scholarly journals Lentisphaera profundi sp. nov., isolated from deep-sea water

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4186-4190 ◽  
Author(s):  
Ahyoung Choi ◽  
Jaeho Song ◽  
Yochan Joung ◽  
Kazuhiro Kogure ◽  
Jang-Cheon Cho
Keyword(s):  
Deep Sea ◽  
Sea Water ◽  
Sequence Similarity ◽  
North Pacific Ocean ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Deep Sea Water ◽  
Gram Staining ◽  
The 16S Rrna Gene

A Gram-staining-negative, aerobic, non-motile, coccus-shaped bacterium, designated SAORIC-696T, was isolated from deep-sea water at a depth of 1700 m in the western North Pacific Ocean. Optimal growth of strain SAORIC-696T was observed at 15 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Strain SAORIC-696T formed a robust phylogenetic clade with members of the genus Lentisphaera. The 16S rRNA gene sequence similarity showed that strain SAORIC-696T was most closely related to Lentisphaera marina (98.0 % similarity) and Lentisphaera araneosa (97.3 %). The DNA–DNA relatedness between SAORIC-696T and two species of the genus Lentisphaera was only 27–42 %. The DNA G+C content of strain SAORIC-696T was 43.1 mol% and predominant cellular fatty acids were C16 : 1ω9c (36.8 %), C14 : 0 (22.5 %) and C14 : 0 3-OH and/or iso-C16 : 1 I (10.8 %). Strain SAORIC-696T contained MK-7 as the only respiratory quinone. On the basis of taxonomic data collected in this study, it was concluded that strain SAORIC-696T represents a novel species of the genus Lentisphaera, for which the name Lentisphaera profundi sp. nov. is proposed, with the type strain SAORIC-696T ( = NBRC 110692T = KCTC 42681T).

scholarly journals Parvibaculum indicum sp. nov., isolated from deep-sea water

2011 ◽  
Vol 61 (2) ◽  
pp. 271-274 ◽  
Author(s):  
Qiliang Lai ◽  
Liping Wang ◽  
Yuhui Liu ◽  
Jun Yuan ◽  
Fengqin Sun ◽  
...  
Keyword(s):  
Deep Sea ◽  
Sea Water ◽  
Sequence Similarity ◽  
Tween 80 ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Deep Sea Water ◽  
Polycyclic Aromatic

A taxonomic study was carried out on strain P31T, which was isolated from a polycyclic aromatic hydrocarbon (PAH)-degrading consortium enriched with deep-sea water of the Indian Ocean. The isolate was Gram-reaction-negative, rod-shaped, motile by means of a polar flagellum and incapable of reducing nitrate to nitrite. Growth was observed at 0.5–8 % NaCl and at 10–41 °C. Strain P31T was unable to degrade Tween 80 or gelatin. The major respiratory quinone was ubiquinone 11 (Q-11). The dominant fatty acids were C18 : 1 ω7c (39.79 %), 11-methyl C18 : 1 ω7c (17.84 %), C19 : 0 cyclo ω8c (12.05 %) and C18 : 0 (6.09 %). The G+C content of the chromosomal DNA was 62.1 mol%. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain P31T and Parvibaculum lavamentivorans DS-1T formed a distinct lineage in the family Phyllobacteriaceae; these two strains showed 95.7 % sequence similarity, while similarities between P31T and other members of the genus Parvibaculum were below 93 %. Based on the genotypic and phenotypic data, strain P31T represents a novel species of the genus Parvibaculum, for which the name Parvibaculum indicum sp. nov. is proposed. The type strain is P31T (=CCTCC AB 208230T =LMG 24712T =MCCC 1A01132T).

