Sphingomonas sabuli sp. nov., a carotenoid-producing bacterium isolated from beach sand

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Minchung Kang ◽  
Geeta Chhetri ◽  
Jiyoun Kim ◽  
Inhyup Kim ◽  
Taegun Seo
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Beach Sand ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Bacterium Strain

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).

scholarly journals Tabrizicola algicola sp. nov. isolated from culture of microalga Ettlia sp.

2020 ◽  
Vol 70 (12) ◽  
pp. 6133-6141 ◽  
Author(s):  
Chan-Yeong Park ◽  
Seong-Jun Chun ◽  
Chunzhi Jin ◽  
Ve Van Le ◽  
Yingshun Cui ◽  
...  
Keyword(s):  
Type Species ◽  
Optimal Growth ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Major Respiratory Quinone ◽  
Bacterium Strain

A novel Gram-stain-negative, aerobic, non-spore-forming, non-motile, and rod-shaped bacterium, strain ETT8T was isolated from a chemostat culture of microalga Ettlia sp. YC001. Optimal growth was with 0–2% NaCl and at 25–37 °C on R2A medium. Phylogenetic analysis based on the 16S rRNA gene and genome sequence showed that strain ETT8T belongs to the genus Tabrizicola , with the close neighbours being T. sediminis DRYC-M-16T (98.1 %), T. alkalilacus DJCT (97.6 %), T. fusiformis SY72T (96.9 %), T. piscis K13M18T (96.8 %), and T. aquatica RCRI19T (96.5 %). The genomic comparison of strain ETT8T with type species in the genus Tabrizicola was analysed using the genome-to-genome distance calculator (GGDC), average nucleotide identity (ANI), and average amino acid identity (AAI) (values indicated ≤17.7, ≤75.4 and ≤71.9 %, respectively). The genomic DNA G+C content of strain ETT8T was 64.4 %, plus C18 : 1  ω6c and C18 : 0-iso were the major fatty acids and Q-10 the major respiratory quinone. Strain ETT8T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine aminolipid, and four unidentified lipids as the major polar lipids. Based on the chemotaxonomic, genotypic, and phenotype results, strain ETT8T was recognized as a novel species of the genus Tabrizicola for which the name Tabrizicola algicola sp. nov. is proposed. The type strain is ETT8T (=KCTC 72206T=JCM 31893T=MCC 4339T).

scholarly journals Pontibacter mangrovi sp. nov., isolated from mangrove sediment

2020 ◽  
Vol 70 (7) ◽  
pp. 4245-4249 ◽  
Author(s):  
kun-lian Mo ◽  
Ling Wang ◽  
Qing-juan Wu ◽  
Lin Ye ◽  
Xing-di Liu ◽  
...  
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Polar Lipids ◽  
Mangrove Sediment ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity

A Gram-stain-negative, short-rod-shaped and pink-pigmented bacterial strain (HB172049T) was isolated from mangrove sediment. Cells grew at 10–45 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.0) and with 0.5–9.0 % (w/v) NaCl (optimum, 2–5 %). Analysis of the 16S rRNA gene sequence revealed that the isolate had highest sequence similarities to Pontibacter mucosus DSM 100162T (96.5 %) and Pontibacter korlensis X14-1T (96.5 %). The values of average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization between the isolate and its close neighbours were, respectively, less than 80.1, 81.7 and 23.2 %. Chemotaxonomic analysis indicated that the sole respiratory quinone was MK-7 and the predominant cellular fatty acids were summed feature 4 and iso-C15 : 0 (42.2 and 24.6 %, respectively). The major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid, one unidentified aminophospholipid and two unidentified polar lipids. The genomic DNA G+C content was 52.6 mol%. Based on polyphasic taxonomic characterization, it is proposed that strain HB172049T belongs to the genus Pontibacter and represents a novel species, for which the name Pontibacter mangrovi sp. nov. is proposed. The type strain is HB172049T (=CGMCC 1.16729T=JCM 33333T).

