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 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 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 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 Sphingobacterium shayense sp. nov., isolated from forest soil

2010 ◽  
Vol 60 (10) ◽  
pp. 2377-2381 ◽  
Author(s):  
Xiang He ◽  
Ting Xiao ◽  
Haiju Kuang ◽  
Xiaojun Lan ◽  
Maripat Tudahong ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Populus Euphratica ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A Gram-staining-negative, yellow-coloured, strictly aerobic, non-spore-forming, rod-shaped bacterium, designated HS39T, isolated from a soil sample collected from a natural Populus euphratica forest in Xinjiang, China, was characterized using a polyphasic approach. The isolate grew optimally at 30–37 °C, at pH 6.5–8.0 and with 0–3 % NaCl. Analysis of the 16S rRNA gene sequence of strain HS39T revealed that it is a member of the genus Sphingobacterium. Sphingobacterium mizutaii ATCC 33299T was the nearest relative (94.0 % 16S rRNA gene sequence similarity). The G+C content of the genomic DNA was 40.2 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c). The predominant isoprenoid quinone was MK-7. On the basis of phenotypic properties and phylogenetic inference, strain HS39T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium shayense sp. nov. is proposed. The type strain is HS39T (=CCTCC AB 209006T =NRRL B-59203T).

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 Salinisphaera dokdonensis sp. nov., isolated from surface seawater

2010 ◽  
Vol 60 (3) ◽  
pp. 680-685 ◽  
Author(s):  
Gi Duk Bae ◽  
Chung Yeon Hwang ◽  
Hye Min Kim ◽  
Byung Cheol Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

A Gram-negative, strictly aerobic bacterium, designated CL-ES53T, was isolated from surface water of the East Sea in Korea. Cells of strain CL-ES53T were short rods and motile by means of monopolar flagella. Strain CL-ES53T grew with 4–21 % NaCl (optimum 10 %) and at 5–40 °C (optimum 25 °C) and pH 5.2–8.8 (optimum pH 6.3–7.2). The major isoprenoid quinone was Q-8. The major fatty acids were C18 : 1 ω7c (42.0 %), C18 : 1 ω9c (14.8 %) and C14 : 0 (9.4 %). The genomic DNA G+C content was 64.9 mol%. Analysis of the 16S rRNA gene sequence of strain CL-ES53T revealed that it was a member of the genus Salinisphaera and most closely related to Salinisphaera shabanensis E1L3A T (96.9 % sequence similarity) and Salinisphaera hydrothermalis EPR70T (93.8 %). Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain CL-ES53T formed a robust cluster with S. shabanensis E1L3A T. Although the 16S rRNA gene sequence similarity between strain CL-ES53T and S. shabanensis E1L3A T was rather high (96.9 %), DNA–DNA relatedness between these strains was 12 %, suggesting that they represent genomically distinct species. Strain CL-ES53T was differentiated from S. shabanensis E1L3A T and S. hydrothermalis EPR70T on the basis of optimum temperature for growth and certain phenotypic characteristics. The phylogenetic analysis and physiological and chemotaxonomic data show that strain CL-ES53T should be classified in the genus Salinisphaera within a novel species, for which the name Salinisphaera dokdonensis sp. nov. is proposed. The type strain is CL-ES53T (=KCCM 90064T =DSM 19549T).

scholarly journals Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella rosea sp. nov., acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs

2010 ◽  
Vol 60 (12) ◽  
pp. 2951-2959 ◽  
Author(s):  
Timofey A. Pankratov ◽  
Svetlana N. Dedysh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Peat Bogs ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence

