Halomonas diversa sp. nov., isolated from deep-sea sediment of the Pacific Ocean

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Liping Wang ◽  
Xiupian Liu ◽  
Qiliang Lai ◽  
Li Gu ◽  
Zongze Shao
Keyword(s):  
Pacific Ocean ◽  
16S Rrna ◽  
Deep Sea ◽  
Type Species ◽  
Sequence Similarity ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type ◽  
The Pacific ◽  
The Pacific Ocean

A novel Gram-stain-negative, facultatively anaerobic, rod-shaped bacterium, designated as D167-6-1T, was isolated from deep-sea sediment collected from the Pacific Ocean. The cells were catalase- and oxidase-positive, and motile by means of peritrichous flagella. Growth occurred at NaCl concentrations ranging from 0 to 19 % (optimum, 2–8 %, w/v), from pH 6 to 11 (optimum, 7–8) and at temperatures between 4 and 45 °C (optimum, 33 °C). Phylogenetic analysis based on 16S rRNA, gyrB and rpoD gene sequences and its genome sequence revealed that strain D167-6-1T formed a monophyletic branch within the genus Halomonas and was most closely related to Halomonas saliphila , Halomonas pellis , Halomonas kenyensis , Halomonas daqingensis , Halomonas desiderata and Halomonas lactosivorans (with 98.5, 98.5, 98.4, 98.1, 97.5 and 97.8 % 16S rRNA sequence similarity, respectively). The complete genome size of strain D167-6-1T was 4.49 Mb, with a DNA G+C content of 62.8 mol%. The estimated averagenucleotide identity and DNA–DNA hybridization values between strain D167-6-1T and other closely related species were 77.59–85.35 % and 22.0–30.6 %, respectively. The principal cellular fatty acids (>5 %) were C18 : 1  ω7c, C16 : 0, C19 : 0 cyclo ω8c, summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c) and C17 : 0 cyclo. The polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, aminophospholipid and two unidentified phospholipids. The predominant respiratory quinones were Q-9 and Q-8. The combined genotypic and phenotypic data show that strain D167-6-1T represents a novel species of the genus Halomonas , for which the name Halomonas diversa sp. nov. is proposed, with the type strain D167-6-1T (=MCCC 1A13316T=KCTC 72441T).

scholarly journals Pseudooceanicola pacificus sp. nov., isolated from deep-sea sediment of the Pacific Ocean

2020 ◽  
Vol 70 (7) ◽  
pp. 4372-4377 ◽  
Author(s):  
Lina Lyu ◽  
Qiliang Lai ◽  
Jianyang Li ◽  
Zongze Shao ◽  
Zhiqiang Yu
Keyword(s):  
Pacific Ocean ◽  
Deep Sea ◽  
Type Species ◽  
Aerobic Bacterium ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type ◽  
The Pacific ◽  
The Pacific Ocean ◽  
Gene Similarity

A Gram-strain-negative, rod-shaped, aerobic bacterium, designated 216_PA32_1T, was isolated from deep-sea sediment of the Pacific Ocean. Cells of strain 216_PA32_1T were non-motile, oxidase-positive and catalase-negative. The strain could grow at temperatures of 10–45 °C (optimum, 32–35 °C), at pH 5.0–10.0 (optimum, 6.0–7.0) and at salinities of 0–10% (optimum, 2–8%). The principal fatty acid (>10 %) was summed feature 8 (C18:1 ω6c/ω7c). The sole respiratory quinone was Q10 (100 %). The polar lipids included phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, two unidentified phospholipids and five unidentified aminolipids. The G+C content of the chromosomal DNA was 66.3 mol%. According to the 16S rRNA gene similarity, strain 216_PA32_1T showed the highest sequence similarity to Pseudooceanicola nitratireducens JLT 1210T (97.3 %), followed by Pseudooceanicola nanhaiensis SS011B1-20T (97.1 %). Phylogenetic trees indicated that strain 216_PA32_1T clustered with strain P. nanhaiensis SS011B1-20T. The average nucleotide identity and the DNA–DNA hybridization values between strain 216_PA32_1T and all species of the genus Pseudooceanicola were below 79.5 and 20.6%, respectively. A combination of the phylogenetic, phenotypic, chemotaxonomic and genomic evidence demonstrated that strain 216_PA32_1T represents a novel species of the genus Pseudooceanicola , for which the name Pseudooceanicola pacificus sp. nov. is proposed. The type strain is 216_PA32_1T (=MCCC 1A14128T=KCTC 72688T).

