmented, rod-shaped and non-motile bacterium designated strain MMS17-SY002T was isolated from island soil. The isolate grew at 20–37 °C (optimum, 30 °C), at pH 6.0–9.5 (optimum, pH 7) and in the presence of 0.5–4.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MMS17-SY002T was mostly related to the genus Muriicola of the family Flavobacteriaceae and had highest sequence similarity of 96.82 % to Muriicola marianensis A6B8T and Muriicola jejuensis EM44T, but formed a distinct phylogenetic line within the genus. Chemotaxonomic analyses showed that menaquinone 6 was the predominant isoprenoid quinone, the major fatty acids were iso-C15 : 1 G and iso-C15 : 0, and the diagnostic polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 42.4 mol%. Strain MMS17-SY002T could be distinguished from related species by the combination of trypsin, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase and β-glucosidase activities. The orthologous average nucleotide identity between the genomes of strain MMS17-SY002T and M. jejuensis and that between the strain and M. marianensis A6B8T were 73.26 and 73.33%, respectively, thus confirming the separation of the strain from related species at species level. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic characterization, MMS17-SY002T should be recognized as a novel species of the genus Muriicola , for which the name Muriicola soli sp. nov. is proposed. The type strain is MMS17-SY002T (=KCTC 62790T=JCM 32370T).

scholarly journals Mesoflavibacter aestuarii sp. nov., a zeaxanthin-producing marine bacterium isolated from seawater

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1932-1937 ◽  
Author(s):  
Ji Hee Lee ◽  
Yeoung Min Hwang ◽  
Keun Sik Baik ◽  
Kap Seong Choi ◽  
Jong-Ok Ka ◽  
...  
Keyword(s):  
Marine Bacterium ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Carotenoid Pigment ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Gwangyang Bay

An orange, rod-shaped, Gram-reaction-negative, aerobic and gliding bacterial strain devoid of flagella, designated strain KYW614T, was isolated from seawater collected from Gwangyang Bay, Republic of Korea. Zeaxanthin was the major carotenoid pigment produced and flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain KYW614T belonged to the family Flavobacteriaceae and it was most closely related to Mesoflavibacter zeaxanthinifaciens TD-ZX30T (96.5 %, sequence similarity). The predominant cellular fatty acids of strain KYW614T were iso-C15 : 1 G (10.5 %), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 10.0 %), iso-C15 : 0 (9.5 %), C15 : 0 (7.5 %) and iso-C17 : 0 3-OH (7.4 %). MK-6 was the only isoprenoid quinone and the DNA G+C content was 32.6 mol%. Data from a polyphasic taxonomic study suggested that the isolate represents a novel species in the genus Mesoflavibacter , for which the name Mesoflavibacter aestuarii sp. nov. is proposed. The type strain is KYW614T ( = KCTC 32269T = JCM 19524T).

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