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Junghoon Yoon - One of the best experts on this subject based on the ideXlab platform.
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erythrobacter insulae sp nov isolated from a Tidal Flat
International Journal of Systematic and Evolutionary Microbiology, 2020Co-Authors: Sooyeon Park, Siyu Chen, Junghoon YoonAbstract:A Gram-staining-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated as JBTF-M21T, was isolated from a Tidal Flat sediment on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences indicated that JBTF-M21T fell within the clade comprising the type strains of species of the genus Erythrobacter . JBTF-M21T exhibited 16S rRNA gene sequence similarities of 97.0–98.4 % to the type strains of Erythrobacter longus , Erythrobacter aquimaris , Erythrobacter nanhaisediminis , Erythrobacter vulgaris , Erythrobacter seohaensis , Erythrobacter litoralis and Erythrobacter citreus and 93.7–96.6 % to the type strains of the other species of the genus Erythrobacter . The ANI and dDDH values between JBTF-M21T and the type strains of E. longus , E. nanhaisediminis , E. seohaensis and E. litoralis were 70.83–72.93 % and 18.0–18.8 %, respectively. Mean DNA–DNA relatedness values between JBTF-M21T and the type strains of E. aquimaris , E. vulgaris and E. citreus were 12–24 %. The DNA G+C content of JBTF-M21T was 57.0 mol%. JBTF-M21T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C17 : 1ω6c as the major fatty acids. The major polar lipids ofJBTF-M21T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. Distinguishing phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that JBTF-M21T is separated from species of the genus Erythrobacter with validly published names. On the basis of the data presented, strain JBTF-M21T is considered to represent a novel species of the genus Erythrobacter , for which the name Erythrobacter insulae sp. nov. is proposed. The type strain is JBTF-M21T (=KACC 19864T=NBRC 113584T).
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alteromonas aestuariivivens sp nov isolated from a Tidal Flat
International Journal of Systematic and Evolutionary Microbiology, 2017Co-Authors: Sooyeon Park, Su Jung Choi, Jimin Park, Junghoon YoonAbstract:A Gram-stain-negative, aerobic, non-spore-forming, motile and ovoid or rod-shaped bacterial strain, JDTF-113T, was isolated from a Tidal Flat in Jindo, an island of South Korea. Strain JDTF-113T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree, based on 16S rRNA gene sequences, revealed that strain JDTF-113T fell within the clade enclosing the type strains of species of the genus Alteromonas . Strain JDTF-113T exhibited 16S rRNA gene sequence similarity values of 97.1–98.1 % to the type strains of Alteromonas lipolytica , Alteromonas litorea , Alteromonas mediterranea , Alteromonas confluentis , Alteromonas hispanica , Alteromonas genovensis and Alteromonas marina , and of 94.8–96.9 % to those of the other species of the genus Alteromonas . Strain JDTF-113T contained Q-8 as the predominant ubiquinone and C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C18 : 1ω7c as the major fatty acids. The major polar lipids of strain JDTF-113T were phosphatidylethanolamine, phosphatidylglycerol and one unidentified glycolipid. The DNA G+C content of strain JDTF-113T was 51.1 mol% and its mean DNA–DNA relatedness values with the type strains of seven closely phylogenetically related species of the genus Alteromonas were was 10–23 %. The differential phenotypic properties and phylogenetic and genetic distinctiveness support strain JDTF-113T being separated from species of the genus Alteromonas with validly published names . On the basis of the data presented, strain JDTF-113T is considered to represent a novel species of the genus Alteromonas , for which the name Alteromonas aestuariivivens sp. nov. is proposed. The type strain is JDTF-113T (=KCTC 52655T=NBRC 112708T).
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erythrobacter lutimaris sp nov isolated from a Tidal Flat sediment
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Yongtaek Jung, Sooyeon Park, Jungsook Lee, Junghoon YoonAbstract: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).
