Marinomonas dokdonensis sp. nov., isolated from sea water

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.

2004 ◽  
Vol 54 (5) ◽  
pp. 1845-1848 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Soo-Hwan Yeo ◽  
Tae-Kwang Oh

Two Gram-negative, non-motile, non-spore-forming, rod-shaped strains, SW-2T and SW-26, were isolated from sea water of the East Sea in Korea. These organisms grew optimally at 37 °C and in the presence of 2–3 % (w/v) NaCl. They did not grow without NaCl or in the presence of >9 % (w/v) NaCl. Strains SW-2T and SW-26 were characterized chemotaxonomically as having MK-7 as the predominant isoprenoid quinone and iso-C15 : 0 as the major fatty acid. The DNA G+C content of strains SW-2T and SW-26 was 43 mol%. A neighbour-joining tree based on 16S rRNA gene sequences showed that strains SW-2T and SW-26 fell within the Cytophaga–Flavobacterium–Bacteroides group and formed a coherent cluster with Hongiella species. Strains SW-2T and SW-26 showed a 16S rRNA gene sequence similarity value of 99·9 % and a mean DNA–DNA relatedness level of 87 % to each other. Levels of 16S rRNA gene sequence similarity between strains SW-2T and SW-26 and the type strains of two Hongiella species ranged from 94·2 to 96·6 %. On the basis of phenotypic and chemotaxonomic properties and phylogenetic distinctiveness, strains SW-2T and SW-26 should be placed in the genus Hongiella as members of a novel species, for which the name Hongiella marincola sp. nov. is proposed. The type strain is SW-2T (=KCTC 12180T=DSM 16067T).


2005 ◽  
Vol 55 (4) ◽  
pp. 1453-1456 ◽  
Author(s):  
S. Shivaji ◽  
Pratima Gupta ◽  
Preeti Chaturvedi ◽  
K. Suresh ◽  
Daniel Delille

A psychrotolerant, Gram-negative, motile bacterium, designated CK 47T, was isolated from sea water off the subantarctic Kerguelen islands (50° 40′ S 68° 25′ E). The isolate grew optimally at 22 °C and minimum and maximum temperature of growth were 4 and 37 °C, respectively. It required Na+ for growth and exhibited optimum growth at pH 8·5 and 4 % NaCl. It utilized hexane, heptane and petroleum ether as sole sources of carbon. Strain CK 47T had Q9 as the major respiratory quinone and C16 : 0 (21·7 %), C17 : 0 (21·3 %), C18 : 0 (5·7 %), C18 : 1 ω7c (9·0 %) and C18 : 1 ω9c (31·4 %) as predominant fatty acids. The G+C content of the DNA was 58 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that CK 47T formed a coherent cluster within the genus Marinobacter. It exhibited highest 16S rRNA gene sequence similarity of 96·8 % with Marinobacter lipolyticus. However, the level of DNA–DNA relatedness between strain CK47T and M. lipolyticus was only 55 %. On the basis of phenotypic characteristics, and phylogenetic and genotypic distinctiveness, strain CK 47T is considered to represent a novel species of the genus Marinobacter. The name Marinobacter maritimus sp. nov. is proposed, with CK 47T (=JCM 12521T=MTCC 6519T) as the type strain.


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).


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.


2011 ◽  
Vol 61 (6) ◽  
pp. 1386-1391 ◽  
Author(s):  
Qiliang Lai ◽  
Zhiwei Yu ◽  
Jianning Wang ◽  
Huanzi Zhong ◽  
Fengqin Sun ◽  
...  

