scholarly journals Gaetbulibacter saemankumensis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat sediment in Korea

2005 ◽  
Vol 55 (5) ◽  
pp. 1845-1849 ◽  
Author(s):  
Seo-Youn Jung ◽  
So-Jung Kang ◽  
Mi-Hwa Lee ◽  
Soo-Young Lee ◽  
Tae-Kwang Oh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Tidal Flat Sediment ◽  
Distinct Evolutionary Lineage ◽  
The Family

Three Gram-negative, yellow-pigmented, rod-shaped bacterial strains, SMK-12T, SMK-36 and SMK-45, were isolated from a tidal flat sediment of the Yellow Sea in Korea, and their taxonomic positions were investigated by a polyphasic approach. The three strains grew optimally at 25–30 °C and in the presence of 2–3 % (w/v) NaCl. They contained MK-6 as the predominant menaquinone. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1, anteiso-C15 : 0, iso-C15 : 0 3-OH and C16 : 1 ω7c and/or iso-C15 : 0 2-OH. The DNA G+C contents of the three strains were 34·7–34·9 mol%. The phylogenetic tree based on 16S rRNA gene sequences revealed that the three strains form one distinct evolutionary lineage supported by a bootstrap value of 100 % within the family Flavobacteriaceae. The three strains exhibited 16S rRNA gene sequence similarity levels of 93·8–94·9 % to the nearest phylogenetic neighbours, the genera Algibacter, Bizionia and Formosa. On the basis of differences in phenotypic characteristics and phylogenetic distinctiveness, strains SMK-12T, SMK-36 and SMK-45 were classified in a novel genus and species, for which the name Gaetbulibacter saemankumensis gen. nov., sp. nov. is proposed. The type strain for the novel species is SMK-12T (=KCTC 12379T=DSM 17032T).

scholarly journals Algoriphagus aestuarii sp. nov., a member of the Cyclobacteriaceae isolated from a tidal-flat sediment of the Yellow Sea in Korea

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3439-3446 ◽  
Author(s):  
Yong-Taek Jung ◽  
Jung-Sook Lee ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Tidal Flat Sediment ◽  
The Mean ◽  
Type Strains

A Gram-strain-negative, coccoid or oval-shaped, non-motile bacterial strain, designated MDM-1T, was isolated from a tidal-flat sediment on the Korean peninsula. Strain MDM-1T was found to grow optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain MDM-1T falls within the clade comprising species of the genus Algoriphagus, clustering with the type strains of Algoriphagus halophilus, A. lutimaris, A. chungangensis and A. machipongonensis, with which it exhibited 97.2–98.5 % 16S rRNA gene sequence similarity. Sequence similarities to the type strains of the other recognized species of the genus Algoriphagus were 92.8–97.6 %. Strain MDM-1T was found to contain MK-7 as the predominant menaquinone and iso-C15 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) as the major fatty acids. The major polar lipids were identified as phosphatidylcholine, phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain MDM-1T was determined to be 42.7 mol% and the mean DNA–DNA relatedness with A. halophilus KCTC 12051T, A. lutimaris S1-3T, A. chungangensis KCTC 23759T, A. machipongonensis DSM 24695T and A. ratkowskyi CIP 107452T was 19.7–5.2 %. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain MDM-1T is distinguishable from recognized species of the genus Algoriphagus. On the basis of the data presented, strain MDM-1T is proposed to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus aestuarii sp. nov. is proposed. The type strain is MDM-1T ( = KCTC 42199T = NBRC 110552T).

scholarly journals Jannaschia seohaensis sp. nov., isolated from a tidal flat sediment

2010 ◽  
Vol 60 (1) ◽  
pp. 191-195 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Ki-Hoon Oh ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Tidal Flat Sediment ◽  
The Mean ◽  
Type Strains

