scholarly journals Tenacibaculum litoreum sp. nov., isolated from tidal flat sediment

2006 ◽  
Vol 56 (3) ◽  
pp. 635-640 ◽  
Author(s):  
Dong Han Choi ◽  
Yoon-Gon Kim ◽  
Chung Yeon Hwang ◽  
Hana Yi ◽  
Jongsik Chun ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Physiological Data ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Ph Range

A rod-shaped bacterium, designated CL-TF13T, was isolated from a tidal flat in Ganghwa, Korea. Analysis of the 16S rRNA gene sequence revealed an affiliation with the genus Tenacibaculum. The sequence similarities between CL-TF13T and type strains of members of the genus Tenacibaculum were from 94·2 to 97·4 %. Cells were motile by means of gliding. Strain CL-TF13T grew on solid medium as pale-yellow colonies with an irregular spreading edge. The strain was able to grow in NaCl at a range of 3–5 %. They grew within a temperature range of 5–40 °C and at pH range of 6–10. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH, 19·6 %), iso-C15 : 0 (18·8 %) and iso-C17 : 0 3-OH (13·6 %). Fatty acids such as C18 : 3 ω6c (6,9,12) (1·5 %) and summed feature 4 (iso I- and/or anteiso B-C17 : 1, 1·3 %) were uniquely found in minor quantities in CL-TF13T among Tenacibaculum species. The DNA G+C content was 30 mol%. According to physiological data, fatty-acid composition and 16S rRNA gene sequence, CL-TF13T could be assigned to the genus Tenacibaculum but distinguished from the recognized species of the genus. Therefore, strain CL-TF13T (=KCCM 42115T=JCM 13039T) represents a novel species, for which the name Tenacibaculum litoreum sp. nov. is proposed.

scholarly journals Exiguobacterium aestuarii sp. nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

2005 ◽  
Vol 55 (2) ◽  
pp. 885-889 ◽  
Author(s):  
In-Gi Kim ◽  
Mi-Hwa Lee ◽  
Seo-Youn Jung ◽  
Jae Jun Song ◽  
Tae-Kwang Oh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Yellow Sea ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Three Gram-variable, rod-shaped bacterial strains, TF-16T, TF-19 and TF-80T, were isolated from a tidal flat of Daepo Beach (Yellow Sea) near Mokpo City, Korea, and their taxonomic positions were investigated by a polyphasic approach. These isolates grew optimally in the presence of 2 % NaCl and at 30 °C. Their peptidoglycan types were based on l-Lys–Gly. The predominant menaquinone detected in the three strains was MK-7. The three strains contained large amounts of the branched fatty acids iso-C17 : 0, anteiso-C13 : 0, iso-C13 : 0 and iso-C15 : 0. The DNA G+C contents of strains TF-16T, TF-19 and TF-80T were 48·6, 48·4 and 48·0 mol%, respectively. The three strains formed a coherent cluster with Exiguobacterium species in a phylogenetic tree based on 16S rRNA gene sequences. They showed closest phylogenetic affiliation to Exiguobacterium aurantiacum, with 16S rRNA gene sequence similarity values of 98·1–98·3 %. The three strains exhibited 16S rRNA gene sequence similarity values of 94·0–94·6 % to the type strains of other Exiguobacterium species. Levels of DNA–DNA relatedness indicated that strains TF-16T and TF-19 and strain TF-80T are members of two species that are separate from E. aurantiacum. On the basis of phenotypic, phylogenetic and genetic data, strains TF-16T and TF-19 and strain TF-80T represent two novel species in the genus Exiguobacterium; the names Exiguobacterium aestuarii sp. nov. (type strain TF-16T=KCTC 19035T=DSM 16306T; reference strain TF-19) and Exiguobacterium marinum sp. nov. (type strain TF-80T=KCTC 19036T=DSM 16307T) are proposed.