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aestuariivita boseongensis gen nov sp nov isolated from a Tidal Flat sediment
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Sooyeon Park, Sungmin Won, Hyangmi Kim, Doosang Park, Junghoon YoonAbstract:A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, BS-B2T, which was isolated from a Tidal Flat sediment at Boseong in South Korea, was characterized taxonomically. Strain BS-B2T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. The novel strain exhibited highest 16S rRNA gene sequence similarity (97.4 %) to Marivita geojedonensis DPG-138T. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain BS-B2T is closely related to Primorskyibacter sedentarius KMM 9018T, showing 96.5 % sequence similarity. Strain BS-B2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The polar lipid profile of strain BS-B2T comprised phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid as major components, and differentiated it from the type strains of P. sedentarius and M. geojedonensis . The DNA G+C content of strain BS-B2T was 62.2 mol%. Differential phenotypic properties, together with the phylogenetic and chemotaxonomic data, demonstrated that strain BS-B2T can be distinguished from phylogenetically related genera as well as P. sedentarius and M. geojedonensis . On the basis of the data presented, strain BS-B2T is considered to represent a novel species of a new genus, for which the name Aestuariivita boseongensis gen. nov., sp. nov. is proposed. The type strain of Aestuariivita boseongensis is BS-B2T ( = KCTC 42052T = CECT 8532T).
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mucilaginibacter lutimaris sp nov isolated from a Tidal Flat sediment
International Journal of Systematic and Evolutionary Microbiology, 2012Co-Authors: Jihoon Kim, Sojung Kang, Junghoon Yoon, Yongtaek JungAbstract:A Gram-staining-negative, non-spore-forming, facultatively aerobic, non-motile, rod-shaped bacterial strain, BR-3T, was isolated from a Tidal Flat on the western coast of Korea, and subjected to a polyphasic study. Strain BR-3T grew optimally at 25 °C, at pH 6.5–7.0 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BR-3T fell within the clade comprising species of the genus Mucilaginibacter, joining the type strain of Mucilaginibacter rigui, with which it exhibited highest 16S rRNA gene sequence similarity (98.2 %). 16S rRNA gene sequence similarity values between strain BR-3T and the type strains of the other species of the genus Mucilaginibacter were in the range 93.8–95.9 %. A mean DNA–DNA relatedness value between strain BR-3T and M. rigui KCTC 12534T was 21 %. Strain BR-3T contained MK-7 as the predominant menaquinone and C16 : 1ω7c and/or iso-C15 : 0 2-OH and iso-C15 : 0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine and an unidentified aminophospholipid. The DNA G+C content was 49.8 mol%. Differential phenotypic properties and phylogenetic and genetic distinctiveness of strain BR-3T demonstrated that this strain is separate from M. rigui as well as the other species of the genus Mucilaginibacter. On the basis of the data presented, strain BR-3T is considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter lutimaris sp. nov. is proposed. The type strain is BR-3T ( = KCTC 23461T = CCUG 60742T).
Jongsik Chun - One of the best experts on this subject based on the ideXlab platform.
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marinifilum fragile gen nov sp nov isolated from Tidal Flat sediment
International Journal of Systematic and Evolutionary Microbiology, 2009Co-Authors: Seil Kim, Eun Young Moon, Jongsik ChunAbstract:A facultatively anaerobic, moderately halophilic, Gram-negative, filamentous bacterium, designated JC2469T, was isolated from Tidal Flat sediment in Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the phylum Bacteroidetes and its closest taxonomic relative was Cytophaga fermentans NCIMB 2218T (89.6% sequence similarity). Cells appeared as filaments during exponential growth, but became fragmented to rods at stationary phase. Spherical cells were also observed in aged cultures. Strain JC2469T contained iso-C15:0 (56.2%) and MK-7 as the predominant fatty acid and respiratory quinone, respectively. On the basis of evidence from this polyphasic study, the isolate showed substantial differences from other genera. The phylogenetic and physiological data of the present study strongly suggest that the isolate represents a novel genus and species, for which the name Marinifilum fragile gen. nov., sp. nov. is proposed. The type strain of Marinifilum fragile is JC2469T (=IMSNU 14138T=KCTC 22488T=JCM 15579T).
