scholarly journals Shewanella marisflavi sp. nov. and Shewanella aquimarina sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea

2004 ◽  
Vol 54 (6) ◽  
pp. 2347-2352 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Soo-Hwan Yeo ◽  
In-Gi Kim ◽  
Tae-Kwang Oh

Two Gram-negative, motile, non-spore-forming, rod-shaped organisms, strains SW-117T and SW-120T, were isolated from sea water of the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. Strains SW-117T and SW-120T simultaneously contained both menaquinones (MK) and ubiquinones (Q) as isoprenoid quinones; the predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acid detected in the two strains was iso-C15 : 0. The DNA G+C content of strains SW-117T and SW-120T was 51 and 54 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-117T and SW-120T fall within the radiation of the cluster comprising Shewanella species. Strains SW-117T and SW-120T showed a 16S rRNA gene sequence similarity of 97·4 % and a DNA–DNA relatedness level of 10·1 %. Strains SW-117T and SW-120T exhibited 16S rRNA gene sequence similarity levels of 93·8–98·5 % and 92·4–97·0 %, respectively, to Shewanella species. Strain SW-117T exhibited DNA–DNA relatedness levels of 8·3–20·3 % to the type strains of six phylogenetically related Shewanella species. On the basis of phenotypic, phylogenetic and genetic data, strains SW-117T and SW-120T were classified in the genus Shewanella as two distinct novel species, for which the names Shewanella marisflavi sp. nov. (type strain, SW-117T=KCCM 41822T=JCM 12192T) and Shewanella aquimarina sp. nov. (type strain, SW-120T=KCCM 41821T=JCM 12193T) are proposed, respectively.

2004 ◽  
Vol 54 (5) ◽  
pp. 1799-1803 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Soo-Hwan Yeo ◽  
In-Gi Kim ◽  
Tae-Kwang Oh

Two Gram-negative, motile, non-spore-forming and slightly halophilic rods (strains SW-145T and SW-156T) were isolated from sea water of the Yellow Sea in Korea. Strains SW-145T and SW-156T grew optimally at 37 and 30–37 °C, respectively, and in the presence of 2–6 % (w/v) NaCl. Strains SW-145T and SW-156T were chemotaxonomically characterized as having ubiquinone-9 as the predominant respiratory lipoquinone and C16 : 0, C18 : 1 ω9c, C16 : 1 ω9c and C12 : 0 3-OH as the major fatty acids. The DNA G+C contents of strains SW-145T and SW-156T were 58 and 57 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-145T and SW-156T fell within the evolutionary radiation enclosed by the genus Marinobacter. The 16S rRNA gene sequences of strains SW-145T and SW-156T were 94·8 % similar. Strains SW-145T and SW-156T exhibited 16S rRNA gene sequence similarity levels of 94·3–98·1 and 95·4–97·7 %, respectively, with respect to the type strains of all Marinobacter species. Levels of DNA–DNA relatedness, together with 16S rRNA gene sequence similarity values, indicated that strains SW-145T and SW-156T are members of two species that are distinct from seven Marinobacter species with validly published names. On the basis of phenotypic properties and phylogenetic and genotypic distinctiveness, strains SW-145T (=KCTC 12185T=DSM 16070T) and SW-156T (=KCTC 12184T=DSM 16072T) should be placed in the genus Marinobacter as the type strains of two distinct novel species, for which the names Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov. are proposed.


2005 ◽  
Vol 55 (2) ◽  
pp. 793-798 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh

Four Gram-negative, rod-shaped bacterial strains, TF-26T, TF-28, TF-42 and TF-53, were isolated from a tidal flat in the Yellow Sea, Korea, and their taxonomic positions were determined by a polyphasic characterization. The strains grew optimally in the presence of 2–3 % (w/v) NaCl and at 30–37 °C. The predominant menaquinone detected in the four strains was MK-6. These strains contained large amounts of fatty acids C16 : 1 ω7c and/or iso-C15 : 0 2-OH, iso-C15 : 0, iso-C16 : 0 3-OH, C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C contents of the four strains were 32·3–32·8 mol%. Strains TF-26T, TF-28, TF-42 and TF-53 showed 16S rRNA gene sequence similarity levels of 99·8–100 % and DNA–DNA relatedness levels of 82–87 %. The four strains exhibited 16S rRNA gene sequence similarity levels of 95·0–98·0 % to the type strains of the five current Tenacibaculum species, and DNA–DNA relatedness levels between the four strains and two phylogenetic relatives, Tenacibaculum mesophilum DSM 13764T and Tenacibaculum skagerrakense DSM 14836T, were less than 21 %. On the basis of phenotypic, phylogenetic and genetic data, strains TF-26T, TF-28, TF-42 and TF-53 were classified in the genus Tenacibaculum as members of a novel species, for which the name Tenacibaculum lutimaris sp. nov. (type strain, TF-26T=KCTC 12302T=DSM 16505T) is proposed.


