scholarly journals Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm

2006 ◽  
Vol 56 (8) ◽  
pp. 1869-1873 ◽  
Author(s):  
Dong H. Choi ◽  
Byung C. Cho
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Coastal Fish ◽  
The Family ◽  
The 16S Rrna Gene

A rod-shaped marine bacterium, CL-TA03T, isolated from a biofilm in a coastal fish farm in Tongyeong, Korea, was characterized for physiological and biochemical features, fatty acid profile and phylogenetic position based on 16S rRNA gene sequences. Analysis of the 16S rRNA gene sequence revealed a clear affiliation with the family Rhodobacteraceae. Phylogenetic analysis of the 16S rRNA gene sequence showed that the closest relatives of CL-TA03T were Thalassobius gelatinovorus and Thalassobius mediterraneus (95.6 % similarity). The sequence similarities between CL-TA03T and other type species of the Roseobacter lineage ranged from 92.4 to 95.4 %. Strain CL-TA03T is motile and grows on marine agar as colourless or beige colonies. The strain is able to grow optimally in the range of 3–5 % sea salts. It grows within a temperature range of 15–35 °C and at pH 6–10. The fatty acids are dominated by 18 : 1ω7c (64.1 %) and 11-methyl 18 : 1ω7c (10.6 %). The DNA G+C content is 57.2 mol%. According to physiological data, fatty acid composition and phylogenetic analysis of the 16S rRNA gene sequence, CL-TA03T is considered to represent a new genus in the family Rhodobacteraceae and the name Shimia marina gen. nov., sp. nov. is proposed. The type strain of Shimia marina is CL-TA03T (=KCCM 42117T=JCM 13038T).

scholarly journals Citreimonas salinaria gen. nov., sp. nov., a member of the Roseobacter clade isolated from a solar saltern

2006 ◽  
Vol 56 (12) ◽  
pp. 2799-2803 ◽  
Author(s):  
Dong H. Choi ◽  
Byung C. Cho
Keyword(s):  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Rrna Gene Sequence ◽  
The Family ◽  
The 16S Rrna Gene

A lemon-shaped marine bacterium, strain CL-SP20T, isolated from hypersaline water from a solar saltern in Korea, was characterized in terms of its physiological and biochemical features, its fatty acid profile and its phylogenetic position based on 16S rRNA gene sequences. Analysis of the 16S rRNA gene sequence revealed a clear affiliation with the Roseobacter lineage (91.0–96.3 % similarity) of the family Rhodobacteraceae. However, strain CL-SP20T did not form a robust clade with any species of the Roseobacter clade, forming a distinct subline. Strain CL-SP20T is non-motile and forms beige colonies on marine agar. The strain is able to grow with sea salts at concentrations in the range 1–10 %, with optimal growth between 5 and 6 %. It grows at temperatures in the range 15–40 °C and at pH 6–10. The strain cannot oxidize thiosulfate. The fatty acids are dominated by 18 : 1ω7c (54.3 %) and 19 : 0 cyclo ω8c (20.4 %). The DNA G+C content is 67.3 mol%. According to the physiological data, fatty acid composition and phylogenetic analysis of the 16S rRNA gene sequence, strain CL-SP20T represents a novel species in a novel genus of the family Rhodobacteraceae, for which the name Citreimonas salinaria gen. nov., sp. nov. is proposed. The type strain of Citreimonas salinaria is CL-SP20T (=KCCM 42116T=JCM 13036T).

scholarly journals Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite

2011 ◽  
Vol 61 (9) ◽  
pp. 2186-2190 ◽  
Author(s):  
De-Chao Zhang ◽  
Mersiha Redzic ◽  
Franz Schinner ◽  
Rosa Margesin
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Good Growth ◽  
Rrna Gene Sequence ◽  
Alpine Glacier ◽  
The Family

