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Complete Genome Sequence of Croceibacter Bacteriophage P2559S
Kang, Ilnam,Kang, Dongmin,Cho, Jang-Cheon American Society for Microbiology 2012 Journal of virology Vol.86 No.16
<P>Croceibacter atlanticusHTCC2559<SUP>T</SUP>, a marine bacterium isolated from the Sargasso Sea, is a phylogenetically unique member of the familyFlavobacteriaceae. Strain HTCC2559<SUP>T</SUP>possesses genes related to interaction with primary producers, which makes studies on bacteriophages infecting the strain interesting. Here we report the genome sequence of bacteriophage P2559S, which was isolated off the coast of the Republic of Korea and lytically infects HTCC2559<SUP>T</SUP>. Many genes predicted in the P2559S genome had their homologs inBacteroidesphages.</P>
Complete Genome Sequence of Marinomonas Bacteriophage P12026
Kang, Ilnam,Jang, Hani,Oh, Hyun-Myung,Cho, Jang-Cheon American Society for Microbiology 2012 Journal of virology Vol.86 No.16
<P>Members of the genusMarinomonasin theGammaproteobacteriaare broadly distributed in marine environments where they could be infected by bacteriophages. Here we report the genome sequence of bacteriophage P12026 that can lytically infect bacterial strain IMCC12026, a member of the genusMarinomonas. To our knowledge, this is the first genome sequence of a lytic bacteriophage infecting the genusMarinomonas.</P>
Kang, Ilnam,Oh, Hyun-Myung,Lim, Seung-Il,Ferriera, Steve,Giovannoni, Stephen J.,Cho, Jang-Cheon American Society for Microbiology 2010 Journal of Bacteriology Vol.192 No.18
<B>ABSTRACT</B><P><I>Fulvimarina pelagi</I> is a Mn(II)-oxidizing marine heterotrophic bacterium in the order <I>Rhizobiales</I>. Here we announce the draft genome sequence of <I>F. pelagi</I> HTCC2506<SUP>T</SUP>, which was isolated from the Sargasso Sea by using dilution-to-extinction culturing. The genome sequence contained a xanthorhodopsin gene as well as a photosynthetic gene cluster, which suggests the coexistence of two different phototrophic mechanisms in a single microorganism.</P>
Genome Sequence of the Marine Alphaproteobacterium HTCC2150, Assigned to the Roseobacter Clade
Kang, Ilnam,Oh, Hyun-Myung,Vergin, Kevin L.,Giovannoni, Stephen J.,Cho, Jang-Cheon American Society for Microbiology 2010 Journal of Bacteriology Vol.192 No.23
<B>ABSTRACT</B><P>Here we announce the genome sequence of a marine bacterium, HTCC2150, that was isolated off the Oregon coast using dilution-to-extinction culturing and that is affiliated with the <I>Roseobacter</I> clade. The 16S rRNA phylogeny showed that the strain was closely related to members of the RCA clade. The genome sequence suggests that strain HTCC2150 is an organoheterotroph carrying diverse metabolic potential, including a close relationship with phytoplankton.</P>
Kang, Ilnam,Lim, Yeonjung,Cho, Jang-Cheon Elsevier 2018 MARINE GENOMICS Vol.37 No.-
<P><B>Abstract</B></P> <P> <I>Granulosicoccus</I>, the only genus of the family <I>Granulosicoccaceae</I>, occupies a distinct phylogenetic position within the order <I>Chromatiales</I> of the <I>Gammaproteobacteria</I>. The genus has been found in various marine regions, especially associated with diverse marine macroalgae. No genomes have been reported for the genus <I>Granulosicoccus</I> thus far, hampering studies on physiology and lifestyles of this genus. Here we report the complete genome sequence of strain IMCC3135<SUP>T</SUP>, the type strain of <I>Granulosicoccus antarcticus</I> isolated from Antarctic coastal seawater. The genome was 7.78Mbp long and harbored many genes involved in sulfur metabolism. In particular, a gene for dimethylsulfoniopropionate (DMSP) demethylase was found in the genome, rendering strain IMCC3135<SUP>T</SUP> one of the few marine gammaproteobacteria equipped with the potential for DMSP demethylation.</P>