2006 ◽  
Vol 56 (4) ◽  
pp. 805-810 ◽  
Author(s):  
Ida Romano ◽  
Licia Lama ◽  
Barbara Nicolaus ◽  
Annarita Poli ◽  
Agata Gambacorta ◽  
...  

A halophilic, alkalitolerant bacterium, strain 20AGT, was isolated from an algal mat collected from a sulfurous spring located in Santa Maria Incaldana (Mondragone, Campania Region, southern Italy). The isolate is Gram-positive, ferments several carbohydrates and has motile, rod-shaped cells that do not sporulate. The isolate grows at pH 6·5–9·5 and in 5–20 % NaCl. On the basis of 16S rRNA gene sequence similarity, the strain was shown to belong to the genus Oceanobacillus; strain 20AGT showed 96·6 % 16S rRNA gene sequence similarity to the type strain of Oceanobacillus iheyensis, DSM 14371T, and 99·5 % similarity to Oceanobacillus oncorhynchi NCIMB 14022T. Levels of DNA–DNA relatedness between strain 20AGT and O. iheyensis DSM 14371T and O. oncorhynchi NCIMB 14022T were respectively 29·4 and 59·0 %. The G+C content of the DNA of strain 20AGT was 40·1 mol%. The predominant respiratory quinone was MK-7, phosphatidylglycerol and phosphatidylcholine were the predominant polar lipids and minor phospholipids were also detected. ai-C14 : 0, ai-C15 : 0 and i-C15 : 0 were the major fatty acids. Strain 20AGT accumulated osmolytes and produced exopolysaccharide. On the basis of phenotypic characteristics, phylogenetic data and DNA–DNA relatedness data, isolate 20AGT should be designated as the type strain of a subspecies of Oceanobacillus oncorhynchi, for which the name Oceanobacillus oncorhynchi subsp incaldanensis subsp. nov. is proposed. The type strain is 20AGT (=DSM 16557T=ATCC BAA-954T).


2006 ◽  
Vol 56 (12) ◽  
pp. 2853-2859 ◽  
Author(s):  
Pham Thi Ngoc Lan ◽  
Mitsuo Sakamoto ◽  
Shinji Sakata ◽  
Yoshimi Benno

Eight bacterial strains isolated from the caecum of chicken, BL2T, BL66, EG3, EG6, M27, BL78T, C35T and C43, were characterized by determining their phenotypic characteristics, cellular fatty acid profiles, menaquinone profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that these isolates belonged to the genus Bacteroides. One group of five strains (BL2T, BL66, EG3, EG6 and M27) was related most closely to Bacteroides coprocola JCM 12979T, with approximately 93 % 16S rRNA gene sequence similarity, and to Bacteroides plebeius JCM 12973T, with about 92 % similarity, and shared ⩾99.6 % similarity with each other. Strain BL78T exhibited 90.5 % similarity to B. plebeius JCM 12973T and 89.8 % similarity to B. coprocola JCM 12979T and differed from the above group of five strains at ⩾10 % sequence divergence. Strains C35T and C43 were related most closely to Bacteroides eggerthii JCM 12986T, with 95.1 % sequence similarity, to Bacteroides stercoris JCM 9496T, with 94.6 % similarity, and to Bacteroides uniformis JCM 5828T, with 94.4 % similarity, and shared 100 % similarity with each other. From results of phenotypic examination, cellular fatty acid composition analysis, menaquinone composition analysis and DNA G+C contents, the group of five strains as well as strain BL78T were shown to differ from the type strains of B. coprocola and B. plebeius. Strain BL78T differed from the others based on its menaquinone composition, which included MK-11 and MK-12. Strains C35T and C43 could also be differentiated from the type strains of B. eggerthii, B. stercoris and B. uniformis. The group of five strains, strain BL78T, B. coprocola JCM 12979T and B. plebeius JCM 12973T showed low levels of DNA–DNA relatedness (<35 %) with each other. High levels of DNA–DNA relatedness were obtained within the group of five strains (>75 %). Strains C35T and C43 exhibited a high level of DNA–DNA relatedness (>88 %) with each other, but low levels with B. eggerthii JCM 12986T (<40 %), B. stercoris JCM 9496T (<37 %) and B. uniformis JCM 5828T (<16 %). On the basis of these data, three novel Bacteroides species are proposed: Bacteroides barnesiae sp. nov. (type strain BL2T=JCM 13652T=DSM 18169T), Bacteroides salanitronis sp. nov. (type strain BL78T=JCM 13657T=DSM 18170T) and Bacteroides gallinarum sp. nov. (type strain C35T=JCM 13658T=DSM 18171T).