Five strains of strictly aerobic, heterotrophic bacteria that form pink–red colonies and are capable of hydrolysing pectin, xylan, laminarin, lichenan and starch were isolated from acidic Sphagnum peat bogs and were designated OB1010T, LCBR1, TPB6011T, TPB6028T and TPO1014T. Cells of these isolates were Gram-negative, non-motile rods that produced an amorphous extracellular polysaccharide-like substance. Old cultures contained spherical bodies of varying sizes, which represent starvation forms. Cells of all five strains were acidophilic and psychrotolerant, capable of growth at pH 3.0–7.5 (optimum pH 3.8–4.5) and at 2–33 °C (optimum 15–22 °C). The major fatty acids were iso-C15 : 0, C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The major menaquinone detected was MK-8. The pigments were carotenoids. The genomic DNA G+C contents were 57.3–59.3 mol%. The five isolates were found to be members of subdivision 1 of the phylum Acidobacteria and displayed 95.3–98.9 % 16S rRNA gene sequence similarity to each other. The closest described relatives to strains OB1010T, LCBR1, TPB6011T, TPB6028T, and TPO1014T were members of the genera Terriglobus (94.6–95.8 % 16S rRNA gene sequence similarity) and Edaphobacter (94.2–95.4 %). Based on differences in cell morphology, phenotypic characteristics and hydrolytic capabilities, we propose a novel genus, Granulicella gen. nov., containing four novel species, Granulicella paludicola sp. nov. with type strain OB1010T (=DSM 22464T =LMG 25275T) and strain LCBR1, Granulicella pectinivorans sp. nov. with type strain TPB6011T (=VKM B-2509T =DSM 21001T), Granulicella rosea sp. nov. with type strain TPO1014T (=DSM 18704T =ATCC BAA-1396T) and Granulicella aggregans sp. nov. with type strain TPB6028T (=LMG 25274T =VKM B-2571T).

scholarly journals Aquimarina spongiae sp. nov., isolated from marine sponge Halichondria oshoro

2011 ◽  
Vol 61 (2) ◽  
pp. 417-421 ◽  
Author(s):  
Byoung-Jun Yoon ◽  
Han-Su You ◽  
Dong-Heon Lee ◽  
Duck-Chul Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sponge ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence

A Gram-stain-negative, yellow-pigmented, rod-shaped, strictly aerobic, non-flagellated, non-gliding and oxidase- and catalase-positive bacterium, designated A6T, was isolated from a marine sponge, Halichondria oshoro, collected on the coast of Jeju Island, South Korea. Phylogenetic analysis based on the nearly complete 16S rRNA gene sequence revealed that strain A6T was a member of the family Flavobacteriaceae. The closest relatives were Aquimarina intermedia LMG 23204T, A. latercula ATCC 23177T, A. brevivitae SMK-19T and A. muelleri KMM 6020T, with which strain A6T shared 95.7, 95.1, 94.7 and 94.6 % 16S rRNA gene sequence similarity, respectively. The dominant fatty acids of strain A6T were iso-C15 : 0 (32.2 %), iso-C17 : 0 3-OH (20.0 %), iso-C15 : 0 3-OH (12.3 %), iso-C15 : 1 G (7.2 %) and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 6.8 %). The DNA G+C content of strain A6T was 36.0 mol% and the major respiratory quinone was MK-6. On the basis of combined phenotypic and phylogenetic analyses, strain A6T represents a novel species of the genus Aquimarina, for which the name Aquimarina spongiae sp. nov. is proposed. The type strain is A6T (=KCTC 22663T =DSM 22623T).

Sphingobacterium thermophilum sp. nov., of the phylum Bacteroidetes , isolated from compost

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1584-1588 ◽  
Author(s):  
Shuhei Yabe ◽  
Yoshifumi Aiba ◽  
Yasuteru Sakai ◽  
Masaru Hazaka ◽  
Kazuyoshi Kawahara ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A Gram-negative bacterium, designated CKTN2T, was isolated from compost. Cells of strain CKTN2T were strictly aerobic rods. The isolate grew at 20–50 °C (optimum 40–45 °C), but not below 15 °C or above 52 °C, and at pH 5.9–8.8 (optimum pH 7.0), but not below pH 5.4 or above pH 9.3. The DNA G+C content was 40.3 mol%. The predominant menaquinone was MK-7. The major fatty acids were iso-C15 : 0 (45.2 %), iso-C17 : 0 3-OH (11.1 %) and C18 : 0 (14.5 %). Analysis of the 16S rRNA gene sequence of strain CKTN2T revealed that it is a member of the genus Sphingobacterium and is most closely related to Sphingobacterium alimentarium DSM 22362T (93.2 % 16S rRNA gene sequence similarity). Strain CKTN2T could be distinguished from its closest phylogenetic relatives by different phenotypic characteristics. According to the phenotypic and genotypic characteristics, strain CKTN2T represents a novel species of the genus Sphingobacterium , for which the name Sphingobacterium thermophilum sp. nov. is proposed. The type strain is CKTN2T ( = JCM 17858T  = KCTC 23708T).

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).

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