송재호,Ilnam Kang,Yochan Joung,Susumu Yoshizawa,Ryo Kaneko,Kenshiro Oshima,Masahira Hattori,Koji Hamasaki,Kazuhiro Kogure,Soochan Kim,Kangseok Lee,Jang-Cheon Cho 한국미생물학회 2019 The journal of microbiology Vol.57 No.5
Although culture-independent studies have shown the presence of Verrucomicrobia in the deep sea, verrucomicrobial strains from deep-sea environments have been rarely cultured and characterized. Recently, Rubritalea profundi SAORIC- 165T, a psychrophilic bacterium of the phylum Verrucomicrobia, was isolated from a depth of 2,000 m in the northwestern Pacific Ocean. In this study, the genome sequence of R. profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, is reported with description of the genome properties and comparison to surface-borne Rubritalea genomes. The draft genome consisted of four contigs with an entire size of 4,167,407 bp and G+C content of 47.5%. The SAORIC-165T genome was predicted to have 3,844 proteincoding genes and 45 non-coding RNA genes. The genome contained a repertoire of metabolic pathways, including the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, tricarboxylic acid cycle, assimilatory sulfate reduction, and biosynthesis of nicotinate/nicotinamide, pantothenate/ coenzyme A, folate, and lycopene. The comparative genomic analyses with two surface-derived Rubritalea genomes showed that the SAORIC-165T genome was enriched in genes involved in transposition of mobile elements, signal transduction, and carbohydrate metabolism, some of which might be related to bacterial enhancement of ecological fitness in the deep-sea environment. Amplicon sequencing of 16S rRNA genes from the water column revealed that R. profundi-related phylotypes were relatively abundant at 2,000 m and preferred a particle-associated life style in the deep sea. These findings suggest that R. profundi represents a genetically unique and ecologically relevant verrucomicrobial group well adapted to the deep-sea environment.
( Suhyun Kim ),( Ilnam Kang ),( Jang-cheon Cho ) 한국미생물 · 생명공학회 2017 Journal of microbiology and biotechnology Vol.27 No.4
Strain IMCC26207 was isolated from the surface layer of Lake Soyang in Korea by the dilutionto- extinction culturing method, using a liquid medium prepared with filtered and autoclaved lake water. The strain could neither be maintained in a synthetic medium other than natural freshwater medium nor grown on solid agar plates. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain IMCC26207 formed a distinct lineage in the order Acidimicrobiales of the phylum Actinobacteria. The closest relative among the previously identified bacterial taxa was “Candidatus Microthrix parvicella” with 16S rRNA gene sequence similarity of 91.7%. Here, the draft genome sequence of strain IMCC26207, a freshwater actinobacterium, is reported with the description of the genome properties and annotation summary. The draft genome consisted of 10 contigs with a total size of 3,316,799 bp and an average G+C content of 57.3%. The IMCC26207 genome was predicted to contain 2,975 protein-coding genes and 51 non-coding RNA genes, including 45 tRNA genes. Approximately 76.8% of the protein coding genes could be assigned with a specific function. Annotation of the IMCC26207 genome showed several traits of adaptation to living in oligotrophic freshwater environments, such as phosphorus-limited condition. Comparative genomic analysis revealed that the genome of strain IMCC26207 was distinct from that of “Candidatus Microthrix” strains; therefore, we propose the name “Candidatus Limnosphaera aquatica” for this bacterium.