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Rapid phylogenetic dissection of prokaryotic community structure in Tidal Flat using pyrosequencing
The Journal of Microbiology, 2008Co-Authors: Jongsik ChunAbstract:Dissection of prokaryotic community structure is prerequisite to understand their ecological roles. Various methods are available for such a purpose which amplification and sequencing of 16S rRNA genes gained its popularity. However, conventional methods based on Sanger sequencing technique require cloning process prior to sequencing, and are expensive and labor-intensive. We investigated prokaryotic community structure in Tidal Flat sediments, Korea, using pyrosequencing and a subsequent automated bioinformatic pipeline for the rapid and accurate taxonomic assignment of each amplicon. The combination of pyrosequencing and bioinformatic analysis showed that bacterial and archaeal communities were more diverse than previously reported in clone library studies. Pyrosequencing analysis revealed 21 bacterial divisions and 37 candidate divisions. Proteobacteria was the most abundant division in the bacterial community, of which Gamma-and Delta-Proteobacteria were the most abundant. Similarly, 4 archaeal divisions were found in Tidal Flat sediments. Euryarchaeota was the most abundant division in the archaeal sequences, which were further divided into 8 classes and 11 unclassified euryarchaeota groups. The system developed here provides a simple, in-depth and automated way of dissecting a prokaryotic community structure without extensive pretreatment such as cloning.
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thalassobius aestuarii sp nov isolated from Tidal Flat sediment
Journal of Microbiology, 2006Co-Authors: Jongsik ChunAbstract:A strictly aerobic, non-motile, ovoid-shaped Alphaproteobacteria, designated strain JC2049(T), was isolated from a Tidal Flat sediment sample. The results of 16S rRNA gene sequence analysis indicated that this isolate belonged to the genus Thalassobius, with a sequence similarity of 96.9-97.3% to other valid Thalassobius spp. The cells required 1-7% NaCl for growth (optimum 2%) and accumulated poly-beta-hydroxybutyrate. Nitrite was reduced to nitrogen, but nitrate was not reduced to nitrite. No genetic potential for aerobic anoxygenic photosynthesis was detected. The primary isoprenoid quinone (Ubiquinone-10), predominant cellular fatty acids (C(18:1)omega7c, 11 methyl C(18:1)omega7c and C(16:0)) and DNA G+C content (61 mol%) were all consistent with the assignment of this isolate to the genus Thalassobius. Several phenotypic characteristics clearly distinguished our isolate from other Thalassobius species. The degree of genomic relatedness between strain JC2049(T) and other Thalassobius species was in a range of 20-43%. The polyphasic data presented in this study indicates that our isolate should be classified as a novel species within the genus Thalassobius. The name Thalassobius aestuarii sp. nov. is therefore proposed for this isolate; the type strain is JC2049(T) (= IMSNU 14011(T) = KCTC 12049(T) = DSM 15283(T)).
