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Metagenomic and metatranscriptomic analysis of rice paddy soil

Research Project

Project/Area Number 25252013
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Plant nutrition/Soil science
Research InstitutionThe University of Tokyo

Principal Investigator

Senoo Keishi  東京大学, 大学院農学生命科学研究科(農学部), 教授 (40206652)

Co-Investigator(Kenkyū-buntansha) 大塚 重人  東京大学, 農学生命科学研究科, 准教授 (10313074)
磯部 一夫  東京大学, 農学生命科学研究科, 助教 (30621833)
Co-Investigator(Renkei-kenkyūsha) HATTORI Masahira  早稲田大学, 先進理工学研究科, 教授 (70175537)
KUROKAWA Ken  国立遺伝学研究所, 生命情報研究センター, 教授 (20343246)
TAKAMI Hideto  (独)海洋研究開発機構, 海洋・極限環境生物領域, チームリーダー (70359165)
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥47,580,000 (Direct Cost: ¥36,600,000、Indirect Cost: ¥10,980,000)
Fiscal Year 2015: ¥9,880,000 (Direct Cost: ¥7,600,000、Indirect Cost: ¥2,280,000)
Fiscal Year 2014: ¥9,880,000 (Direct Cost: ¥7,600,000、Indirect Cost: ¥2,280,000)
Fiscal Year 2013: ¥27,820,000 (Direct Cost: ¥21,400,000、Indirect Cost: ¥6,420,000)
Keywords水田土壌 / メタゲノム解析 / メタトランスクリプトーム解析 / メタン生成・消去 / 窒素固定 / DNRA / 脱窒 / 脱窒反応 / DNRA反応 / 窒素固定反応 / デルタプロテオバクテリア / 鉄還元菌 / 土壌微生物 / 土壌学
Outline of Final Research Achievements

Waterlogged paddy soil is characterized by surface oxidized and lower reduced layers, where various kind of oxidation/reduction reactions proceed. Shotgun DNA/RNA sequencing analysis (metagenomics and metatranscriptomics) of both layers soil samples revealed whole picture of microbial communities involved in methane generation and oxidation. Our analysis also revealed that most reductive nitrogen transformation (nitrogen fixation, DNRA and denitrification) gene transcripts were derived from Deltaproteobacteria, particularly the genera Anaeromyxobacter and Geobacter, previously known as iron reducers. This finding suggests the important role of these bacteria for nitrogen fertility of paddy soil.

Report

(4 results)
  • 2016 Final Research Report ( PDF )
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (15 results)

All 2017 2016 2015 2014

All Journal Article (1 results) (of which Peer Reviewed: 1 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (14 results) (of which Int'l Joint Research: 4 results,  Invited: 5 results)

  • [Journal Article] Predominant but Previously-overlooked Prokaryotic Drivers of Reductive Nitrogen Transformation in Paddy Soils, Revealed by Metatranscriptomics2017

    • Author(s)
      Masuda Y, Itoh H, Shiratori Y, Isobe K, Otsuka S, Senoo K.
    • Journal Title

      Microbes and Environments

      Volume: 32 Issue: 2 Pages: 180-183

    • DOI

      10.1264/jsme2.ME16179

    • NAID

      130006789873

    • ISSN
      1342-6311, 1347-4405
    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] 水田土壌の窒素変換微生物:特定・分離とN2O削減への利用2017

    • Author(s)
      妹尾啓史
    • Organizer
      第34回 土・水研究会
    • Place of Presentation
      つくば農林ホール(茨城県つくば市)
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 水田土壌オミクス解析から見えた陸域生態系における鉄還元菌の新たな機能-還元的窒素変換(Predominant but previously-unseen prokaryotic drivers of reductive nitrogen transformation in paddy soils, unveiled by metatranscriptomics)2017

    • Author(s)
      増田曜子、伊藤英臣、白鳥豊、磯部一夫、大塚重人、妹尾啓史
    • Organizer
      JpGU-AGU Joint Meeting 2017
    • Place of Presentation
      幕張メッセ(千葉県千葉市)
    • Related Report
      2015 Annual Research Report
  • [Presentation] Overlooked but pivotal prokaryotic drivers involved in reductive nitrogen transformations in paddy soils, captured by metatranscriptomics2016

    • Author(s)
      Masuda Y., Itoh H. , Shiratori Y. , Isobe K., Otsuka S., Senoo K.
    • Organizer
      3rd Thunen Symposium on Soil Metagenomics
    • Place of Presentation
      Braunschweig, Germany
    • Year and Date
      2016-12-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 水田土壌に優占する微生物の新機能:鉄還元菌こそが窒素循環に重要である2016