2005 ◽  
Vol 55 (6) ◽  
pp. 2303-2307 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh

Two Gram-negative, motile, non-spore-forming, slightly halophilic bacteria (strains DSW10-10T and DSW10-19) were isolated from sea water and subjected to a polyphasic taxonomic study. They grew optimally at 30 °C and in the presence of 2–3 % (w/v) NaCl. Strains DSW10-10T and DSW10-19 were characterized chemotaxonomically as containing Q-8 as the predominant ubiquinone and C18 : 1 ω7c, C16 : 0 and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. Their DNA G+C contents were 45·3–45·7 mol%. Strains DSW10-10T and DSW10-19 exhibited a 16S rRNA gene sequence similarity value of 100 % and possessed a mean DNA–DNA relatedness level of 85 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains DSW10-10T and DSW10-19 fell within the radiation of the cluster encompassed by the genus Marinomonas. Strains DSW10-10T and DSW10-19 had 16S rRNA gene sequence similarity levels of 95·7–97·7 % with respect to the type strains of Marinomonas species with validly published names. Levels of DNA–DNA relatedness were low enough to indicate that the two strains constitute a distinct Marinomonas species. On the basis of phenotypic data and phylogenetic and genetic distinctiveness, strains DSW10-10T (=KCTC 12394T=DSM 17202T) and DSW10-19 were placed in the genus Marinomonas as members of a novel species, Marinomonas dokdonensis sp. nov.


2011 ◽  
Vol 61 (8) ◽  
pp. 1933-1937 ◽  
Author(s):  
Dong Wan Lee ◽  
Soo-Young Lee ◽  
Jung-Hoon Yoon ◽  
Soon Dong Lee

Two novel Gram-reaction-positive, rod-shaped actinobacterial strains, designated RP-B26T and RP-B30T, were isolated from rhizosphere soil of a cliff-associated plant (Peucedanum japonicum Thunb.) which was collected from Mara Island, Republic of Korea. The colonies of the isolates were circular, smooth, convex and moderately yellow–light-yellow in colour. 16S rRNA gene sequence analysis revealed that the isolates belonged to the family Nocardioidaceae and formed two distinct sublineages within the radiation of the genus Nocardioides. 16S rRNA gene sequence similarity between the isolates was 98.2 %. The closest phylogenetic neighbours of strain RP-B26T were Nocardioides humi DCY24T and Nocardioides kongjuensis A2-4T with 97.4 and 97.0 % 16S rRNA gene sequence similarity, respectively, whereas 16S rRNA gene sequence similarities between strain RP-B30T and N. humi DCY24T and N. kongjuensis A2-4T were 96.5 and 96.0 %, respectively. Both of the isolates contained ll-diaminopimelic acid as the diagnostic diamino acid in the cell walls. The predominant menaquinone was MK-8(H4). The polar lipids were phosphatidylinositol and phosphatidylglycerol. The fatty acid profiles of the isolates were characterized by the presence of saturated, unsaturated, 10-methyl and hydroxyl fatty acids, with small amounts of branched fatty acids. The DNA G+C contents of strains RP-B26T and RP-B30T were 73.0 and 71.7 mol%, respectively. Levels of DNA–DNA relatedness between the isolates were 44.9±1.5 % (thermal renaturation method) and 43.2 % (photobiotin-labelled method); the isolates showed low DNA–DNA relatedness values (<11 %) to the most closely related strain, N. humi KCTC 19265T. On the basis of the phenotypic, genotypic and DNA–DNA hybridization data presented here, the isolates are considered to represent two novel species of the genus Nocardioides, for which the names Nocardioides ultimimeridianus sp. nov. (type strain RP-B26T  = KCTC 19368T  = DSM 19768T) and Nocardioides maradonensis sp. nov. (type strain RP-B30T  = KCTC 19384T  = DSM 19769T) are proposed.