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tenacibaculum litoreum sp nov isolated from Tidal Flat sediment
International Journal of Systematic and Evolutionary Microbiology, 2006Co-Authors: Dong Han Choi, Jongsik Chun, Yoon Gon Kim, Chung Yeon Hwang, Byung Cheol ChoAbstract:A rod-shaped bacterium, designated CL-TF13T, was isolated from a Tidal Flat in Ganghwa, Korea. Analysis of the 16S rRNA gene sequence revealed an affiliation with the genus Tenacibaculum. The sequence similarities between CL-TF13T and type strains of members of the genus Tenacibaculum were from 94·2 to 97·4 %. Cells were motile by means of gliding. Strain CL-TF13T grew on solid medium as pale-yellow colonies with an irregular spreading edge. The strain was able to grow in NaCl at a range of 3–5 %. They grew within a temperature range of 5–40 °C and at pH range of 6–10. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH, 19·6 %), iso-C15 : 0 (18·8 %) and iso-C17 : 0 3-OH (13·6 %). Fatty acids such as C18 : 3 ω6c (6,9,12) (1·5 %) and summed feature 4 (iso I- and/or anteiso B-C17 : 1, 1·3 %) were uniquely found in minor quantities in CL-TF13T among Tenacibaculum species. The DNA G+C content was 30 mol%. According to physiological data, fatty-acid composition and 16S rRNA gene sequence, CL-TF13T could be assigned to the genus Tenacibaculum but distinguished from the recognized species of the genus. Therefore, strain CL-TF13T (=KCCM 42115T=JCM 13039T) represents a novel species, for which the name Tenacibaculum litoreum sp. nov. is proposed.
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archaeal diversity in Tidal Flat sediment as revealed by 16s rdna analysis
Journal of Microbiology, 2005Co-Authors: Huynmyung Oh, Hojeong Kang, Jongsik ChunAbstract:: During the past ten years, Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages. More recently, the presence of novel archaeal phylogenetic lineages has been discovered in coastal marine environments, freshwater lakes, polar seas, and deep-sea hydrothermal vents. Therefore, we conducted an investigation into the archaeal community existing in Tidal Flat sediment collected from Ganghwa Island, Korea. Phylogenetic analysis of archaeal 16S rDNA amplified directly from Tidal Flat sediment DNA revealed the presence of two major lineages, belonging to the Crenarchaeota (53.9%) and Euryarchaeota (46.1%) phyla. A total of 102 clones were then sequenced and analyzed by comprehensive phylogenetic analysis. The sequences determined in our samples were found to be closely related to the sequences of clones which had been previously obtained from a variety of marine environments. Archaeal clones exhibited higher similarities (83.25-100%) to sequences from other environments in the public database than did those (75.22-98.46%) of previously reported bacterial clones obtained from Tidal Flat sediment. The results of our study suggest that the archaeal community in Tidal Flat sediment is remarkably diverse.
Che Ok Jeon - One of the best experts on this subject based on the ideXlab platform.
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genome wide transcriptional responses of alteromonas naphthalenivorans sn2 to contaminated seawater and marine Tidal Flat sediment
Scientific Reports, 2016Co-Authors: Hye Im Jeong, Yoonsoo Hahn, Eugene L Madsen, Che Ok JeonAbstract:A genome-wide transcriptional analysis of Alteromonas naphthalenivorans SN2 was performed to investigate its ecophysiological behavior in contaminated Tidal Flats and seawater. The experimental design mimicked these habitats that either added naphthalene or pyruvate; Tidal Flat-naphthalene (TF-N), Tidal Flat-pyruvate (TF-P), seawater-naphthalene (SW-N), and seawater-pyruvate (SW-P). The transcriptional profiles clustered by habitat (TF-N/TF-P and SW-N/SW-P), rather than carbon source, suggesting that the former may exert a greater influence on genome-wide expression in strain SN2 than the latter. Metabolic mapping of cDNA reads from strain SN2 based on KEGG pathway showed that metabolic and regulatory genes associated with energy metabolism, translation, and cell motility were highly expressed in all four test conditions, probably highlighting the copiotrophic properties of strain SN2 as an opportunistic marine r-strategist. Differential gene expression analysis revealed that strain SN2 displayed specific cellular responses to environmental variables (Tidal Flat, seawater, naphthalene, and pyruvate) and exhibited certain ecological fitness traits –– its notable PAH degradation capability in seasonally cold Tidal Flat might be reflected in elevated expression of stress response and chaperone proteins, while fast growth in nitrogen-deficient and aerobic seawater probably correlated with high expression of glutamine synthetase, enzymes utilizing nitrite/nitrate, and those involved in the removal of reactive oxygen species.
