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- 저자 : Ajit Kumar Patra (검색결과 6 건)
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Ajit Kumar Patra,조현희,권용민,권개경,Takako Sato,Chiaki Kato,강성균,김상진 한국해양과학기술원 2016 Ocean science journal Vol.51 No.3
Vestimentiferan tubeworms acquire their symbionts through horizontal transmission from the surrounding environment. In the present study, we constructed a 16S rRNA gene clone library to investigate the phylogenetic relationship between diverse microbes in the sediment and symbiotic bacteria in the trophosome of the tubeworm, Lamellibrachia satsuma, from Kagoshima Bay, Japan. Two symbiotic bacterial phylotypes belonging to the classes γ- and ε-Proteobacteria were found from this tubeworm trophosome. They were very closely related to the symbionts of several other marine invertebrates. The most predominant bacteria in the sediment were ε-Proteobacteria. A broad diversity of bacteria belonged to nonproteobacterial phyla such as Planctomycetes, Acidobacteria, and Chloroflexi was observed. The presence of sulfur oxidizers (i.e., ε-Proteobacteria and γ-Proteobacteria) and sulfur reducers (i.e., δ-Proteobacteria) may play a significant role in the sulfur cycle in these habitats and provide multiple sources of nutrition to the cold-seep communities. Closely related clones of ε-Proteobacteria symbiont in the species level and of γ-Proteobacteria symbiont in the genus level were found in the surrounding sediment. The similarity of symbiont clones of L. satsuma with other symbionts and free-living bacteria suggests the possibility of opportunistic symbiosis in ε-Proteobacteria and the co-evolution of γ-Proteobacteria having occurred after symbiosis with the tubeworms.
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Patra, Ajit Kumar,Cho, Hyun Hee,Kwon, Yong Min,Kwon, Kae Kyoung,Sato, Takako,Kato, Chiaki,Kang, Sung Gyun,Kim, Sang-Jin Korean Ocean Research & Development Institute and 2016 OCEAN SCIENCE JOURNAL Vol.51 No.3
Vestimentiferan tubeworms acquire their symbionts through horizontal transmission from the surrounding environment. In the present study, we constructed a 16S rRNA gene clone library to investigate the phylogenetic relationship between diverse microbes in the sediment and symbiotic bacteria in the trophosome of the tubeworm, Lamellibrachia satsuma, from Kagoshima Bay, Japan. Two symbiotic bacterial phylotypes belonging to the classes <TEX>${\gamma}$</TEX>- and <TEX>${\varepsilon}$</TEX>-Proteobacteria were found from this tubeworm trophosome. They were very closely related to the symbionts of several other marine invertebrates. The most predominant bacteria in the sediment were <TEX>${\varepsilon}$</TEX>-Proteobacteria. A broad diversity of bacteria belonged to non-proteobacterial phyla such as Planctomycetes, Acidobacteria, and Chloroflexi was observed. The presence of sulfur oxidizers (i.e., <TEX>${\varepsilon}$</TEX>-Proteobacteria and <TEX>${\gamma}$</TEX>-Proteobacteria) and sulfur reducers (i.e., <TEX>${\delta}$</TEX>-Proteobacteria) may play a significant role in the sulfur cycle in these habitats and provide multiple sources of nutrition to the cold-seep communities. Closely related clones of <TEX>${\varepsilon}$</TEX>-Proteobacteria symbiont in the species level and of <TEX>${\gamma}$</TEX>-Proteobacteria symbiont in the genus level were found in the surrounding sediment. The similarity of symbiont clones of L. satsuma with other symbionts and free-living bacteria suggests the possibility of opportunistic symbiosis in <TEX>${\varepsilon}$</TEX>-Proteobacteria and the co-evolution of <TEX>${\gamma}$</TEX>-Proteobacteria having occurred after symbiosis with the tubeworms.
