Pseudooceanicola endophyticus sp. nov., a novel endophytic bacterium isolated from bark Aegiceras corniculatum

Author(s):  
Zhou-Qing Zheng ◽  
Ming-Sheng Chen ◽  
Xiao-Rui Yan ◽  
Li Tuo

A Gram-stain-negative, aerobic, short-rod-shaped bacterium, designated strain CBS1P-1T, was isolated from a surface-sterilized bark of Aegiceras corniculatum. Growth of strain CBS1P-1T was observed with between 0 and 12.0 % (w/v) NaCl (optimally with 5.0 %) and at between pH 6.0–9.0. It grew at temperatures between 25–37 °C (optimum, 30 °C). Chemotaxonomic analysis showed that ubiquinone-10 was the respiratory quinone. The lipids comprised diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, an unidentified phospholipid and an unidentified aminolipid. The major fatty acids of strain CBS1P-1T were C18 : 1  ω7c, C16 : 0 and C19 : 0 cyclo ω8c. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CBS1P-1T was most related to Pseudooceanicola antarcticus CGMCC 1.12662T with a sequence similarity of 96.5 %. The average nucleotide identity and digital DNA–DNA hybridization values between strain CBS1P-1T and P. antarcticus 1.12662T were 77.5 and 21.1 %, respectively. The G+C content of the genomic DNA was 67.3 mol%. Based on phylogenetic, chemotaxonomic and phenotypic data, strain CBS1P-1T is considered to represent a novel species of the genus Pseudooceanicola , for which the name Pseudooceanicola endophyticus is proposed. The type strain is CBS1P-1T (=KCTC 62836T=CGMCC 1.13743T).

Author(s):  
Renju Liu ◽  
Qiliang Lai ◽  
Li Gu ◽  
Peisheng Yan ◽  
Zongze Shao

A novel Gram-stain-negative, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9T, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1–8 %, at pH 6.5–8 and at temperatures of 10–40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9T formed a monophyletic branch affiliated to the family Schleiferiaceae , and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with Owenweeksia hongkongensis DSM 17368T, followed by similarities of 90.4, 90.1 and 88.8 % with Phaeocystidibacter luteus MCCC 1F01079T, Vicingus serpentipes DSM 103558T and Salibacter halophilus MCCC 1K02288T, respectively. Its complete genome size was 4 035 598 bp, the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9T and O. hongkongensis DSM 17368T shared 67.8 % average nucleotide identity, 62.7 % average amino acid identity value, 46.6% of conserved proteins and 17.8 % digital DNA–DNA hybridization identity. A20-9T contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C15 : 0 (37.5 %), iso-C16 : 0 3-OH (12.4 %), and summed feature 3 (C16 : 1ω7c /C16 : 1ω6c, 11.6 %). Combining the genotypic and phenotypic data, A20-9T could be distinguished from the members of other genera within the family Schleiferiaceae and represents a novel genus, for which the name Croceimicrobium hydrocarbonivorans gen. nov., sp. nov. is proposed. The type strain is A20-9T (=MCCC 1A17358T =KCTC 72878T).


Author(s):  
Si Chen ◽  
Mengyuan He ◽  
Qiliang Lai ◽  
Ying Xu ◽  
Chenjing Shang

A taxonomic study was carried out on strain SHC163T, which was isolated from the gut of Onchidium reevesii. The bacterium was Gram-stain-negative, oxidase-positive, catalase-negative and rod-shaped. Growth was observed at salinities of 0–4.0 % NaCl and at temperatures of 15–35 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SHC163T belonged to the genus Jannaschia , with the highest sequence similarity to Jannaschia seosinensis CL-SP26T (97.9%), followed by Jannaschia faecimaris DSM 100420T (97.8 %), Jannaschia rubra CECT 5088T (97.5%) and eight species of the genus Jannaschia (94.7−97.1 %). The average amino acid identity, average nucleotide identity and the digital DNA–DNA hybridization estimate values between strain SHC163T and the type strains of the genus Jannaschia were 64.33−79.78 %, 71.0−78.4 % and 19.2−21.0%, respectively. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c, 56.5 %), C18 : 1  ω7c 11-methyl (23.1 %), C18 : 0 (8.7 %). The G+C content of the chromosomal DNA was 67.8 mol%. The respiratory quinone was determined to be Q-10 (100 %). The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and aminophospholipid. The combined genotypic and phenotypic data show that strain SHC163T represents a novel species within the genus Jannaschia , for which the name Jannaschia marina sp. nov. is proposed, with the type strain SHC163T (=MCCC 1K04032T=KCTC 72524T).


2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1810-1816 ◽  
Author(s):  
Wen-Ming Chen ◽  
Hsing-Wei Huang ◽  
Jo-Shu Chang ◽  
Yin-Lung Han ◽  
Tai-Rong Guo ◽  
...  

