scholarly journals Nitratireductor indicus sp. nov., isolated from deep-sea water

2011 ◽  
Vol 61 (2) ◽  
pp. 295-298 ◽  
Author(s):  
Qiliang Lai ◽  
Zhiwei Yu ◽  
Jun Yuan ◽  
Fengqin Sun ◽  
Zongze Shao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Gene Sequence ◽  
Sea Water ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Chromosomal Dna ◽  
Deep Sea Water

A taxonomic study was carried out on a novel bacterial strain, designated C115T, isolated from a crude-oil-degrading consortium, enriched from deep-sea water of the Indian Ocean. Cells were Gram-negative short rods, mobile by means of a monopolar flagellum. Growth was observed at salinities of 0–7 % and at 10–43 °C. It was unable to degrade Tween 80 or gelatin. 16S rRNA gene sequence analysis showed that strain C115T was related most closely to Nitratireductor aquibiodomus NL21T (96.5 % similarity), Nitratireductor kimnyeongensis KY 101T (96.4 %) and Nitratireductor basaltis J3T (96.2 %). The predominant fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c, 81.8 %) and C18 : 0 (7.0 %). The G+C content of the chromosomal DNA of strain C115T was 59 mol%. Based on its morphology, physiology and fatty acid composition together with 16S rRNA gene sequence comparisons, the novel strain most appropriately belongs to the genus Nitratireductor, but can be distinguished readily from recognized species of the genus. Strain C115T is therefore considered to represent a novel species of the genus Nitratireductor, for which the name Nitratireductor indicus sp. nov. is proposed. The type strain is C115T (=RC92-7T =CCTCC AB 209298T =LMG 25540T =MCCC 1A01260T).

Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the ‘deep sea-1’ clade of marine methanotrophs

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 251-259 ◽  
Author(s):  
Patricia L. Tavormina ◽  
Roland Hatzenpichler ◽  
Shawn McGlynn ◽  
Grayson Chadwick ◽  
Katherine S. Dawson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Sequence Identity ◽  
Link Type

We report the isolation and growth characteristics of a gammaproteobacterial methane-oxidizing bacterium (Methylococcaceae strain WF1T, ‘whale fall 1’) that shares 98 % 16S rRNA gene sequence identity with uncultivated free-living methanotrophs and the methanotrophic endosymbionts of deep-sea mussels, ≤94.6 % 16S rRNA gene sequence identity with species of the genus Methylobacter and ≤93.6 % 16S rRNA gene sequence identity with species of the genera Methylomonas and Methylosarcina . Strain WF1T represents the first cultivar from the ‘deep sea-1’ clade of marine methanotrophs, which includes members that participate in methane oxidation in sediments and the water column in addition to mussel endosymbionts. Cells of strain WF1T were elongated cocci, approximately 1.5 µm in diameter, and occurred singly, in pairs and in clumps. The cell wall was Gram-negative, and stacked intracytoplasmic membranes and storage granules were evident. The genomic DNA G+C content of WF1T was 40.5 mol%, significantly lower than that of currently described cultivars, and the major fatty acids were 16 : 0, 16 : 1ω9c, 16 : 1ω9t, 16 : 1ω8c and 16 : 2ω9,14. Growth occurred in liquid media at an optimal temperature of 23 °C, and was dependent on the presence of methane or methanol. Atmospheric nitrogen could serve as the sole nitrogen source for WF1T, a capacity that had not been functionally demonstrated previously in members of Methylobacter . On the basis of its unique morphological, physiological and phylogenetic properties, this strain represents the type species within a new genus, and we propose the name Methyloprofundus sedimenti gen. nov., sp. nov. The type strain of Methyloprofundus sedimenti is WF1T ( = LMG 28393T = ATCC BAA-2619T).

Leucobacter salsicius sp. nov., from a salt-fermented food

2011 ◽  
Vol 61 (3) ◽  
pp. 502-506 ◽  
Author(s):  
Ji-Hyun Yun ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Mi-Ja Jung ◽  
Eun-Jin Park ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Fermented Food ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Chromosomal Dna

