scholarly journals Bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in Canada

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3202-3207 ◽  
Author(s):  
Xiumei Yu ◽  
Sylvie Cloutier ◽  
James T. Tambong ◽  
Eden S. P. Bromfield
Keyword(s):  
Glycine Max ◽  
Glycine Soja ◽  
Root Nodules ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Content Type ◽  
Carbon And Nitrogen ◽  
Link Type ◽  
Macroptilium Atropurpureum

Sixteen strains of symbiotic bacteria from root nodules of Glycine max grown in Ottawa, Canada, were previously characterized and placed in a novel group within the genus Bradyrhizobium . To verify their taxonomic status, these strains were further characterized using a polyphasic approach. All strains possessed identical 16S rRNA gene sequences that were 99.79 % similar to the closest relative, Bradyrhizobium liaoningense LMG 18230T. Phylogenetic analysis of concatenated atpD, glnII, recA, gyrB, rpoB and dnaK genes divided the 16 strains into three multilocus sequence types that were placed in a highly supported lineage distinct from named species of the genus Bradyrhizobium consistent with results of DNA–DNA hybridization. Based on analysis of symbiosis gene sequences (nodC and nifH), all novel strains were placed in a phylogenetic group with five species of the genus Bradyrhizobium that nodulate soybeans. The combination of phenotypic characteristics from several tests including carbon and nitrogen source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium . Novel strain OO99T elicits effective nodules on Glycine max, Glycine soja and Macroptilium atropurpureum, partially effective nodules on Desmodium canadense and Vigna unguiculata, and ineffective nodules on Amphicarpaea bracteata and Phaseolus vulgaris. Based on the data presented, we conclude that our strains represent a novel species for which the name Bradyrhizobium ottawaense sp. nov. is proposed, with OO99T ( = LMG 26739T = HAMBI 3284T) as the type strain. The DNA G+C content is 62.6 mol%.

Sediminihaliea albiluteola gen. nov., sp. nov., a new member of the family Halieaceae, isolated from marine sediment

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Shan Jiang ◽  
Feng-Bai Lian ◽  
You-Yang Sun ◽  
Xiao-Kui Zhang ◽  
Zong-Jun Du
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Sequence Similarities

A Gram-stain-negative, rod-shaped and facultatively aerobic bacterial strain, designated F7430T, was isolated from coastal sediment collected at Jingzi Wharf in Weihai, PR China. Cells of strain F7430T were 0.3–0.4 µm wide, 2.0–2.6 µm long, non-flagellated, non-motile and formed pale-beige colonies. Growth was observed at 4–40 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.5–8.0) and at NaCl concentrations of 1.0–10.0 % (w/v; optimum, 1.0 %). The sole respiratory quinone of strain F7430T was ubiquinone 8 and the predominant cellular fatty acids were summed feature 8 (C18 : 1  ω7c / C18 : 1  ω6c; 60.7 %), summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c; 30.2 %) and C15 : 0 iso (13.9 %). The polar lipids of strain F7430T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid and three unidentified lipids. Results of 16S rRNA gene sequences analyses indicated that this strain belonged to the family Halieaceae and had high sequence similarities to Parahaliea aestuarii JCM 51547T (95.3 %) and Halioglobus pacificus DSM 27932T (95.2 %) followed by 92.9–95.0 % sequence similarities to other type species within the aforementioned family. The rpoB gene sequences analyses indicated that the novel strain had the highest sequence similarities to Parahaliea aestuarii JCM 51547T (82.2 %) and Parahaliea mediterranea DSM 21924T (82.2 %) followed by 75.2–80.5 % sequence similarities to other type species within this family. Phylogenetic analyses showed that strain F7430T constituted a monophyletic branch clearly separated from the other genera of family Halieaceae . Whole-genome sequencing of strain F7430T revealed a 3.3 Mbp genome size with a DNA G+C content of 52.6 mol%. The genome encoded diverse metabolic pathways including the Entner–Doudoroff pathway, assimilatory sulphate reduction and biosynthesis of dTDP-l-rhamnose. Based on results from the current polyphasic study, strain F7430T is proposed to represent a novel species of a new genus within the family Halieaceae , for which the name Sediminihaliea albiluteola gen. nov., sp. nov. is proposed. The type strain of the type species is F7430T (=KCTC 72873T=MCCC 1H00420T).