A slightly thermophilic bacterial strain, designated AT-A2T, was isolated from a hot spring water sample taken from the Antun hot spring in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain AT-A2T were aerobic, Gram-negative, motile by a single polar flagellum and formed non-pigmented colonies. Growth occurred at 35–60 °C (optimum, 55 °C), with 0–1.0 % NaCl (optimum, 0.2 %) and at pH 7.0–9.0 (optimum, pH 7.0). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain AT-A2T belonged to the genus Tepidimonas and its closest neighbour was Tepidimonas thermarum AA-1T with a sequence similarity of 97.5 %. The predominant cellular fatty acids were C16 : 0 (40.2 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 20.1 %) and C17 : 0 cyclo (11.5 %). The major respiratory quinone was Q-8. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminolipid and several uncharacterized phospholipids. The DNA G+C content of strain AT-A2T was 70.1 mol%. The mean level of DNA–DNA relatedness between strain AT-A2T and Tepidimonas thermarum AA-1T was 23.9 %. On the basis of the phylogenetic and phenotypic data, strain AT-A2T should be classified as representing a novel species, for which the name Tepidimonas fonticaldi sp. nov. is proposed. The type strain is AT-A2T ( = LMG 26746T = KCTC 23862T = BCRC 80391T).


2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3043-3049 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Jhen-Ci Chen ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen

A bacterial strain designated Npb-07T was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomic approach. Strain Npb-07T was Gram-negative, aerobic, rod-shaped and motile by means of a single polar flagellum. Growth occurred at 10–37 °C (optimum, 20–30 °C), at pH 6.0–9.0 (optimum, pH 6.0–7.0) and with 0–1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-07T belonged to the genus Vogesella and its most closely related neighbour was Vogesella indigofera ATCC 19706T with sequence similarity of 98.4 %. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 44.4 %) and C16 : 0 (31.9 %). The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 65.3 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two uncharacterized aminophospholipids and an uncharacterized phospholipid. The DNA–DNA relatedness of strain Npb-07T with respect to V. indigofera ATCC 19706T was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Npb-07T represents a novel species in the genus Vogesella , for which the name Vogesella fluminis sp. nov. is proposed. The type strain is Npb-07T ( = LMG 26669T = BCRC 80377T = KCTC 23713T).


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).


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

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).


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).


2020 ◽  
Vol 70 (3) ◽  
pp. 2132-2136 ◽  
Author(s):  
Hyo-Jin Lee ◽  
Kyung-Sook Whang

A Gram-stain-negative bacterium, designated strain PF-30T, was isolated from floodwater of a paddy field in South Korea. Strain PF-30T was found to be a strictly aerobic, motile and pink-pigmented rods which can grow at 25–40 °C (optimum, 28 °C), at pH 5.0–9.0 (optimum pH 7.0) and at salinities of 0.5–3.0 % NaCl (optimum 0.5 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain PF-30T belongs to the genus Elioraea , showing highest sequence similarity to Elioraea tepidiphila TU-7T (97.1%) and less than 91.3 % similarity with other members of the family Acetobacteraceae . The average nucleotide identity (ANI) and DNA–DNA relatedness between the strain PF-30T and E. tepidiphila TU-7T yielded an ANI value of 75.1 % and DNA–DNA relatedness of 11.7±0.7 %, respectively. The major fatty acids were identified as C18 : 0 and C18 : 1 ω7c. The predominant respiratory quinone was identified as Q-10. The DNA G+C content was determined to be 69.9 mol%. The strain PF-30T was observed to produce plant-growth-promoting materials such as indole-3-acetic acid (IAA), siderophore and phytase. On the basis of the results from phylogenetic, chemotaxonomic and phenotypic data, we concluded that strain PF-30T represents a novel species of the genus Elioraea , for which the name Elioraea rosea sp. nov. is proposed. The type strain is PF-30T (=KACC 19985T=NBRC 113984T).


Author(s):  
Xiao-Xian Huang ◽  
Jia Shang ◽  
Lian Xu ◽  
Rui Yang ◽  
Ji-Quan Sun

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, named SJ-16T, was isolated from desert soil collected in Inner Mongolia, northern PR China. Strain SJ-16T grew at pH 6.0–11.0 (optimum, pH 8.0–9.0), 4–40 °C (optimum, 30–35 °C) and in the presence of 0–8 % (w/v) NaCl (optimum, 0–2 %). The strain was negative for catalase and positive for oxidase. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SJ-16T clustered with Luteimonas chenhongjianii 100111T and Luteimonas terrae THG-MD21T, and had 98.8, 98.6, 98.3 and <97.9 % of 16S rRNA gene sequence similarity to strains L. chenhongjianii 100111T, L. terrae THG-MD21T, L. aestuarii B9T and all other type strains of the genus Luteimonas , respectively. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1  ω9c). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids, and ubiquinone-8 was the only respiratory quinone. The genomic DNA G+C content was 69.3 mol%. The digital DNA–DNA hybridization and average nucleotide identity values of strain SJ-16T to L. chenhongjianii 100111T, L. terrae THG-MD21T, L. rhizosphaerae 4-12T and L. aestuarii B9T were 36.9, 37.5, 24.0 and 21.1 %, and 80.9, 80.6, 80.7 and 76.3 %, respectively. Based on phenotypic, physiological and phylogenetic results, strain SJ-16T represents a novel species of the genus Luteimonas , for which the name Luteimonas deserti is proposed. The type strain is SJ-16T (=CGMCC 1.17694T=KCTC 82207T).


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