Ruegeria marina sp. nov., isolated from Marine Sediment

2011 ◽  
Vol 61 (2) ◽  
pp. 347-350 ◽  
Author(s):  
Ying-Yi Huo ◽  
Xue-Wei Xu ◽  
Xue Li ◽  
Chen Liu ◽  
Heng-Lin Cui ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Dna Reassociation ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Ruegeria Pomeroyi ◽  
Ubiquinone 10

A Gram-negative, neutrophilic and rod-shaped bacterium, strain ZH17T, was isolated from a marine sediment of the East China Sea and subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0–7.5 % (w/v) NaCl and at pH 6.5–9.0; optimum growth was observed with 0.5–3.0 % (w/v) NaCl and at pH 7.5. Chemotaxonomic analysis showed ubiquinone-10 as predominant respiratory quinone and C18 : 1 ω7c, 11-methyl C18 : 1 ω7c, C16 : 0, C12 : 0 3-OH and C16 : 0 2-OH as major fatty acids. The genomic DNA G+C content was 63.5 mol%. Comparative 16S rRNA gene sequence analysis revealed that the isolate belongs to the genus Ruegeria. Strain ZH17T exhibited the closest phylogenetic affinity to the type strain of Ruegeria pomeroyi, with 97.2 % sequence similarity, and less than 97 % sequence similarity with respect to other described species of the genus Ruegeria. The DNA–DNA reassociation value between strain ZH17T and R. pomeroyi DSM 15171T was 50.7 %. On the basis of phenotypic and genotypic data, strain ZH17T represents a novel species of the genus Ruegeria, for which the name Ruegeria marina sp. nov. (type strain ZH17T =CGMCC 1.9108T =JCM 16262T) is proposed.

scholarly journals Bacillus panaciterrae sp. nov., isolated from soil of a ginseng field

2006 ◽  
Vol 56 (12) ◽  
pp. 2861-2866 ◽  
Author(s):  
Leonid N. Ten ◽  
Sang-Hoon Baek ◽  
Wan-Taek Im ◽  
Qing-Mei Liu ◽  
Zubair Aslam ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Distinct Phylogenetic Lineage

A Gram-positive, non-motile, endospore-forming bacterium, designated Gsoil 1517T, was isolated from soil of a ginseng field in Pocheon Province (South Korea) and was characterized in order to determine its taxonomic position, using a polyphasic approach. It was found to rod-shaped and aerobic or facultatively anaerobic. It grew optimally at 30 °C and at pH 6.5–7.0. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 1517T forms a distinct phylogenetic lineage within the genus Bacillus, being related to Bacillus funiculus JCM 11201T (96.8 %). The strain showed less than 94.3 % sequence similarity with other Bacillus species. The G+C content of the genomic DNA was found to be 47.8 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C15 : 0 (42.4 %), anteiso-C15 : 0 (17.4 %), iso-C14 : 0 (9.7 %) and C16 : 0 (6.0 %). On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1517T represents a novel species of the genus Bacillus, for which the name Bacillus panaciterrae sp. nov. is proposed. The type strain is Gsoil 1517T (=KCTC 13929T=CCUG 52470T=LMG 23408T).

scholarly journals Marinobacter nitratireducens sp. nov., a halophilic and lipolytic bacterium isolated from coastal surface sea water

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2056-2063 ◽  
Author(s):  
Bhumika Vaidya ◽  
Ravinder Kumar ◽  
Suresh Korpole ◽  
Naga Radha Srinivas Tanuku ◽  
Anil Kumar Pinnaka
Keyword(s):  
Type Strain ◽  
Sea Water ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Pairwise Sequence Similarity ◽  
The Mean ◽  
Type Strains

