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Preparation method of environmental DNA sample for conservation of the genetic resource in the deep subsurface biosphere and analysis of biodiviersity harbored in the DNA

Research Project

Project/Area Number 20310124
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Applied genomics
Research InstitutionJapan Agency for Marine-Earth Science and Technology

Principal Investigator

TAKAMI Hideto  Japan Agency for Marine-Earth Science and Technology, 海洋・極限環境生物圏領域, チームリーダー (70359165)

Co-Investigator(Kenkyū-buntansha) HORI Sayaka  独立行政法人海洋研究開発機構, 海洋・極限環境生物圏領域, ポストドクトラル研究員 (20470122)
TSUBOUCHI Taishi  独立行政法人海洋研究開発機構, 海洋・極限環境生物圏領域, ポストドクトラル研究員 (30442990)
Co-Investigator(Renkei-kenkyūsha) TOYODA Atsushi  国立遺伝学研究所, 特任准教授 (10267495)
HORI Sayaka  独立行政法人海洋研究開発機構, 海洋・極限環境生物圏領域, ポストドクトラル研究員 (20470122)
Research Collaborator NISHI Shinro  独立行政法人海洋研究開発機構, 海洋・極限環境生物圏領域, 技術研究副主事
Project Period (FY) 2008 – 2010
Project Status Completed (Fiscal Year 2010)
Budget Amount *help
¥18,590,000 (Direct Cost: ¥14,300,000、Indirect Cost: ¥4,290,000)
Fiscal Year 2010: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2009: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000)
Fiscal Year 2008: ¥10,530,000 (Direct Cost: ¥8,100,000、Indirect Cost: ¥2,430,000)
Keywordsゲノム資源 / メタゲノム / メタゲノム情報解析 / 地下生命圏 / 代謝パスウェイ / Chloroflexi / アセチルCoAパスウェイ / Candidate division OP1 / 比較ゲノム解析 / メタゲノム解析 / 極限環境 / 16S rRNA遺伝子 / 微生物多様性 / 遺伝子資源 / メタグノム解析
Research Abstract

We attempted to extract environmental DNA mainly from ocean drilling core samples recovered offshore Shimokita Peninsula. The extracted DNA decreased with increasing of depth but the estimated cell number from DNA amount was not so different from those counted by microscopy. Thus, It is though that the DNA extraction method was almost successfully established. We also analyzed to figure out biodiversity based on 16S rDNA and the predicted metabolic potential from the identified genes in the DNA samples. JS1 and Chloroflexi were found to be predominant taxa as described previously up to a depth of 100m. In each DNA sample from different depth, 60,000-80,000 genes were identified. The sulfur respiration-related genes and methanogenesis-related genes were highlighted in sallower and deeper horizons, respectively.

Report

(4 results)
  • 2010 Annual Research Report   Final Research Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (42 results)

All 2011 2010 2009 2008 Other

All Journal Article (5 results) (of which Peer Reviewed: 2 results) Presentation (31 results) Book (5 results) Remarks (1 results)

  • [Journal Article] Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal division.2011

    • Author(s)
      Nunoura T., Takaki Y., Kakuta J., Nishi S., Takami H., 他14人中14番目
    • Journal Title

      Nucleic Acids Res. 39

      Pages: 3204-3223

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal division.2010

    • Author(s)
      Nunourra T.
    • Journal Title

      Nucleic Acids Research

      Volume: 39 Pages: 3204-3223

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article]2009

    • Author(s)
      高見英人
    • Journal Title

      マリンメタゲノムの有効利用(CMC出版)

    • Related Report
      2009 Annual Research Report
  • [Journal Article] 地下生命圏におけるメタゲノム解析2008

    • Author(s)
      布浦拓郎, 高見英人
    • Journal Title

      バイオインダストリー 25

      Pages: 61-69

    • Related Report
      2010 Final Research Report
  • [Journal Article] 地下生命圏におけるメタゲノム解析2008