A Gram-negative, motile and pleomorphic bacterial strain, SMK-146T, was isolated from a tidal flat sediment of the Yellow Sea, Korea, and its taxonomic position was investigated. Strain SMK-146T grew optimally at pH 7.0–8.0 and 30 °C. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and 11-methyl C18 : 1 ω7c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 68.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SMK-146T belongs to the genus Jannaschia. Strain SMK-146T exhibited 16S rRNA gene sequence similarity values of 95.3–97.0 % to the type strains of the five recognized Jannaschia species. The mean DNA–DNA relatedness value between strain SMK-146T and Jannaschia seosinensis KCCM 42114T, the closest phylogenetic neighbour, was 17 %. Differential phenotypic properties also revealed that strain SMK-146T differs from the recognized Jannaschia species. On the basis of phenotypic, phylogenetic and genetic data, strain SMK-146T represents a novel species of the genus Jannaschia, for which the name Jannaschia seohaensis sp. nov. is proposed. The type strain is SMK-146T (=KCTC 22172T =CCUG 55326T).

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

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4184-4190 ◽  
Author(s):  
Yong-Taek Jung ◽  
Sooyeon Park ◽  
Jung-Sook Lee ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment

A Gram-stain-negative, non-motile, coccoid- or oval-shaped bacterial strain, designated S-5T, belonging to the class Alphaproteobacteria , was isolated from a tidal flat sediment of the Yellow Sea, Korea and was subjected to a polyphasic taxonomic study. Strain S-5T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining analysis based on 16S rRNA gene sequences showed that strain S-5T fell within the clade comprising the species of the genus Erythrobacter , clustering with the type strains of Erythrobacter pelagi , Erythrobacter citreus and Erythrobacter seohaensis with which it exhibited the highest 16S rRNA gene sequence similarity (96.0–96.7 %). The DNA G+C content was 66.0 mol%. Strain S-5T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 1ω6c as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, an unidentified glycolipid and two unidentified lipids. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain S-5T is distinguishable from other species of the genus Erythrobacter . On the basis of the data presented, strain S-5T is considered to represent a novel species of the genus Erythrobacter , for which the name Erythrobacter lutimaris sp. nov. is proposed. The type strain is S-5T ( = KCTC 42109T = CECT 8624T).

scholarly journals Wenxinia saemankumensis sp. nov., isolated from a tidal flat sediment

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1958-1963 ◽  
Author(s):  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Link Type ◽  
Tidal Flat Sediment

A Gram-stain-negative, non-motile, ovoid- or rod-shaped bacterial strain, designated S-22T, belonging to the class Alphaproteobacteria , was isolated from a tidal flat sediment of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain S-22T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain S-22T joined Wenxinia marina HY34T, with which it exhibited highest 16S rRNA gene sequence similarity (98.0 %). The DNA G+C content was 72.3 mol% and the mean DNA–DNA relatedness value between strain S-22T and the type strain of W. marina was 3.7 %. Strain S-22T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain S-22T is distinguishable from W. marina . On the basis of the data presented, strain S-22T is considered to represent a novel species of the genus Wenxinia , for which the name Wenxinia saemankumensis sp. nov. is proposed. The type strain of is S-22T ( = KCTC 32548T = CECT 8456T).

scholarly journals Erythrobacter luteolus sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

2005 ◽  
Vol 55 (3) ◽  
pp. 1167-1170 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Kook Hee Kang ◽  
Soo-Hwan Yeo ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Yellow Sea ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties

A Gram-negative, non-spore-forming, yellow-pigmented, slightly halophilic bacterial strain, SW-109T, was isolated from a tidal flat of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. This isolate did not produce bacteriochlorophyll a and contained ubiquinone-10 as the predominant respiratory lipoquinone and C18 : 1 ω7c as the major fatty acid. The DNA G+C content was 60·3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SW-109T is phylogenetically affiliated to the genus Erythrobacter of the family Sphingomonadaceae. Strain SW-109T exhibited levels of 16S rRNA gene sequence similarity to the type strains of Erythrobacter species of 94·0–96·3 %, making it possible to categorize strain SW-109T as a species that is separate from previously recognized Erythrobacter species. On the basis of its phenotypic properties and phylogenetic distinctiveness, SW-109T (=KCTC 12311T=JCM 12599T) was classified as the type strain of a novel Erythrobacter species, for which the name Erythrobacter luteolus sp. nov. is proposed.