Flavobacterium chungbukense sp. nov., isolated from soil

2011 ◽  
Vol 61 (11) ◽  
pp. 2734-2739 ◽  
Author(s):  
Chae-Sung Lim ◽  
Yong-Sik Oh ◽  
Jae-Kwan Lee ◽  
A-Rum Park ◽  
Jae-Soo Yoo ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Gram Staining ◽  
Flavobacterium Johnsoniae ◽  
The Family ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A yellow-pigmented, Gram-staining-negative, non-motile, strictly aerobic and rod-shaped bacterium, designated CS100T, was isolated from soil in Chungbuk, Korea. Phylogenetic analysis and comparative studies based on the 16S rRNA gene sequence showed that strain CS100T belonged to the genus Flavobacterium in the family Flavobacteriaceae. Strain CS100T showed the highest sequence similarities to Flavobacterium glaciei JCM 13953T (97.6 %) and Flavobacterium johnsoniae KACC 11410T (97.1 %). Sequence similarity to other members of the genus Flavobacterium was 91.5–97.0 %. Growth occurred at 4–30 °C, at pH 5.0–9.0 and in the presence of 0–2 % (w/v) NaCl. Flexirubin-type pigments were produced. Menaquinone-6 (MK-6) was the major respiratory quinone and the major fatty acids were iso-C15 : 0 (17.3 %), summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c, 15.5 %) and C16 : 0 (11.8 %). The DNA G+C content was 36.4 mol%. Strain CS100T hydrolysed skimmed milk and gelatin, but not chitin or pectin, and showed oxidase and catalase activities. DNA–DNA relatedness was 3.0 % with F. glaciei JCM 13953T and 11.5 % with F. johnsoniae KACC 11410T. On the basis of the evidence from this study, strain CS100T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium chungbukense sp. nov. is proposed. The type strain is CS100T ( = KACC 15048T = JCM 17386T).

scholarly journals Thiobacimonas profunda gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from deep-sea water

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 359-364 ◽  
Author(s):  
Shuhui Li ◽  
Kai Tang ◽  
Keshao Liu ◽  
Nianzhi Jiao
Keyword(s):  
Deep Sea ◽  
Sea Water ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Deep Sea Water ◽  
Link Type ◽  
Novel Genus And Species ◽  
Family Rhodobacteraceae

A bacterial strain, JLT2016T, was isolated from a sample of South-eastern Pacific deep-sea water. Cells were Gram-stain-negative, aerobic, devoid of flagella, motile by gliding and rod-shaped. Colonies were mucoid and cream. Growth occurred at 1.0–11.0 % (w/v) NaCl, 10–40 °C and pH 4.0–9.0. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) (60.5 %), C19 : 0 cyclo ω8c (10.9 %) and C16 : 0 (9.0 %). The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two sphingoglycolipids. The DNA G+C content was 67.1 mol%. The closest relative of strain JLT2016T was Salipiger mucosus A3T (96.7 % 16S rRNA gene sequence similarity). The results of phylogenetic analyses with different treeing algorithms indicated that this strain belonged to the Roseobacter clade in the order Rhodobacterales . Based on polyphasic analysis, strain JLT2016T is considered to represent a novel genus and species, for which the name Thiobacimonas profunda gen. nov., sp. nov. is proposed. The type strain is JLT2016T ( = LMG 27365T = CGMCC 1.12377T).

scholarly journals Aestuariivita atlantica sp. nov., isolated from deep-sea sediment

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3281-3285 ◽  
Author(s):  
Guizhen Li ◽  
Qiliang Lai ◽  
Yaping Du ◽  
Xiupian Liu ◽  
Fengqin Sun ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Deep Sea ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Deep Sea Sediment ◽  
Gram Staining

A novel strain, 22II-S11-z3T, was isolated from the deep-sea sediment of the Atlantic Ocean. The bacterium was aerobic, Gram-staining-negative, oxidase-positive and catalase-negative, oval- to rod-shaped, and non-motile. Growth was observed at salinities of 1–9 % NaCl and temperatures of 10–45 °C. The isolate could hydrolyse aesculin and Tweens 20, 40 and 80, but not gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II-S11-z3T belonged to the genus Aestuariivita, with highest sequence similarity to Aestuariivita boseongensis KCTC 42052T (97.5 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain 22II-S11-z3T and A. boseongensis KCTC 42052T were 71.5 % and 20.0 ± 2.3 %, respectively. The G+C content of the chromosomal DNA was 65.5 mol%. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1ω7c/ω6c) (35.2 %), C19 : 0 cyclo ω8c (20.9 %), C16 : 0 (11.8 %), 11-methyl C18 : 1ω7c (11.4 %) and C12 : 1 3-OH (9.4 %). The respiratory quinone was determined to be Q-10. Diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, nine unidentified phospholipids, one unidentified aminolipid and two unidentified lipids were present. The combined genotypic and phenotypic data show that strain 22II-S11-z3T represents a novel species of the genus Aestuariivita, for which the name Aestuariivita atlantica sp. nov. is proposed, with the type strain 22II-S11-z3T ( = KCTC 42276T = MCCC 1A09432T).