    • Author(s)
      布浦拓郎
    • Journal Title

      バイオインダストリー 25

      Pages: 61-69

    • Related Report
      2008 Annual Research Report
  • [Presentation] メタゲノム解析から見える世界最深部マリアナ海溝底泥の優先種ゲノム2011

    • Author(s)
      西真郎
    • Organizer
      日本ゲノム微生物学会
    • Place of Presentation
      東北学院大学
    • Year and Date
      2011-03-15
    • Related Report
      2010 Annual Research Report
  • [Presentation] 多様度指数からみたアーキア菌叢層序変遷2011

    • Author(s)
      坪内泰志
    • Organizer
      日本ゲノム微生物学会
    • Place of Presentation
      東北学院大学
    • Year and Date
      2011-03-15
    • Related Report
      2010 Annual Research Report
  • [Presentation] 多様度指数から見たアーキア菌叢層序変遷2011

    • Author(s)
      坪内泰志
    • Organizer
      日本ゲノム微生物学会
    • Place of Presentation
      東北学院大学
    • Year and Date
      2011-03-12
    • Related Report
      2010 Final Research Report
  • [Presentation] メタゲノム解析から見えるマリアナ海溝最深部の優先種ゲノム2011

    • Author(s)
      西真郎
    • Organizer
      日本ゲノム微生物学会
    • Place of Presentation
      東北学院大学
    • Year and Date
      2011-03-12
    • Related Report
      2010 Final Research Report
  • [Presentation] 海洋性堆積物365m鉛直プロファイルはアーキアとの生息域の相関を解く手がかりとなるか2010

    • Author(s)
      坪内泰志
    • Organizer
      日本微生物生態学会
    • Place of Presentation
      筑波大学
    • Year and Date
      2010-11-25
    • Related Report
      2010 Final Research Report
  • [Presentation] Candidate division OP1は祖先的acetyl-CoA pathwayを有する好熱性acetogen2010

    • Author(s)
      高見英人
    • Organizer
      日本微生物生態学会
    • Place of Presentation
      筑波大学
    • Year and Date
      2010-11-25
    • Related Report
      2010 Final Research Report
  • [Presentation] Candidate division OP 1は祖先的acety1-CoA pathwayを有する好熱性acetogen2010

    • Author(s)
      高見英人
    • Organizer
      日本微生物生態学会
    • Place of Presentation
      筑波大学
    • Year and Date
      2010-11-25
    • Related Report
      2010 Annual Research Report
  • [Presentation] 海洋堆積物365m鉛直プロファイルはアーキアとその生息域の相関を解く手掛かりとなるか2010

    • Author(s)
      坪内泰志
    • Organizer
      日本微生物生態学会
    • Place of Presentation
      筑波大学
    • Year and Date
      2010-11-25
    • Related Report
      2010 Annual Research Report
  • [Presentation] メタゲノムから見える地下微生物群集の代謝ポテンシャル, 日本微生物生態学会2010

    • Author(s)
      高木善弘
    • Organizer
      日本微生物生態学会
    • Place of Presentation
      筑波大学
    • Year and Date
      2010-11-25
    • Related Report
      2010 Annual Research Report
  • [Presentation] メタゲノム解析から見える世界最深部マリアナ海溝底泥の微生物生態系2010

    • Author(s)
      西真郎
    • Organizer
      日本微生物生態学会
    • Place of Presentation
      筑波大学
    • Year and Date
      2010-11-24
    • Related Report
      2010 Annual Research Report 2010 Final Research Report
  • [Presentation] メタゲノム解析から極限環境を見る2010

    • Author(s)
      高見英人
    • Organizer
      日本水産学会シンポジウム
    • Place of Presentation
      京都大学
    • Year and Date
      2010-09-25
    • Related Report
      2010 Annual Research Report
  • [Presentation] メタゲノム解析から見える下北半島沖地下生命圏生態系2010

    • Author(s)
      高木善弘
    • Organizer
      日本ゲノム微生物学会
    • Place of Presentation
      九州大学
    • Year and Date
      2010-03-09
    • Related Report
      2009 Annual Research Report
  • [Presentation] 下北半島掘削コアのメタゲノム解析から見える微生物代謝の可能性2010

