scholarly journals Dyadobacter jiangsuensis sp. nov., a methyl red degrading bacterium isolated from a dye-manufacturing factory

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1138-1143 ◽  
Author(s):  
Li Wang ◽  
Liang Chen ◽  
Qi Ling ◽  
Chen-chen Li ◽  
Yong Tao ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Methyl Red ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
Low Levels

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, L-1T, which was capable of degrading methyl red was isolated from a dye-manufacturing factory in China. Phenotypic, chemotaxonomic and phylogenetic analyses established affiliation of the isolate to the genus Dyadobacter . Cells occurred in pairs in young cultures but became chains of coccoid cells in old cultures, and produced a flexirubin-like yellow pigment. Strain L-1T could not hydrolyse cellulose, and had a DNA G+C content of 51.3 mol%. The major cellular fatty acids were iso-C15 : 0, C16 : 1ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). C16 : 0, iso-C15 : 0 3-OH and C16 : 0 3-OH were the other major fatty acid components. Comparative 16S rRNA gene sequence analysis showed that strainL-1T was most closely related to Dyadobacter fermentans DSM 18053T (99.2 %), Dyadobacter soli JCM 16232T (98.9 %) and Dyadobacter beijingensis CGMCC 1.6375T (98.7 %). However, the new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to JCM 16232T (41.2±1.8 %), DSM 18053T (38.6±2.6 %) and CGMCC 1.6375T (35.0±2.1 %). Strain L-1T could also be differentiated from its closest phylogenetic relatives based on differences in several phenotypic characteristics. These data suggest that strain L-1T represents a novel species of the genus Dyadobacter , for which the name Dyadobacter jiangsuensis sp. is proposed. The type strain is L-1T (DSM 29057T = CGMCC 1.12969T).

Isolation and description of Selenomonas timonae sp. nov., a novel Selenomonas species detected in a gingivitis patient

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Angéline Antezack ◽  
Manon Boxberger ◽  
Mariem Ben Khedher ◽  
Bernard La Scola ◽  
Virginie Monnet-Corti
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
Optimum Ph

A Gram-stain-negative bacterium, designated strain Marseille-Q3039T, was isolated from subgingival dental plaque of a woman with gingivitis in Marseille, France. Strain Marseille-Q3039T was found to be an anaerobic, motile and spore-forming crescent-shaped bacterium that grew at 25–41.5 °C (optimum, 37 °C), pH 5.5–8.5 (optimum, pH 7.5) and salinity of 5.0 g l−1 NaCl. The results of 16S rRNA gene sequence analysis revealed that strain Marseille-Q3039T was closely related to Selenomonas infelix ATCC 43532T (98.42 % similarity), Selenomonas dianae ATCC 43527T (97.25 %) and Centipedia periodontii DSM 2778T (97.19 %). The orthologous average nucleotide identity and digital DNA–DNA hybridization relatedness between strain Q3039T and its closest phylogenetic neighbours were respectively 84.57 and 28.2 % for S. infelix ATCC 43532T and 83.93 and 27.2 % for C. periodontii DSM 2778T. The major fatty acids were identified as C13 : 0 (27.7 %), C15 : 0 (24.4 %) and specific C13 : 0 3-OH (12.3 %). Genome sequencing revealed a genome size of 2 351 779 bp and a G+C content of 57.2 mol%. On the basis of the results from phenotypic, chemotaxonomic, genomic and phylogenetic analyses and data, we concluded that strain Marseille-Q3039T represents a novel species of the genus Selenomonas , for which the name Selenomonas timonae sp. nov. is proposed (=CSUR Q3039=CECT 30128).

scholarly journals Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa

2020 ◽  
Vol 70 (3) ◽  
pp. 1720-1728 ◽  
Author(s):  
Anusha Rai ◽  
Smita N ◽  
Suresh G ◽  
Shabbir A ◽  
Deepshikha G ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Western Ghats Of India

