scholarly journals Gimesia chilikensis sp. nov., a haloalkali-tolerant planctomycete isolated from Chilika lagoon and emended description of the genus Gimesia

2020 ◽  
Vol 70 (6) ◽  
pp. 3647-3655 ◽  
Author(s):  
Dhanesh Kumar ◽  
Kumar Gaurav ◽  
Sreya PK ◽  
Shabbir A. ◽  
Jagadeeshwari Uppada ◽  
...  

A Gram-stain-negative, aerobic, non-motile, salt- and alkali-tolerant, pear to oval shaped, rosette-forming, white coloured, bacterium, designated as strain JC646T, was isolated from a sediment sample collected from Chilika lagoon, India. Strain JC646T reproduced through budding, grew well at up to pH 9.0 and tolerated up to 7 % NaCl. Strain JC 646T utilized α-d-glucose, fumarate, lactose, sucrose, fructose, d-galactose, mannose, maltose and d-xylose as carbon sources. Peptone, l-isoleucine, l-serine, l-lysine, l-glutamic acid, l-aspartic acid, dl-threonine and l-glycine were used by the strain as nitrogen sources for growth. The respiratory quinone was MK6. Major fatty acids were C16 : 1 ω7c/C16 : 1 ω6c and C16 : 0. The polar lipids of strain JC646T comprised phosphatidyl-dimethylethanolamine, phosphatidylcholine, diphosphatidylglycerol, an unidentified amino lipid and two unidentified lipids. Strain JC646T had highest (97.3 %) 16S rRNA gene sequence identity to the only species of the genus Gimesia , Gimesia maris DSM 8797T. The genome of strain JC646T was 7.64 Mbp with a DNA G+C content of 53.2 mol%. For the resolution of the phylogenetic congruence of the novel strain, the phylogeny was also reconstructed with the sequences of 92 housekeeping genes. Based on phylogenetic analyses, digital DNA–DNA hybridization (19.0 %), genome average nucleotide identity (74.5 %) and average amino acid identity/percentageof conserved proteins (77 %) results, chemotaxonomic characteristics, and differential physiological properties, strain JC646T is recognized as representing a new species of the genus Gimesia , for which we propose the name Gimesia chilikensis sp. nov. The type strain is JC646T (=KCTC 72175T=NBRC 113881T).

Author(s):  
Minchung Kang ◽  
Geeta Chhetri ◽  
Jiyoun Kim ◽  
Inhyup Kim ◽  
Taegun Seo

A Gram-stain-negative, aerobic and non-motile bacterium, strain sand1-3T, was isolated from beach sand collected from Haeundae Beach located in Busan, Republic of Korea. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, Sphingomonas daechungensis CH15-11T (97.0 %), Sphingomonas edaphi DAC4T (96.8 %), Sphingomonas xanthus AE3T (96.5 %) and Sphingomonas oryziterrae YC6722T (96.0 %) were selected for comparing phenotypic and chemotaxonomic characteristics. Cells of strain sand1-3T grew at 7–50 °C (optimum, 30–35 °C), pH 5.0–8.0 (optimum, pH 7.0–8.0) and in the presence of 0–0.5 % (w/v) NaCl (optimum, 0 %). Major polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, one unidentified glycolipid and one unidentified phosphoglycolipid. The major fatty acids were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) and C18 : 1 2-OH. Moreover, the sole respiratory quinone and major polyamine were identified as ubiquinone-10 and homospermidine, respectively. The genomic DNA G+C content was 65.9 mol%. The digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values of strain sand1-3T and its reference strains with publicly available genomes were 17.9–18.9 %, 72.0–75.3 % and 63.3–76.5 % respectively. Based on polyphasic evidence, we propose Sphingomonas sabuli sp. nov. as a novel species within the genus Sphingomonas . The type strain is sand1-3T (=KCTC 82358T=NBRC 114538T).


