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 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 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).

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).

scholarly journals Sediminicola luteus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae

2006 ◽  
Vol 56 (4) ◽  
pp. 841-845 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Yasuyoshi Nakagawa ◽  
Shigeaki Harayama
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Golden Yellow ◽  
The Family

The taxonomic position of four Gram-negative, rod-shaped, golden-yellow-coloured bacteria isolated from marine sediments was determined. Analysis of the almost complete 16S rRNA gene sequences indicated that these isolates belong to the family Flavobacteriaceae. An unclassified bacterium, NBRC 15975, was found to be the closest relative, showing 16S rRNA gene sequence similarity of 93 %; other related genera shared only 87·9–90·5 % similarity. In contrast, the four isolates shared high levels of 16S rRNA gene sequence similarity (99·3–99·7 %) and high DNA–DNA reassociation values (93–104 %). The isolates could be differentiated phenotypically from other genera by the abilities to reduce nitrate and to degrade gelatin, casein and starch. The only respiratory quinone was MK-6, and the major fatty acids were iso-C15 : 0, iso-C15 : 1, anteiso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH. The DNA G+C content was 38–40 mol%. Differentiating phenotypic characteristics and large phylogenetic distances between the isolates and previously published genera indicated that the isolates constitute a novel genus, for which the name Sediminicola gen. nov. is proposed. The type species is Sediminicola luteus sp. nov. (type strain CNI-3T=NBRC 100966T=LMG 23246T).

scholarly journals Candidimonas nitroreducens gen. nov., sp. nov. and Candidimonas humi sp. nov., isolated from sewage sludge compost

2011 ◽  
Vol 61 (9) ◽  
pp. 2238-2246 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
Vânia Figueira ◽  
Ana R. Lopes ◽  
Evie De Brandt ◽  
Peter Vandamme ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sludge Compost ◽  
The Family

Two bacterial strains (SC-089T and SC-092T) isolated from sewage sludge compost were characterized by using a polyphasic approach. The isolates were Gram-negative short rods, catalase- and oxidase-positive, and showed good growth at 30 °C, at pH 7 and with 1 % (w/v) NaCl. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, the strains were observed to be members of the family Alcaligenaceae, but could not be identified as members of any validly described genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa, together with comparative analysis of phenotypic traits and chemotaxonomic markers, supported the proposal of a new genus within the family Alcaligenaceae, for which the name Candidimonas gen. nov. is proposed. Strains SC-089T and SC-092T, which shared 99.1 % 16S rRNA gene sequence similarity, could be differentiated at the phenotypic level, and DNA–DNA hybridization results supported their identification as representing distinct species. The names proposed for these novel species are Candidimonas nitroreducens sp. nov. (type strain, SC-089T = LMG 24812T = CCUG 55806T) and Candidimonas humi sp. nov. (type strain, SC-092T = LMG 24813T = CCUG 55807T).

scholarly journals Sphingobium qiguonii sp. nov., a carbaryl-degrading bacterium isolated from a wastewater treatment system

2010 ◽  
Vol 60 (12) ◽  
pp. 2724-2728 ◽  
Author(s):  
Qiu-Xiang Yan ◽  
Yong-Xia Wang ◽  
Shun-Peng Li ◽  
Wen-Jun Li ◽  
Qing Hong
Keyword(s):  
Phylogenetic Analysis ◽  
Wastewater Treatment ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Treatment System ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