Strain M1-8T was isolated from jeotgal, a Korean salt-fermented food. Cells were aerobic, non-motile, Gram-reaction-positive and rod-shaped. Colonies were cream-coloured and circular with entire margins. Strain M1-8T exhibited optimal growth at 25–30 °C and pH 7.0–8.0 and in 0–4 % (w/v) NaCl. The strain tolerated up to 10.0 mM Cr(VI). Phylogenetic analyses of 16S rRNA gene sequences indicated that strain M1-8T represents a novel species in the genus Leucobacter. The 16S rRNA gene sequence of M1-8T exhibited 98.1 % similarity to that of Leucobacter chromiireducens subsp. chromiireducens L-1T. The new isolate was clustered with Leucobacter species on a 16S rRNA gene sequence-based phylogenetic tree. The chromosomal DNA G+C content of strain M1-8T was 62.8 mol%. Its cell-wall peptidoglycan contained 2,4-diaminobutyric acid, glutamic acid, alanine, glycine and γ-aminobutyric acid. The major menaquinone was MK-11 and the predominant fatty acids were anteiso-C15 : 0 (63.6 %), anteiso-C17 : 0 (16.7 %) and iso-C16 : 0 (14.2 %). The polar lipid profile of strain M1-8T contained diphosphatidylglycerol and one unknown glycolipid. Significant genotypic and phenotypic differences were found between strain M1-8T and other Leucobacter species. These differentiating characteristics indicate that strain M1-8T represents a novel species of the genus Leucobacter, for which the name Leucobacter salsicius sp. nov. is proposed. The type strain is M1-8T (=KACC 21127T =JCM 16362T).

scholarly journals Hongiella marincola sp. nov., isolated from sea water of the East Sea in Korea

2004 ◽  
Vol 54 (5) ◽  
pp. 1845-1848 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Soo-Hwan Yeo ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sea Water ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
East Sea ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Two Gram-negative, non-motile, non-spore-forming, rod-shaped strains, SW-2T and SW-26, were isolated from sea water of the East Sea in Korea. These organisms grew optimally at 37 °C and in the presence of 2–3 % (w/v) NaCl. They did not grow without NaCl or in the presence of >9 % (w/v) NaCl. Strains SW-2T and SW-26 were characterized chemotaxonomically as having MK-7 as the predominant isoprenoid quinone and iso-C15 : 0 as the major fatty acid. The DNA G+C content of strains SW-2T and SW-26 was 43 mol%. A neighbour-joining tree based on 16S rRNA gene sequences showed that strains SW-2T and SW-26 fell within the Cytophaga–Flavobacterium–Bacteroides group and formed a coherent cluster with Hongiella species. Strains SW-2T and SW-26 showed a 16S rRNA gene sequence similarity value of 99·9 % and a mean DNA–DNA relatedness level of 87 % to each other. Levels of 16S rRNA gene sequence similarity between strains SW-2T and SW-26 and the type strains of two Hongiella species ranged from 94·2 to 96·6 %. On the basis of phenotypic and chemotaxonomic properties and phylogenetic distinctiveness, strains SW-2T and SW-26 should be placed in the genus Hongiella as members of a novel species, for which the name Hongiella marincola sp. nov. is proposed. The type strain is SW-2T (=KCTC 12180T=DSM 16067T).

scholarly journals Marinobacter maritimus sp. nov., a psychrotolerant strain isolated from sea water off the subantarctic Kerguelen islands

2005 ◽  
Vol 55 (4) ◽  
pp. 1453-1456 ◽  
Author(s):  
S. Shivaji ◽  
Pratima Gupta ◽  
Preeti Chaturvedi ◽  
K. Suresh ◽  
Daniel Delille
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sea Water ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Maximum Temperature ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Kerguelen Islands

A psychrotolerant, Gram-negative, motile bacterium, designated CK 47T, was isolated from sea water off the subantarctic Kerguelen islands (50° 40′ S 68° 25′ E). The isolate grew optimally at 22 °C and minimum and maximum temperature of growth were 4 and 37 °C, respectively. It required Na+ for growth and exhibited optimum growth at pH 8·5 and 4 % NaCl. It utilized hexane, heptane and petroleum ether as sole sources of carbon. Strain CK 47T had Q9 as the major respiratory quinone and C16 : 0 (21·7 %), C17 : 0 (21·3 %), C18 : 0 (5·7 %), C18 : 1 ω7c (9·0 %) and C18 : 1 ω9c (31·4 %) as predominant fatty acids. The G+C content of the DNA was 58 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that CK 47T formed a coherent cluster within the genus Marinobacter. It exhibited highest 16S rRNA gene sequence similarity of 96·8 % with Marinobacter lipolyticus. However, the level of DNA–DNA relatedness between strain CK47T and M. lipolyticus was only 55 %. On the basis of phenotypic characteristics, and phylogenetic and genotypic distinctiveness, strain CK 47T is considered to represent a novel species of the genus Marinobacter. The name Marinobacter maritimus sp. nov. is proposed, with CK 47T (=JCM 12521T=MTCC 6519T) as the type strain.