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 Kaistia terrae sp. nov., isolated from a wetland in Korea

2010 ◽  
Vol 60 (4) ◽  
pp. 949-952 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Rangasamy Anandham ◽  
Seung-Hee Yoo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).

scholarly journals Paucibacter toxinivorans gen. nov., sp. nov., a bacterium that degrades cyclic cyanobacterial hepatotoxins microcystins and nodularin

2005 ◽  
Vol 55 (4) ◽  
pp. 1563-1568 ◽  
Author(s):  
Jarkko Rapala ◽  
Katri A. Berg ◽  
Christina Lyra ◽  
R. Maarit Niemi ◽  
Werner Manz ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Thirteen bacterial isolates from lake sediment, capable of degrading cyanobacterial hepatotoxins microcystins and nodularin, were characterized by phenotypic, genetic and genomic approaches. Cells of these isolates were Gram-negative, motile by means of a single polar flagellum, oxidase-positive, weakly catalase-positive and rod-shaped. According to phenotypic characteristics (carbon utilization, fatty acid and enzyme activity profiles), the G+C content of the genomic DNA (66·1–68·0 mol%) and 16S rRNA gene sequence analysis (98·9–100 % similarity) the strains formed a single microdiverse genospecies that was most closely related to Roseateles depolymerans (95·7–96·3 % 16S rRNA gene sequence similarity). The isolates assimilated only a few carbon sources. Of the 96 carbon sources tested, Tween 40 was the only one used by all strains. The strains were able to mineralize phosphorus from organic compounds, and they had strong leucine arylamidase and chymotrypsin activities. The cellular fatty acids identified from all strains were C16 : 0 (9·8–19 %) and C17 : 1 ω7c (<1–5·8 %). The other predominant fatty acids comprised three groups: summed feature 3 (<1–2·2 %), which included C14 : 0 3-OH and C16 : 1 iso I, summed feature 4 (54–62 %), which included C16 : 1 ω7c and C15 : 0 iso OH, and summed feature 7 (8·5–28 %), which included ω7c, ω9c and ω12t forms of C18 : 1. A more detailed analysis of two strains indicated that C16 : 1 ω7c was the main fatty acid. The phylogenetic and phenotypic features separating our strains from recognized bacteria support the creation of a novel genus and species, for which the name Paucibacter toxinivorans gen. nov., sp. nov. is proposed. The type strain is 2C20T (=DSM 16998T=HAMBI 2767T=VYH 193597T).

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 Henriciella litoralis sp. nov., isolated from a tidal flat, transfer of Maribaculum marinum Lai et al. 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. and emended description of the genus Henriciella

2011 ◽  
Vol 61 (4) ◽  
pp. 722-727 ◽  
Author(s):  
Se Hee Lee ◽  
Jae Kuk Shim ◽  
Jeong Myeong Kim ◽  
Hyung-Kyoon Choi ◽  
Che Ok Jeon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Gene Sequence ◽  
The Yellow Sea ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Emended Description

A Gram-staining-negative, strictly aerobic bacterium, designated strain SD10T, was isolated from a tidal flat of the Yellow Sea, South Korea. Cells were non-spore-forming rods that showed catalase- and oxidase-positive reactions. Growth of strain SD10T was observed at 15–40 °C (optimum, 25–30 °C), at pH 6.0–9.0 (optimum, pH 6.5–8.5) and in the presence of 1–10 % (w/v) NaCl. Strain SD10T contained ubiquinone-10 (Q-10) as a major isoprenoid quinone and C18 : 1ω7c (39.3 %), C16 : 0 (20.2 %), C17 : 0 (8.9 %) and C17 : 1ω6c (8.1 %) as major fatty acids. The cellular polar lipids were identified as phosphatidylglycerol, monoglycosyldiglyceride, glucuronopyranosyldiglyceride and two unidentified glycolipids. The G+C content of the genomic DNA was 55.2 mol%. Based on 16S rRNA gene sequence similarities, the strain was most closely related to Henriciella marina Iso4T and Maribaculum marinum P38T, with similarities of 97.8 and 97.0 %, respectively. The DNA–DNA relatedness between strain SD10T and H. marina Iso4T was 12.0±3.2 %. A phylogenetic analysis based on 16S rRNA gene sequences showed that M. marinum P38T and H. marina Iso4T formed a monophyletic cluster and that their 16S rRNA gene sequence similarity was 98.1 %. DNA–DNA hybridization between H. marina Iso4T and M. marinum LMG 24711T was 22.9±2.7 %, indicating that the two strains belong to separate species. On the basis of chemotaxonomic data and molecular properties, we propose that strain SD10T represents a novel species of the genus Henriciella, for which the name Henriciella litoralis sp. nov. is proposed. The type strain is SD10T ( = KACC 13700T  = DSM 22014T). In addition, we propose to transfer Maribaculum marinum Lai et al. 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. (type strain P38T  = CCTCC AB 208227T  = LMG 24711T  = MCCC 1A01086T), and we present an emended description of the genus Henriciella.