Pseudomonas bijieensis sp. nov., isolated from cornfield soil

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Jingling Liang ◽  
Sai Wang ◽  
Ayizekeranmu Yiming ◽  
Luoyi Fu ◽  
Iftikhar Ahmad ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Novel Species ◽  
Guizhou Province ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Genome Comparisons

Strain L22-9T, a Gram-stain-negative and rod-shaped bacterium, motile by one polar flagellum, was isolated from cornfield soil in Bijie, Guizhou Province, PR China. Based on 16S rRNA gene sequences, it was identified as a Pseudomonas species. Multilocus sequence analysis of concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences showed that strain L22-9T formed a clearly separated branch, located in a cluster together with Pseudomonas brassicacearum LMG 21623T, Pseudomonas kilonensis DSM 13647T and Pseudomonas thivervalensis DSM 13194T. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) confirmed that strain L22-9T should be classified as a novel species. It was most closely related to P. kilonensis DSM 13647T with ANI and dDDH values of 91.87 and 46.3 %, respectively. Phenotypic features that can distinguish strain L22-9T from P. kilonensis DSM 13647T are the assimilation ability of N-acetyl-d-glucosamine, poor activity of arginine dihydrolase and failure to ferment ribose and d-fucose. The predominant cellular fatty acids of strain L22-9T are C16 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The respiratory quinones consist of Q-9 and Q-8. The polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phosphoglycolipids, two unidentified aminophospholipids and an unidentified glycolipid. Based on the evidence, we conclude that strain L22-9T represents a novel species, for which the name Pseudomonas bijieensis sp. nov. is proposed. The type strain is L22-9T (=CGMCC 1.18528T=LMG 31948T), with a DNA G+C content of 60.85 mol%.

Reclassification of Parvularcula flava as Aquisalinus luteolus nom. nov. and emended description of the genus Aquisalinus

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Jun-Jie Ying ◽  
Zhi-Cheng Wu ◽  
Yuan-Chun Fang ◽  
Lin Xu ◽  
Cong Sun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Parvularcula flava was proposed as a novel member of genus Parvularcula in 2016. Some time earlier, Aquisalinus flavus has been proposed as a novel species of a novel genus named Aquisalinus . When comparing the 16S rRNA gene sequences of type strains P. flava NH6-79T and A. flavus D11M-2T, they showed 97.9 % sequence identity, much higher than the sequence identities 92.7–94.3 % between P. flava NH6-79T and type strains in the genus Parvularcula , indicating that the later proposed novel taxon Parvularcula flava need reclassification. The phylogenetic trees based on 16S rRNA gene sequences and genome sequences both showed that P. flava NH6-79T and A. flavus D11M-2T formed a separated branch away from strains in the genera Parvularcula , Marinicaulis and Amphiplicatus . The average amino acid identity and average nucleotide identity values of P. flava NH6-79T and A. flavus D11M-2T were 87.9 and 85.0 %, respectively, much higher than the values between P. flava NH6-79T and other closely related type strains (54.3 %–58.1 % and 68.6–70.4 %, respectively). P. flava NH6-79T and A. flavus D11M-2T also contained summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c) and C16 : 0 as major fatty acids, distinguishing them from other closely related taxa. Based on the results of the phylogenetic, comparative genomic and phenotypic analyses, Parvularcula flava should be reclassified as Aquisalinus luteolus nom. nov. and the description of genus Aquisalinus is emended.

Limosilactobacillus urinaemulieris sp. nov. and Limosilactobacillus portuensis sp. nov. isolated from urine of healthy women

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Magdalena Ksiezarek ◽  
Teresa Gonçalves Ribeiro ◽  
Joana Rocha ◽  
Filipa Grosso ◽  
Svetlana Ugarcina Perovic ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Gram Stain ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Healthy Women ◽  
Genome Distance

Two Gram-stain-positive strains, c9Ua_26_MT and c11Ua_112_MT, were isolated from voided urine samples from two healthy women. Comparative 16S rRNA gene sequences demonstrated that these novel strains were members of the genus Limosilactobacillus . Phylogenetic analysis based on pheS gene sequences and core genomes showed that each strain formed a separated branch and are closest to Limosilactobacillus vaginalis DSM 5837T. The average nucleotide identity (ANI) and Genome-to-Genome Distance Calculator (GGDC) values between c9Ua_26_MT and the closest relative DSM 5837T were 90.7 and 42.9 %, respectively. The ANI and GGDC values between c11Ua_112_MT and the closest relative DSM 5837T were 91.2 and 45.0 %, and those among the strains were 92.9% and 51,0 %, respectively. The major fatty acids were C12 : 0 (40.2 %), C16 : 0 (26.7 %) and C18 : 1 ω9c (17.7 %) for strain c9Ua_26_MT, and C18 : 1 ω9c (38.0 %), C16 : 0 (33.3 %) and C12 : 0 (17.6 %) for strain c11Ua_112_MT. The genomic DNA G+C content of strains c9Ua_26_MT and c11Ua_112_MT was 39.9 and 39.7 mol%, respectively. On the basis of the data presented here, strains c9Ua_26_MT and c11Ua_112_MT represent two novel species of the genus Limosilactobacillus , for which the names Limosilactobacillus urinaemulieris sp. nov. (c9Ua_26_MT=CECT 30144T=LMG 31899T) and Limosilactobacillus portuensis sp. nov. (c11Ua_112_MT=CECT 30145T=LMG 31898T) are proposed.

