Alkalimonas collagenimarina sp. nov., a psychrotolerant, obligate alkaliphile isolated from deep-sea sediment

2007 ◽  
Vol 57 (7) ◽  
pp. 1549-1553 ◽  
Author(s):  
Atsushi Kurata ◽  
Masayuki Miyazaki ◽  
Tohru Kobayashi ◽  
Yuichi Nogi ◽  
Koki Horikoshi
Keyword(s):  
Dna Hybridization ◽  
Deep Sea ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Deep Sea Sediment ◽  
Hybridization Data ◽  
Physiological Properties ◽  
Initial Ph

A psychrotolerant, obligately alkaliphilic, collagenolytic enzyme-producing bacterium, strain AC40T, was isolated from a deep-sea sediment off Torishima Island, Japan, at a depth of 4026 m. Phylogenetic analysis of 16S rRNA gene sequences indicated that this bacterium was closely related to members of the genus Alkalimonas, with highest sequence similarity (97.9 %) to Alkalimonas delamerensis 1E1T. DNA–DNA hybridization experiments of strain AC40T with A. delamerensis 1E1T revealed a level of relatedness of less than 30 %. Cells of strain AC40T were strictly aerobic, rod-shaped, Gram-negative and motile by means of a single polar flagellum. The organism grew over a range of temperatures from 5 to 37 °C and at initial pH values between 7.0 and 10.5. Optimal growth was observed at 33 °C and at pH 8.5–10.0. Cellular fatty acids of strain AC40T were predominantly saturated and mono-unsaturated straight-chain components (C16 : 0 and C18 : 1). The major isoprenoid quinone was Q-8. The G+C content of the DNA was 49.3 mol%. Phylogenetic characteristics, physiological properties and DNA–DNA hybridization data indicate that strain AC40T represents a novel species of the genus Alkalimonas, for which the name Alkalimonas collagenimarina sp. nov. is proposed. The type strain is AC40T (=JCM 14267T=NCIMB 14266T).

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

2011 ◽  
Vol 61 (4) ◽  
pp. 728-731 ◽  
Author(s):  
Qiliang Lai ◽  
Yuanyuan Fu ◽  
Jianning Wang ◽  
Shuangxi Chen ◽  
Huanzi Zhong ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Deep Sea ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Phenotypic Data ◽  
Deep Sea Sediment ◽  
South West Indian Ocean ◽  
West Indian Ocean ◽  
Ocean Ridge

A taxonomic study was carried out on a novel strain, designated CK-I3-6T, which was isolated from deep-sea sediment of the south-west Indian Ocean Ridge. Cells were Gram-reaction-negative, oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at 4–38 °C and in 1–12 % (w/v) NaCl. Cells were able to degrade gelatin and oxidize thiosulfate but did not reduce nitrate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CK-I3-6T belonged to the genus Citreicella with a sequence similarity of 97.3 % to Citreicella thiooxidans CHLG 1T, while similarities with other taxa were <95.7 %. DNA–DNA hybridization showed that strain CK-I3-6T and C. thiooxidans CHLG 1T showed a low DNA–DNA relatedness (48±3 %). The principal fatty acids were C16 : 0 (7.8 %), C18 : 1ω7c (66.6 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 6.3 %) and C19 : 0ω8c cyclo (10.0 %). The chromosomal DNA G+C content was 67.5 mol%. On the basis of the combined genotypic and phenotypic data, strain CK-I3-6T represents a novel species of the genus Citreicella, for which the name Citreicella marina sp. nov. is proposed. The type strain is CK-I3-6T ( = CCTCC AB 209064T  = LMG 25230T  = MCCC 1A03060T).

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 Dactylosporangium darangshiense sp. nov., isolated from rock soil

2010 ◽  
Vol 60 (6) ◽  
pp. 1256-1260 ◽  
Author(s):  
Seong Hae Seo ◽  
Soon Dong Lee
Keyword(s):  
Dna Hybridization ◽  
Unsaturated Fatty Acids ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Aerial Mycelium ◽  
Rock Surface ◽  
Rrna Gene ◽  
Hybridization Data ◽  
Physiological Properties ◽  
Type Strains

A novel actinomycete was isolated from soil of a rock surface collected from the peak of Darangshi Oreum (Small Mountain) in Jeju, Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that strain DLS-44T belonged to the genus Dactylosporangium, with the type strains of Dactylosporangium roseum (99.1 % sequence similarity) and Dactylosporangium fulvum (99.0 %) as the nearest phylogenetic relatives. Substrate mycelium was abundant, irregularly branched, twisted and vivid orange–yellow in colour. Aerial mycelium was not produced on most media tested. Finger-shaped sporangia and globose bodies were formed directly from the vegetative mycelium. The combination of morphological and chemotaxonomic characteristics supported assignment of the actinomycete to the genus Dactylosporangium. Strain DLS-44T could be distinguished clearly from all type strains of the genus based on its physiological properties (utilization of methyl α-d-mannoside and glycerol, nitrate reduction and growth at 20 °C and pH 9.1) and some chemotaxonomic characteristics (absence of unsaturated fatty acids). DNA–DNA relatedness values between strain DLS-44T and its closest phylogenetic relatives were 12.2–14.8 % with D. roseum DSM 43916T and 2.5–3.6 % with D. fulvum IMSNU 22055T. On the basis of phenotypic, phylogenetic and DNA–DNA hybridization data, strain DLS-44T represents a novel species of the genus Dactylosporangium, for which the name Dactylosporangium darangshiense sp. nov. is proposed. The type strain is strain DLS-44T (=KCTC 19560T =DSM 45260T).