scholarly journals Oceanisphaera psychrotolerans sp. nov., isolated from coastal sediment samples

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2797-2802 ◽  
Author(s):  
Shan Zhou ◽  
Huimin Wang ◽  
Yanwei Wang ◽  
Kedong Ma ◽  
Mingxiong He ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Coastal Sediment ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Sediment Samples ◽  
Gram Staining ◽  
Optimum Ph ◽  
Method Analysis ◽  
Reference Strains ◽  
The 16S Rrna Gene

A novel aerobic, Gram-staining-negative bacterium, designated strain LAM-WHM-ZCT, was isolated from coastal sediment samples from the Bohai Sea, near Yantai, China. Cells of LAM-WHM-ZCT were non-motile, short-rod- or coccoid-shaped. The temperature and pH ranges for growth were 4–40  °C (optimum: 20–33  °C) and pH 5–9 (optimum: pH 7.5). The strain did not require NaCl for growth but tolerated up to 10 % NaCl (w/v). The major fatty acids of strain LAM-WHM-ZCT were summed feature 3, C12 : 0, C16 : 0, summed feature 2 and summed feature 8. The predominant respiratory quinone was ubiquinone Q-8. The main polar lipids were diphosphatidyglycerol, phosphatigylethanolamine, phosphatidyglycerol, one phospholipid and four unidentified glycolipids. The DNA G+C content was 59.3 mol% as determined by the melting temperature (T m) method. Analysis of the 16S rRNA gene sequence indicated that the isolate represented a member of the genus Oceanisphaera and was closely related to Oceanisphaera arctica KCTC 23013T, Oceanisphaera litoralis DSM 15406T, Oceanisphaera sediminis KACC 15117T and Oceanisphaera donghaensis KCTC 12522T with 97.7 %, 97.1 %, 96.6 % and 96.6 % sequence similarity, respectively. The DNA–DNA hybridization values between strain LAM-WHM-ZCT and the four reference strains were 47.4 ± 2.8 %, 33.5 ± 2.2 %, 28.4 ± 1.8 % and 13.7 ± 0.8 %, respectively. Based on its phenotypic and genotypic properties, strain LAM-WHM-ZCT is suggested to represent a novel species of the genus Oceanisphaera, for which the name Oceanisphaera psychrotolerans sp. nov. is proposed. The type strain is LAM-WHM-ZCT ( = ACCC 06516T = JCM 30466T).

Polyphasic taxonomic analysis of Parasedimentitalea marina gen. nov., sp. nov., a psychrotolerant bacterium isolated from deep sea water of the New Britain Trench

2019 ◽  
Vol 366 (22) ◽  
Author(s):  
Wanzhen Ding ◽  
Ping Liu ◽  
Yunping Xu ◽  
Jiasong Fang ◽  
Junwei Cao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Sea Water ◽  
Sequence Similarity ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Circular Chromosome ◽  
Deep Sea Water ◽  
New Britain