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aquamicrobium aestuarii sp nov a marine bacterium isolated from a Tidal Flat
International Journal of Systematic and Evolutionary Microbiology, 2013Co-Authors: Hyun Mi Jin, Jeong Myeong Kim, Che Ok JeonAbstract:A Gram-negative, strictly aerobic, motile bacterium with flagella, designated strain G210T, was isolated from a crude-oil-contaminated Tidal Flat of the Taean coast in South Korea. Cells were non-spore-forming, ovoid rods showing catalase- and oxidase-positive reactions. Growth of strain G210T was observed between 15 and 45 °C (optimum, 30–35 °C) and between pH 5.5 and 9.0 (optimum, pH 6.5–7.5). Strain G210T contained Q-10 as the sole isoprenoid quinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0 cyclo ω8c as the major fatty acids. Putrescine and spermidine were identified as the major polyamines. Strain G210T contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, an unidentified phospholipid and an unidentified aminolipid as polar lipids. The G+C content of the genomic DNA was 56.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain G210T formed a phyletic lineage with members of the genus Aquamicrobium . Strain G210T was most closely related to Aquamicrobium ahrensii 905/1T (97.9 % similarity). The DNA–DNA relatedness between strain G210T and the type strain of A. ahrensii was 24±0.5 %. On the basis of phenotypic, chemotaxonomic and molecular properties, strain G210T represents a novel species within the genus Aquamicrobium , for which the name Aquamicrobium aestuarii sp. nov. is proposed. The type strain is G210T ( = KACC 14931T = JCM 16876T).
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isolation of a btex degrading bacterium janibacter sp sb2 from a sea Tidal Flat and optimization of biodegradation conditions
Bioresource Technology, 2013Co-Authors: Hyun Mi Jin, Eun Jin Choi, Che Ok JeonAbstract:Abstract An enrichment culture was established using seawater containing BTEX (benzene, toluene, ethylbenzene and xylene) compounds to isolate a BTEX-degrading bacterium from contaminated sea-Tidal Flat. The enriched microbial communities were characterized by 16S rRNA-based DGGE profiling, which indicated that a Janibacter species was dominant during the enrichment. Strain SB2, corresponding to the major band and able to degrade all BTEX compounds, was isolated and characterized. NH 4 Cl, NaH 2 PO 4 , cell mass and BTEX concentrations were used as independent variables to optimize the degradation of BTEX by strain SB2 in a Tidal Flat and a statistically significant ( R 2 = 0.8933, p 7 cells/L, 45.5% BTEX removal was observed under the optimum condition of NH 4 Cl and NaH 2 PO 4 , while 32.2% BTEX removal was observed under the untreated condition of NH 4 Cl and NaH 2 PO 4 .
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altererythrobacter gangjinensis sp nov a marine bacterium isolated from a Tidal Flat
International Journal of Systematic and Evolutionary Microbiology, 2013Co-Authors: Sang Hyeon Jeong, Hyun Mi Jin, Hyo Jung Lee, Che Ok JeonAbstract:A Gram-stain-negative, ochre-pigmented, strictly aerobic bacterium, designated strain KJ7T, was isolated from a Tidal Flat of the Gangjin bay in South Korea. Cells were halotolerant, non-motile, catalase- and oxidase-positive rods. Growth of strain KJ7T was observed at 5–35 °C (optimum, 25 °C), at pH 6.0–9.5 (optimum, pH 6.5–7.0) and in the presence of 0–9 % (w/v) NaCl (optimum, 2 %). The major cellular fatty acids were C18 : 1ω7c, C17 : 1ω6c, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid pattern indicated the presence of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, a sphingoglycolipid, an unidentified phospholipid and two unidentified lipids. The G+C content of the genomic DNA was 60.2±0.9 mol% and the predominant respiratory quinone was Q-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KJ7T formed a phyletic lineage distinct from other members of the genus Altererythrobacter and was most closely related to Altererythrobacter luteolus SW-109T and Altererythrobacter namhicola KYW48T (95.6 and 95.0 % 16S rRNA gene sequence similarity, respectively). On the basis of phenotypic, chemotaxonomic and molecular features, strain KJ7T represents a novel species of the genus Altererythrobacter , for which the name Altererythrobacter gangjinensis sp. nov. is proposed. The type strain is KJ7T ( = KACC 16190T = JCM 17802T).