scholarly journals Solimonas marina sp. nov., isolated from deep seawater of the Pacific Ocean

2021 ◽  
Vol 71 (1) ◽  
Author(s):  
Xiupian Liu ◽  
Qiliang Lai ◽  
Fengqin Sun ◽  
Yaping Du ◽  
Yingbao Gai ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Deep Seawater ◽  
Content Type ◽  
Link Type ◽  
The Pacific ◽  
The Pacific Ocean

A taxonomic study was carried out on strain C16B3T, which was isolated from deep seawater of the Pacific Ocean. The bacterium was Gram-stain-negative, oxidase- and catalase- positive and rod-shaped. Growth was observed at salinities of 0–8.0 % and at temperatures of 10–45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C16B3T belonged to the genus Solimonas , with the highest sequence similarity to Solimonas terrae KIS83-12T (97.2 %), followed by Solimonas variicoloris MN28T (97.0 %) and the other four species of the genus Solimonas (94.5 –96.8 %). The average nucleotide identity and estimated DNA–DNA hybridization values between strain C16B3T and the type strains of the genus Solimonas were 74.05−79.48 % and 19.5–22.5 %, respectively. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c; 20.9 %), iso-C16 : 0 (14.6 %), C16 : 1  ω5c (9.4 %), iso-C12 : 0 (8.4 %), summed feature 2 (C14 : 0 3-OH/iso I-C16 : 1 and C12 : 0 aldehyde; 6.8 %) and C16 : 0 (5.5 %). The G+C content of the chromosomal DNA was 65.37 mol%. The respiratory quinone was determined to be Q-8 (100 %). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified aminolipids, six unidentified phospholipids and one unidentified polar lipid. The combined genotypic and phenotypic data show that strain C16B3T represents a novel species within the genus Solimonas , for which the name Solimonas marina sp. nov. is proposed, with the type strain C16B3T (=MCCC 1A04678T=KCTC 52314T).

Luteimonas abyssi sp. nov., isolated from deep-sea sediment

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 668-674 ◽  
Author(s):  
Xiaoyang Fan ◽  
Tong Yu ◽  
Zhao Li ◽  
Xiao-Hua Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type

Three Gram-stain-negative, strictly aerobic, rod-shaped with single polar flagellum, yellow-pigmented bacteria, designated strains XH031T, XH038-3 and XH80-1, were isolated from deep-sea sediment of the South Pacific Gyre (41° 51′ S 153° 6′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates belonged to the genus Luteimonas and showed the highest 16S rRNA gene sequence similarity with Luteimonas aestuarii B9T (96.95 %), Luteimonas huabeiensis HB2T (96.93 %) and Xanthomonas cucurbitae LMG 690T (96.92 %). The DNA G+C contents of the three isolates were 70.2–73.9 mol%. The major fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C11 : 0 and C16 : 010-methyl and/or iso-C17 : 1ω9c. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unknown phospholipid. On the basis of data from polyphasic analysis, the three isolates represent a novel species of the genus Luteimonas , for which the name Luteimonas abyssi sp. nov. is proposed. The type strain is XH031T ( = DSM 25880T = CGMCC 1.12611T).

scholarly journals Oceanobacillus pacificus sp. nov., isolated from a deep-sea sediment

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1278-1283 ◽  
Author(s):  
Cong Yu ◽  
Shaolan Yu ◽  
Zenghu Zhang ◽  
Zhao Li ◽  
Xiao-Hua Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Deep Sea ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type