Acerihabitans arboris gen. nov., sp. nov., a new member of the family Pectobacteriaceae isolated from sap drawn from Acer pictum

2021 ◽  
Author(s):  
Soon Dong Lee ◽  
In Seop Kim ◽  
Hanna Choe ◽  
Ji-Sun Kim
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Amino Acid Identity ◽  
Core Gene ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-negative, facultatively anaerobic bacterium, designated SAP-6T, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea and its precise taxonomic status was determined by a polyphasic approach. Cells were non-sporulating, motile, short rods and showed growth at 4–37 °C, pH 6.0–8.0 and 0–4% NaCl. Phylogenomic analysis based on 92 core gene sequences showed that strain SAP-6T belonged to the family Pectobacteriaceae and formed a distinct clade between members of the genera Sodalis and Biostraticola with gene support index of 89. The closest phylogenetic neighbours were Biostraticola tofi DSM 19580T (97.3% 16S rRNA gene sequence similarity) and Sodalis praecaptivus HS1T (96.8%), with the average amino acid identity values of 75.3% and 74.0%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The major isoprenoid quinones were Q-7 and Q-8. The predominant fatty acids were C16:0, C17:0 cyclo and summed feature 3. The DNA G+C content was 57.0%. On the basis of data presented here, strain SAP-6T (=KCTC 52622T=DSM 104038T) represents a novel species of a new genus in the family Pectobacteriaceae , for which the name Acerihabitans arboris gen. nov., sp. nov. is proposed.

Taxonomic status of the species Clostridium methoxybenzovorans Mechichi et al. 1999

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Hisami Kobayashi ◽  
Yasuhiro Tanizawa ◽  
Mitsuo Sakamoto ◽  
Moriya Ohkuma ◽  
Masanori Tohno
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

The taxonomic status of the species Clostridium methoxybenzovorans was assessed. The 16S rRNA gene sequence, whole-genome sequence and phenotypic characterizations suggested that the type strain deposited in the American Type Culture Collection ( C. methoxybenzovorans ATCC 700855T) is a member of the species Eubacterium callanderi . Hence, C. methoxybenzovorans ATCC 700855T cannot be used as a reference for taxonomic study. The type strain deposited in the German Collection of Microorganism and Cell Cultures GmbH (DSM 12182T) is no longer listed in its online catalogue. Also, both the 16S rRNA gene and the whole-genome sequences of the original strain SR3T showed high sequence identity with those of Lacrimispora indolis (recently reclassified from Clostridium indolis ) as the most closely related species. Analysis of the two genomes showed average nucleotide identity based on blast and digital DNA–DNA hybridization values of 98.3 and 87.9 %, respectively. Based on these results, C. methoxybenzovorans SR3T was considered to be a member of L. indolis .

Pseudomonas cyclaminis sp. nov., a pathogen causing bacterial bud blight of cyclamen in Japan

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Hiroyuki Sawada ◽  
Takashi Fujikawa ◽  
Shigeru Osada ◽  
Mamoru Satou
Keyword(s):  
Fatty Acids ◽  
Type Species ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Total Fatty Acids

Five phytopathogenic bacterial strains, MAFF 301449T, MAFF 301450, MAFF 301451, MAFF 301452, and MAFF 301453, which were isolated from bud blight lesions of cyclamen (Cyclamen persicum Mill.) in Miyagi, Japan, were subjected to polyphasic taxonomic characterisation. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one to five polar flagella, and rod-shaped. Analysis of 16S rRNA gene sequences showed that they belong to the genus Pseudomonas , with Pseudomonas extremaustralis 14-3T (99.79 % sequence similarity), Pseudomonas trivialis DSM 14937T (99.79 %), Pseudomonas poae DSM 14936T (99.72 %), and Pseudomonas antarctica CMS 35T (99.72 %) as their relatives. The genomic DNA G+C content was 60.3 mol% and the major fatty acids (>5 % of the total fatty acids) were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), and C17 : 0 cyclo. Phylogenetic analysis using the rpoD gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas fluorescens subgroup, but form a monophyletic and robust clade separated from their relatives. Average nucleotide identity and digital DNA–DNA hybridisation analyses with the closely related Pseudomonas species corroborated their novel species status. The strains were differentiated from their relatives by phenotypic characteristics, pathogenicity towards cyclamen, cellular fatty acid composition, and whole-cell MALDI-TOF mass spectrometry profiles. Based on the phenotypic, chemotaxonomic, and genotypic data obtained, we conclude that the strains represent a novel Pseudomonas species, for which we propose the name Pseudomonas cyclaminis sp. nov.; the type strain is MAFF 301449T (=ICMP 23720T).