    • Author(s)
      西真郎
    • Organizer
      日本ゲノム微生物学会
    • Place of Presentation
      九州大学
    • Year and Date
      2010-03-08
    • Related Report
      2010 Final Research Report
  • [Presentation] 16S rRNA遺伝子のコンセンサス配列の差異に基づく下北半島掘削コアからのarchaeaの探索2010

    • Author(s)
      坪内泰志
    • Organizer
      日本ゲノム微生物学会
    • Place of Presentation
      九州大学
    • Year and Date
      2010-03-08
    • Related Report
      2010 Final Research Report
  • [Presentation] OP1様バクテリアに支持される微生物マットのメタゲノム解析2010

    • Author(s)
      高見英人
    • Organizer
      日本ゲノム微生物学会
    • Place of Presentation
      九州大学
    • Year and Date
      2010-03-08
    • Related Report
      2010 Final Research Report 2009 Annual Research Report
  • [Presentation] 16S rRNA遺伝子のコンセンサス配列の差異に基づく下北半島掘削コアからの archaea の探索2010

    • Author(s)
      坪内泰志
    • Organizer
      日本ゲノム微生物学会
    • Place of Presentation
      九州大学
    • Year and Date
      2010-03-08
    • Related Report
      2009 Annual Research Report
  • [Presentation] 下北半島沖掘削コアのメタゲノム解析から見える微生物代謝の可能性2010

    • Author(s)
      西真郎
    • Organizer
      日本ゲノム微生物学会
    • Place of Presentation
      九州大学
    • Year and Date
      2010-03-08
    • Related Report
      2009 Annual Research Report
  • [Presentation] メタゲノム解析から見た掘削コアの遺伝子多様性2009

    • Author(s)
      高見英人
    • Organizer
      日本微生物生態学会
    • Place of Presentation
      広島大学
    • Year and Date
      2009-11-21
    • Related Report
      2010 Final Research Report 2009 Annual Research Report
  • [Presentation] Metagenomics in the deep subsurface environments.2009

    • Author(s)
      高見英人
    • Organizer
      The 8^th International Workshop on Advanced Genomics. (Invited speaker)
    • Place of Presentation
      National Center of Science Tokyo
    • Year and Date
      2009-05-20
    • Related Report
      2010 Final Research Report
  • [Presentation] Metagenomics in the deep subsurface environments2009

    • Author(s)
      高見英人
    • Organizer
      The 8^<th> International Workshop on Advanced Genomics(Invited speaker)
    • Place of Presentation
      Tokyo(National Center of Science)
    • Year and Date
      2009-05-17
    • Related Report
      2009 Annual Research Report
  • [Presentation] primer mismatchingを介した希少アーキアの探索2009

    • Author(s)
      坪内泰志
    • Organizer
      日本ゲノム微生物学会
    • Place of Presentation
      中央大学,東京
    • Year and Date
      2009-03-05
    • Related Report
      2010 Final Research Report
  • [Presentation] 下北半島東方沖掘削コアのメタゲノミクス2008

    • Author(s)
      高見英人
    • Organizer
      日本微生物生態学会
    • Place of Presentation
      北海道大学,札幌
    • Year and Date
      2008-11-26
    • Related Report
      2010 Final Research Report
  • [Presentation] 下北半島東方沖掘削コアのメタゲノミクス2008

    • Author(s)
      高見英人
    • Organizer
      第24回日本微生物生態学会
    • Place of Presentation
      札幌、北海道大学
    • Year and Date
      2008-11-26
    • Related Report
      2008 Annual Research Report
  • [Presentation] Metagenomic analysis of deep subsurface core samples collected in an offing of the Shimokita Peninsula on the northwest Honshu, Japan2008