Strain pht-3BT was isolated from a pyrene-degrading consortium of an enriched sediment from the Pacific Ocean, collected during the screening of polycyclic aromatic hydrocarbon-degrading bacteria. Cells were Gram-negative, short rods that were motile by means of flagella. Growth was observed at 0–7 % NaCl and 10–41 °C. The isolate was able to reduce nitrate to nitrite, but not to nitrogen. 16S rRNA gene sequence comparisons showed that strain pht-3BT was most closely related to Nitratireductor aquibiodomus NL21T (97.3 % 16S rRNA gene sequence similarity), N. indicus C115T (97.1 %), N. basaltis J3T (96.8 %) and N. kimnyeongensis KY 101T (96.7 %). DNA–DNA hybridization between strain pht-3BT and these reference strains revealed 55, 54, 28 and 42 % DNA–DNA relatedness, respectively. The dominant fatty acids were C19 : 0ω8c cyclo (22.6 %) and summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c; 60.4 %). The G+C content of the chromosomal DNA was 63 mol%. These characteristics were in good agreement with those of members of the genus Nitratireductor. According to cell morphology, physiology, fatty acid composition, 16S rRNA gene sequence analysis and DNA–DNA relatedness, the isolate belonged to the genus Nitratireductor but could be readily distinguished from recognized species of the genus. Therefore a novel species is proposed to accommodate strain pht-3BT, for which the name Nitratireductor pacificus sp. nov. is proposed. The type strain is pht-3BT ( = CCTCC AB 209302T = LMG 25541T = MCCC 1A01024T).


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).


2010 ◽  
Vol 60 (12) ◽  
pp. 2813-2817 ◽  
Author(s):  
Ahyoung Choi ◽  
Jang-Cheon Cho

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).


2006 ◽  
Vol 56 (5) ◽  
pp. 1079-1083 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Mi-Hwa Lee ◽  
Hyun Woo Oh ◽  
Tae-Kwang Oh

A Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strain, DSW-74T, was isolated from sea water off the island of Dokdo, Korea, and its taxonomic position was investigated by a polyphasic study. Strain DSW-74T grew optimally at 37 °C and in the presence of 2 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C17 : 1 ω6c and C18 : 1 ω7c as the major fatty acids. Its DNA G+C content was 65.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DSW-74T was most closely related to Porphyrobacter species. Similarity values between the 16S rRNA gene sequence of strain DSW-74T and those of the type strains of recognized Porphyrobacter species and of Erythromicrobium ramosum were in the range 97.4–98.7 %. Strain DSW-74T exhibited 16S rRNA gene sequence similarity values of <97.5 % to recognized Erythrobacter species and the other species used in the phylogenetic analysis. DNA–DNA relatedness levels and differential phenotypic properties made it possible to categorize strain DSW-74T as representing a novel Porphyrobacter species. On the basis of the taxonomic data presented, it is proposed that DSW-74T (=KCTC 12395T=DSM 17193T) should be classified in the genus Porphyrobacter as the type strain of a novel species, Porphyrobacter 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.


2004 ◽  
Vol 54 (6) ◽  
pp. 1975-1980 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Hyang Burm Lee ◽  
Soo-Hwan Yeo ◽  
Jae-Eul Choi

Two Gram-positive bacterial strains, CM2104T and CM2110, isolated from the inner part of abnormally spoiled oriental melon (Cucumis melo) in Korea, were subjected to a polyphasic taxonomic study. The cell-wall peptidoglycan of strains CM2104T and CM2110 contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-8(H4). The major fatty acids detected in the two strains were iso-C16 : 0, C17 : 1 ω8c and C18 : 1 ω9c or C17 : 0. The DNA G+C content of the two strains was 73 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed a coherent cluster with a clade comprising two Janibacter species, Janibacter limosus and Janibacter terrae. Strains CM2104T and CM2110 exhibited a 16S rRNA gene sequence similarity value of 99·7 % and a mean DNA–DNA relatedness level of 89 %. Strains CM2104T and CM2110 showed 16S rRNA gene sequence similarity levels of 97·8–98·4 % to the type strains of J. limosus and J. terrae. DNA–DNA relatedness between strains CM2104T and CM2110 and the type strains of these two Janibacter species was 7–11 %. On the basis of the phenotypic and phylogenetic data and genomic distinctiveness, strains CM2104T and CM2110 should be placed within the genus Janibacter as members of a novel species, for which the name Janibacter melonis sp. nov. is proposed. The type strain is CM2104T (=KCTC 9987T=DSM 16063T=JCM 12321T).


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