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comparative genomics reveals adaptation by alteromonas sp sn2 to marine Tidal Flat conditions cold tolerance and aromatic hydrocarbon metabolism
PLOS ONE, 2012Co-Authors: Renukaradhya K Math, Yoonsoo Hahn, Eugene L Madsen, Woojun Park, Che Ok JeonAbstract:Alteromonas species are globally distributed copiotrophic bacteria in marine habitats. Among these, sea-Tidal Flats are distinctive: undergoing seasonal temperature and oxygen-tension changes, plus periodic exposure to petroleum hydrocarbons. Strain SN2 of the genus Alteromonas was isolated from hydrocarbon-contaminated sea-Tidal Flat sediment and has been shown to metabolize aromatic hydrocarbons there. Strain SN2's genomic features were analyzed bioinformatically and compared to those of Alteromonas macleodii ecotypes: AltDE and ATCC 27126. Strain SN2's genome differs from that of the other two strains in: size, average nucleotide identity value, tRNA genes, noncoding RNAs, dioxygenase gene content, signal transduction genes, and the degree to which genes collected during the Global Ocean Sampling project are represented. Patterns in genetic characteristics (e.g., GC content, GC skew, Karlin signature, CRISPR gene homology) indicate that strain SN2's genome architecture has been altered via horizontal gene transfer (HGT). Experiments proved that strain SN2 was far more cold tolerant, especially at 5°C, than the other two strains. Consistent with the HGT hypothesis, a total of 15 genomic islands in strain SN2 likely confer ecological fitness traits (especially membrane transport, aromatic hydrocarbon metabolism, and fatty acid biosynthesis) specific to the adaptation of strain SN2 to its seasonally cold sea-Tidal Flat habitat.
Sooyeon Park - One of the best experts on this subject based on the ideXlab platform.
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erythrobacter insulae sp nov isolated from a Tidal Flat
International Journal of Systematic and Evolutionary Microbiology, 2020Co-Authors: Sooyeon Park, Siyu Chen, Junghoon YoonAbstract:A Gram-staining-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated as JBTF-M21T, was isolated from a Tidal Flat sediment on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences indicated that JBTF-M21T fell within the clade comprising the type strains of species of the genus Erythrobacter . JBTF-M21T exhibited 16S rRNA gene sequence similarities of 97.0–98.4 % to the type strains of Erythrobacter longus , Erythrobacter aquimaris , Erythrobacter nanhaisediminis , Erythrobacter vulgaris , Erythrobacter seohaensis , Erythrobacter litoralis and Erythrobacter citreus and 93.7–96.6 % to the type strains of the other species of the genus Erythrobacter . The ANI and dDDH values between JBTF-M21T and the type strains of E. longus , E. nanhaisediminis , E. seohaensis and E. litoralis were 70.83–72.93 % and 18.0–18.8 %, respectively. Mean DNA–DNA relatedness values between JBTF-M21T and the type strains of E. aquimaris , E. vulgaris and E. citreus were 12–24 %. The DNA G+C content of JBTF-M21T was 57.0 mol%. JBTF-M21T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C17 : 1ω6c as the major fatty acids. The major polar lipids ofJBTF-M21T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. Distinguishing phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that JBTF-M21T is separated from species of the genus Erythrobacter with validly published names. On the basis of the data presented, strain JBTF-M21T is considered to represent a novel species of the genus Erythrobacter , for which the name Erythrobacter insulae sp. nov. is proposed. The type strain is JBTF-M21T (=KACC 19864T=NBRC 113584T).