2020 ◽  
Vol 70 (3) ◽  
pp. 1720-1728 ◽  
Author(s):  
Anusha Rai ◽  
Smita N ◽  
Suresh G ◽  
Shabbir A ◽  
Deepshikha G ◽  
...  

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).


2020 ◽  
Vol 70 (8) ◽  
pp. 4610-4615 ◽  
Author(s):  
Xiao-Yu Zhang ◽  
Rui Zhang ◽  
Jia-Cheng Wang ◽  
Ting Zhang ◽  
Zong-Jun Du

A novel Gram-stain-negative, strictly aerobic, gliding and rod-shaped bacterial strain, designated strain C33T, was isolated from Yuncheng Salt Lake, Shanxi, PR China. Strain C33T grows optimally at 37 °C, pH 7.5 and 5.0 % (w/v) NaCl. Cells of strain C33T are 0.3–0.5 µm wide and 1.0–2.0 µm long, catalase-positive and oxidase-positive. The major cellular fatty acids are iso-C15 : 0 and iso-C16 : 0. The sole respiratory quinone is Q-8. The major polar lipids include phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophospholipid, one unidentified glycolipid and four unidentified lipids. The results of phylogenetic analysis based on 16S rRNA gene sequences indicate that strain C33T has the highest similarities to Wenzhouxiangella marina KCTC 42284T (97.4 %), Wenzhouxiangella sediminis XDB06T (96.5 %) and ‘Wenzhouxiangella salilacus’ MCCC 1K03442T (95.2 %). The percentage of conserved proteins and average amino acid identity values between strain C33T and its close related species are higher than the threshold for dividing genera, the average nucleotide identity and digital DNA–DNA hybridization values are well below the threshold limits for species delineation. The genomic DNA G+C content is 63.7 mol%. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain C33T is considered to represent a novel species of the genus Wenzhouxiangella , for which the name Wenzhouxiangella limi sp. nov. is proposed. The type strain is C33T (=MCCC 1H00413T=KCTC 72874T).


2020 ◽  
Vol 70 (4) ◽  
pp. 2616-2623 ◽  
Author(s):  
Dhanesh Kumar ◽  
Kumar Gaurav ◽  
Jagadeeshwari U ◽  
Deepshikha G ◽  
Sasikala Ch. ◽  
...  

Strain JC651T was isolated from a sediment sample collected from Chilika lagoon, which is one of the world’s most important brackish water lakes with estuarine characteristics. Colonies of this strain are light pink and cells are Gram-stain negative, spherical to pear shaped and form rosettes. Strain JC651T grows well up to pH 9.0 and tolerates up to 5 % NaCl (w/v). The respiratory quinone is MK6. The detected major fatty acids are C18 : 1 ω9c and C16 : 0. Its polar lipids are diphosphatidylglycerol, an unidentified phospholipid, phosphatidylglycerol and phosphatidylcholine. Strain JC651T shows highest 16S rRNA gene sequence similarity (97.8%) to the type species of the genus Roseimaritima , Roseimaritima ulvae UC8T. The genome size of strain JC651T is 6.2 Mb with a G+C content of 62.4 mol%. For the resolution of the phylogenetic congruence of the novel strain, the phylogeny was also reconstructed with the sequences of 92 core genes. Based on the phylogenetic analyses, low digital DNA–DNA hybridization values (19.5%), low (74.9%) genome average nucleotide identity results, chemotaxonomic characteristics and differential physiological properties, strain JC651T is recognized as a new species of the genus Roseimaritima for which we propose the name Roseimaritima sediminicola sp. nov. The type strain is JC651T (=KCTC 72178T=NBRC 113926T).


2020 ◽  
Vol 70 (11) ◽  
pp. 5950-5957 ◽  
Author(s):  
Jia Zhou ◽  
Wen-Wen Ma ◽  
Jian-Hang Qu ◽  
Hai-Feng Li ◽  
Bang-Bang Yang ◽  
...  