A novel Gram-stain-negative, rod-shaped, motile bacterium, designated strain AK21T, was isolated from coastal surface sea water at Visakhapatnam, India. The strain was positive for oxidase, catalase, lipase, l-proline arylamidase and tyrosine arylamidase activities. The predominant fatty acids were C12:0, C12:0 3-OH, C16:0, C16:1ω9c, C18:1ω9c and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, two unidentified phospholipids and one unidentified lipid. Q-10 was the predominant respiratory quinone. The DNA G+C content of the strain was 54.6 mol%. 16S rRNA gene sequence analysis indicated that strain AK21T was a member of the genus Marinobacter and was closely related to Marinobacter xestospongiae, with pairwise sequence similarity of 97.2 % to the type strain, with similarity to other members of the genus of 94.0–96.8 %. The mean DNA–DNA relatedness of strain AK21T with M. xestospongiae JCM 17469T was 34.5 %, and relatedness with Marinobacter mobilis JCM 15154T was 40.5 %. Phylogenetic analysis showed that strain AK21T clustered with the type strains of M. xestospongiae and M. mobilis at distances of 2.9 and 2.8 % (97.1 and 97.2 % similarity), respectively. Based on the phenotypic characteristics and on phylogenetic inference, it appears that strain AK21T represents a novel species of the genus Marinobacter, for which the name Marinobacter nitratireducens sp. nov. is proposed. The type strain of Marinobacter nitratireducens is AK21T ( = MTCC 11704T = JCM 18428T).

scholarly journals Luteimonas composti sp. nov., a moderately thermophilic bacterium isolated from food waste

2007 ◽  
Vol 57 (4) ◽  
pp. 741-744 ◽  
Author(s):  
Chiu-Chung Young ◽  
Peter Kämpfer ◽  
Wen-Ming Chen ◽  
Wen-Shao Yen ◽  
A. B. Arun ◽  
...  
Keyword(s):  
Food Waste ◽  
Type Strain ◽  
Sequence Similarity ◽  
Thermophilic Bacterium ◽  
Physiological Data ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Moderately Thermophilic ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

A yellow-pigmented, Gram-negative, rod-shaped bacterium (strain CC-YY255T) was isolated from compost generated from food waste collected from Kinmen County, Taiwan. 16S rRNA gene sequence analysis indicated that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Luteimonas; its closest neighbour was the type strain of Luteimonas mephitis (94.4 % sequence similarity). The isolate was distinguished from Luteimonas mephitis on the basis of several phenotypic properties. The organism utilized glucose, maltose, gentiobiose, melibiose and turanose and only a few organic acids (acetate, propionate) and amino acids (l-alanyl glycine, glycyl l-aspartic acid and glycyl l-glutamic acid) as substrates. The fatty acid profile was slightly different from that reported for Luteimonas mephitis. It is evident from the genotypic, chemotaxonomic and physiological data presented that strain CC-YY255T represents a novel species of the genus Luteimonas, for which the name Luteimonas composti sp. nov. is proposed. The type strain is CC-YY255T (=CCUG 53595T=CIP 109311T=BCRC 17598T).

scholarly journals Amorphus orientalis sp. nov., an exopolysaccharide-producing bacterium isolated from salt mine sediment

2010 ◽  
Vol 60 (8) ◽  
pp. 1750-1754 ◽  
Author(s):  
Yong-Xia Wang ◽  
Ji-Hui Liu ◽  
Yi-Guang Chen ◽  
Xiao-Xia Zhang ◽  
Zhi-Gang Wang ◽  
...  
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Salt Mine ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
West China ◽  
Unknown Phospholipid ◽  
Ubiquinone 10