Oh, Hyun-Myung,Kang, Ilnam,Ferriera, Steve,Giovannoni, Stephen J.,Cho, Jang-Cheon American Society for Microbiology 2010 Journal of Bacteriology Vol.192 No.17
<B>ABSTRACT</B><P>Strain HTCC2143 was isolated from Oregon Coast surface waters using dilution-to-extinction culturing. Here we present the genome of strain HTCC2143 from the BD1-7 clade of the oligotrophic marine <I>Gammaproteobacteria</I> group. The genome of HTCC2143 contains genes for carotenoid biosynthesis and proteorhodopsin and for proteins that have potential biotechnological significance: epoxide hydrolases, Baeyer-Villiger monooxygenases, and polyketide synthases.</P>
<i>Kordia</i> <i>antarctica</i> sp. nov., isolated from Antarctic seawater
Baek, Kiwoon,Choi, Ahyoung,Kang, Ilnam,Lee, Kiyoung,Cho, Jang-Cheon International Union of Microbiological Societies 2013 International journal of systematic and evolutiona Vol.63 No.10
<P>A Gram-staining-negative, chemoheterotrophic, yellow-pigmented, non-motile, flexirubin-negative, facultatively anaerobic bacterium, designated strain IMCC3317<SUP>T</SUP>, was isolated from a coastal seawater sample from the Antarctic Penninsula. Optimal growth of strain IMCC3317<SUP>T</SUP> was observed at 20 °C, pH 8.0 and in the presence of 2–3 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC3317<SUP>T</SUP> belonged to the genus <I>Kordia</I> and was closely related to <I>Kordia algicida</I> OT-1<SUP>T</SUP> (96.7 % sequence similarity) and <I>Kordia periserrulae</I> IMCC1412<SUP>T</SUP> (96.1 % sequence similarity). The major fatty acids were 10-methyl C<SUB>16 : 0</SUB> and/or iso-C<SUB>16 : 1</SUB>ω9<I>c</I>, iso-C<SUB>17 : 0</SUB> 3-OH, iso-C<SUB>15 : 0</SUB> and anteiso-C<SUB>15 : 0</SUB>. The G+C content of the genomic DNA was 35.1 mol%. The strain contained menaquinone-6 (MK-6) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine and unknown aminophospholipids, aminolipids and polar lipids. On the basis of phylogenetic distinction and differential phenotypic characteristics, it is suggested that strain IMCC3317<SUP>T</SUP> ( = KCTC 32292<SUP>T</SUP> = NBRC 109401<SUP>T</SUP>) be assigned to the genus <I>Kordia</I> as the type strain of a novel species, for which the name <I>Kordia</I> <I>antarctica</I> sp. nov. is proposed.</P>
Baek, Kiwoon,Choi, Ahyoung,Kang, Ilnam,Im, Mihye,Cho, Jang-Cheon International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.12
<P>A Gram-staining-negative, motile by flagella, non-pigmented, poly-β-hydroxybutyrate-producing, strictly aerobic and sphere-shaped bacterium, IMCC3490<SUP>T</SUP>, was isolated from a coastal seawater sample from the Antarctic Peninsula. Optimal growth of strain IMCC3490<SUP>T</SUP> was observed at 20 °C, pH 8.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain IMCC3490<SUP>T</SUP> belonged to the genus <I>Granulosicoccus</I> in the family <I>Granulosicoccaceae</I>. The strain was closely related to <I>Granulosicoccus antarcticus</I> IMCC3135<SUP>T</SUP> (98.8 % 16S rRNA gene sequence similarity) and <I>Granulosicoccus coccoides</I> Z 271<SUP>T</SUP> (98.5 %). The DNA–DNA relatedness values between IMCC3490<SUP>T</SUP> and type strains of the two species of the genus were far lower than 70 %, which indicated strain IMCC3490<SUP>T</SUP> is a novel genomic species of the genus <I>Granulosicoccus</I>. The major fatty acids of strain IMCC3490<SUP>T</SUP> were summed feature 8 (C<SUB>18 : 1</SUB>ω7<I>c</I> and/or C<SUB>18 : 1</SUB>ω6<I>c</I>) and summed feature 3 (C<SUB>16 : 1</SUB>ω7<I>c</I> and/or C<SUB>16 : 1</SUB>ω6<I>c</I>). The isoprenoid quinone detected was ubiquinone-8 (Q-8) and predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 61.0 mol%. On the basis of phylogenetic analyses, DNA–DNA relatedness values and phenotypic data, it is suggested that strain IMCC3490<SUP>T</SUP> represents a novel species of the genus <I>Granulosicoccus</I>, for which the name <I>Granulosicoccus marinus</I> sp. nov. is proposed. The type strain is IMCC3490<SUP>T</SUP> ( = KACC 17483<SUP>T</SUP> = NBRC 109704<SUP>T</SUP>). An emended description of the genus <I>Granulosicoccus</I> is also provided.</P>