A moderately halophilic bacterial strain, designated XH204T, was isolated from deep-sea sediment core (45° 58′ S 163° 11′ W) of the South Pacific Gyre during the Integrated Ocean Drilling Program Expedition 329. The strain was Gram-stain-positive, rod-shaped, motile by peritrichous flagella and produced ellipsoidal endospores subterminally positioned within swollen sporangia. Growth of strain XH204T occurred at 15–42 °C (optimum 37 °C), in the presence of 0–14 % (w/v) NaCl (optimum 4 %) and at pH 7.0–10.0 (optimum pH 8.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH204T belonged to the genus Oceanobacillus and showed the highest sequence similarity to Oceanobacillus profundus CL-MP28T (95.6 %); strain XH204T exhibited 93.4 % 16S rRNA gene sequence similarity to the type strain of the type species of the genus Oceanobacillus , Oceanobacillus iheyensis HTE831T. The dominant fatty acids of strain XH204T were anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The cell wall of strain XH204T contained meso-diaminopimelic acid as the diagnostic diamino acid, and ribose, glucose and galactose as the major whole-cell sugars. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. Menaquinone-7 (MK-7) was the only isoprenoid quinone and the DNA G+C content was 38.8 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic analysis, strain XH204T represents a novel species of the genus Oceanobacillus , for which the name Oceanobacillus pacificus sp. nov. is proposed. The type strain is XH204T ( = DSM 25873T = JCM 18381T).

scholarly journals Alcanivorax sediminis sp. nov., isolated from deep-sea sediment of the Pacific Ocean

2020 ◽  
Vol 70 (7) ◽  
pp. 4280-4284 ◽  
Author(s):  
Xianzhi Liao ◽  
Qiliang Lai ◽  
Junpeng Yang ◽  
Chunming Dong ◽  
Dengfeng Li ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Deep Sea ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type

A taxonomic study was carried out on strain PA15-N-34T, which was isolated from deep-sea sediment of Pacific Ocean. The bacterium was Gram-stain-positive, oxidase- and catalase-positive and rod-shaped. Growth was observed at salinity of 0–15.0% NaCl and at temperatures of 10–45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PA15-N-34T belonged to the genus Alcanivorax , with the highest sequence similarity to Alcanivorax profundi MTEO17T (97.7 %), followed by Alcanivorax nanhaiticus 19 m-6T (97.3 %) and 12 other species of the genus Alcanivorax (93.4 %–97.0 %). The average nucleotide identity and DNA–DNA hybridization values between strain PA15-N-34T and type strains of the genus Alcanivorax were 71.46–81.78% and 18.7–25.2 %, respectively. The principal fatty acids (>10 %) were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c; 31.2 %), C16 : 0 (25.0 %) and summed feature 3 (14.6 %). The DNA G+C content was 57.15 mol%. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, four unidentified aminolipids and three unidentified lipids. The novel strain can be differentiated from its closest type strain by a negative test for urease and the presence of diphosphatidylglycerol and aminolipid. The combined genotypic and phenotypic data show that strain PA15-N-34T represents a novel species within the genus Alcanivorax , for which the name Alcanivorax sediminis sp. nov. is proposed, with the type strain PA15-N-34T (=MCCC 1A14738T=KCTC 72163T).

scholarly journals Algibacter pacificus sp. nov., isolated from a deep-sea seamount

2020 ◽  
Vol 70 (4) ◽  
pp. 2907-2911 ◽  
Author(s):  
Jie Liu ◽  
Sheng-Dong Cai ◽  
Yu-Jing Wang ◽  
Qian Wang ◽  
De-Chao Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
The Pacific ◽  
The Pacific Ocean