A Gram-negative, moderately halophilic, non-motile, aerobic bacterium, designated strain YIM D10T, was isolated from a salt mine sediment sample from Yunnan, south-west China. The strain grew optimally in the presence of 3–8 % NaCl and at 28 °C and pH 7.5. The polar lipid profile of strain YIM D10T comprised diphosphatidylglycerol, an unknown phospholipid and two unknown aminolipids. The major cellular fatty acids were C18 : 1 ω7c (30.5 %), C19 : 0 cyclo ω8c (29.3 %) and C18 : 0 (13.2 %). The respiratory quinone was ubiquinone 10 (Q-10). The genomic DNA G+C content was 65.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM D10T was closely related to Amorphus coralli RS.Sph.026T (96.8 % gene sequence similarity). Results confirmed the placement of isolate YIM D10T within the genus Amorphus. However, DNA–DNA hybridization between strain YIM D10T and the type strain of the only recognized species of the genus Amorphus, A. coralli RS.Sph.026T, was 16.7 %, showing clearly that the isolate constitutes a new genospecies. Strain YIM D10T could be clearly differentiated from A. coralli and other phylogenetic neighbours on the basis of some phenotypic, genotypic and chemotaxonomic features. Therefore, strain YIM D10T is considered to represent a novel species of the genus Amorphus, for which the name Amorphus orientalis sp. nov. is proposed; the type strain is YIM D10T (=DSM 21202T=CCTCC AA 208035T).

scholarly journals Tolumonas osonensis sp. nov., isolated from anoxic freshwater sediment, and emended description of the genus Tolumonas

2011 ◽  
Vol 61 (11) ◽  
pp. 2659-2663 ◽  
Author(s):  
Matthew E. Caldwell ◽  
Toby D. Allen ◽  
Paul A. Lawson ◽  
Ralph S. Tanner
Keyword(s):  
Type Strain ◽  
Freshwater Sediment ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Respiratory Quinone ◽  
Fermentation Products ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Emended Description ◽  
Bacterium Strain

A polyphasic taxonomic study was performed on a strain of an unknown Gram-negative, non-motile, saccharolytic, facultatively anaerobic bacterium, strain OCF 7T, isolated from anoxic freshwater sediment. The strain grew optimally at 22 °C and pH 7.5, and was able to grow under strictly anaerobic conditions. Major fermentation products from glucose metabolism were formate, acetate, ethanol and lactate. Comparative 16S rRNA gene sequence analysis indicated that strain OCF 7T was phylogenetically related to the type strain of Tolumonas auensis (97.2 % similarity) within the family Aeromonadaceae of the Gammaproteobacteria. However, OCF 7T did not produce toluene from phenylacetate, phenylalanine, phenoxyacetate, phenylsuccinate or phenylbutyrate in the presence of glucose. Phenol was not produced from tyrosine or phenoxyacetate in the presence of glucose. Dominant fatty acids of this micro-organism included C16 : 0, C18 : 1ω7c and C16 : 1ω7c (and/or iso-C15 : 0 2-OH). Major polar lipids were phosphatidylglycerol and phosphatidylethanolamine, and the respiratory quinone was menaquinone MK-8. The genomic DNA G+C content of strain OCF 7T was 52.1 mol%. Based on phylogenetic and phenotypic evidence, strain OCF 7T should be classified as a representative of a novel species of Tolumonas, for which the name Tolumonas osonensis sp. nov. is proposed; the type strain is OCF 7T ( = DSM 22975T  = ATCC BAA-1908T). An emended description of the genus Tolumonas is also given.

Tropicimonas sediminicola sp. nov., isolated from marine sediment

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2424-2429 ◽  
Author(s):  
Na-Ri Shin ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Bora Yun ◽  
Tae Woong Whon ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

A novel Gram-negative, obligately aerobic, non-motile, rod-shaped bacterium, strain M97T, was isolated from marine sediment of a cage-cultured ark clam farm on the south coast of Korea. Strain M97T was positive for oxidase and catalase. Optimal growth occurred at 37 °C, with 1–2 % (w/v) NaCl and at pH 7–8. The main cellular fatty acids were C16 : 0, C18 : 1ω7c, C12 : 0 3-OH and cyclo-C19 : 0ω8c. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unknown aminolipid and three unknown lipids. The predominant respiratory quinone was ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain M97T belongs to the genus Tropicimonas , with highest sequence similarity to Tropicimonas aquimaris DPG-21T (99.0 %). The DNA G+C content of strain M97T was 68.5 mol%. Mean DNA–DNA relatedness between strain M97T and T. aquimaris DPG-21T was 46±10 %. Based on phylogenetic, phenotypic and genotypic analyses, strain M97T is considered to represent a novel species of the genus Tropicimonas , for which the name Tropicimonas sediminicola sp. nov. is proposed. The type strain is M97T ( = KACC 15544T = JCM 17731T).