    • Author(s)
      Hideto Takami
    • Organizer
      International symposium for subsurface microbiology
    • Place of Presentation
      静岡、グランシップ
    • Year and Date
      2008-11-20
    • Related Report
      2008 Annual Research Report
  • [Presentation] Metagenomic analysis of deep subsurface core samples collected in an offing of the Shimokita Peninsula on the northwest Honshu, Japan.2008

    • Author(s)
      高見英人
    • Organizer
      ISSM 2008
    • Place of Presentation
      グランシップ,静岡
    • Year and Date
      2008-11-18
    • Related Report
      2010 Final Research Report
  • [Presentation] Metagenomic analysis of deep subsurface environments.2008

    • Author(s)
      高見英人
    • Organizer
      Metagenomics 2008 (Invited speaker)
    • Place of Presentation
      UC San Diego, USA
    • Year and Date
      2008-11-05
    • Related Report
      2010 Final Research Report
  • [Presentation] Metagenomic analysis of deep subsurface environments2008

    • Author(s)
      Hideto Takami
    • Organizer
      Metagenomics 2008 (Invited speaker)
    • Place of Presentation
      米国、San Diego, UC San Diego
    • Year and Date
      2008-11-05
    • Related Report
      2008 Annual Research Report
  • [Presentation] Metagenomic analysis of deep subsurface core samples collected in an offing of the Shimokita Peninsula on the northwest Honshu, Japan.2008

    • Author(s)
      高見英人
    • Organizer
      ISME12
    • Place of Presentation
      ケアンズコンベンションセンター,オーストラリア
    • Year and Date
      2008-08-20
    • Related Report
      2010 Final Research Report
  • [Presentation] Metagenomic analysis of deep subsurface core samples collected in an offing of the Shimokita Peninsula on the northwest Honshu, Japan2008

    • Author(s)
      Hideto Takami
    • Organizer
      International symposium on microbial ecology12
    • Place of Presentation
      オーストラリア、ケアンズコンベンションセンター
    • Year and Date
      2008-08-19
    • Related Report
      2008 Annual Research Report
  • [Presentation] 地下深部をメタゲノムから探る2008

    • Author(s)
      高見英人
    • Organizer
      文科省特定領域研究「ゲノム研究」主催シンポジウム新しいシーケンス技術とメタゲノム解析のインパクト(招待講演)
    • Place of Presentation
      東京大学弥生講堂
    • Year and Date
      2008-05-28
    • Related Report
      2010 Final Research Report
  • [Presentation] 地下深部をメタゲノム解析から探る2008

    • Author(s)
      高見英人
    • Organizer
      文科省特定領域研究「ゲノム研究」主催シンポジウム 新しいシークエンス技術とメタゲノム解析のインパクト(招待講演)
    • Place of Presentation
      東京大学 弥生講堂
    • Year and Date
      2008-05-23
    • Related Report
      2008 Annual Research Report
  • [Book] 極限環境生物学2010

    • Author(s)
      高見英人
    • Publisher
      岩波書店
    • Related Report
      2010 Final Research Report
  • [Book] メタゲノム解析技術の最前線2010

    • Author(s)
      高見英人, 高木善弘
    • Publisher
      CMC出版
    • Related Report
      2010 Final Research Report
  • [Book] メタゲノム解析技術の最前線第3章海洋・環境、メタゲノム解析から地下深部を探る2010

    • Author(s)
      高見英人
    • Publisher
      CMC出版
    • Related Report
      2010 Annual Research Report
  • [Book] 現代生物科学入門第10極限環境生物学第3章深海環境生物圏2010

    • Author(s)
      高見英人
    • Publisher
      岩波書店
    • Related Report
      2010 Annual Research Report
  • [Book] マリンメタゲノムの有効利用2009

    • Author(s)
      高見英人
    • Publisher
      CMC出版
    • Related Report
      2010 Final Research Report
  • [Remarks] ホームページ等

    • URL

      http://www.jamstec.go.jp/biogeos/j/xbr/emrt/index.html

    • Related Report
      2010 Final Research Report

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Published: 2008-04-01   Modified: 2016-04-21  

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