scholarly journals Pareuzebyella sediminis gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae, isolated from a tidal flat sediment

2020 ◽  
Author(s):  
Zhaobin Huang ◽  
Xiaomei Wei ◽  
Qiliang Lai ◽  
Shiyong Chen ◽  
Jianjun Yuan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family

Two marine bacterial strains, designated S2-4-21T and MT2-5-19, were isolated from two tidal flat sediments of cordgrass Spartina alterniflora and adjacent oyster culture field in Quanzhou bay, China, respectively. Both strains were Gram-staining-negative, rod-shaped, non-flagellated, non-motile, aerobic, had NaCl requirements, and contained carotenoid and flexirubin pigments. The 16S rRNA gene sequence similarity (99.8%), average nucleotide identity value (99.4%) and average amino acid identity (99.3%) between strain S2-4-21T and strain MT2-5-19 strongly supported that they belonged to a single species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2-4-21T and strain MT2-5-19 formed a monophyletic branch affiliated to the family Flavobacteriaceae , sharing similarities of 94.6% with Euzebyella marina CY01T and E. saccharophila 7SM30T, and of 94.1 and 92.8% with E. algicola MEBiC 12267T and Pseudozobellia thermophile DSM 19858T, respectively. Phylogenomic analysis based on the whole genome sequences supported that the two strains formed a distinct monophyletic clade within Flavobacteriaceae members, which was phylogenetically different from the clades of Euzebyella and Pseudozobellia . The major respiratory quinone was menaquinone MK-6. The major fatty acids (>10%) consisted of C15 : 0 iso, C16 : 0, summed feature 9 (C17 : 1 iso ω9c/C16 : 0 10-methyl) and C17 : 0 iso 3-OH. The polar lipid profiles of strain S2-4-21T and strain MT2-5-19 are identical, including phosphatidylethanolamine, four unidentified aminolipids, and four unidentified lipids. The genomic size was 4.9–5.0 Mb with genomic DNA G+C content of 41.5 mol%. Based on the above characteristics, strains S2-4-21T and MT2-5-19 represented a novel species of a novel genus in the family Flavobacteriaceae . Thus, Pareuzebyella sediminis gen. nov. sp. nov. is proposed with type strain S2-4-21T (=MCCC 1K03818T=KCTC 72152T), and another strain MT2-5-19 (=KCTC 72539=MCCC 1K03874).

scholarly journals Ruegeria faecimaris sp. nov., isolated from a tidal flat sediment

2011 ◽  
Vol 61 (5) ◽  
pp. 1182-1188 ◽  
Author(s):  
Ki-Hoon Oh ◽  
Yong-Taek Jung ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Phenotypic Properties

A Gram-negative-staining, non-motile and rod-shaped bacterial strain, HD-28T, was isolated from a tidal flat of the Yellow Sea, Korea. Strain HD-28T grew optimally at pH 7.0–8.0 and 30 °C in the presence of 2–3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HD-28T was most closely related to species of the genus Ruegeria and exhibited 95.5–96.9 % 16S rRNA gene sequence similarity to the type strains of Ruegeria species. A neighbour-joining phylogenetic tree based on gyrB gene sequences also showed that strain HD-28T fell within the cluster comprising recognized species of the genus Ruegeria, showing 77.5–83.9 % sequence similarity. Strain HD-28T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids detected in strain HD-28T were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. The DNA G+C content was 57.9 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain HD-28T could be distinguished from recognized species of the genus Ruegeria. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain HD-28T is considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria faecimaris sp. nov. is proposed. The type strain is HD-28T ( = KCTC 23044T = CCUG 58878T).

