scholarly journals Clostridium ganghwense sp. nov., isolated from tidal flat sediment

2006 ◽  
Vol 56 (4) ◽  
pp. 691-693 ◽  
Author(s):  
Seil Kim ◽  
Hyunyoung Jeong ◽  
Sanggoo Kim ◽  
Jongsik Chun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Sea Salts ◽  
Tidal Flat Sediment

A Gram-negative, strictly anaerobic, halophilic, motile, sporulating and rod-shaped bacterium, designated strain HY-42-06T, was isolated from tidal flat sediment from Ganghwa Island in South Korea. The isolate produced glycerol, ethanol and CO2 as fermentation end-products from glucose. Strain HY-42-06T grew optimally at 35 °C, pH 7·5 and 3 % (w/v) artificial sea salts. No growth was observed in the absence of sea salts. In phylogenetic analyses based on 16S rRNA gene sequence, strain HY-42-06T showed a distinct phyletic line within the members of cluster I of the order Clostridiales. The closest phylogenetic neighbour to strain HY-42-06T was Clostridium novyi ATCC 17861T (94·91 % 16S rRNA gene sequence similarity). Several phenotypic characters readily differentiate the tidal flat isolate from phylogenetically related clostridia. On the basis of polyphasic evidence, strain HY-42-06T should be classified as a representative of a novel species, for which the name Clostridium ganghwense sp. nov. is proposed. The type strain is HY-42-06T (=IMSNU 40127T=KCTC 5146T=JCM 13193T).

Desulfatitalea tepidiphila gen. nov., sp. nov., a sulfate-reducing bacterium isolated from tidal flat sediment

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 761-765 ◽  
Author(s):  
Yuriko Higashioka ◽  
Hisaya Kojima ◽  
Miho Watanabe ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Sulfate Reducing ◽  
Tidal Flat Sediment

A novel sulfate-reducing bacterium, strain S28bFT, was isolated from tidal flat sediment from Tokyo Bay, Japan. Cells of strain S28bFT were rod-shaped (0.5–0.6×1.7–3.8 µm), motile and Gram-stain-negative. For growth, the optimum pH was pH 6.8–7.3 and the optimum temperature was 34–42 °C. Strain S28bFT used sulfate and thiosulfate as electron acceptors, but not nitrate. The G+C content of the genomic DNA was 56.6 mol%. The fatty acid profile of strain S28bFT was characterized by the presence of anteiso-C15 : 0 and C16 : 0 as the major components. Phylogenetic analyses based on genes for 16S rRNA, the alpha subunit of dissimilatory sulfite reductase (dsrA) and adenosine-5′-phosphosulfate reductase (aprA) revealed that the isolated strain belonged to the class Deltaproteobacteria . Its closest relative was Desulfosarcina cetonica DSM 7267T with a 16S rRNA gene sequence similarity of 93.3 %. Two other strains, S28OL1 and S28OL2 were also isolated from the same sediment. These strains were closely related to S28bFT with 16S rRNA gene sequence similarities of 99 %, and the same physiological characteristics were shared with strain S28bFT. On the basis of phylogenetic and phenotypic characterization, a novel species in a new genus, Desulfatitalea tepidiphila gen. nov., sp. nov., is proposed to accommodate the strains obtained in this study. The type strain is S28bFT ( = NBRC 107166T = DSM 23472T).

scholarly journals Caloranaerobacter ferrireducens sp. nov., an anaerobic, thermophilic, iron (III)-reducing bacterium isolated from deep-sea hydrothermal sulfide deposits

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1714-1718 ◽  
Author(s):  
Xiang Zeng ◽  
Zhao Zhang ◽  
Xi Li ◽  
Mohamed Jebbar ◽  
Karine Alain ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Sea Salts ◽  
Content Type ◽  
Link Type