Strains Cr9-30T and Cr9-12 were isolated from alpine glacier cryoconite. Both strains were Gram-negative-staining, non-motile, rod-shaped and psychrophilic, showing good growth over the temperature range 1–20 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that the two strains formed a distinct branch within the family Oxalobacteraceae and were most closely related to members of the genus Collimonas. The 16S rRNA gene sequence similarity between strains Cr9-30T and Cr9-12 was 99.0 %. The two strains showed highest 16S rRNA gene sequence pairwise similarity with Collimonas pratensis LMG 23965T (96.6 and 96.1 % for strains Cr9-30T and Cr9-12, respectively), Collimonas arenae LMG 23964T (96.5 and 96.3 %, respectively) and Collimonas fungivorans LMG 21973T (96.4 and 96.2 %, respectively). The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. The DNA G+C content of strain Cr9-30T was 51.0 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strains Cr9-30T and Cr9-12 represent a novel species in a new genus of the family Oxalobacteraceae, for which the name Glaciimonas immobilis gen. nov., sp. nov. is proposed. The type strain of Glaciimonas immobilis is Cr9-30T ( = DSM 23240T = LMG 25547T).

scholarly journals Chryseomicrobium imtechense gen. nov., sp. nov., a new member of the family Planococcaceae

2011 ◽  
Vol 61 (8) ◽  
pp. 1859-1864 ◽  
Author(s):  
Pankaj Kumar Arora ◽  
Archana Chauhan ◽  
Bhawana Pant ◽  
Suresh Korpole ◽  
Shanmugam Mayilraj ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Major Fatty Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

A Gram-stain-positive, rod-shaped, yellow, non-motile, non-spore-forming, strictly aerobic bacterial strain, designated MW 10T, was isolated from seawater of the Bay of Bengal, India, and was subjected to a polyphasic taxonomic study. Analysis of the 16S rRNA gene sequence revealed that strain MW 10T showed highest similarity to the type strains of Psychrobacillus psychrodurans (96.15 %) and Psychrobacillus psychrotolerans (96.01 %) and showed less than 96 % similarity to members of the genera Paenisporosarcina, Planococcus, Sporosarcina and Planomicrobium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain MW 10T formed a clade separate from members of closely related genera. The morphological, physiological and chemotaxonomic characteristics of strain MW 10T differed from those of members of closely related genera. The major fatty acid in strain MW 10T was iso-C15 : 0 and the menaquinones were MK-7 (48.4 %), MK-8 (32.3 %), MK-7(H2) (13.7 %) and MK-6 (5.6 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unknown phospholipid, an unknown lipid and an unknown glycolipid. The cell-wall peptidoglycan type was l-Lys–d-Asp. The genomic DNA G+C content (53.4 mol%) of strain MW 10T was significantly different from those of members of closely related genera. On the basis of its morphological, physiological and chemotaxonomic characteristics as well as our phylogenetic analysis, we conclude that strain MW 10T is a member of a novel genus and species, for which the name Chryseomicrobium imtechense gen. nov., sp. nov., is proposed. The type strain of Chryseomicrobium imtechense is MW 10T ( = MTCC 10098T  = JCM 16573T).

scholarly journals Denitratisoma oestradiolicum gen. nov., sp. nov., a 17β-oestradiol-degrading, denitrifying betaproteobacterium

2006 ◽  
Vol 56 (7) ◽  
pp. 1547-1552 ◽  
Author(s):  
Michael Fahrbach ◽  
Jan Kuever ◽  
Ruth Meinke ◽  
Peter Kämpfer ◽  
Juliane Hollender
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Municipal Wastewater ◽  
Treatment Plant ◽  
16S Rrna Gene Sequence ◽  
Physiological Data ◽  
Rrna Gene ◽  
Rrna Gene Sequence

