scholarly journals Devosia pacifica sp. nov., isolated from deep-sea sediment

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2637-2641 ◽  
Author(s):  
Yan-Yu Jia ◽  
Cong Sun ◽  
Jie Pan ◽  
Wei-Yan Zhang ◽  
Xin-Qi Zhang ◽  
...  
Keyword(s):  
Deep Sea ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Content Sharing ◽  
Link Type ◽  
Lateral Flagellum

A novel bacterial strain, NH131T, was isolated from deep-sea sediment of South China Sea. Cells were strictly aerobic, Gram-stain negative, short rod-shaped and motile with a single lateral flagellum. Strain NH131T grew optimally at pH 6.5–7.0 and 25–30 °C. 16S rRNA gene sequence analysis revealed that strain NH131T belonged to the genus Devosia , sharing the highest sequence similarity with the type strain, Devosia geojensis BD-c194T (96.2 %). The predominant fatty acids were C18 : 1ω7c, 11-methyl C18 : 1ω7c, C18 : 0 and C16 : 0. Ubiquinone 10 was the predominant ubiquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid, three glycolipids and two unknown lipids. The DNA G+C content of strain NH131T was 63.0 mol%. On the basis of the results of polyphasic identification, it is suggested that strain NH131T represents a novel species of the genus Devosia for which the name Devosia pacifica sp. nov. is proposed. The type strain is NH131T ( = JCM 19305T = KCTC 32437T).

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 Oceanisphaera profunda sp. nov., a marine bacterium isolated from deep-sea sediment, and emended description of the genus Oceanisphaera

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1252-1256 ◽  
Author(s):  
Zhong Xu ◽  
Xi-Ying Zhang ◽  
Hai-Nan Su ◽  
Zi-Chao Yu ◽  
Chang Liu ◽  
...  
Keyword(s):  
Deep Sea ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type ◽  
Emended Description ◽  
Type Strains

A Gram-stain-negative, aerobic, oxidase- and catalase-positive, flagellated, rod-shaped bacterial strain, designated SM1222T, was isolated from the deep-sea sediment of the South China Sea. The strain grew at 4–35 °C and with 0.5–8 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1222T was affiliated with the genus Oceanisphaera in the class Gammaproteobacteria . It shared the highest sequence similarity with the type strain of Oceanisphaera ostreae (96.8 %) and 95.4–96.6 % sequence similarities with type strains of other species of the genus Oceanisphaera with validly published names. Strain SM1222T contained summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C18 : 1ω7c, C16 : 0, C12 : 0 and summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I) as the major fatty acids and ubiquinone Q-8 as the predominant respiratory quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of strain SM1222T was 51.5 mol%. On the basis of the evidence presented in this study, strain SM1222T represents a novel species of the genus Oceanisphaera , for which the name Oceanisphaera profunda sp. nov. is proposed. The type strain of Oceanisphaera profunda is SM1222T ( = CCTCC AB 2013241T = KCTC 32510T). An emended description of the genus Oceanisphaera Romanenko et al. 2003 emend. Choi et al. 2011 is also proposed.

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 .

Saccharobesus litoralis gen. nov., sp. nov., a novel alginate-degrading bacterium isolated from the surface of intertidal algal turf

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Rosyada Amran Amrina ◽  
Go Furusawa ◽  
Nyok-Sean Lau
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Algal Turf ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
Lateral Flagellum

A novel rod-shaped, Gram-stain-negative, strictly aerobic and alginate-degrading marine bacterium, designated CCB-QB4T, was isolated from a surface of algal turf collected from a coastal area of Penang, Malaysia. The cells showed motility by a lateral flagellum. The rod-shaped cells formed long chains end-to-end. Phylogenetic analysis based on the 16S rRNA gene sequence of strain CCB-QB4T showed 94.07, 92.69, 91.52 and 90.90 % sequence similarity to Algibacillus agarilyticus RQJ05T, Catenovulum maritimum Q1T, Catenovulum agarivorans YM01T and Catenovulum sediminis D2T, respectively. Strain CCB-QB4T formed a cluster with A. agarilyticus RQJ05T. Strain CCB-QB4T was catalase-negative, oxidase-positive, and degraded agar, alginate, and starch. Cell growth was observed at 15–40 °C, at pH 7.0–10.0 and in the presence of 1–6 % (w/v) NaCl and glucose. The major fatty acids were summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH), C16 : 0 and C18 : 1 ω7c. The polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two unidentified glycolipids, an unidentified phospholipid and unidentified lipid. The major respiratory quinone was ubiquinone-8. The genomic DNA G+C content was 46.7 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain CCB-BQ4T represents a novel species in a new genus, for which the name Saccharobesus litoralis gen. nov., sp. nov. is proposed. The type strain is CCB-QB4T (=JCM 33513T=CCB-MBL 5008T).

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).

Litoreibacter roseus sp. nov., a novel bacteriochlorophyll a-containing bacterium

2021 ◽  
Author(s):  
Masataka Kanamuro ◽  
Yuki Sato-Takabe ◽  
So Muramatsu ◽  
Setsuko Hirose ◽  
Yuki Muramatsu ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Near Infrared ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A strictly aerobic, bacteriochlorophyll (BChl) a-containing alphaproteobacterium, designated strain K6T, was isolated from seawater around an aquaculture site in the Uwa Sea in Japan. The novel strain grew optimally at 30 °C at pH 7.0–7.5 and in the presence of 2.0 % (w/v) NaCl. The nonmotile and coccoid or rod-shaped cells formed pink-pigmented colonies on agar plates containing organic compounds. Cells showed an in vivo absorption maximum at 870 nm in the near-infrared region, indicating the presence of BChl a in the light-harvesting 1 complex. The new bacterial strain was Gram-stain-negative and oxidase- and catalase-positive. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain K6T was closely related to species in the genus Litoreibacter . The closest phylogenetic relatives of strain K6T were Litoreibacter ponti GJSW-31T (98.56 % sequence similarity), Litoreibacter janthinus KMM 3842T (97.63 %) and Litoreibacter albidus KMM 3851T (96.88 %). The G+C content of the genomic DNA was 58.26 mol%. The average nucleotide identity value of strain K6T with the type strain of L. ponti was 77.16 % (SD 4.79 %). The digital DNA−DNA hybridization value of strain K6T with the type strain of L. ponti was 19.40 %. The respiratory quinone was ubiquinone-10. The major cellular fatty acids were C18 : 1 ω7c, C16 : 0 and 11-methyl C18 : 1 ω7c. The dominant polar lipids were phosphatidylcholine and phosphatidylglycerol. On the basis of the genetic and phenotypic data obtained in the present study, we propose a new species in the genus Litoreibacter : Litoreibacter roseus sp. nov., whose type strain is K6T (=DSM 110109T=NBRC 114114T). Strain K6T represents the first confirmed species that produces BChl a within the genus Litoreibacter .

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).

Sign in / Sign up

Export Citation Format

Share Document