The Gram-stain-negative, rod-shaped, yellow-pigmented and facultative anaerobic bacterial strain, designated H164T, was isolated from seawater collected from the Caroline Seamounts in the Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H164T was related to the genus Algibacter and had highest 16S rRNA gene sequence similarity to Algibacter wandonensis WS-MY22T (97.4 %). The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. The predominant menaquinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The genomic DNA G+C content of strain H164T was 33.2 mol%. The values of in silico DNA–DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain H164T and A. wandonensis KCTC 32381T were 26.10 and 81.88 %. The isDDH and ANI values between strain H164T and Algibacter lectus DSM 15365T were 25.40 and 81.79 %. Combined data from phenotypic, phylogenetic, isDDH and ANI analyses demonstrated that strain H164T represents a novel species of the genus Algibacter , for which we propose the name Algibacter pacificus sp. nov. (type strain H164T=KCTC 72432T=CGMCC 1.17117T).

Description of Novosphingopyxis iocasae sp. nov., isolated from deep sea sediment from the Mariana Trench, and emended description of the genus Novosphingopyxis

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Hai-zhen Zhou ◽  
Jian Zhang ◽  
Qing-lei Sun
Keyword(s):  
Deep Sea ◽  
Type Species ◽  
Sequence Similarity ◽  
Metal Resistance ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Mariana Trench ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type

In this study, we reported a Gram-stain-negative, orange-coloured, rod-shaped, motile and faculatively anaerobic bacterium named strain PB63T, which was isolated from the deep-sea sediment from the Mariana Trench. Growth of PB63T occurred at 10–35 °C (optimum, 28 °C), pH 5.0–8.0 (optimum, 5.0–6.0) and with 0–7 % (w/v) NaCl (optimum, 2–3 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PB63T represented a member of the genus Novosphingopyxis and was closely related to Novosphingopyxis baekryungensis DSM 16222T (97.9 % sequence similarity). PB63T showed tolerance to a variety of heavy metals, including Co2+, Zn2+, Mn2+ and Cu2+. The complete genome of PB63T was obtained, and many genes involved in heavy metal resistance were found. The genomic DNA G+C content of PB63T was 62.8 mol%. The predominant respiratory quinone of PB63T was ubiquinone-10 (Q-10). The polar lipids of PB63T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, glycolipid, phosphatidylcholines and three unidentified lipids. The major fatty acids of PB63T included summed feature 8 (C18 : 1ω7c or/and C18 : 1ω6c), C14 : 0 2-OH, 11-methyl C18 : 1ω7c, C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C17 : 1ω6c. The results of phylogenetic, physiological, biochemical and morphological analyses indicated that strain PB63T represents a novel species of the genus Novosphingopyxis , and the name Novosphingopyxis iocasae sp. nov. is proposed with the type species PB63T (=CCTCC AB 2019195T=JCM 34178T).

scholarly journals Acuticoccus sediminis sp. nov., isolated from deep-sea sediment of the Indian Ocean and proposal of Acuticoccaceae fam. nov

2019 ◽  
Vol 69 (4) ◽  
pp. 1173-1178 ◽  
Author(s):  
Qiliang Lai ◽  
Xiupian Liu ◽  
Fenqing Sun ◽  
Zongze Shao
Keyword(s):  
Indian Ocean ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type ◽  
The Indian Ocean

A Gram-staining negative, aerobic, oval-shaped bacterium, designated strain PTG4-2T, was isolated from deep-sea sediment of the Indian Ocean. Growth was observed with 1–9 % (w/v) NaCl with optimal growth with 3 %, at pH 6.0–10.0 with an optimum of pH 7.0, and at 4–40 °C with an optimum of 30 °C. Positive for catalase and oxidase. The results of a 16S rRNA gene sequence comparison indicated that PTG4-2T was most closely related to Acuticoccus yangtzensis JL1095T (97.3 %), followed by Acuticoccus kandeliae J103T (96.5 %), all other species shared <93 % sequence similarity. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PTG4-2T forms a distinct lineage within the genus Acuticoccus , and revealed that the genus Acuticoccus forms a novel family-level clade in the order Rhizobiales . The ANI and the DNA–DNA hybridization estimate values between PTG4-2T and two type strains (A. yangtzensis JL1095T and A. kandeliae J103T) were 79.9–76.2 % and 23.1–20.8 %, respectively. PTG4-2T contained Q-10 as the predominant ubiquinone. The principal fatty acids (>5 %) were summed feature 8 [C18 : 1 ω7c/ω6c (72.2 %)], C18 : 0 (8.4 %), C20 : 1 ω7c (6.4 %) and C16 : 0 (6.3 %). The polar lipids consisted of phosphatidylglycerol, three unidentified phospholipids, two unidentified glycolipids, one unidentified aminolipid and one unknown lipid. The DNA G+C content of PTG4-2T is 69.2 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, PTG4-2T should be classified as representing a novel species of the genus Acuticoccus , for which the name Acuticoccus sediminis sp. nov. is proposed, with the type strain PTG4-2T (=MCCC 1A01274T=KCTC 52323T). In addition, a novel family, Acuticoccaceae fam. nov., is proposed to accommodate the genus Acuticoccus .