A thermophilic, anaerobic, iron-reducing bacterium (strain DY22619T) was isolated from a sulfide sample collected from an East Pacific Ocean hydrothermal field at a depth of 2901 m. Cells were Gram-stain-negative, motile rods (2–10 µm in length, 0.5 µm in width) with multiple peritrichous flagella. The strain grew at 40–70 °C inclusive (optimum 60 °C), at pH 4.5–8.5 inclusive (optimum pH 7.0) and with sea salts concentrations of 1–10 % (w/v) (optimum 3 % sea salts) and NaCl concentrations of 1.5–5.0 % (w/v) (optimum 2.5 % NaCl). Under optimal growth conditions, the generation time was around 55 min. The isolate was an obligate chemoorganoheterotroph, utilizing complex organic compounds, amino acids, carbohydrates and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamate, methionine, threonine, fructose, mannose, galactose, glucose, palatinose, rhamnose, turanose, gentiobiose, xylose, sorbose, pyruvate, tartaric acid, α-ketobutyric acid, α-ketovaleric acid, galacturonic acid and glucosaminic acid. Strain DY22619T was strictly anaerobic and facultatively dependent on various forms of Fe(III) as an electron acceptor: insoluble forms and soluble forms. It did not reduce sulfite, sulfate, thiosulfate or nitrate. The genomic DNA G+C content was 29.0 mol%. Phylogenetic 16S rRNA gene sequence analyses revealed that the closest relative of strain DY22619T was Caloranaerobacter azorensis MV1087T, sharing 97.41 % 16S rRNA gene sequence similarity. On the basis of physiological distinctness and phylogenetic distance, the isolate is considered to represent a novel species of the genus Caloranaerobacter , for which the name Caloranaerobacter http://dx.doi.org/10.1601/nm.4081 ferrireducens sp. nov. is proposed. The type strain is DY22619T ( = JCM 19467T = DSM 27799T = MCCC1A06455T).

scholarly journals Reinekea aestuarii sp. nov., isolated from tidal flat sediment

2010 ◽  
Vol 60 (12) ◽  
pp. 2813-2817 ◽  
Author(s):  
Ahyoung Choi ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Dna Relatedness ◽  
Tidal Flat Sediment

Two Gram-negative, non-motile, non-pigmented and curved rod-shaped bacterial strains, designated IMCC4489T and IMCC4451, were isolated from a tidal flat sediment of the Yellow Sea. Strains IMCC4489T and IMCC4451 shared 99.9 % 16S rRNA gene sequence similarity and 78.5 % DNA–DNA relatedness, which suggested that they belonged to the same species. The isolates were most closely related to Reinekea blandensis MED297T (98.7–98.8 % 16S rRNA gene sequence similarity) and Reinekea marinisedimentorum DSM 15388T (95.3–95.4 %). DNA–DNA relatedness between the strains and R. blandensis CCUG 52066T was 31–34 %. Strains IMCC4489T and IMCC4451 could also be differentiated from the type strains of the two recognized Reinekea species by several phenotypic properties. The DNA G+C content was 51.3–51.5 mol% and the major isoprenoid quinone was Q-8. On the basis of the data obtained in this study, it is proposed that strains IMCC4489T and IMCC4451 represent a novel species, Reinekea aestuarii sp. nov. The type strain is IMCC4489T (=KCTC 22813T =KCCM 42938T =NBRC 106079T).

scholarly journals Marinimicrobium koreense gen. nov., sp. nov. and Marinimicrobium agarilyticum sp. nov., novel moderately halotolerant bacteria isolated from tidal flat sediment in Korea

2006 ◽  
Vol 56 (3) ◽  
pp. 653-657 ◽  
Author(s):  
Jee-Min Lim ◽  
Che Ok Jeon ◽  
Jae-Chan Lee ◽  
Sung-Min Song ◽  
Kwang-Yup Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Tidal Flat Sediment