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Patra Ajit Kumar,Kwon Yong Min,Yang Youngik 한국미생물학회 2022 The journal of microbiology Vol.60 No.9
Siboglinid tubeworms thrive in hydrothermal vent and seep habitats via a symbiotic relationship with chemosynthetic bacteria. Difficulties in culturing tubeworms and their symbionts in a laboratory setting have hindered the study of host-microbe interactions. Therefore, released symbiont genomes are fragmented, thereby limiting the data available on the genome that affect subsequent analyses. Here, we present a complete genome of gammaproteobacterial endosymbiont from the tubeworm Lamellibrachia satsuma collected from a seep in Kagoshima Bay, assembled using a hybrid approach that combines sequences generated from the Illumina and Oxford Nanopore platforms. The genome consists of a single circular chromosome with an assembly size of 4,323,754 bp and a GC content of 53.9% with 3,624 protein-coding genes. The genome is of high quality and contains no assembly gaps, while the completeness and contamination are 99.33% and 2.73%, respectively. Comparative genome analysis revealed a total of 1,724 gene clusters shared in the vent and seep tubeworm symbionts, while 294 genes were found exclusively in L. satsuma symbionts such as transposons, genes for defense mechanisms, and inorganic ion transportations. The addition of this complete endosymbiont genome assembly would be valuable for comparative studies particularly with tubeworm symbiont genomes as well as with other chemosynthetic microbial communities.
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Complete genome sequence of Falsirhodobacter sp. PG104, an alginate-degrading marine bacterium
권용민,Ajit Kumar Patra,정다운,양영익 한국미생물학회 2020 미생물학회지 Vol.56 No.3
A novel marine bacterium belonging to the family Rhodobacteraceae was designated as strain PG104 after being isolated from red algae collected in the coastal region of Pohang, South Korea. The genome consists of one circular chromosome of 2,279,458 bp with 66.68 GC mol% content and five plasmids; pL104-1 to pL104-5 with lengths ranging from 44,911 bp to 175,961 bp. Furthermore, the genome contains 2,643 protein-coding sequences (CDSs), 51 tRNA genes, as well as 9 rRNA operons as 16S-23S-5S rRNA. Genome analysis revealed that the PG104 strain harbors alginate lyase genes, which are responsible for the degradation of algal polysaccharides.
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해양 Flavobacteria Flagellimonas eckloniae DOKDO 007<sup>T</sup> 의 유전체 염기서열 해독
권용민,김상진,권개경,Kwon, Yong Min,Kumar, Patra Ajit,Kim, Sang-Jin,Kwon, Kae Kyoung The Microbiological Society of Korea 2018 미생물학회지 Vol.54 No.4
Flavobacteriaceae에 속하는 해양 Flavobacteria인 Flagellimonas eckloniae DOKDO $007^T$은 독도에서 서식하는 조류(Ecklonia kurome)에서 분리되었다. DOKDO $007^T$ 균주의 유전체는 4,132,279 bp 크기로 3,527개의 코딩 서열과 37.85%의 GC 함량을 가지며, 하나의 스케폴드에서 두 개의 콘티그로 구성되어 있다. 이 균주는 태양광을 에너지원으로써 이용할 수 있는 여러 레티날 생합성 유전자들과 마찬가지로 프로테오로돕신을 인코딩하는 유전자를 함유하고 있다. 속명과는 달리 편모 형성에 관여하는 유전자가 충분하지 못한 것을 감안하여 속명의 개정이 필요하다. Flagellimonas eckloniae DOKDO $007^T$, isolated from the rhizosphere of the marine algae Ecklonia kurome collected from Dokdo Island, South Korea, is a marine Flavobacteria belonging to the family Flavobacteriaceae. The genome consists of 4,132,279 bp, 3,527 coding sequences with 37.85% G + C contents and two contigs in one scaffold chromosome. This strain contains a gene encoding proteorhodopsin, as well as other retinal biosynthesis genes, allowing it to utilize sunlight as an energy source. The strain contained only few segment of flagellar constructing gene cluster and this is not consistent with genus name Flagellimonas, therefore, revision of the genus name is required.
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