Tropicimonas sediminicola sp. nov., isolated from marine sediment

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2424-2429 ◽  
Author(s):  
Na-Ri Shin ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Bora Yun ◽  
Tae Woong Whon ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

A novel Gram-negative, obligately aerobic, non-motile, rod-shaped bacterium, strain M97T, was isolated from marine sediment of a cage-cultured ark clam farm on the south coast of Korea. Strain M97T was positive for oxidase and catalase. Optimal growth occurred at 37 °C, with 1–2 % (w/v) NaCl and at pH 7–8. The main cellular fatty acids were C16 : 0, C18 : 1ω7c, C12 : 0 3-OH and cyclo-C19 : 0ω8c. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unknown aminolipid and three unknown lipids. The predominant respiratory quinone was ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain M97T belongs to the genus Tropicimonas , with highest sequence similarity to Tropicimonas aquimaris DPG-21T (99.0 %). The DNA G+C content of strain M97T was 68.5 mol%. Mean DNA–DNA relatedness between strain M97T and T. aquimaris DPG-21T was 46±10 %. Based on phylogenetic, phenotypic and genotypic analyses, strain M97T is considered to represent a novel species of the genus Tropicimonas , for which the name Tropicimonas sediminicola sp. nov. is proposed. The type strain is M97T ( = KACC 15544T = JCM 17731T).

scholarly journals Wenzhouxiangella limi sp. nov., isolated from a salt lake

2020 ◽  
Vol 70 (8) ◽  
pp. 4610-4615 ◽  
Author(s):  
Xiao-Yu Zhang ◽  
Rui Zhang ◽  
Jia-Cheng Wang ◽  
Ting Zhang ◽  
Zong-Jun Du
Keyword(s):  
Type Species ◽  
Salt Lake ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Pr China

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).

scholarly journals Marinilabilia rubra sp. nov., isolated from a marine solar saltern

2019 ◽  
Vol 69 (4) ◽  
pp. 914-919 ◽  
Author(s):  
Rui Zhang ◽  
Shuo Wang ◽  
Chong Wang ◽  
Guang-Yu Wang ◽  
Zong-Jun Du
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Marine Solar Saltern ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity

A novel cherry-red-pigmented, Gram-stain-negative, gliding, facultatively anaerobic and rod-shaped bacterium, designated strain WTE16T, was isolated from a sediment sample taken from a marine solar saltern of Wendeng, China (36° 59′ 56.49′′ N 122° 1′ 38.84′′ E). The novel isolate was able to grow at 20–40 °C (optimum 33 °C), at pH 6.0–9.0 (optimum pH 7.0) and with 1.0–12.0 % (w/v) NaCl (optimum 3.0–5.0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the most closely related validly published species is Marinilabilia salmonicolor JCM 21150T (96.0 % similarity). Average nucleotide identity, average amino acid identity, percentage of conserved proteins and digital DNA–DNA hybridization values between strain WTE16T and Marinilabilia salmonicolor JCM 21150T were 73.8 %, 73.5 %, 63.4 % and 19.5–24.2 %, respectively. The genomic DNA G+C content of strain WTE16T was 40.8 mol%. Chemotaxonomic analysis showed that the sole respiratory quinone was menaquinone 7 (MK-7), and the major fatty acids included iso-C15 : 0 and anteiso-C15 : 0. The polar lipid profile of strain WTE16T included phosphatidylethanolamine, three unidentified phospholipids and three unidentified lipids. On the basis of its phylogenetic, phenotypic, chemotaxonomic, genotypic and genomic characteristics, strain WTE16T is suggested to represent a novel species of the genus Marinilabilia , for which the name Marinilabilia rubra sp. nov. is proposed. The type strain is WTE16T (=KCTC 62599T=MCCC 1H00311T).