Barrientosiimonas humi gen. nov., sp. nov., an actinobacterium of the family Dermacoccaceae

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 241-248 ◽  
Author(s):  
Learn-Han Lee ◽  
Yoke-Kqueen Cheah ◽  
Shiran Mohd Sidik ◽  
Qing-Yi Xie ◽  
Yi-Li Tang ◽  
...  
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Cell Wall Polysaccharide ◽  
Content Type ◽  
Link Type ◽  
The Family

Three novel actinobacteria, strains 39T, 40 and 41, were isolated from soil collected from Barrientos Island in the Antarctic. The taxonomic status of these strains was determined using a polyphasic approach. Comparison of 16S rRNA gene sequences revealed that strain 39T represented a novel lineage within the family Dermacoccaceae and was most closely related to members of the genera Demetria (96.9 % 16S rRNA gene sequence similarity), Branchiibius (95.7 %), Dermacoccus (94.4–95.3 %), Calidifontibacter (94.6 %), Luteipulveratus (94.3 %), Yimella (94.2 %) and Kytococcus (93.1 %). Cells were irregular cocci and short rods. The peptidoglycan type was A4α with an l-Lys–l-Ser–d-Asp interpeptide bridge. The cell-wall sugars were galactose and glucose. The major menaquinone was MK-8(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphoglycolipid, two glycolipids and one unknown phospholipid. The acyl type of the cell-wall polysaccharide was N-acetyl. The major cellular fatty acids were anteiso-C17 : 0 (41.97 %), anteiso-C17 : 1ω9c (32.16 %) and iso-C16 : 0 (7.68 %). The DNA G+C content of strain 39T was 68.4 mol%. On the basis of phylogenetic and phenotypic differences from other genera of the family Dermacoccaceae , a novel genus and species, Barrientosiimonas humi gen. nov., sp. nov., is proposed; the type strain of the type species is 39T ( = CGMCC 4.6864T  = DSM 24617T).

scholarly journals Reclassification of Deinococcus xibeiensis Wang et al. 2010 as a heterotypic synonym of Deinococcus wulumuqiensis Wang et al. 2010

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 1083-1085 ◽  
Author(s):  
Sunhee Hong ◽  
Christine E. Farrance ◽  
Anne Russell ◽  
Hana Yi
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Taxonomic Status ◽  
Single Species ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Genomic Relatedness

Two species of the genus Deinococcus , namely Deinococcus wulumuqiensis Wang et al. 2010 and Deinococcus xibeiensis Wang et al. 2010, were simultaneously proposed and described in the same publication. However, the identical 16S rRNA gene sequence of the two type strains strongly raised the probability of their relatedness at the species level. Thus, the genomic relatedness of the two species of the genus Deinococcus was investigated here to clarify their taxonomic status. The high (99.9 %) average nucleotide identity (ANI) between the genome sequences of the two type strains suggested that the two species are synonymous. Additional phenotypic data including enzymic activities and substrate-utilization profiles showed no pronounced differences between the type strains of the two species. Data from this study demonstrated that the two taxa constitute a single species. According to Rule 42 of the Bacteriological Code, we propose that D. xibeiensis Wang et al. 2010 should be reclassified as a subjective heterotypic synonym of D. wulumuqiensis Wang et al. 2010.

Sphingobium fontiphilum sp. nov., isolated from a freshwater spring

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1906-1911 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yu-Wen Shiau ◽  
Yan-Ting Wei ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

To investigate the biodiversity of bacteria in the spring water of the Chengcing Lake Park in Taiwan, a Gram-stain-negative, rod-shaped, non-motile, non-spore-forming and aerobic bacterial strain, designated strain Chen16-4T, was isolated and characterized in a taxonomic study using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the closest relatives of strain Chen16-4T were Sphingobium amiense YTT, Sphingobium yanoikuyae GIFU 9882T and Sphingobium scionense WP01T, with sequence similarities of 97.6, 97.1 and 97.0 %, respectively. A phylogenetic tree obtained with 16S rRNA gene sequences indicated that strain Chen16-4T and these three closest relatives formed an independent phylogenetic clade within the genus Sphingobium . The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of C18 : 1ω7c in the cellular fatty acid profile and the DNA G+C content also supported affiliation of the isolate to the genus Sphingobium . The DNA–DNA relatedness of strain Chen16-4T with respect to recognized species of the genus Sphingobium was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Chen16-4T represents a novel species in the genus Sphingobium , for which the name Sphingobium fontiphilum sp. nov. is proposed. The type strain is Chen16-4T ( = BCRC 80308T = LMG 26342T = KCTC 23559T).

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