Ferrimonas gelatinilytica sp. nov., isolated from tidal flat sediment

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4309-4314 ◽  
Author(s):  
Mohammad Mizanur Rahman ◽  
Chang-Jun Cha
Keyword(s):  
16S Rrna ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Anaerobic Bacteria ◽  
Minor Component ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment

A novel beige-pigmented, Gram-staining-negative, coccoid, motile and facultatively anaerobic bacteria, designated strain CJ24T, was isolated from the tidal flat sediment of the Yellow Sea in South Korea. Characterization of this strain was performed on the basis of polyphasic taxonomic methods. Phylogenetic analysis of the 16S rRNA and gyrB genes revealed that strain CJ24T belongs to the genus Ferrimonas , sharing the highest 16S rRNA gene sequence similarity of 96.9 % with Ferrimonas marina DSM 16917T. Strain CJ24T was able to grow optimally at 30 °C, at pH 6.0 and in the presence of 2 % NaCl (w/v). As an isoprenoid quinone, menaquinone (MK-7) was predominantly identified from this strain, while ubiquinone (Q-7) was also present as a minor component. The DNA G+C content of strain CJ24T was 60.2 mol%. The most abundant cellular fatty acids were C15 : 0 iso, C18 : 1ω9c, C16 : 0 and C17 : 0 iso. Therefore, strain CJ24T represents a novel species in the genus Ferrimonas for which the name Ferrimonas gelatinilytica sp. nov. is proposed; the type strain is CJ24T ( = KACC 17065T = JCM 18720T).

scholarly journals Mariniflexile aquimaris sp. nov., isolated from seawater, and emended description of the genus Mariniflexile Nedashkovskaya et al. 2006

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 539-544 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Polar Lipid Profile ◽  
The Family ◽  
Emended Description

A Gram-staining-negative, non-flagellated, non-gliding and rod-shaped bacterial strain, designated HWR-17T, was isolated from seawater of the Yellow Sea in Korea. Strain HWR-17T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HWR-17T clustered with the two Mariniflexile species in the family Flavobacteriaceae, exhibiting 16S rRNA gene sequence similarity of 97.1–97.2 % to their type strains and less than 95.7 % sequence similarity to other members of the family Flavobacteriaceae. Strain HWR-17T contained MK-6 as the predominant menaquinone and iso-C15 : 0 as the major fatty acid. The polar lipid profile of strain HWR-17T contained phosphatidylethanolamine, an unidentified aminolipid and four unidentified lipids. The DNA G+C content of strain HWR-17T was 35.7 mol% and it exhibited 11 and 10 % DNA–DNA relatedness, respectively, with Mariniflexile gromovii KCTC 12570T and Mariniflexile fucanivorans DSM 18792T. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain HWR-17T is distinguishable from the two recognized Mariniflexile species. On the basis of the data presented, strain HWR-17T is considered to represent a novel species of the genus Mariniflexile, for which the name Mariniflexile aquimaris sp. nov. is proposed. The type strain is HWR-17T ( = KCTC 23346T  = CCUG 60529T). An emended description of the genus Mariniflexile is also proposed.

Kangiella sediminilitoris sp. nov., isolated from a tidal flat sediment

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1001-1006 ◽  
Author(s):  
Soo-Young Lee ◽  
Sooyeon Park ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment

A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped bacterial strain, BB-Mw22T, was isolated from a tidal flat sediment of the South Sea in South Korea. It grew optimally at 30–37 °C, at pH 7.0–7.5 and in the presence of 2–3 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain BB-Mw22T belonged to the genus Kangiella and the cluster comprising Kangiella species and strain BB-Mw22T was clearly separated from other taxa. Strain BB-Mw22T exhibited 95.3–98.7 % 16S rRNA gene sequence similarity to the type strains of recognized Kangiella species. Strain BB-Mw22T contained Q-8 as the predominant ubiquionone and iso-C15 : 0 and iso-C11 : 0 3-OH as the major fatty acids. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and one unidentified aminolipid. The DNA G+C content of strain BB-Mw22T was 48.9 mol%, and its mean DNA–DNA hybridization values with Kangiella geojedonensis YCS-5T, Kangiella japonica JCM 16211T and Kangiella taiwanensis JCM 17727T were 14–28 %. Phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain BB-Mw22T is distinguishable from all recognized Kangiella species. On the basis of the data presented, strain BB-Mw22T is considered to represent a novel species of the genus Kangiella , for which the name Kangiella sediminilitoris sp. nov. is proposed. The type strain is BB-Mw22T ( = KCTC 23892T  = CCUG 62217T).

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