A Gram-stain-negative, non-motile, coccoid-shaped, catalase- and oxidase-positive, non-denitrifying, neutrophilic bacterium designated as strain JC501T was isolated from an epiphytic rhizosphere of an orchid, Aerides maculosa, growing in the Western Ghats of India. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that strain JC501T belonged to the genus Paracoccus and had the highest levels of sequence identity with Paracoccus marinus KKL-A5T (98.9 %), Paracoccus contaminans WPAn02T (97.3 %) and other members of the genus Paracoccus (<97.3 %). Strain JC501T produced indole-3 acetic acid and other indole derivatives from tryptophan. The dominant respiratory quinone was Q-10 and the major fatty acid was C18 : 1ω7c/C18 : 1ω6c, with significant quantities of C18 : 1ω9c, C17 : 0 and C16 : 0. The polar lipids of strain JC501T comprised phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an unidentified glycolipid, two unidentified aminolipids, two unidentified lipids and four unidentified phospholipids. The genome of strain JC501T was 3.3 Mbp with G+C content of 69.4 mol%. For the resolution of the phylogenetic congruence of the novel strain, the phylogeny was also reconstructed with the sequences of eight housekeeping genes. Based on the results of phylogenetic analyses, low (<85.9 %) average nucleotide identity, digital DNA–DNA hybridization (<29.8 %), chemotaxonomic analysis and physiological properties, strain JC501T could not be classified into any of the recognized species of the genus Paracoccus . Strain JC501T represents a novel species, for which the name Paracoccus aeridis sp. nov. is proposed. The type strain is JC501T (=LMG 30532T=NBRC 113644T).

Ruania rhizosphaerae sp. nov., a novel actinobacterium isolated from rhizosphere of Suaeda aralocaspica

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Wan-Ni Lu ◽  
Yi-Zhuo Xu ◽  
Yuan-Guo Xie ◽  
Rui Gao ◽  
Jie-Qiong Song ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
West China ◽  
Content Type ◽  
North West ◽  
Link Type

A Gram-stain-positive, non-motile and short rod-shaped actinobacterium, designated strain LNNU 22110T, was isolated from the rhizosphere soil of the halophyte Suaeda aralocaspica (Bunge) Freitag and Schütze, which collected in Xinjiang, north-west China. Growth occurred at 10–45 °C, pH 6.0–10.0 and in the presence of 0–11 % NaCl (w/v). Based on the results of 16S rRNA gene sequence phylogenetic analyses, strain LNNU 22110T belonged to the genus Ruania and had 97.5 and 95.5 % sequence similarity to Ruania alba KCTC 19413T and Ruania albidiflava CGMCC 4.3142T, respectively. The digital DNA–DNA hybridization relatedness values between strain LNNU 22110T and R. alba KCTC 19413T and R. albidiflava CGMCC 4.3142T were 23.2 and 19.9 %, respectively. The highest average nucleotide identity value between strain LNNU 22110T and its closest related strain ( R. alba KCTC 19413T) was 80.2 %, much lower than the species delineation threshold of 95–96 %. The genome of strain LNNU 22110T was 4.4 Mb, with a genomic DNA G+C content of 68.4 mol%. The diagnostic diamino acids in the peptidoglycan layer of strain LNNU 22110T were lysine, alanine, glycine, glutamic acid and aspartic acid. The predominant menaquinone was MK-8(H4). The major fatty acid (>10 %) was anteiso-C15 : 0. The polar lipid profile of strain LNNU 22110T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, diacylated phosphatidyl dimannoside, one unidentified glycolipid and two unidentified phospholipids. According to the phenotypic, phylogenetic and chemotaxonomic results, strain LNNU 22110T is considered to represent a novel species of the genus Ruania , for which the name Ruania rhizosphaerae sp. nov. is proposed. The type strain is LNNU 22110T (=KCTC 39807T=CGMCC 1.17105T).

scholarly journals Deinococcus citri sp. nov., isolated from citrus leaf canker lesions

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4134-4140 ◽  
Author(s):  
Iftikhar Ahmed ◽  
Saira Abbas ◽  
Takuji Kudo ◽  
Muhammad Iqbal ◽  
Toru Fujiwara ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Content Type ◽  
Citrus Leaf ◽  
Link Type ◽  
Physiological And Biochemical Characteristics ◽  
Gene Sequence Analysis