scholarly journals Inquilinus ginsengisoli sp. nov., isolated from soil of a ginseng field

2011 ◽  
Vol 61 (1) ◽  
pp. 201-204 ◽  
Author(s):  
Hae-Min Jung ◽  
Jung-Sook Lee ◽  
Heon-Meen Bae ◽  
Tae-Hoo Yi ◽  
Se-Young Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Physiological Data ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterium Strain ◽  
Taxonomic Approach

A Gram-reaction-negative, chemo-organotrophic, non-motile, non-spore-forming, rod-shaped bacterium (strain Gsoil 080T) was isolated from soil collected in a ginseng field in Pocheon Province, South Korea, and was investigated by using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 080T was related most closely to Inquilinus limosus strains AU0476T and AU1979 (98.9 % similarity to both). Strain Gsoil 080T shared ≤91.3 % 16S rRNA gene sequence similarity with the type strains of other recognized species examined. The genus Inquilinus belongs to the family Rhodospirillaceae in the order Rhodospirillales, class Alphaproteobacteria. The predominant ubiquinone was Q-10 and the major fatty acids were summed feature 7 (C18 : 1 ω9c/ω12t/ω7c) and C19 : 0 cyclo ω8c. The G+C content of the genomic DNA of strain Gsoil 080T was 69.9 mol%. The level of DNA–DNA relatedness between strain Gsoil 080T and I. limosus LMG 20952T was 12 %. The results of genotypic analyses in combination with chemotaxonomic and physiological data demonstrated that strain Gsoil 080T represents a novel species of the genus Inquilinus, for which the name Inquilinus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 080T (=KCTC 12574T =LMG 23638T).

Gaetbulicola byunsanensis gen. nov., sp. nov., isolated from tidal flat sediment

2010 ◽  
Vol 60 (1) ◽  
pp. 196-199 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Yong-Taek Jung ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences

A Gram-negative, non-motile and pleomorphic bacterial strain, SMK-114T, which belongs to the class Alphaproteobacteria, was isolated from a tidal flat sample collected in Byunsan, Korea. Strain SMK-114T grew optimally at pH 7.0–8.0 and 25–30 °C and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain SMK-114T formed a cluster with Octadecabacter species, with which it exhibited 16S rRNA gene sequence similarity values of 95.2–95.4 %. This cluster was part of the clade comprising Thalassobius species with a bootstrap resampling value of 76.3 %. Strain SMK-114T exhibited 16S rRNA gene sequence similarity values of 95.1–96.3 % to members of the genus Thalassobius. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The DNA G+C content was 60.0 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SMK-114T is considered to represent a novel species in a new genus for which the name Gaetbulicola byunsanensis gen. nov., sp. nov. is proposed. The type strain of Gaetbulicola byunsanensis is SMK-114T (=KCTC 22632T =CCUG 57612T).

scholarly journals Sphingomonas rubra sp. nov., isolated from bioreactor wastewater