A taxonomic identification using a polyphasic approach was performed on strain NBS58-1T, which was isolated from the interfacial sediment of Taihu Lake in China. Strain NBS58-1T was Gram-stain-negative, aerobic, non-spore-forming and catalase-positive. Phylogenetic analyses based on 16S rRNA gene and three housekeeping genes (rpoB, gyrB and dnaK) sequences supported the position that strain NBS58-1T should be classified within the genus Rufibacter . The 16S rRNA gene sequence of strain NBS58-1T possessed the highest similarity to Rufibacter sediminis H-1T (96.60 %), followed by Rufibacter glacialis MDT1-10-3T (96.17 %). And the ANI value between strain NBS58-1T and R. glacialis MDT1-10-3T was 79.3 %. The respiratory quinone was menaquinone 7 (MK-7). The major cellular fatty acids comprised iso-C15 : 0 and summed feature 3. Phosphatidylethanolamine, two unidentified phospholipids and four unidentified lipids were the main polar lipids. The genomic DNA G+C content was 51.3 mol%. Based on phenotypic features and phylogenetic position, a novel species with the name Rufibacter hautae sp. nov. is proposed. The type strain is NBS58-1T=(KACC 21309T=MCCC 1K04037T). We also proposed Rufibacter quisquiliarum as a latter heterotypic synonym of Rufibacter ruber .


2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 676-680 ◽  
Author(s):  
Ying-Yi Huo ◽  
Hong You ◽  
Zheng-Yang Li ◽  
Chun-Sheng Wang ◽  
Xue-Wei Xu

A Gram-stain-negative, aerobic, short rod-shaped bacterium, strain LA53T, was isolated from a deep-sea water sample collected from the eastern Pacific Ocean. Strain LA53T grew in the presence of 0–7.0 % (w/v) NaCl and at 15-37 °C; optimum growth was observed with 1.0–2.0 % (w/v) NaCl and at 35 °C. Chemotaxonomic analysis showed ubiquinone-10 as the predominant respiratory quinone, C18 : 1ω7c and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) as major fatty acids, and diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid as major polar lipids. The genomic DNA G+C content was 57.7 mol%. Phylogenetic analyses revealed that strain LA53T belongs to the genus Novosphingobium . 16S rRNA gene sequence similarities between strain LA53T and the type strains of species of the genus Novosphingobium with validly published names ranged from 93.1 to 96.3 %. In addition, strain LA53T could be differentiated from Novosphingobium pentaromativorans DSM 17173T and Novosphingobium indicum DSM 23608T as well as the type strain of the type species of the genus, Novosphingobium capsulatum DSM 30196T, by some phenotypic characteristics, including hydrolysis of substrates, utilization of carbon sources and susceptibility to antibiotics. On the basis of phenotypic and genotypic data, strain LA53T represents a novel species within the genus Novosphingobium , for which the name Novosphingobium marinum sp. nov. is proposed. The type strain is LA53T ( = CGMCC 1.12918T = JCM 30307T).


2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1766-1770 ◽  
Author(s):  
Joon Yong Kim ◽  
Jina Lee ◽  
Na-Ri Shin ◽  
Ji-Hyun Yun ◽  
Tae Woong Whon ◽  
...  

A novel Gram-stain-negative, facultatively anaerobic, non-motile and coccus-shaped bacterium, strain C7T, was isolated from the gut of the butterfly Sasakia charonda. Strain C7T grew optimally at 20–25 °C, at pH 7–8 and with 1 % (w/v) NaCl. The strain was negative for oxidase activity but positive for catalase activity. The 16S rRNA gene sequences of strain C7T and Orbus hercynius CN3T shared 96.8 % similarity. The major fatty acids identified were C14 : 0, C16 : 0, C18 : 1ω7c and summed feature 2 (comprising C14 : 0 3-OH/iso-C16 : 1). The major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids of strain C7T were phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid and two unidentified aminophospholipids. The G+C content of the genomic DNA extracted from strain C7T was 32.1 mol%. Taken together, the phenotypic, genotypic and phylogenetic analyses indicate that strain C7T represents a novel species of the genus Orbus , for which the name Orbus sasakiae sp. nov. is proposed. The type strain is C7T ( = KACC 16544T = JCM 18050T). An emended description of the genus Orbus is provided.