scholarly journals Paracoccus homiensis sp. nov., isolated from a sea-sand sample

2006 ◽  
Vol 56 (10) ◽  
pp. 2387-2390 ◽  
Author(s):  
Byung-Yong Kim ◽  
Hang-Yeon Weon ◽  
Seung-Hee Yoo ◽  
Soon-Wo Kwon ◽  
Yang-Hee Cho ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Rrna Gene ◽  
Sand Sample ◽  
Respiratory Quinone ◽  
Sea Sand ◽  
Gene Sequence Analysis ◽  
Major Respiratory Quinone ◽  
Genotypic Characteristics ◽  
Ubiquinone 10 ◽  
Type Strains

Strain DD-R11T, isolated from a sea-sand sample from Homi Cape, Pohang city, South Korea, was a Gram-negative, aerobic, motile, non-spore-forming, rod- to ovoid-shaped bacterium. Colonies grown on marine agar were circular, convex and colourless to creamy white. Growth occurred between 10 and 40 °C (optimum 25–30 °C) and at pH 5.0–9.0 (optimum pH 6.0–8.0). The strain could grow in up to 15 % NaCl (optimum 3–5 % NaCl). According to 16S rRNA gene sequence analysis, the strain was a member of the genus Paracoccus in the Alphaproteobacteria. Sequence similarities to type strains of the genus Paracoccus were between 94.6 and 98.3 %, showing the highest sequence similarity to Paracoccus zeaxanthinifaciens ATCC 21588T. The DNA–DNA relatedness value of strain DD-R11T and P. zeaxanthinifaciens ATCC 21588T was 27 %. Strain DD-R11T was characterized by having ubiquinone 10 as the major respiratory quinone and C18 : 1 ω7c as the predominant fatty acid. The DNA G+C content was 63.0 mol%. On the basis of its phenotypic and genotypic characteristics, it is suggested that DD-R11T represents a novel species of the genus Paracoccus, for which the name Paracoccus homiensis sp. nov. is proposed, with DD-R11T (=KACC 11518T=DSM 17862T) as the type strain.

scholarly journals Arenimonas malthae sp. nov., a gammaproteobacterium isolated from an oil-contaminated site

2007 ◽  
Vol 57 (12) ◽  
pp. 2790-2793 ◽  
Author(s):  
Chiu-Chung Young ◽  
Peter Kämpfer ◽  
Mann-Jing Ho ◽  
Hans-Jürgen Busse ◽  
Birgit E. Huber ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Contaminated Site ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Phylogenetic Affiliation ◽  
Dna Reassociation ◽  
Gene Sequence Analysis

A Gram-negative, rod-shaped bacterium (CC-JY-1T) was isolated on nutrient agar from a soil sample collected from an oil-contaminated site located in Chyai county, Taiwan. 16S rRNA gene sequence analysis demonstrated that this isolate is unique, showing 96.7 % sequence similarity to the type strain of Arenimonas donghaensis and similarities of 93.0–93.8 % to species of the genera Thermomonas, Lysobacter and Silanimonas. The presence of ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and the fatty acid profile were in accordance with the phylogenetic affiliation of CC-JY-1T. DNA–DNA reassociation experiments between CC-JY-1T and A. donghaensis KACC 11381T resulted in a mean relatedness value of 32 %, indicating that strain CC-JY1T represents a novel species in the genus Arenimonas, for which we propose the name Arenimonas malthae sp. nov. The type strain is CC-JY-1T (=CCUG 53596T =CIP 109310T).