A Gram-stain-positive, strictly aerobic, non-motile, coccoid bacterium, designated NCCP-154T, was isolated from citrus leaf canker lesions and was subjected to a polyphasic taxonomic study. Strain NCCP-154T grew at 10–37 °C (optimum 30 °C) and at pH 7.0–8.0 (optimum pH 7.0). The novel strain exhibited tolerance of UV irradiation (>1000 J m−2). Based on 16S rRNA gene sequence analysis, strain NCCP-154T showed the highest similarity to Deinococcus gobiensis CGMCC 1.7299T (98.8 %), and less than 94 % similarity to other closely related taxa. The chemotaxonomic data [major menaquinone, MK-8; cell-wall peptidoglycan type, A3β (Orn–Gly2); major fatty acids, summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH; 35.3 %) followed by C16 : 0 (12.7 %), iso-C17 : 1ω9c (9.2 %), C17 : 1ω8c (7.4 %) and iso-C17 : 0 (6.9 %); major polar lipids made up of several unidentified phosphoglycolipids and glycolipids and an aminophospholipid, and mannose as the predominant whole-cell sugar] also supported the affiliation of strain NCCP-154T to the genus Deinococcus . The level of DNA–DNA relatedness between strain NCCP-154T and D. gobiensis JCM 16679T was 63.3±3.7 %. The DNA G+C content of strain NCCP-154T was 70.0 mol%. Based on the phylogenetic analyses, DNA–DNA hybridization and physiological and biochemical characteristics, strain NCCP-154T can be differentiated from species with validly published names. Therefore, it represents a novel species of the genus Deinococcus . The name Deinococcus citri sp. nov. is proposed, with the type strain NCCP-154T ( = JCM 19024T = DSM 24791T = KCTC 13793T).

Texcoconibacillus texcoconensis gen. nov., sp. nov., alkalophilic and halotolerant bacteria isolated from soil of the former lake Texcoco (Mexico)

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3336-3341 ◽  
Author(s):  
Erick Ruiz-Romero ◽  
María de los Angeles Coutiño-Coutiño ◽  
César Valenzuela-Encinas ◽  
María Patricia López-Ramírez ◽  
Rodolfo Marsch ◽  
...  
Keyword(s):  
Type Species ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Bacillus Agaradhaerens

A novel Gram-positive, rod-shaped, spore-forming bacterium, designated 13CCT was isolated from soil of the former lake Texcoco. The strain was aerobic, catalase-positive and oxidase-negative. It grew at salinities of 0–26 % (w/v) NaCl with an optimum at 9–16 % (w/v) NaCl. The cells contain peptidoglycan type A1γ, A1γ′ with glycine instead of l-alanine and three variations of peptidoglycan type A4γ. The only quinone detected was MK-7. The major fatty acid was anteiso-C15 : 0. The polar lipids fraction consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three different phospholipids. The DNA G+C content was 37.5 mol%. Maximum-likelihood phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 13CCT was closely related to members of the genus Bacillus and shared 92.35 % similarity with Bacillus agaradhaerens , 92.28 % with Bacillus neizhouensis and 92.21 % with Bacillus locisalis . It is proposed based on the phenotypic, genotypic and phylogenetic analyses that the novel isolate should be classified as a representative of a new genus and novel species, for which the name Texcoconibacillus texcoconensis gen. nov., sp. nov. is proposed. The type strain of Texcoconibacillus texcoconensis is 13CCT ( = JCM 17654T = DSM 24696T).