Roseococcus microcysteis sp. nov., isolated from a Microcystis aeruginosa culture sample

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Wonjae Kim ◽  
Minkyung Kim ◽  
Woojun Park
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Genomic Comparison ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Major Respiratory Quinone ◽  
Obligate Aerobic

Strain NIBR12T (=KACC 22094T=HAMBI 3739T), a novel Gram-stain-negative, obligate aerobic, non-spore-forming, non-motile and coccobacillus-shaped bacterium, was isolated from a cyanobacterial sample culture (Microcysitis aeruginosa NIBRCYC000000452). The newly identified bacterial strain grew optimally in modified Reasoner's 2A medium under the following conditions: 0 % (w/v) NaCl, pH 7.5 and 35 °C. Phylogenetic analysis using the 16S rRNA gene sequence confirmed that strain NIBR12T belongs to the genus Roseococcus , with its closest neighbours being Roseococcus suduntuyensis SHETT (98.8%), Roseococcus thiosulfatophilus RB-3T (97.7%), “Sediminicoccus rosea” R-30T (95.7 %) and Rubritepida flocculans H-8T (95.0 %). Genomic comparison of strain NIBR12T with type species in the genus Roseococcus was conducted using digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity analyses, resulting in values of ≤53.7, ≤93.7 and ≤96.1 %, respectively. The genomic DNA G+C content of strain NIBR12T was 70.9 mol%. The major fatty acids of strain NIBR12T were summed feature 8 (C18 : 1  ω7c and/or C18:1 ω6c) and summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c). Q-9 was its major respiratory quinone. Moreover, the major polar lipids of strain NIBR12T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Based on our chemotaxonomic, genotypic and phenotype analyses, strain NIBR12T is identified as represeting a novel species of the genus Roseococcus , for which the name Roseococcus microcysteis sp. nov. is proposed.

scholarly journals Novosphingobium marinum sp. nov., isolated from seawater

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 676-680 ◽  
Author(s):  
Ying-Yi Huo ◽  
Hong You ◽  
Zheng-Yang Li ◽  
Chun-Sheng Wang ◽  
Xue-Wei Xu
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sea Water ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

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).

Orbus sasakiae sp. nov., a bacterium isolated from the gut of the butterfly Sasakia charonda, and emended description of the genus Orbus

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1766-1770 ◽  
Author(s):  
Joon Yong Kim ◽  
Jina Lee ◽  
Na-Ri Shin ◽  
Ji-Hyun Yun ◽  
Tae Woong Whon ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Major Respiratory Quinone ◽  
Bacterium Strain ◽  
Sasakia Charonda

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.

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).

Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Silvio Hering ◽  
Moritz K. Jansson ◽  
Michael E. J. Buhl
Keyword(s):  
Type Species ◽  
Throat Swab ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Routine Care ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

A novel species within the genus Eikenella is described, based on the phenotypical, biochemical and genetic characterization of a strain of a facultatively anaerobic, Gram-negative rod-shaped bacterium. Strain S3360T was isolated from the throat swab of a patient sampled during routine care at a hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequences) placed the strain in the genus Eikenella , separate from all recognized species but with the closest relationship to Eikenella longinqua (NML 02-A-017T). Eikenella is one of the genera in the HACEK group known to be responsible for rare cases of endocarditis in humans. Until the recent descriptions of Eikenella exigua , Eikenella halliae and Eikenella longinqua , Eikenella corrodens had been the only validly published species in this genus since its description as Bacteroides corrodens in 1958. Unlike these species, strain S3360T is able to metabolize carbohydrates (glucose). The average nucleotide identities of strain S3360T with E. longinqua (NML 02-A-017T) and E. corrodens (NCTC 10596T), the type species of the genus, were 90.5 and 84.7 %, respectively, and the corresponding genome-to-genome distance values were 41.3 and 29.0 %, respectively. The DNA G+C content of strain S3360T was 58.4 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3360T is considered to represent a novel species within the genus Eikenella , for which the name Eikenella glucosivorans sp. nov. is proposed. The type strain is S3360T (DSM 110714T=CCOS 1935T=CCUG 74293T). In addition, an emendation of the genus Eikenella is proposed to include species which are saccharolytic.

Sign in / Sign up

Export Citation Format

Share Document