A Gram-staining-negative, catalase-positive, carbaryl-degrading, non-spore-forming, non-motile, rod-shaped bacterium, designated strain X23T, was isolated from a wastewater treatment system. Phylogenetic analysis based on 16S rRNA gene sequence indicated that the strain belongs to the genus Sphingobium. The highest 16S rRNA gene sequence similarity observed for the isolate was 96.6 % with the type strain of Sphingobium amiense. Chemotaxonomic data [major ubiquinone: Q-10; major polar lipids: diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, sphingoglycolipid, phosphatidylethanolamine and unknown aminolipids and phospholipids; major fatty acids: summed feature 7 (C18 : 1 ω7c, C18 : 1 ω9t and/or C18 : 1 ω12t), C16 : 1 ω5c, C14 : 0 2-OH and C16 : 0 2-OH] as well as the inability to reduce nitrate and the presence of spermidine as the major polyamine supported the affiliation of the strain to the genus Sphingobium. Based on the phylogenetic analysis, whole-cell fatty acid composition and biochemical characteristics, the strain could be separated from all recognized species of the genus Sphingobium. Strain X23T should be classified as a novel species of the genus Sphingobium, for which the name Sphingobium qiguonii sp. nov. is proposed, with strain X23T (=CCTCC AB 208221T =DSM 21541T) as the type strain.

scholarly journals Pseudosphingobacterium domesticum gen. nov., sp. nov., isolated from home-made compost

2007 ◽  
Vol 57 (7) ◽  
pp. 1535-1538 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
M. Fernanda Nobre ◽  
Olga C. Nunes ◽  
Célia M. Manaia
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family

A bacterial strain, DC-186T, isolated from home-made compost, was characterized for its phenotypic and phylogenetic properties. The isolate was a Gram-negative rod that was able to grow at 15–36 °C and pH 5.5–8.0. Strain DC-186T was positive in tests for catalase, oxidase and β-galactosidase activities and aesculin hydrolysis. The predominant fatty acids were the summed feature C16 : 1/iso-C15 : 0 2-OH (42 %) and iso-C15 : 0 (26 %), the major respiratory quinone was menaquinone-7 and the genomic DNA G+C content was 42 mol%. 16S rRNA gene sequence analysis and phenetic characterization indicated that this organism belongs to the phylum Bacteroidetes and revealed its affiliation to the family Sphingobacteriaceae. Of recognized taxa, strain DC-186T was most closely related to Sphingobacterium daejeonense (90 % sequence similarity) based on 16S rRNA gene sequence analysis. The low 16S rRNA gene sequence similarity with other recognized taxa and the identification of distinctive phenetic features for this isolate support the definition of a new genus within the family Sphingobacteriaceae. The name Pseudosphingobacterium domesticum gen. nov., sp. nov. is proposed, with strain DC-186T (=CCUG 54353T=LMG 23837T) as the type strain.

Paracoccus caeni sp. nov., isolated from sludge

2011 ◽  
Vol 61 (8) ◽  
pp. 1968-1972 ◽  
Author(s):  
Myungjin Lee ◽  
Song-Geun Woo ◽  
Giho Park ◽  
Myung Kyum Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Type Strains ◽  
Sequence Similarities

A Gram-negative, non-motile bacterium, designated MJ17T, was isolated from sludge at the Daejeon sewage disposal plant in South Korea. Comparative 16S rRNA gene sequence analysis showed that strain MJ17T belonged to the genus Paracoccus in the family Rhodobacteraceae of the class Alphaproteobacteria. 16S rRNA gene sequence similarities between strain MJ17T and type strains of species of the genus Paracoccus were 94.1–97.4 %. The highest similarities were between strain MJ17T and Paracoccus homiensis DD-R11T, Paracoccus zeaxanthinifaciens ATCC 21588T and Paracoccus alcaliphilus JCM 7364T (97.4, 97.2 and 96.3 %, respectively). Strain MJ17T exhibited <22 % DNA–DNA relatedness with P. homiensis KACC 11518T and P. zeaxanthinifaciens JCM 21774T. The G+C content of the genomic DNA was 58.7 mol%. Strain MJ17T contained ubiquinone Q-10. The major fatty acids were C18 : 0 (11.3 %), C16 : 0 (10.2 %) and summed feature 7 (containing one or more of C18 : 1ω7c, C18 : 1ω9c and C18 : 1ω12t; 54.3 %). Poly-β-hydroxybutyrate granules are formed. On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, strain MJ17T should be classified in a novel species of the genus Paracoccus, for which the name Paracoccus caeni sp. nov. is proposed. The type strain is MJ17T ( = KCTC 22480T  = JCM 16385T  = KEMB 9004-001T).

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