2005 ◽  
Vol 55 (1) ◽  
pp. 149-152 ◽  
Author(s):  
Jie Feng ◽  
Peijin Zhou ◽  
Yu-Guang Zhou ◽  
Shuang-Jiang Liu ◽  
Kimberly Warren-Rhodes

A novel haloalkaliphilic archaeon, strain DZ-1T, was isolated from a soda lake in Xinjiang, China. The taxonomy of strain DZ-1T was studied by polyphasic methods. According to 16S rRNA gene sequence similarity, strain DZ-1T was phylogenetically related to Halorubrum tibetense (97·5 %), Halorubrum vacuolatum (95·7 %) and Halorubrum saccharovorum (95·9 %). Strain DZ-1T was able to grow at 20–44 °C and was also physiologically different from the above-mentioned species with respect to assimilation of sugars and utilization of organic acids. The DNA G+C content of strain DZ-1T was 62·1 mol% (T m). The DNA–DNA relatedness of strain DZ-1T to H. tibetense and H. vacuolatum was 22 and 13 %, respectively. It was concluded that strain DZ-1T represents a novel species of the genus Halorubrum, for which the name Halorubrum alkaliphilum (type strain, DZ-1T=AS 1.3528T=JCM 12358T) is proposed.


2004 ◽  
Vol 54 (5) ◽  
pp. 1829-1835 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park

Two Gram-negative, non-motile, non-spore-forming, rod-shaped organisms, strains SW-125T and SW-154T, were isolated from tidal flat sediment of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. Strains SW-125T and SW-154T grew optimally at 30–37 °C and in the presence of 2–3 % (w/v) NaCl. They contained ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and iso-C15 : 0 as the major fatty acid. The DNA G+C contents of strains SW-125T and SW-154T were 44 mol%. Phylogenetic trees based on 16S rRNA gene sequences revealed that the two strains form deep evolutionary lineages of descent within the γ-Proteobacteria. Strains SW-125T and SW-154T exhibited 16S rRNA gene sequence similarity levels of less than 90 % to members of the γ-Proteobacteria used in this analysis. Strains SW-125T and SW-154T showed a 16S rRNA gene sequence similarity level of 98·5 % and a mean DNA–DNA relatedness level of 9·4 %. Therefore, on the basis of phenotypic, phylogenetic and genomic data, a new genus, Kangiella gen. nov., is proposed to accommodate the novel strains, comprising two novel species, Kangiella koreensis sp. nov. (type strain, SW-125T=KCTC 12182T=DSM 16069T) and Kangiella aquimarina sp. nov. (type strain, SW-154T=KCTC 12183T=DSM 16071T).


2005 ◽  
Vol 55 (2) ◽  
pp. 885-889 ◽  
Author(s):  
In-Gi Kim ◽  
Mi-Hwa Lee ◽  
Seo-Youn Jung ◽  
Jae Jun Song ◽  
Tae-Kwang Oh ◽  
...  

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.


2011 ◽  
Vol 61 (8) ◽  
pp. 1954-1961 ◽  
Author(s):  
An Coorevits ◽  
Niall A. Logan ◽  
Anna E. Dinsdale ◽  
Gillian Halket ◽  
Patsy Scheldeman ◽  
...  

A polyphasic taxonomic study was performed on 22 thermotolerant, aerobic, endospore-forming bacteria from dairy environments. Seventeen isolates were retrieved from raw milk, one from a filter cloth and four from grass, straw or milking equipment. These latter four isolates (R-6546, R-7499, R-7764 and R-7440) were identified as Bacillus thermoamylovorans based on DNA–DNA hybridizations (values above 70 % with Bacillus thermoamylovorans LMG 18084T) but showed discrepancies in characteristics with the original species description, so an emended description of this species is given. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization experiments, the remaining 18 isolates (R-6488T, R-28193, R-6491, R-6492, R-7336, R-33367, R-6486, R-6770, R-31288, R-28160, R-26358, R-7632, R-26955, R-26950, R-33520, R-6484, R-26954 and R-7165) represented one single species, most closely related to Bacillus thermoamylovorans (93.9 % 16S rRNA gene sequence similarity), for which the name Bacillus thermolactis is proposed. Cells were Gram-stain-positive, facultatively anaerobic, endospore-forming rods that grew optimally at 40–50 °C. The cell wall peptidoglycan type of strain R-6488T, the proposed type strain, was A1γ based on meso-diaminopimelic acid. Major fatty acids of the strains were C16 : 0 (28.0 %), iso-C16 : 0 (12.1 %) and iso-C15 : 0 (12.0 %). MK-7 was the predominant menaquinone, and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and some unidentified phospholipids. DNA G+C content was 35.0 mol%. Phenotypic properties allowed discrimination from other thermotolerant species of the genus Bacillus and supported the description of the novel species Bacillus thermolactis, with strain R-6488T ( = LMG 25569T  = DSM 23332T) as the proposed type strain.


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