scholarly journals Nitratireductor pacificus sp. nov., isolated from a pyrene-degrading consortium

2011 ◽  
Vol 61 (6) ◽  
pp. 1386-1391 ◽  
Author(s):  
Qiliang Lai ◽  
Zhiwei Yu ◽  
Jianning Wang ◽  
Huanzi Zhong ◽  
Fengqin Sun ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Chromosomal Dna ◽  
Dna Relatedness ◽  
Degrading Bacteria

Strain pht-3BT was isolated from a pyrene-degrading consortium of an enriched sediment from the Pacific Ocean, collected during the screening of polycyclic aromatic hydrocarbon-degrading bacteria. Cells were Gram-negative, short rods that were motile by means of flagella. Growth was observed at 0–7 % NaCl and 10–41 °C. The isolate was able to reduce nitrate to nitrite, but not to nitrogen. 16S rRNA gene sequence comparisons showed that strain pht-3BT was most closely related to Nitratireductor aquibiodomus NL21T (97.3 % 16S rRNA gene sequence similarity), N. indicus C115T (97.1 %), N. basaltis J3T (96.8 %) and N. kimnyeongensis KY 101T (96.7 %). DNA–DNA hybridization between strain pht-3BT and these reference strains revealed 55, 54, 28 and 42 % DNA–DNA relatedness, respectively. The dominant fatty acids were C19 : 0ω8c cyclo (22.6 %) and summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c; 60.4 %). The G+C content of the chromosomal DNA was 63 mol%. These characteristics were in good agreement with those of members of the genus Nitratireductor. According to cell morphology, physiology, fatty acid composition, 16S rRNA gene sequence analysis and DNA–DNA relatedness, the isolate belonged to the genus Nitratireductor but could be readily distinguished from recognized species of the genus. Therefore a novel species is proposed to accommodate strain pht-3BT, for which the name Nitratireductor pacificus sp. nov. is proposed. The type strain is pht-3BT ( = CCTCC AB 209302T = LMG 25541T = MCCC 1A01024T).

Marinomonas dokdonensis sp. nov., isolated from sea water

2005 ◽  
Vol 55 (6) ◽  
pp. 2303-2307 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sea Water ◽  
Sequence Similarity ◽  
Halophilic Bacteria ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Dna Relatedness

Two Gram-negative, motile, non-spore-forming, slightly halophilic bacteria (strains DSW10-10T and DSW10-19) were isolated from sea water and subjected to a polyphasic taxonomic study. They grew optimally at 30 °C and in the presence of 2–3 % (w/v) NaCl. Strains DSW10-10T and DSW10-19 were characterized chemotaxonomically as containing Q-8 as the predominant ubiquinone and C18 : 1 ω7c, C16 : 0 and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. Their DNA G+C contents were 45·3–45·7 mol%. Strains DSW10-10T and DSW10-19 exhibited a 16S rRNA gene sequence similarity value of 100 % and possessed a mean DNA–DNA relatedness level of 85 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains DSW10-10T and DSW10-19 fell within the radiation of the cluster encompassed by the genus Marinomonas. Strains DSW10-10T and DSW10-19 had 16S rRNA gene sequence similarity levels of 95·7–97·7 % with respect to the type strains of Marinomonas species with validly published names. Levels of DNA–DNA relatedness were low enough to indicate that the two strains constitute a distinct Marinomonas species. On the basis of phenotypic data and phylogenetic and genetic distinctiveness, strains DSW10-10T (=KCTC 12394T=DSM 17202T) and DSW10-19 were placed in the genus Marinomonas as members of a novel species, Marinomonas dokdonensis sp. nov.

scholarly journals Porphyrobacter dokdonensis sp. nov., isolated from sea water

2006 ◽  
Vol 56 (5) ◽  
pp. 1079-1083 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Mi-Hwa Lee ◽  
Hyun Woo Oh ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sea Water ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strain, DSW-74T, was isolated from sea water off the island of Dokdo, Korea, and its taxonomic position was investigated by a polyphasic study. Strain DSW-74T grew optimally at 37 °C and in the presence of 2 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C17 : 1 ω6c and C18 : 1 ω7c as the major fatty acids. Its DNA G+C content was 65.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DSW-74T was most closely related to Porphyrobacter species. Similarity values between the 16S rRNA gene sequence of strain DSW-74T and those of the type strains of recognized Porphyrobacter species and of Erythromicrobium ramosum were in the range 97.4–98.7 %. Strain DSW-74T exhibited 16S rRNA gene sequence similarity values of <97.5 % to recognized Erythrobacter species and the other species used in the phylogenetic analysis. DNA–DNA relatedness levels and differential phenotypic properties made it possible to categorize strain DSW-74T as representing a novel Porphyrobacter species. On the basis of the taxonomic data presented, it is proposed that DSW-74T (=KCTC 12395T=DSM 17193T) should be classified in the genus Porphyrobacter as the type strain of a novel species, Porphyrobacter dokdonensis sp. nov.