Pontivivens ytuae sp. nov., isolated from deep sea sediment of the Mariana Trench

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Zhen Wang ◽  
Rong-bin Du ◽  
Qing-lei Sun ◽  
Yuan-yuan Sun ◽  
Jian Zhang ◽  
...  
Keyword(s):  
Deep Sea ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Circular Chromosome ◽  
Mariana Trench ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type

A Gram-stain-negative, light pink-coloured, rod-shaped, flagellated and facultative anaerobic bacterial strain, designated MT2928T, was isolated from deep-sea sediment collected from the Mariana Trench. Growth of strain MT2928T occurred optimally at 28 °C, pH 8.0–9.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MT2928T belongs to the genus Pontivivens and has the highest sequence similarity to Pontivivens insulae GYSW-23T (96.6 %). Genomic analysis indicated that strain MT2928T contains a circular chromosome of 4 199 362 bp with G+C content of 67.2 mol%. The strain did not produce bacteriochlorophyll a, but produced carotenoid. The predominant respiratory quinone of MT2928T was ubiquinone-10. The polar lipids of MT2928T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified lipids and two unidentified phospholipids. The major fatty acids of strain MT2928T contained summed feature 8 (C18 : 1  ω7c or/and C18 : 1  ω6c), C18 : 0 and summed feature 2 (iso-C16 : 1 I and/or C14 : 0 3-OH). On the basis of phylogenetic, physiological, biochemical and other phenotypic properties, strain MT2928T represents a novel species of the genus Pontivivens , and the name Pontivivens ytuae sp. nov. is proposed with the type species MT2928T (=MCCC 1K05575T=JCM 34320T).

Aurantimonas marina sp. nov., isolated from deep-sea sediment

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Lei Song ◽  
Hongcan Liu ◽  
Qinglei Sun ◽  
Xiuzhu Dong ◽  
Yuguang Zhou
Keyword(s):  
Deep Sea ◽  
Type Species ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type ◽  
Aurantimonas Coralicida

A novel bacterial strain, designated SW136T, was isolated from a deep-sea sediment sample collected from the South China Sea. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW136T represented a novel member of the genus Aurantimonas , forming a distinct cluster with ‘ Aurantimonas litoralis ’, Aurantimonas coralicida and Aurantimonas manganoxydans (98.2, 98.1 and 97.9% sequence similarity, respectively). The predominant cellular fatty acid of strain SW136T was C18 : 1  ω7c. Strain SW136T contained ubiquinone-10 as the dominant respiratory quinone, and diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G+C content was 64.3 mol%. The average nucleotide identity and digital DNA–DNA hybridization values of strain SW136T with A. coralicida CGMCC 1.12222T and A. manganoxydans CGMCC 1.12225T were 78.8 and 78.6 % and 21.5 and 25.5 %, respectively. On the basis of phylogenetic inference and phenotypic characteristics, we propose that strain SW136T represents a novel species of the genus Aurantimonas , with the name Aurantimonas marina sp. nov. The type strain is SW136T (=CGMCC 1.17725T=KCTC 82366T).

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