A Gram-negative, motile, denitrifying bacterium (strain AcBE2-1T) was isolated from activated sludge of a municipal wastewater treatment plant using 17β-oestradiol (E2) as sole source of carbon and energy. Cells were curved rods, 0.4–0.8×0.8–2.0 μm in size, non-fermentative, non-spore-forming, oxidase-positive and catalase-negative. E2 was oxidized completely to carbon dioxide and water by reduction of nitrate to a mixture of dinitrogen monoxide and dinitrogen, with the intermediate accumulation of nitrite. Electron recoveries were between 90 and 100 %, taking assimilated E2 into account. With nitrate as the electron acceptor, the bacterium also grew on fatty acids (C2 to C6), isobutyrate, crotonate, dl-lactate, pyruvate, fumarate and succinate. Phylogenetic analysis of its 16S rRNA gene sequence revealed that strain AcBE2-1T represents a separate line of descent within the family Rhodocyclaceae (Betaproteobacteria). The closest relatives are the cholesterol-degrading, denitrifying bacteria Sterolibacterium denitrificans DSM 13999T and strain 72Chol (=DSM 12783), with <93.9 % sequence similarity. The G+C content of the DNA was 61.4 mol%. Detection of a quinone system with ubiquinone Q-8 as the predominant compound and a fatty acid profile that included high concentrations of C16 : 1 ω7c/iso-C15 : 0 2-OH and C16 : 0, in addition to C18 : 1 ω7c and small amounts of C8 : 0 3-OH, supported the results of the phylogenetic analysis. On the basis of 16S rRNA gene sequence data in combination with chemotaxonomic and physiological data, strain AcBE2-1T (=DSM 16959T=JCM 12830T) is placed in a new genus Denitratisoma gen. nov. as the type strain of the type species Denitratisoma oestradiolicum gen. nov., sp. nov.

scholarly journals Crenobacter luteus gen. nov., sp. nov., isolated from a hot spring

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 214-219 ◽  
Author(s):  
Lei Dong ◽  
Hong Ming ◽  
En-Min Zhou ◽  
Yi-Rui Yin ◽  
Lan Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
Polar Lipids ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
The Family

A slightly thermophilic, Gram-staining-negative and strictly aerobic bacteria, designated strain YIM 78141T, was isolated from a sediment sample collected at Hehua hot spring, Tengchong, Yunnan province, south-west China. Cells of the strain were short-rod-shaped and colonies were yellowish and circular. The strain grew at pH 6.0–10.0 (optimum, pH 8.0–9.0) and 10–55 °C (optimum, 40–50 °C). Phylogenetic analyses based on 16S rRNA gene sequence comparison demonstrated that strain YIM 78141T belongs to the family Neisseriaceae , and strain YIM 78141T also showed low levels of 16S rRNA gene sequence similarity (below 93.4 %) with all other genera in this family. The only quinone was ubiquinone 8 and the genomic DNA G+C content was 67.3 mol%. Major fatty acids (>5 %) were C12 : 0, C16 : 0, C18 : 1ω7c and summed feature 3. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phospholipids of unknown structure containing aminoglycophospholipid and three unidentified polar lipids. On the basis of the morphological, physiological and biochemical characteristics as well as genotypic data, this strain should be classified as a representative of a novel genus and species of the family Neisseriaceae , for which the name Crenobacter luteus gen. nov., sp. nov. is proposed. The type strain is YIM 78141T ( = BCRC 80650T = KCTC 32558T = DSM 27258T).

scholarly journals Kistimonas asteriae gen. nov., sp. nov., a gammaproteobacterium isolated from Asterias amurensis

2010 ◽  
Vol 60 (4) ◽  
pp. 938-943 ◽  
Author(s):  
Eun Ju Choi ◽  
Hak Cheol Kwon ◽  
Young Chang Sohn ◽  
Hyun Ok Yang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Asterias Amurensis ◽  
Light Yellow ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A novel marine bacterium, strain KMD 001T, was isolated from the starfish Asterias amurensis, which inhabits the East Sea of Korea. Strain KMD 001T was aerobic, light-yellow pigmented and Gram-stain-negative. Analyses of the 16S rRNA gene sequence revealed that strain KMD 001T represents a novel lineage within the class Gammaproteobacteria. Strain KMD 001T is closely related to the genera Endozoicomonas and Zooshikella, which belong to the family Hahellaceae and to the order Oceanospirillales. The 16S rRNA gene sequence of strain KMD 001T shows similarities of approximately 91.8–94.6 % with the above-mentioned genera. The DNA G+C content of KMD 001T is 47.6 mol%. It contains Q-9 as the major isoprenoid quinone. The predominant fatty acids were determined to be anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. Strain KMD 001T should be assigned to a novel bacterial genus within the class Gammaproteobacteria based on its phylogenetic, chemotaxonomic and phenotypic characteristics. The name Kistimonas asteriae gen. nov., sp. nov. is proposed. The type strain is KMD 001T (=KCCM 90076T =JCM 15607T).