Algimonas ampicilliniresistens sp. nov., isolated from the red alga Porphyra yezoensis, and emended description of the genus Algimonas

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4407-4412 ◽  
Author(s):  
Youhei Fukui ◽  
Masahiro Kobayashi ◽  
Hiroaki Saito ◽  
Hiroshi Oikawa ◽  
Yutaka Yano ◽  
...  
Keyword(s):  
Type Species ◽  
Porphyra Yezoensis ◽  
Red Alga ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Emended Description

Three strains (14A-2-7T, 14A-3-1 and 14A-3) of Gram-stain-negative, prosthecate, motile bacteria were isolated from an algal medium supplemented with 10 mg ampicillin l−1 (w/v), in which the red alga Porphyra yezoensis had been cultured. Based on the 16S rRNA gene sequence analysis, the three isolates formed a cluster with the genus Algimonas of the family Hyphomonadaceae . The sequences of the three isolates had high similarity with those of Algimonas porphyrae 0C-2-2T (97.6 % similarity) and Litorimonas taeanensis G5T (95.6 % similarity). The DNA G+C contents of the three isolates ranged from 54.3 to 55.0 mol%, which were more similar to that of A. porphyrae 0C-2-2T (58.5 mol%) than to that of L. taeanensis G5T (47.1 mol%). The DNA–DNA relatedness showed that the three isolates were representatives of the same species (88.1–94.0 % relatedness) and that strain 14A-2-7T was a representative of a different species from A. porphyrae 0C-2-2T and L. taeanensis G5T (1.2–8.6 % relatedness). The phenotypic characteristics of strain 14A-2-7T differed by 20 results and 30 results from A. porphyrae 0C-2-2T and L. taeanensis G5T, respectively. The three isolates contained ubiquinone-10 as the predominant quinone and C18 : 1ω7c as the major fatty acid. Based on the polyphasic taxonomic analysis, the three isolates represent a novel species of the genus Algimonas , for which the name Algimonas ampicilliniresistens sp. nov. is proposed. The type strain is 14A-2-7T ( = LMG 26421T = NBRC 108219T). An emended description of the genus Algimonas is also proposed.

scholarly journals Methylobacterium nonmethylotrophicum sp. nov., isolated from tungsten mine tailing

2020 ◽  
Vol 70 (4) ◽  
pp. 2867-2872 ◽  
Author(s):  
Guang-Da Feng ◽  
Wendi Chen ◽  
Xian-Jiao Zhang ◽  
Jun Zhang ◽  
Sheng-Nan Wang ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Jiangxi Province ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Tungsten Mine

A novel pink-pigmented strain, designated 6HR-1T, was isolated from tungsten mine tailings in Jiangxi Province, PR China. Cells were Gram-stain-negative, aerobic, non-spore-forming, rod-shaped and motile with a polar flagellum (monotrichous). It could not utilize methanol, methylamine, formaldehyde or formate as a sole carbon source. The methanol dehydrogenase mxaF gene was absent but the xoxF gene was present. Phylogenomic and 16S rRNA gene phylogenetic analyses clearly showed that strain 6HR-1T was affiliated to the genus Methylobacterium and closely related to ‘Methylobacterium terrae’ 17Sr1-28T (98.6 %), Methylobacterium platani JCM 14648T (97.7 %), Methylobacterium variabile DSM 16961T (97.7 %) and Methylobacterium currus KACC 19662T (97.4 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain 6HR-1T and its closely related type species were 87.4–88.7 and 33.2–36.3 %, respectively. It had summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) as the major fatty acid and ubiquinone 10 as the predominant respiratory quinone. Polyphasic characterization supported that strain 6HR-1T represents a novel species of the genus Methylobacterium , for which the name Methylobacterium nonmethylotrophicum sp. nov. is proposed with the type strain 6HR-1T (=GDMCC 1.662T=KCTC 42760T).

scholarly journals Ulvibacter marinus sp. nov., isolated from coastal seawater

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2041-2046 ◽  
Author(s):  
Kiwoon Baek ◽  
Hwanhui Jo ◽  
Ahyoung Choi ◽  
Ilnam Kang ◽  
Jang-Cheon Cho
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Coastal Seawater ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-stain-negative, aerobic, chemoheterotrophic, yellow, non-motile and flexirubin-positive bacterium, designated strain IMCC12008T, was isolated from coastal seawater of the Yellow Sea and subjected to polyphasic taxonomy. Optimal growth was observed at 25 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Based on 16S rRNA gene sequence analysis and subsequent phylogenetic analyses, strain IMCC12008T belonged to the genus Ulvibacter of the family Flavobacteriaceae , with Ulvibacter antarcticus IMCC3101T (96.0 %) and Ulvibacter litoralis KMM 3912T (95.8 %) having the highest sequence similaries. The major fatty acids were iso-C15 : 0 (26.2 %) and iso-C15 : 1 G (10.5 %). The DNA G+C content was 38.1 mol%. Strain IMCC12008T contained menaquinone-6 (MK-6) as the respiratory quinone, and polar lipids comprising phosphatidylethanolamine, two unidentified aminolipids and an unknown aminophospholipid. On the basis of data collected from this study, strain IMCC12008T ( = NBRC 109484T = KCTC 32322T) represents a novel species of the genus Ulvibacter , for which the name Ulvibacter marinus sp. nov. is proposed.