ABSTRACT A novel Rhodobacteraceae bacterium, strain W43T, was isolated from a deep-sea water sample from the New Britain Trench. Strain W43T exhibited the highest 16S rRNA gene sequence similarity of 96.5% to Sedimentitalea nanhaiensis DSM 24252T, Phaeobacter gallaeciensis DSM 26640T, Phaeobacter inhibens DSM 16374T, and Phaeobacter porticola P97T. Phylogenetic analysis of the 16S rRNA gene and phylogenomic analysis of the genome showed that strain W43T formed an independent monophyletic branch within the family Rhodobacteraceae. Strain W43T was Gram-stain-negative, rod-shaped, and grew optimally at 16–20°C, pH 6.5–7.0 and 2% (w/v) NaCl. The principal fatty acids were C18:1ω7c/C18:1ω6c, major respiratory quinone was ubiquinone-10 and predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The 5 080 916 bp long genome, comprising a circular chromosome and four plasmids, exhibits a G + C content of 55.9 mol%. The combined phenotypic, chemotaxonomic and molecular data show that strain W43T represents a novel species of a novel genus, for which the name Parasedimentitalea marina gen. nov. sp. nov. is proposed (type strain W43T = MCCC 1K03532T = KCTC 62635T).

Kordia antarctica sp. nov., isolated from Antarctic seawater

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3617-3622 ◽  
Author(s):  
Kiwoon Baek ◽  
Ahyoung Choi ◽  
Ilnam Kang ◽  
Kiyoung Lee ◽  
Jang-Cheon Cho
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
The Antarctic

A Gram-staining-negative, chemoheterotrophic, yellow-pigmented, non-motile, flexirubin-negative, facultatively anaerobic bacterium, designated strain IMCC3317T, was isolated from a coastal seawater sample from the Antarctic Penninsula. Optimal growth of strain IMCC3317T was observed at 20 °C, pH 8.0 and in the presence of 2–3 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC3317T belonged to the genus Kordia and was closely related to Kordia algicida OT-1T (96.7 % sequence similarity) and Kordia periserrulae IMCC1412T (96.1 % sequence similarity). The major fatty acids were 10-methyl C16 : 0 and/or iso-C16 : 1ω9c, iso-C17 : 0 3-OH, iso-C15 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 35.1 mol%. The strain contained menaquinone-6 (MK-6) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine and unknown aminophospholipids, aminolipids and polar lipids. On the basis of phylogenetic distinction and differential phenotypic characteristics, it is suggested that strain IMCC3317T ( = KCTC 32292T = NBRC 109401T) be assigned to the genus Kordia as the type strain of a novel species, for which the name Kordia antarctica sp. nov. is proposed.

Muricauda zhangzhouensis sp. nov., isolated from mangrove sediment

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2320-2325 ◽  
Author(s):  
Caiyun Yang ◽  
Yi Li ◽  
Qian Guo ◽  
Qiliang Lai ◽  
Jun Wei ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Optimal Growth ◽  
Bacterial Consortium ◽  
Mangrove Sediment ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

A Gram-staining-negative, rod-shaped and non-motile bacterial strain, designated 12C25T, was isolated from the crude-oil-degrading bacterial consortium enriched from mangrove sediment collected in Fujian Province, China. Optimal growth was observed at 25–28 °C, at pH 7.0 and in the presence of 2 % (w/v) NaCl + 2 % (w/v) KCl. Comparative 16S rRNA gene sequence analysis demonstrated that strain 12C25T shared the highest sequence similarity with members of the genus Muricauda (97.7–93.9 %), exhibiting 97.7 % sequence similarity and 33.7±4 % DNA–DNA relatedness to Muricauda aquimarina SW-63T. The DNA G+C content of strain 12C25T was 39.9 mol%. The dominant fatty acids were iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C15 : 0, C18 : 0 and iso-C15 : 0 3-OH, and menaquinone with six isoprene units (MK-6) was the only respiratory quinone. On the basis of phenotypic data and phylogenetic inference, the novel strain belongs to the genus Muricauda , but can readily be distinguished from known species of this genus and thus represents a novel species of the genus Muricauda. The name Muricauda zhangzhouensis sp. nov. is proposed and the type strain is 12C25T ( = CGMCC 1.11028T = MCCC 1F01096T = DSM 25030T).

scholarly journals Bizionia fulviae sp. nov., isolated from the gut of an egg cockle, Fulvia mutica

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3066-3072 ◽  
Author(s):  
Hyun Sik Kim ◽  
Dong-Wook Hyun ◽  
Pil Soo Kim ◽  
June-Young Lee ◽  
Na-Ri Shin ◽  
...  
Keyword(s):  
Intestinal Tract ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Marine Agar ◽  
Respiratory Quinone ◽  
Gram Staining ◽  
Optimum Ph ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene

A novel Gram-staining-negative, non-spore-forming, non-flagellated, non-motile, aerobic, saffron-coloured, rod-shaped bacterium that did not produce flexirubin-type pigments was designated strain EM7T and was distinct from other members of the genus Bizionia by produce carotenoid-type pigments and being able to grow independently of NaCl. Strain EM7T was isolated from the intestinal tract of an egg cockle, Fulvia mutica, which had been collected from the West Sea in Korea. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain EM7T belonged to the genus Bizionia, and showed sequence similarity to Bizionia paragorgiae KMM 6029T (97.9 %) and Bizionia saleffrena HFDT (97.73 %). Growth occurred on marine agar 2216 at 0–25 °C (optimum, 20 °C) and at pH 6–9 (optimum, pH 7). Growth occurred in the presence of 0–10 % (w/v) NaCl (optimum, 2 %, w/v, NaCl). The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C16 : 0 3-OH. The major respiratory quinone was menaquinone MK-6. The polar lipids of strain EM7T comprised phosphatidylethanolamine, three unidentified aminolipids, an unidentified aminophospholipid and two unidentified lipids. The genomic DNA G+C content was 34.8 mol%. Bizionia paragorgiae KMM 6029T and Bizionia saleffrena HFDT to Bizionia paragorgiae KCTC 12304T and Bizionia saleffrena CIP 108534T, respectively. Thus, it is proposed that the isolate represents a novel species, Bizionia fulviae sp. nov., with strain EM7T ( = KACC 18255T = JCM 30417T) as the type strain.

scholarly journals Roseovarius indicus sp. nov., isolated from deep-sea water of the Indian Ocean

2011 ◽  
Vol 61 (9) ◽  
pp. 2040-2044 ◽  
Author(s):  
Qiliang Lai ◽  
Huanzi Zhong ◽  
Jianning Wang ◽  
Jun Yuan ◽  
Fengqin Sun ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Indian Ocean ◽  
16S Rrna ◽  
Deep Sea ◽  
Sea Water ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Deep Sea Water ◽  
The Indian Ocean

A taxonomic study was carried out on a novel bacterial strain, designated B108T, which was isolated from a polycyclic aromatic hydrocarbon (PAH)-degrading consortium, enriched from deep-sea water of the Indian Ocean. The isolate was Gram-reaction-negative, rod-shaped and non-motile. Growth of strain B108T was observed in 1–15 % (w/v) NaCl and at 10–39 °C and it was unable to degrade Tween 80 or gelatin. 16S rRNA gene sequence comparisons showed that strain B108T was most closely related to Roseovarius halotolerans HJ50T (97.1 % sequence similarity), followed by Roseovarius pacificus 81-2T (96.6 %) and Roseovarius aestuarii SMK-122T (95.2 %); other species shared <95.0 % sequence similarity. DNA–DNA hybridization tests showed that strain B108T had a low DNA–DNA relatedness to R. halotolerans HJ50T and R. pacificus 81-2T (48±4 % and 44±5 %, respectively). The predominant fatty acids were C16 : 0, C16 : 0 2-OH, summed feature 8 (C18 : 1ω7c/ω6c) and C19 : 0ω8c cyclo, which accounted for 84.2 % of the total cellular fatty acids. The G+C content of the chromosomal DNA was 63.6 mol%. The major respiratory quinone was ubiquinone 10 (Q10). Phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and some unidentified compounds were detected. These characteristics were in good agreement with those of members of the genus Roseovarius. The pufLM gene was also detected. According to its morphology, physiology, fatty acid composition and phylogenetic position based on 16S rRNA sequence data, the novel strain most appropriately belongs to the genus Roseovarius but can be readily distinguished from known species of this genus. Therefore, strain B108T represents a novel species, of the genus Roseovarius, for which the name Roseovarius indicus sp. nov. is proposed. The type strain is B108T ( = 2PR52-14T  = CCTCC AB 208233T  = LMG 24622T  = MCCC 1A01227T).

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