Sandarakinotalea sediminis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae

2006 ◽  
Vol 56 (5) ◽  
pp. 959-963 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Yasuyoshi Nakagawa ◽  
Shigeaki Harayama
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Heterotrophic Bacteria ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The Family

Four Gram-negative, orange-coloured, aerobic, heterotrophic bacteria were isolated from sediment samples collected on the Pacific coast of Japan near the cities of Toyohashi and Katsuura. 16S rRNA gene sequence analysis indicated that these strains form a distinct lineage within the family Flavobacteriaceae. The four isolates shared 99.9–100 % 16S rRNA gene sequence similarity with each other and showed 88–90.9 % similarity with their neighbours in the family Flavobacteriaceae. The four strains also shared high DNA–DNA reassociation values of 67–99 % with each other. All the strains grew at 37 °C but not at 4 °C, and degraded gelatin, starch and DNA. The major fatty acids were i-C15 : 0, a-C15 : 0, i-C16 : 0 and i-C17 : 0 3-OH. However, two common fatty acids of members of the Flavobacteriaceae, i-C15 : 1 and a-C15 : 1, were absent in these strains. The DNA G+C contents of the four strains were in the range 35–37 mol%. On the basis of the polyphasic evidence, it was concluded that these strains should be classified as a novel genus and a novel species in the family Flavobacteriaceae, for which the name Sandarakinotalea sediminis gen. nov., sp. nov. is proposed. The type strain of Sandarakinotalea sediminis is CKA-5T (=NBRC 100970T=LMG 23247T).

scholarly journals Thermasporomyces composti gen. nov., sp. nov., a thermophilic actinomycete isolated from compost

2011 ◽  
Vol 61 (1) ◽  
pp. 86-90 ◽  
Author(s):  
Shuhei Yabe ◽  
Yoshifumi Aiba ◽  
Yasuteru Sakai ◽  
Masaru Hazaka ◽  
Akira Yokota
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Optimum Growth ◽  
Rrna Gene Sequence ◽  
The Family

A thermophilic, Gram-positive bacterium that formed a branched vegetative mycelium was isolated from compost. The strain, designated I3T, grew at temperatures between 35 and 62 °C, with optimum growth at 50–55 °C. No growth was observed below 29 °C or above 65 °C. The pH range for growth was 5.7–10.0, the pH for optimum growth was 7.0 and no growth was observed below pH 5.6 or above pH 10.8. The DNA G+C content of strain I3T was 69.2 mol%. The major fatty acids found were C15 : 0 iso (14.2 %), C15 : 0 anteiso (12.1 %), C17 : 0 iso (16.3 %) and C17 : 0 anteiso (21.7 %). The major menaquinones were MK-9(H4), MK-10(H4) and MK-11(H4). The cell wall contained glutamic acid, glycine, alanine and ll-diaminopimelic acid in a molar ratio of 1.0 : 3.9 : 0.6 : 0.5. The polar lipids consisted of ninhydrin-positive phosphoglycolipids, phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The cell-wall sugars were rhamnose and arabinose. 16S rRNA gene sequence analysis assigned this actinomycete to the family Nocardioidaceae, but its 16S rRNA gene sequence shared no more than 95.5 % similarity with those of other members of the family. The chemotaxonomic and phenotypic characteristics of strain I3T differed in some respects from those of members of the genus Actinopolymorpha, the most closely related genus. Therefore, strain I3T represents a novel species in a new genus of the family Nocardioidaceae, for which the name Thermasporomyces composti gen. nov., sp. nov. is proposed. The type strain of the type species is I3T (=JCM 16421T=DSM 22891T).

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