Two moderately halotolerant Gram-negative bacteria were isolated from tidal flat sediment of the South Sea in Korea (the Korea Strait). The strains, designated M9T and M18T, were strictly aerobic, rod-shaped and non-spore-forming and motile with a flagellum and their major fatty acids were C16 : 0 and C19 : 0 cyclo ω8c. Strains M9T and M18T could grow in the presence of up to 13–15 % (w/v) NaCl, but their optimum salt concentrations were relatively low (0–3 %, w/v). The major predominant isoprenoid quinone was Q-8 and the G+C content of the genomic DNA was 57–58 mol%. Phylogenetic analyses and comparative 16S rRNA gene sequence studies revealed that strains M9T and M18T formed a phylogenetic lineage distinct from the genus Teredinibacter within the class Gammaproteobacteria and were most closely related to the genera Microbulbifer, Saccharophagus and Teredinibacter, with less than 92·5 % 16S rRNA gene sequence similarity. The level of 16S rRNA gene sequence similarity between the two strains was 96·7 %. On the basis of physiological and phylogenetic properties, strains M9T and M18T represent separate species within a novel genus of the class Gammaproteobacteria, for which the names Marinimicrobium koreense gen. nov., sp. nov. (type species) and Marinimicrobium agarilyticum sp. nov. are proposed. The type strains of Marinimicrobium koreense and Marinimicrobium agarilyticum are M9T (=KCTC 12356T=DSM 16974T) and M18T (=KCTC 12357T=DSM 16975T), respectively.

scholarly journals Algoriphagus lutimaris sp. nov., isolated from a tidal flat sediment

2010 ◽  
Vol 60 (1) ◽  
pp. 200-204 ◽  
Author(s):  
Sooyeon Park ◽  
So-Jung Kang ◽  
Ki-Hoon Oh ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Tidal Flat Sediment

A Gram-negative, non-motile, non-spore-forming bacterial strain, S1-3T, was isolated from a tidal flat sediment on the west coast of Korea and its taxonomic position was investigated. Strain S1-3T grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. Strain S1-3T contained MK-7 as the predominant menaquinone and C16 : 1 ω7c and/or iso-C15 : 0 2-OH and iso-C15 : 0 as the major fatty acids. The DNA G+C content was 41.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain S1-3T fell within the clade comprising Algoriphagus species, clustering with Algoriphagus halophilus IMSNU 14013T, with which it exhibited 99.6 % 16S rRNA gene sequence similarity. The 16S rRNA gene sequence similarity between strain S1-3T and the type strains of other Algoriphagus species was 94.0–97.1 %. Differential phenotypic properties and phylogenetic and genetic distinctiveness of strain S1-3T demonstrated that this strain is distinguishable from the other Algoriphagus species as well as A. halophilus. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strain S1-3T is considered to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus lutimaris sp. nov. is proposed. The type strain is S1-3T (=KCTC 22630T =CCUG 57608T).

scholarly journals Clostridium aestuarii sp. nov., from tidal flat sediment

2007 ◽  
Vol 57 (6) ◽  
pp. 1315-1317 ◽  
Author(s):  
Seil Kim ◽  
Hyunyoung Jeong ◽  
Jongsik Chun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

A strictly anaerobic, halophilic, motile, endospore-forming, rod-shaped bacterium, designated strain HY-45-18T, was isolated from a sediment sample of a tidal flat in Korea. The isolate produced butyric acid, propionic acid, glycerol and H2 as fermentation end products from glucose. Strain HY-45-18T is halophilic as it was unable to grow in the absence of sea salts. A 16S rRNA gene sequence analysis clearly indicated that the tidal flat isolate is a member of cluster I of the order Clostridiales, which contains the type species of Clostridium, Clostridium butyricum. The closest phylogenetic neighbour of strain HY-45-18T was Clostridium ganghwense KCTC 5146T (96.5 % 16S rRNA gene sequence similarity). Several phenotypic characteristics can be readily used to differentiate the isolate from phylogenetically related clostridia. Therefore, strain HY-45-18T represents a novel species of the genus Clostridium, for which the name Clostridium aestuarii sp. nov. is proposed. The type strain is HY-45-18T (=IMSNU 40129T=KCTC 5147T=JCM 13194T).

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 Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3965-3970 ◽  
Author(s):  
Estelle Jumas-Bilak ◽  
Philippe Bouvet ◽  
Emma Allen-Vercoe ◽  
Fabien Aujoulat ◽  
Paul A. Lawson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Clinical Isolates ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence

Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5–91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).

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.

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).

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