scholarly journals Georgenia subflava sp. nov., isolated from a deep-sea sediment

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4146-4150 ◽  
Author(s):  
Shuang Wang ◽  
Xianzhong Xu ◽  
Lina Wang ◽  
Kailin Jiao ◽  
Gaiyun Zhang
Keyword(s):  
Deep Sea ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Polar Lipid Profile ◽  
Deep Sea Sediment ◽  
Phosphatidylinositol Mannosides ◽  
The Western Pacific

A Gram-stain-positive, aerobic, motile and non-spore-forming actinobacterium, strain Y32T, was isolated from a deep-sea sediment of the western Pacific Ocean. Phylogenetic and phenotypic properties of the organism supported that it belonged to the genus Georgenia. Strain Y32T shared highest 16S rRNA gene sequence similarity of 97.8 % with Georgenia muralis 1A-CT, followed by Georgenia thermotolerans TT02-04T (97.4 %), Georgenia daeguensis 2C6-43T (97.2 %), Oceanitalea nanhaiensis JLT1488T (97.2 %), Georgenia ruanii YIM 004T (97.0 %) and Georgenia soli CC-NMPT-T3T (97.0 %). The organism grew in the presence of 0–10 % (w/v) NaCl, at 4–40 °C and at pH 6–11, with optimal growth occurring at 30–35 °C, at pH 7 and in the presence of 3.5 % (w/v) NaCl. The polar lipid profile of strain Y32T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two phosphatidylinositol mannosides. Strain Y32T contained MK-8(H4) and MK-7(H4) as the major components of the menaquinone system, and anteiso-C15 : 0, iso-C15 : 0 and iso-C14 : 0 as the predominant fatty acids. Galactose was detected as the cell-wall sugar. The G+C content of the DNA was 71.2 mol%. Based on the results of phenotypic, genotypic and phylogenetic analyses, it is considered that strain Y32T represents a novel species of the genus Georgenia, for which the name Georgenia subflava sp. nov. is proposed. The type strain is Y32T ( = LMG 28101T = CGMCC 1.12782T = JCM 19765T = MCCC 1A09955T).

scholarly journals Anaerobranca californiensis sp. nov., an anaerobic, alkalithermophilic, fermentative bacterium isolated from a hot spring on Mono Lake

2004 ◽  
Vol 54 (3) ◽  
pp. 739-743 ◽  
Author(s):  
Vladimir Gorlenko ◽  
Alexandre Tsapin ◽  
Zorigto Namsaraev ◽  
Tracy Teal ◽  
Tatyana Tourova ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Hot Spring ◽  
Optimal Growth ◽  
Mono Lake ◽  
Rrna Gene ◽  
The Novel ◽  
Hybridization Data ◽  
Physiological Properties ◽  
Concomitant Reduction ◽  
Casamino Acids

A novel, obligately anaerobic, alkalithermophilic, chemo-organotrophic bacterium was isolated from the sediment of an alkaline hot spring located on Paoha Island in Mono Lake, California, USA. This rod-shaped bacterium was motile via peritrichous flagella. Isolated strains grew optimally in 5–25 g NaCl l−1, at pH 9·0–9·5 and at a temperature of 58°C and were fermentative and mainly proteolytic, utilizing peptone, Casamino acids and yeast extract. Optimal growth was seen in the presence of elemental sulfur, polysulfide or thiosulfate with concomitant reduction to hydrogen sulfide. Sulfite was also formed in an equal ratio to sulfide during reduction of thiosulfate. The novel isolate could also reduce Fe(III) and Se(IV) in the presence of organic matter. On the basis of physiological properties, 16S rRNA gene sequence and DNA–DNA hybridization data, strain PAOHA-1T (=DSM 14826T=UNIQEM 227T) belongs to the genus Anaerobranca and represents a novel species, Anaerobranca californiensis sp. nov.