    • Author(s)
      増田曜子、伊藤英臣、白鳥豊、磯部一夫、大塚重人、妹尾啓史
    • Organizer
      日本微生物生態学会第31回大会
    • Place of Presentation
      横須賀市文化会館(神奈川県横須賀市)
    • Year and Date
      2016-10-23
    • Related Report
      2015 Annual Research Report
  • [Presentation] 水田土壌に優占するDeltaproteobacteriaの窒素固定・脱窒・DNRAへの寄与-オミクス解析による水田窒素循環微生物コミュニティの刷新-2016

    • Author(s)
      田伏曜子・伊藤英臣・白鳥豊・磯部一夫・大塚重人・妹尾啓史
    • Organizer
      日本土壌微生物学会2016年度大会
    • Place of Presentation
      岐阜大学(岐阜県岐阜市)
    • Year and Date
      2016-06-11
    • Related Report
      2015 Annual Research Report
  • [Presentation] Denitrifying Microbial Community in Agricultural Soils: Key Players Involved in N2O Generation and Elimination2016

    • Author(s)
      Keishi Senoo
    • Organizer
      105th International Symposium and Annual Meeting of the Korean Society for Applied Biological Chemistry
    • Place of Presentation
      Jeju Island, Korea
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Greenhouse gas and soil microorganisms: N2O generating and eliminating microbial communities in agricultural soils2016

    • Author(s)
      Keishi Senoo
    • Organizer
      China-Japan Environmental Microbiology Forum
    • Place of Presentation
      Chongquing, China
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 水田土壌の窒素循環に寄与する新規微生物群の発見2015

    • Author(s)
      田伏 曜子, 角田 洋子, 伊藤 英臣, 白鳥 豊, 磯部 一夫, 大塚 重人, 妹尾 啓史
    • Organizer
      日本微生物生態学会第30回大会 7th JTK Symposium
    • Place of Presentation
      土浦亀城プラザ(茨城県土浦市)
    • Year and Date
      2015-10-17
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] メタゲノム解析からみた水田土壌における窒素代謝関連遺伝子の詳細2015

    • Author(s)
      角田洋子、伊藤英臣、磯部一夫、白鳥豊、大塚重人、妹尾啓史
    • Organizer
      日本土壌肥料学会2015年度京都大会
    • Place of Presentation
      京都大学吉田キャンパス(京都府京都市)
    • Year and Date
      2015-09-09
    • Related Report
      2015 Annual Research Report
  • [Presentation] 水田土壌のメタトランスクリプトーム解析-微生物群集構造と炭素・窒素循環機能遺伝子の解析-2015

    • Author(s)
      田伏曜子、伊藤英臣、白鳥豊、磯部一夫、大塚重人、妹尾啓史
    • Organizer
      日本土壌肥料学会2015年度京都大会
    • Place of Presentation
      京都大学吉田キャンパス(京都府京都市)
    • Year and Date
      2015-09-09
    • Related Report
      2015 Annual Research Report
  • [Presentation] メタトランスクリプトーム解析から見た水田土壌の炭素・窒素循環とそれを駆動する微生物2015

    • Author(s)
      田伏曜子、伊藤英臣、白鳥豊、磯部一夫、大塚重人、妹尾啓史
    • Organizer
      日本地球惑星連合2015年大会
    • Place of Presentation
      幕張メッセ(千葉県千葉市)
    • Year and Date
      2015-05-19
    • Related Report
      2015 Annual Research Report
  • [Presentation] 水田におけるバルクおよび根圏土壌細菌群集の構造とその周年変動2014

    • Author(s)
      角田洋子、白鳥豊、伊藤英臣、堀知行、西澤智康、磯部一夫、大塚重人、妹尾啓史
    • Organizer
      環境微生物系学会合同大会2014
    • Place of Presentation
      アクトシティ浜松
    • Year and Date
      2014-10-22
    • Related Report
      2014 Annual Research Report
  • [Presentation] 21世紀の土壌微生物研究の目指すもの2014

    • Author(s)
      妹尾啓史
    • Organizer
      環境微生物系学会合同大会2014
    • Place of Presentation
      アクトシティ浜松
    • Year and Date
      2014-10-22
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 水稲根圏の微生物の群集組成とその栽培期間における変動-16Sメタアンプリコンシーケンスによる解析-2014

    • Author(s)
      角田洋子・白鳥豊・伊藤英臣・堀知行・西澤智康・磯部一夫・大塚重人・妹尾啓史
    • Organizer
      日本土壌肥料学会2014年度東京大会
    • Place of Presentation
      東京農工大学工学部
    • Year and Date
      2014-09-09
    • Related Report
      2014 Annual Research Report 2013 Annual Research Report

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Published: 2013-05-15   Modified: 2018-03-22  

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