scholarly journals Bacteroides cellulosilyticus sp. nov., a cellulolytic bacterium from the human gut microbial community

2007 ◽  
Vol 57 (7) ◽  
pp. 1516-1520 ◽  
Author(s):  
Céline Robert ◽  
Christophe Chassard ◽  
Paul A. Lawson ◽  
Annick Bernalier-Donadille
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Cellulolytic Bacterium ◽  
Strictly Anaerobic ◽  
Gene Sequence Analysis ◽  
Human Faecal Sample ◽  
Bacterium Strain ◽  
Gut Microbial Community ◽  
Physiological And Biochemical

A strictly anaerobic cellulolytic bacterium, strain CRE21T, was isolated from a human faecal sample. Cells were Gram-negative non-motile rods that were about 1.7 μm in length and 0.9 μm in width. Strain CRE21T degraded different types of cellulose and was able to grow on a variety of carbohydrates. Cellulose and sugars were mainly converted to acetate, propionate and succinate. The G+C content of the DNA was 41.1 mol%. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Bacteroides with highest sequence similarity to the type strain of Bacteroides intestinalis (98 %). DNA–DNA hybridization results revealed that strain CRE21T was distinct from B. intestinalis (40 % DNA–DNA relatedness). Strain CRE21T also showed several characteristics distinct from B. intestinalis. In particular, it exhibited different capacity to degrade polysaccharides such as cellulose. On the basis of phylogenetic analysis and the morphological, physiological and biochemical data presented in this study, strain CRE21T can be readily differentiated from recognized species of the genus Bacteroides. The name Bacteroides cellulosilyticus sp. nov. is proposed to accommodate this organism. The type strain is CRE21T (=DSM 14838T=CCUG 44979T).

Oceanobacillus neutriphilus sp. nov., isolated from activated sludge in a bioreactor

2010 ◽  
Vol 60 (10) ◽  
pp. 2409-2414 ◽  
Author(s):  
Jun-Yi Yang ◽  
Ying-Yi Huo ◽  
Xue-Wei Xu ◽  
Fan-Xu Meng ◽  
Min Wu ◽  
...  
Keyword(s):  
Activated Sludge ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Tween 40 ◽  
Tween 60 ◽  
Taxonomic Characterization ◽  
Type Strains

A Gram-stain-positive, neutrophilic, rod-shaped bacterium, strain A1gT, was isolated from activated sludge of a bioreactor and was subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0–17.0 % (w/v) NaCl and at pH 6.0–9.0; optimum growth was observed in the presence of 3.0–5.0 % (w/v) NaCl and at pH 7.0. Strain A1gT was motile, formed cream-coloured colonies, was catalase- and oxidase-positive and was able to hydrolyse aesculin, Tween 40 and Tween 60. Chemotaxonomic analysis revealed menaquinone-7 as the predominant respiratory quinone and anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0 as major fatty acids. The genomic DNA G+C content of strain A1gT was 36.3 mol%. Comparative 16S rRNA gene sequence analysis revealed that the new isolate belonged to the genus Oceanobacillus and exhibited closest phylogenetic affinity to the type strains of Oceanobacillus oncorhynchi subsp. incaldanensis (97.9 % similarity) and O. oncorhynchi subsp. oncorhynchi (97.5 %), but less than 97 % sequence similarity with respect to the type strains of other recognized Oceanobacillus species. Levels of DNA–DNA relatedness between strain A1gT and reference strains O. oncorhynchi subsp. incaldanensis DSM 16557T, O. oncorhynchi subsp. oncorhynchi JCM 12661T and Oceanobacillus iheyensis DSM 14371T were 29, 45 and 38 %, respectively. On the basis of phenotypic and genotypic data, strain A1gT is considered to represent a novel species of the genus Oceanobacillus, for which the name Oceanobacillus neutriphilus sp. nov. is proposed. The type strain is A1gT (=CGMCC 1.7693T =JCM 15776T).

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