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).

scholarly journals Shewanella donghaensis sp. nov., a psychrophilic, piezosensitive bacterium producing high levels of polyunsaturated fatty acid, isolated from deep-sea sediments

2007 ◽  
Vol 57 (2) ◽  
pp. 208-212 ◽  
Author(s):  
Sung-Hyun Yang ◽  
Jung-Hyun Lee ◽  
Ji-Sun Ryu ◽  
Chiaki Kato ◽  
Sang-Jin Kim
Keyword(s):  
Dna Hybridization ◽  
Deep Sea ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Psychrophilic Bacterium ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Shewanella Frigidimarina ◽  
Deep Sea Sediments

A Gram-negative, motile, rod-shaped, psychrophilic bacterium, LT17T, was isolated from deep-sea sediments (3300 m depth) of the East Sea (Sea of Japan). Optimal growth of LT17T requires the presence of 2.5 % (w/v) NaCl, a pH of 7.0–7.5 and a temperature of 17 °C. The isolate grows optimally under a hydrostatic pressure of 10 MPa and growth is possible between 0.1 and <30 MPa. The novel strain is positive in tests for catalase, oxidase, lipase, β-glucosidase and gelatinase activities and reduces nitrate to nitrate. The predominant cellular fatty acids are iso-C13 : 0, iso-C15 : 0, C16 : 0, C16 : 1ω7 and C20 : 5ω3. The DNA G+C content of strain LT17T is 38.8 mol%. Phylogenetic analysis of 16S rRNA gene sequences places this bacterium in the class Gammaproteobacteria, within the genus Shewanella. The closest relatives of strain LT17T are Shewanella japonica (97.8 % gene sequence similarity), Shewanella pacifica (97.5 %), Shewanella olleyana (96.8 %), Shewanella frigidimarina (96.5 %) and Shewanella gelidimarina (95.4 %). The DNA–DNA hybridization levels between the novel isolate and its closest known phylogenetic relatives, S. japonica and S. pacifica, are lower than 14 %. On the basis of this polyphasic evidence, strain LT17T represents a novel species of the genus Shewanella, for which the name Shewanella donghaensis sp. nov. is proposed. The type strain is LT17T (=KCTC 10635BPT=JCM 12524T).

scholarly journals Photobacterium frigidiphilum sp. nov., a psychrophilic, lipolytic bacterium isolated from deep-sea sediments of Edison Seamount

2005 ◽  
Vol 55 (4) ◽  
pp. 1661-1666 ◽  
Author(s):  
Hae Jeom Seo ◽  
Seung Seob Bae ◽  
Jung-Hyun Lee ◽  
Sang-Jin Kim
Keyword(s):  
Dna Hybridization ◽  
Deep Sea ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Deep Sea Sediments ◽  
Sequence Similarity Analysis ◽  
Photobacterium Profundum ◽  
The Western Pacific

A Gram-negative, motile, rod-shaped, psychrophilic and weakly halophilic bacterial strain, SL13T, was isolated from deep-sea sediments (1450 m depth) of Edison Seamount in the western Pacific Ocean. Optimal growth of SL13T requires the presence of 1·5 % (w/v) NaCl, a pH of 6·0 and a temperature of 14 °C. The whole-cell fatty acid profile of the isolate includes C16 : 1 and C16 : 0 as major fatty acids and contains C20 : 5ω3. This is consistent with corresponding data for Photobacterium profundum. The DNA G+C content of strain SL13T is 43·8 mol%. Phylogenetic analyses of 16S rRNA gene sequences place this bacterium in the ‘Gammaproteobacteria’, within the genus Photobacterium. Sequence similarity analysis indicates that the closest relatives of strain SL13T are Photobacterium indicum (99·3 %), P. profundum (98·5 %) and Photobacterium lipolyticum (98·2 %). The DNA–DNA hybridization levels between the isolate and its closest known phylogenetic relatives, P. indicum, P. profundum and P. lipolyticum, are 27·1, 52·4 and 20·2 %, respectively. Thus strain SL13T represents a novel species of the genus Photobacterium, for which the name Photobacterium frigidiphilum sp. nov. is proposed. The type strain is SL13T (=KCTC 12384T=JCM 12947T).

scholarly journals Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field

2006 ◽  
Vol 56 (7) ◽  
pp. 1531-1534 ◽  
Author(s):  
Reiji Tanaka ◽  
Satoshi Kawaichi ◽  
Hiroshi Nishimura ◽  
Yoshihiko Sako
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Thermophilic Bacterium ◽  
Hydrothermal Field ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Optimum Ph ◽  
Kagoshima Prefecture ◽  
Bacterium Strain

A novel thermophilic bacterium, strain KW1T, was isolated from a coastal hydrothermal field on the Satsuma Peninsula, Kagoshima Prefecture, Japan. The variably Gram-stained cells were motile rods with flagella, did not form spores and proliferated at 52–78 °C (optimum, 70 °C), pH 5–8 (optimum, pH 7) and 0–4.5 % NaCl (optimum, 1.0 %). The novel isolate was a strictly aerobic heterotroph that utilized complex proteinaceous substrates as well as a variety of carboxylic acids and amino acids. The G+C content of the genomic DNA was 70.8 mol%. Analysis of 16S rRNA gene sequences indicated that strain KW1T is closely related to Thermaerobacter subterraneus C21T (98.4 % sequence similarity). However, the DNA–DNA hybridization value for strain KW1T and T. subterraneus ATCC BAA-137T was below 46 %. On the basis of the molecular and physiological traits of strain KW1T, it represents a novel species of the genus Thermaerobacter, for which the name Thermaerobacter litoralis sp. nov. is proposed. The type strain is KW1T (=JCM 13210T=DSM 17372T).

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