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alteromonas aestuariivivens sp nov isolated from a Tidal Flat
International Journal of Systematic and Evolutionary Microbiology, 2017Co-Authors: Sooyeon Park, Su Jung Choi, Jimin Park, Junghoon YoonAbstract:A Gram-stain-negative, aerobic, non-spore-forming, motile and ovoid or rod-shaped bacterial strain, JDTF-113T, was isolated from a Tidal Flat in Jindo, an island of South Korea. Strain JDTF-113T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree, based on 16S rRNA gene sequences, revealed that strain JDTF-113T fell within the clade enclosing the type strains of species of the genus Alteromonas . Strain JDTF-113T exhibited 16S rRNA gene sequence similarity values of 97.1–98.1 % to the type strains of Alteromonas lipolytica , Alteromonas litorea , Alteromonas mediterranea , Alteromonas confluentis , Alteromonas hispanica , Alteromonas genovensis and Alteromonas marina , and of 94.8–96.9 % to those of the other species of the genus Alteromonas . Strain JDTF-113T contained Q-8 as the predominant ubiquinone and C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C18 : 1ω7c as the major fatty acids. The major polar lipids of strain JDTF-113T were phosphatidylethanolamine, phosphatidylglycerol and one unidentified glycolipid. The DNA G+C content of strain JDTF-113T was 51.1 mol% and its mean DNA–DNA relatedness values with the type strains of seven closely phylogenetically related species of the genus Alteromonas were was 10–23 %. The differential phenotypic properties and phylogenetic and genetic distinctiveness support strain JDTF-113T being separated from species of the genus Alteromonas with validly published names . On the basis of the data presented, strain JDTF-113T is considered to represent a novel species of the genus Alteromonas , for which the name Alteromonas aestuariivivens sp. nov. is proposed. The type strain is JDTF-113T (=KCTC 52655T=NBRC 112708T).
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erythrobacter lutimaris sp nov isolated from a Tidal Flat sediment
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Yongtaek Jung, Sooyeon Park, Jungsook Lee, Junghoon YoonAbstract: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).
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aestuariivita boseongensis gen nov sp nov isolated from a Tidal Flat sediment
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Sooyeon Park, Sungmin Won, Hyangmi Kim, Doosang Park, Junghoon YoonAbstract:A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, BS-B2T, which was isolated from a Tidal Flat sediment at Boseong in South Korea, was characterized taxonomically. Strain BS-B2T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. The novel strain exhibited highest 16S rRNA gene sequence similarity (97.4 %) to Marivita geojedonensis DPG-138T. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain BS-B2T is closely related to Primorskyibacter sedentarius KMM 9018T, showing 96.5 % sequence similarity. Strain BS-B2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The polar lipid profile of strain BS-B2T comprised phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid as major components, and differentiated it from the type strains of P. sedentarius and M. geojedonensis . The DNA G+C content of strain BS-B2T was 62.2 mol%. Differential phenotypic properties, together with the phylogenetic and chemotaxonomic data, demonstrated that strain BS-B2T can be distinguished from phylogenetically related genera as well as P. sedentarius and M. geojedonensis . On the basis of the data presented, strain BS-B2T is considered to represent a novel species of a new genus, for which the name Aestuariivita boseongensis gen. nov., sp. nov. is proposed. The type strain of Aestuariivita boseongensis is BS-B2T ( = KCTC 42052T = CECT 8532T).