scholarly journals Roseovarius mucosus sp. nov., a member of the Roseobacter clade with trace amounts of bacteriochlorophyll a

2005 ◽  
Vol 55 (6) ◽  
pp. 2377-2383 ◽  
Author(s):  
Hanno Biebl ◽  
Martin Allgaier ◽  
Heinrich Lünsdorf ◽  
Rüdiger Pukall ◽  
Brian J. Tindall ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sea Water ◽  
Tricarboxylic Acid Cycle ◽  
16S Rrna Gene Sequence ◽  
Wall Structure ◽  
Rrna Gene ◽  
Reaction Centre ◽  
Rrna Gene Sequence

Among a group of marine isolates that were found to be positive for genes of the bacterial photosynthetic reaction centre, a strain was selected for characterization that was phylogenetically close to the genus Roseovarius. The strain, designated DFL-24T, originated from a culture of Alexandrium ostenfeldii (dinoflagellate) and contained small amounts of bacteriochlorophyll a, corresponding to about 1 % of the amount found in intensely pigmented aerobic phototrophs such as Roseobacter litoralis. Cells were rods of 0·5–0·7×1·3–3·0 μm often with uneven ends, suggesting a budding mode of division. True motility was not observed. Electron micrographs of ultrathin sections revealed a Gram-negative cell-wall structure. Cultures did not grow without addition of sea salts and tolerated up to 10 % (w/v) sea-water salts. Acetate, butyrate, tricarboxylic acid cycle intermediates, glutamate and glycerol were used as growth substrates, but not glucose or fructose. Biotin, thiamine and nicotinic acid were required as growth factors. The DNA G+C content was 63 mol%. 16S rRNA gene sequence analysis placed the strain within the Roseobacter lineage of the ‘Alphaproteobacteria’. Its closest phylogenetic neighbour was Roseovarius tolerans showing 96·4 % 16S rRNA gene sequence similarity. Based also on its physiological and biochemical characteristics, the strain is considered to represent a novel species of the genus Roseovarius, Roseovarius mucosus sp. nov. Strain DFL-24T (=DSM 17069T=NCIMB 14077T) is the type strain. The 16S rRNA gene sequence of DFL-24T was found to have a similarity of 99·7 % with an unidentified strain, 253-13 (=DSM 17070), which was likewise characterized and shown to constitute another strain of the species.

scholarly journals Marinomonas polaris sp. nov., a psychrohalotolerant strain isolated from coastal sea water off the subantarctic Kerguelen islands

2006 ◽  
Vol 56 (2) ◽  
pp. 361-364 ◽  
Author(s):  
Pratima Gupta ◽  
Preeti Chaturvedi ◽  
Suman Pradhan ◽  
Daniel Delille ◽  
Sisinthy Shivaji
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sea Water ◽  
Sequence Data ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Coastal Sea ◽  
Taxonomic Approach

Two aerobic, psychrohalotolerant, motile bacterial isolates, CK13T and CK16, isolated from sea-water samples collected off the subantarctic Kerguelen island, were characterized by using a polyphasic taxonomic approach. On the basis of 16S rRNA gene sequence data, the strains were 99·6 % similar and exhibited 93–97 % similarity with the seven recognized species of Marinomonas. The most closely related species were Marinomonas pontica and Marinomonas primoryensis, with 97 and 96 % similarity at the 16S rRNA gene sequence level, respectively. DNA–DNA hybridization values between strain CK13T and M. pontica and M. primoryensis were only 58 and 40 %, respectively. The major fatty acids present in strain CK13T were iso-C16 : 0, C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. The DNA G+C content of strain CK13T was 41·2 mol%. Phosphatidylethanolamine and phosphatidylglycerol were identified as the predominant phospholipids. All the above characteristics support the affiliation of strain CK13T to the genus Marinomonas. Phylogenetic analysis and phenotypic and genotypic distinctiveness confirmed that strains CK13T and CK16 are members of a novel species of the genus Marinomonas, for which the name Marinomonas polaris sp. nov. is proposed. The type strain is CK13T (=MTCC 6645T=DSM 16579T=JCM 12522T).

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