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Development of procedure for single cell genomics of sedimentary microbial cells

Research Project

Project/Area Number 15K14907
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Environmental agriculture(including landscape science)
Research InstitutionJapan Agency for Marine-Earth Science and Technology

Principal Investigator

HOSHINO Tatsuhiko  国立研究開発法人海洋研究開発機構, 高知コア研究所, 主任研究員 (30386619)

Project Period (FY) 2015-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2016: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2015: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords微生物 / DNA増幅 / 遺伝子解析 / 遺伝子増幅 / シングルセル / 環境微生物学
Outline of Final Research Achievements

Single cell genomics is an effective tool for understanding microbial ecology in the natural environment because it can provide comprehensive information on microbial phylogeny and metabolic function. However, application of single cell genomics to microbial cells in subseafloor environment is hampered by the fact that DNA content in a single cells is very little to be amplified to enough amount for sequencing. In this study, we developed a procedure where proteinase K is used for lysis of cells and a metal plate is used for multiple displacement amplification of genomic DNA. As a result, we successfully amplified genomic DNA from sorted single cells isolated from subseafloor sediment.

Report

(3 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • Research Products

    (12 results)

All 2017 2016 2015

All Journal Article (3 results) (of which Peer Reviewed: 3 results,  Open Access: 1 results,  Acknowledgement Compliant: 3 results) Presentation (9 results) (of which Int'l Joint Research: 4 results,  Invited: 2 results)

  • [Journal Article] Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA genes2017

    • Author(s)
      Tatsuhiko Hoshino, Fumio Inagaki
    • Journal Title

      PLoS One

      Volume: 12 Issue: 1 Pages: e0169431-e0169431

    • DOI

      10.1371/journal.pone.0169431

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Distribution of anaerobic carbon monoxide dehydrogenase genes in deep subseafloor sediments2017

    • Author(s)
      Tatsuhiko Hoshino, Fumio Inagaki
    • Journal Title

      Letters in Applied Microbiology

      Volume: 64 Issue: 5 Pages: 355-363

    • DOI

      10.1111/lam.12727

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Estimation of the influence of sequencing errors and distribution of random-sequence tags on quantitative sequencing2017

    • Author(s)
      Tatsuhiko Hoshino, Yohei Hamada
    • Journal Title

      Journal of Bioscience and Bioengineering

      Volume: 印刷中 Issue: 3 Pages: 359-364

    • DOI

      10.1016/j.jbiosc.2017.04.003

    • NAID

      40021323754

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Biosphere in subseafloor environment and its ecophysiology2017

    • Author(s)
      諸野祐樹、寺田武志、星野辰彦、伊藤元雄、稲垣史生
    • Organizer
      第90回日本細菌学会総会シンポジウム
    • Place of Presentation
      仙台国際センター(宮城県仙台市)
    • Year and Date
      2017-03-20
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Distribution of aerobic microbial activities in ultra-oligotrophic sediments of the South Pacific Gyre2016

    • Author(s)
      Yuki Morono, Takeshi Terada, Motoo Ito, Tatsuhiko Hoshino, Steven D'Hondt, Fumio Inagaki
    • Organizer
      16th International Symposium on Microbial Ecology
    • Place of Presentation
      モントリオール、カナダ
    • Year and Date
      2016-08-22
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] HOSHINO TATSUHIKO , Woemer Lars , Viehweger B , XIAO NAN , MORONO YUKI , Kai-Uwe Hinrichs , INAGAKI FUMIO2016

    • Author(s)
      HOSHINO TATSUHIKO , Woemer Lars , Viehweger B , XIAO NAN , MORONO YUKI , Kai-Uwe Hinrichs , INAGAKI FUMIO
    • Organizer
      Goldschmidt 2016
    • Place of Presentation
      パシフィコ横浜(神奈川県横浜市)
    • Year and Date
      2016-06-30
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Assessing Abundance and Relevance of Bacterial Endospores in the Marine Subsurface2016

    • Author(s)
      Woermer Lars , HOSHINO TATSUHIKO , Viehweger B , Meador T , Gajendra N , Stern B , INAGAKI FUMIO , Hinrichs Kai-Uwe
    • Organizer
      Goldschmidt 2016
    • Place of Presentation
      パシフィコ横浜(神奈川県横浜市)
    • Year and Date
      2016-06-30
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Distribution of Aerobic Microbial Activities in Ultra-Oligotrophic Sediments of the South Pacific Gyre2016

    • Author(s)
      YUKI MORONO, TAKESHI TERADA, MOTOO ITO, TATSUHIKO HOSHINO, STEVEN D'HONDT, FUMIO INAGAKI
    • Organizer
      Goldschmidt 2016
    • Place of Presentation
      パシフィコ横浜(神奈川県横浜市)
    • Year and Date
      2016-06-27
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 海底下微生物圏の解明を目指した技術開発2016

    • Author(s)
      星野辰彦、諸野祐樹、稲垣史生
    • Organizer
      環境バイオテクノロジー学会2016年度大会
    • Place of Presentation
      サテライトキャンパスひろしま、広島県広島市
    • Year and Date
      2016-06-14
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] 海底泥火山から水圏への海底下微生物群集の拡散2016

    • Author(s)
      星野 辰彦, 土岐 知弘, 井尻 暁, 諸野 祐樹, 町山 栄章, 芦 寿一郎, 稲垣 史生
    • Organizer
      日本地球惑星科学連合2016年大会
    • Place of Presentation
      幕張メッセ(千葉県千葉市)
    • Year and Date
      2016-05-24
    • Related Report
      2016 Annual Research Report
  • [Presentation] 海底下生命のセンサス:海底下微生物群集の空間的分布と地球環境との相互作用の解明2015

    • Author(s)
      星野辰彦、諸野祐樹、稲垣史生
    • Organizer
      第16回極限環境生物学会
    • Place of Presentation
      東京海洋大学、東京都港区
    • Year and Date
      2015-11-07
    • Related Report
      2015 Research-status Report
  • [Presentation] 地下深部微生物群集構造解析2015

    • Author(s)
      星野辰彦
    • Organizer
      第4回NGS現場の会
    • Place of Presentation
      エポカルつくば、茨城県つくば市
    • Year and Date
      2015-07-02
    • Related Report
      2015 Research-status Report

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Published: 2015-04-16   Modified: 2018-03-22  

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