2011 ◽  
Vol 61 (5) ◽  
pp. 1028-1032 ◽  
Author(s):  
Ying-Yi Huo ◽  
Xue-Wei Xu ◽  
Sheng-Pan Liu ◽  
Heng-Lin Cui ◽  
Xue Li ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Batch Reactor ◽  
Sensu Stricto ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Similarities

A Gram-reaction-negative, rod-shaped, motile, neutrophilic bacterium, designated strain BH3T, was isolated from wastewater of a sequential batch reactor treating wastewater taken from a leather plant. The isolate grew in 0–8 % (w/v) NaCl, at pH 6–9 and at 4–45 °C. Chemotaxonomic analysis showed that strain BH3T had characteristics typical of members of the genus Sphingomonas, such as the presence of sphingolipids, Q-10 and 2-hydroxymyristic acid and the absence of 3-hydroxy fatty acids. The presence of C18 : 1ω7c (39.2 %) and C16 : 0 (11.2 %) as major fatty acids, C14 : 0 2-OH (20.6 %) as the major 2-hydroxy fatty acid and homospermidine as the major polyamine indicated that strain BH3T belonged to the genus Sphingomonas sensu stricto. The genomic DNA G+C content of strain BH3T was 65.6 mol%. 16S rRNA gene sequence similarities between the isolate and closely related members of the genus Sphingomonas sensu stricto ranged from 92.6 to 97.3 %, the highest sequence similarities being to Sphingomonas melonis DSM 14444T (97.3 %) and Sphingomonas aquatilis DSM 15581T (97.3 %). Based on its phenotypic characteristics and the results of DNA–DNA hybridization studies and 16S rRNA gene sequence comparisons, strain BH3T represents a novel species of the genus Sphingomonas sensu stricto, for which the name Sphingomonas rubra sp. nov. is proposed. The type strain is BH3T ( = CGMCC 1.9113T  = JCM 16230T).

scholarly journals Acidianus sulfidivorans sp. nov., an extremely acidophilic, thermophilic archaeon isolated from a solfatara on Lihir Island, Papua New Guinea, and emendation of the genus description

2007 ◽  
Vol 57 (7) ◽  
pp. 1418-1423 ◽  
Author(s):  
Jason J. Plumb ◽  
Christina M. Haddad ◽  
John A. E. Gibson ◽  
Peter D. Franzmann
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Papua New Guinea ◽  
Electron Acceptor ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Ph Range

A novel, extremely thermoacidophilic, obligately chemolithotrophic archaeon (strain JP7T) was isolated from a solfatara on Lihir Island, Papua New Guinea. Cells of this organism were non-motile, Gram-negative staining, irregular-shaped cocci, 0.5–1.5 μm in size, that grew aerobically by oxidation of sulfur, Fe2+ or mineral sulfides. Cells grew anaerobically using Fe3+ as a terminal electron acceptor and H2S as an electron donor but did not oxidize hydrogen with elemental sulfur as electron acceptor. Strain JP7T grew optimally at 74 °C (temperature range 45–83 °C) and pH 0.8–1.4 (pH range 0.35–3.0). On the basis of 16S rRNA gene sequence similarity, strain JP7T was shown to belong to the Sulfolobaceae, being most closely related to the type strains of Acidianus ambivalens (93.7 %) and Acidianus infernus (93.6 %). Cell-membrane lipid structure, DNA base composition and 16S rRNA gene sequence similarity data support the placement of this strain in the genus Acidianus. Differences in aerobic and anaerobic metabolism, temperature and pH range for growth, and 16S rRNA gene sequence differentiate strain JP7T from recognized species of the genus Acidianus, and an emendation of the description of the genus is proposed. Strain JP7T is considered to represent a novel species of the genus Acidianus, for which the name Acidianus sulfidivorans sp. nov. is proposed. The type strain is JP7T (=DSM 18786T=JCM 13667T).

Sign in / Sign up

Export Citation Format

Share Document