Burkholderia humi sp. nov., Burkholderia choica sp. nov., Burkholderia telluris sp. nov., Burkholderia terrestris sp. nov. and Burkholderia udeis sp. nov.: Burkholderia glathei-like bacteria from soil and rhizosphere soil

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4707-4718 ◽  
Author(s):  
Peter Vandamme ◽  
Evie De Brandt ◽  
Kurt Houf ◽  
Joana Falcão Salles ◽  
Jan Dirk van Elsas ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Rhizosphere Soil ◽  
Fatty Acid Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis

Analysis of partial gyrB gene sequences revealed six taxa in a group of 17 Burkholderia glathei -like isolates which were further examined by (GTG)5-PCR fingerprinting, 16S rRNA gene sequence analysis, DNA–DNA hybridizations, determination of the DNA G+C content, whole-cell fatty acid analysis and an analysis of cell and colony morphology and more than 180 biochemical characteristics. The results demonstrated that one taxon consisting of three human clinical isolates represented Burkholderia zhejiangensis , a recently described methyl-parathion-degrading bacterium isolated from a wastewater-treatment system in China. The remaining taxa represented five novel species isolated from soil or rhizosphere soil samples, and could be distinguished by both genotypic and phenotypic characteristics. We therefore propose to formally classify these bacteria as Burkholderia humi sp. nov. (type strain, LMG 22934T = CCUG 63059T), Burkholderia choica sp. nov. (type strain, LMG 22940T = CCUG 63063T), Burkholderia telluris sp. nov. (type strain, LMG 22936T = CCUG 63060T), Burkholderia udeis sp. nov. (type strain, LMG 27134T = CCUG 63061T) and Burkholderia terrestris sp. nov. (type strain, LMG 22937T = CCUG 63062T).

Luteolibacter yonseiensis sp. nov., isolated from activated sludge using algal metabolites

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1891-1895 ◽  
Author(s):  
Joonhong Park ◽  
Gyu Seok Baek ◽  
Sung-Geun Woo ◽  
Jangho Lee ◽  
Jihoon Yang ◽  
...  
Keyword(s):  
Activated Sludge ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-negative, rod-shaped, aerobic bacterial strain, designated EBTL01T, was isolated from activated sludge by using metabolites of microalgae Ankistrodesmus gracilis SAG278-2. Phylogenetic analyses based on 16S rRNA gene sequence showed that strain EBTL01T belongs to the family Verrucomicrobiaceae , class Verrucomicrobiae , and is related most closely to Luteolibacter pohnpeiensis A4T-83T (95.5 % sequence similarity) and Luteolibacter algae A5J-41-2T (95.2 %). The G+C content of the genomic DNA of strain EBTL01T was 56.3 mol% and the menaquinone MK-9 was detected as the predominant quinone. Major fatty acid components were iso-C14 : 0, C16 : 1ω7c and C16 : 0. The amino acids of the cell-wall peptidoglycan contained muramic acid and meso-diaminopimelic acid. These profile results supported the affiliation of strain EBTL01T to the genus Luteolibacter . On the other hand, based on chemotaxonomic properties and phenotypic characteristics, strain EBTL01T could be clearly differentiated from its phylogenetic neighbours. Therefore, strain EBTL01T represents a novel species of the genus Luteolibacter , for which the name Luteolibacter yonseiensis sp. nov. is proposed. The type strain is EBTL01T ( = KCTC 23678T = JCM 18052T).

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