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aquamicrobium aestuarii sp nov a marine bacterium isolated from a Tidal Flat
International Journal of Systematic and Evolutionary Microbiology, 2013Co-Authors: Hyun Mi Jin, Jeong Myeong Kim, Che Ok JeonAbstract:A Gram-negative, strictly aerobic, motile bacterium with flagella, designated strain G210T, was isolated from a crude-oil-contaminated Tidal Flat of the Taean coast in South Korea. Cells were non-spore-forming, ovoid rods showing catalase- and oxidase-positive reactions. Growth of strain G210T was observed between 15 and 45 °C (optimum, 30–35 °C) and between pH 5.5 and 9.0 (optimum, pH 6.5–7.5). Strain G210T contained Q-10 as the sole isoprenoid quinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0 cyclo ω8c as the major fatty acids. Putrescine and spermidine were identified as the major polyamines. Strain G210T contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, an unidentified phospholipid and an unidentified aminolipid as polar lipids. The G+C content of the genomic DNA was 56.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain G210T formed a phyletic lineage with members of the genus Aquamicrobium . Strain G210T was most closely related to Aquamicrobium ahrensii 905/1T (97.9 % similarity). The DNA–DNA relatedness between strain G210T and the type strain of A. ahrensii was 24±0.5 %. On the basis of phenotypic, chemotaxonomic and molecular properties, strain G210T represents a novel species within the genus Aquamicrobium , for which the name Aquamicrobium aestuarii sp. nov. is proposed. The type strain is G210T ( = KACC 14931T = JCM 16876T).
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isolation of a btex degrading bacterium janibacter sp sb2 from a sea Tidal Flat and optimization of biodegradation conditions
Bioresource Technology, 2013Co-Authors: Hyun Mi Jin, Eun Jin Choi, Che Ok JeonAbstract:Abstract An enrichment culture was established using seawater containing BTEX (benzene, toluene, ethylbenzene and xylene) compounds to isolate a BTEX-degrading bacterium from contaminated sea-Tidal Flat. The enriched microbial communities were characterized by 16S rRNA-based DGGE profiling, which indicated that a Janibacter species was dominant during the enrichment. Strain SB2, corresponding to the major band and able to degrade all BTEX compounds, was isolated and characterized. NH 4 Cl, NaH 2 PO 4 , cell mass and BTEX concentrations were used as independent variables to optimize the degradation of BTEX by strain SB2 in a Tidal Flat and a statistically significant ( R 2 = 0.8933, p 7 cells/L, 45.5% BTEX removal was observed under the optimum condition of NH 4 Cl and NaH 2 PO 4 , while 32.2% BTEX removal was observed under the untreated condition of NH 4 Cl and NaH 2 PO 4 .
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altererythrobacter gangjinensis sp nov a marine bacterium isolated from a Tidal Flat
International Journal of Systematic and Evolutionary Microbiology, 2013Co-Authors: Sang Hyeon Jeong, Hyun Mi Jin, Hyo Jung Lee, Che Ok JeonAbstract:A Gram-stain-negative, ochre-pigmented, strictly aerobic bacterium, designated strain KJ7T, was isolated from a Tidal Flat of the Gangjin bay in South Korea. Cells were halotolerant, non-motile, catalase- and oxidase-positive rods. Growth of strain KJ7T was observed at 5–35 °C (optimum, 25 °C), at pH 6.0–9.5 (optimum, pH 6.5–7.0) and in the presence of 0–9 % (w/v) NaCl (optimum, 2 %). The major cellular fatty acids were C18 : 1ω7c, C17 : 1ω6c, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid pattern indicated the presence of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, a sphingoglycolipid, an unidentified phospholipid and two unidentified lipids. The G+C content of the genomic DNA was 60.2±0.9 mol% and the predominant respiratory quinone was Q-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KJ7T formed a phyletic lineage distinct from other members of the genus Altererythrobacter and was most closely related to Altererythrobacter luteolus SW-109T and Altererythrobacter namhicola KYW48T (95.6 and 95.0 % 16S rRNA gene sequence similarity, respectively). On the basis of phenotypic, chemotaxonomic and molecular features, strain KJ7T represents a novel species of the genus Altererythrobacter , for which the name Altererythrobacter gangjinensis sp. nov. is proposed. The type strain is KJ7T ( = KACC 16190T = JCM 17802T).