2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 122-127 ◽  
Author(s):  
Tong Yu ◽  
Zenghu Zhang ◽  
Xiaoyang Fan ◽  
Xiaochong Shi ◽  
Xiao-Hua Zhang

A novel Gram-stain-negative, rod-shaped, non-flagellated, strictly aerobic strain with gliding motility, designated XH134T, was isolated from surface seawater of the South Pacific Gyre (45° 58′ S 163° 11′ W) during the Integrated Ocean Drilling Program Expedition 329. The major respiratory quinone of strain XH134T was MK-6. The dominant fatty acids of strain XH134T were iso-C15 : 0, iso-C15 : 1 G, C16 : 1ω6c and/or C16 : 1ω7c, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and 10-methyl C16 : 0 and/or iso-C17 : 1ω9c. The polar lipids of strain XH134T comprised phosphatidylethanolamine, one unknown aminolipid and three unknown polar lipids. The DNA G+C content of strain XH134T was 32.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel strain was related most closely to Aquimarina macrocephali JAMB N27T with 96.9 % sequence similarity. A number of phenotypic characteristics distinguished strain XH134T from described members of the genus Aquimarina . On the basis of combined phenotypic and phylogenetic analyses, strain XH134T represents a novel species of the genus Aquimarina , for which the name Aquimarina megaterium sp. nov. is proposed. The type strain is XH134T ( = CGMCC 1.12186T = JCM 18215T).


Author(s):  
Shan Jiang ◽  
Feng-Bai Lian ◽  
You-Yang Sun ◽  
Xiao-Kui Zhang ◽  
Zong-Jun Du

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).


2020 ◽  
Vol 70 (11) ◽  
pp. 5943-5949 ◽  
Author(s):  
Yun-zhen Yang ◽  
Ji-feng Chen ◽  
Wan-ru Huang ◽  
Ran-ran Zhang ◽  
Shuangjiang Liu ◽  
...  

A novel Gram-stain-negative, strictly aerobic, rod-shaped, brick red-pigmented bacterium, designated R-22-1 c-1T, was isolated from water from Baiyang Lake, Hebei Province, PR China. The strain was able to grow at 20–30 °C (optimum, 30 °C) and pH 6–7 (optimum, pH 6) in Reasoner’s 2A medium. 16S rRNA gene sequence and phylogenetic analyses of R-22-1 c-1T revealed closest relationships to Rufibacter immobilis MCC P1T (97.8 %), Rufibacter sediminis H-1T (97.9 %) and Rufibacter glacialis MDT1-10-3T (97.0 %), with other species of the genus Rufibacter showing less than 97.0 % sequence similarity. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids and three unidentified lipids. The major cellular fatty acids were iso-C15 : 0, C15 : 1  ω6c, C17 : 1  ω6c, anteiso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 4 (iso-C17 : 1I and/or anteiso-C17 : 1B). The respiratory quinone was MK-7. The draft genome of R-22-1 c-1T was 5.6 Mbp in size, with a G+C content of 50.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization relatedness values between strain R-22-1 c-1T and related type strains were R. immobilis MCC P1T (77.2 and 21.8 %), R. sediminis H-1T (81.6 and 21.4 %) and R. tibetensis 1351T (78.5 and 22.9 %). Based on these phylogenetic, chemotaxonomic and genotypic results, strain R-22-1 c-1T represents a novel species in the genus Rufibacter , for which the name Rufibacter latericius sp. nov. is proposed. The type strain is R-22-1 c-1T (=CGMCC 1.13570T=KCTC 62781T).


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