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Global systems of symbiotic nitrogen-fixing bradyrhizobia by comparative genomics of phylogenetic super-neighbors

Research Project

Project/Area Number 23658057
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Plant nutrition/Soil science
Research InstitutionTohoku University

Principal Investigator

MINAMISAWA Kiwamu  東北大学, 生命科学研究科, 教授 (70167667)

Project Period (FY) 2011 – 2013
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Fiscal Year 2013: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2012: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2011: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords共生 / ゲノム比較 / 根粒菌 / Bradyrhizobium / 窒素固定 / 土壌低栄養細菌 / タンパク質分泌系 / エンドファイト / 比較ゲノム / 土壌微生物
Research Abstract

Global systems of symbiotic nitrogen-fixing bradyrhizobia were conducted by comparative genomics of phylogenetic super-neighbors of the bacteria. Soil-dwelling Bradyrhizobium sp. strain S23321 lacked symbiosis island with high genomic co-linearity with B. japonicum USDA110, suggesting an ancestral-type genome of symbiotic bradyrhizobia. On the other hand, the genome analysis suggested soil-dwelling Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aechynomeny indica. Indeed, all texted strains of A. oligotrophica are able to nodulate A. indica with symbiotic nitrogen fixation. In addition, the rhcJ and ttsI mutants of B. japonicum for the type III protein secretion system (T3SS) gained the ability to nodulate Rj2 soybean, suggesting the effectors secreted via T3SS trigger incompatibility between these two partners.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (32 results)

All 2014 2013 2012 2011

All Journal Article (11 results) (of which Peer Reviewed: 11 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (21 results) (of which Invited: 4 results)

  • [Journal Article] A Rice Gene for Microbial Symbiosis, Orysa sativa CCaMK, Reduces CH_4 Flux in a Paddy Field with Low Nitrogen Input2014

    • Author(s)
      Zhihua Bao, Aya Watanabe, Kazuhiro Sasaki, Takashi Okubo, Takeshi Tokida, Dongyan Liu, Seishi Ikeda, Haruko Imaizumi-Anraku, Susumu Asakawa, Tadashi Sato, Hisayuki Mitsui, Kiwamu Minamisawa
    • Journal Title

      Applied and Environmental Microbiology

      Volume: VOL.80 Issue: 6 Pages: 1995-2003

    • DOI

      10.1128/aem.03646-13

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Low Nitrogen Fertilization Adapts Rice Root Microbiome to Low Nutrient Environment by Changing Biogeochemical Functions2014

    • Author(s)
      Seishi Ikeda, Kazuhiro Sasaki, Takashi Okubo, Akifumu Yamashita, Kimihiro Terasawa, Zhihua Bao, Dongyan Liu, Takeshi Watanabe, Jun Murase, Susumu Asakawa, Shima Eda, Hisayuki Mitsui, Tadashi Sato, and Kiwamu Minamisawa
    • Journal Title

      Microbes and Environments

      Volume: 29 Issue: 1 Pages: 50-59

    • DOI

      10.1264/jsme2.ME13110

    • NAID

      130003390907

    • ISSN
      1342-6311, 1347-4405
    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] The type III Secretion System of Bradyrhizobium japonicum USDA122 mediates symbiotic incompatibility with Rj2 soybean plants2013

    • Author(s)
      Tsukui T, Eda S, Kaneko T, Sato S,Okazaki S, Kakizaki-Chiba K, Itakura M,Mitsui H, Yamashita A, Terasawa K,Minamisawa K
    • Journal Title

      Appl Environ Microbiol

      Volume: 79 Issue: 3 Pages: 1048-1051

    • DOI

      10.1128/aem.03297-12

    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Genome Analysis Suggests that the Soil Oligotrophic Bacterium Agrmonas oligotrophica (Bradyrhizobium oligotrophicum) Is a Nitrogen-Fixing Symbiont of Aeschynomene indica.2013

    • Author(s)
      大久保 卓
    • Journal Title

      Applied and Environmental Microbiology

      Volume: 79 Issue: 8 Pages: 2542-2551

    • DOI

      10.1128/aem.00009-13

    • Related Report
      2013 Annual Research Report 2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Mitigation of nitrous oxide emissions from soils by Bradyrhizobium japonicum inoculation.2013

    • Author(s)
      Itakura M, Uchida Y, Akiyama H, Takada-Hoshino Y, Shimomura Y, Morimoto S, Tago K, Wang Y, Hayakawa C, Uetake Y, Sanchez C, EdaS, Hayatsu M, Minamisawa K.
    • Journal Title

      Nature Climate Change

      Volume: 3 Issue: 3 Pages: 208-212

    • DOI

      10.1038/nclimate1734

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Evolution of Bradyrhizobium-Aeschynomene mutualism : living testimony of the ancient world or highly evolved state?2012

    • Author(s)
      大久保 卓
    • Journal Title

      Plant & Cell Physiology

      Volume: 53 Issue: 12 Pages: 2000-2007

    • DOI

      10.1093/pcp/pcs150

    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Complete Genome Sequence of <i>Bradyrhizobium</i> sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs2012

    • Author(s)
      大久保 卓
    • Journal Title

      Microbes and Environments

      Volume: 27 Issue: 3 Pages: 306-315

    • DOI

      10.1264/jsme2.ME11321

    • NAID

      10030869620

    • ISSN
      1342-6311, 1347-4405
    • Related Report
      2013 Final Research Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Genetic diversity, symbiotic evolution, and proposed infection process of Bradyrhizobium strains isolated from root nodules of Aeschynomene americana L. in Thailand.2012

    • Author(s)
      Noisangiam R.
    • Journal Title

      Applied and Environmental Microbiology

      Volume: 78 Issue: 17 Pages: 6236-6250

    • DOI

      10.1128/aem.00897-12

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Pyrosequence Read Length of 16S rRNA Gene Affects Phylogenetic Assignment of Plant-associated Bacteria2012

    • Author(s)
      大久保 卓
    • Journal Title

      Microbes and Environments

      Volume: 27 Issue: 2 Pages: 204-208

    • DOI

      10.1264/jsme2.ME11258

    • NAID

      10030432208

    • ISSN
      1342-6311, 1347-4405
    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Complete genome sequence of the soybean symbionts Bradyrhizobium japonicum strain USDA6T2011

    • Author(s)
      Kaneko, T.
    • Journal Title

      Genes

      Volume: 2 Issue: 4 Pages: 763-787

    • DOI

      10.3390/genes2040763

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Nitrate-dependent N2O emissions from intact soybean nodues via denitrification by Bradyrhizobium japonicum bacteroids2011

    • Author(s)
      Hiyama, J
    • Journal Title

      Applied Environmental Microbiology

      Volume: 77 Issue: 24 Pages: 8787-8790

    • DOI

      10.1128/aem.06262-11

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Presentation] 共生アイランド獲得は根粒菌ゲノムの品質低下の危険を招く2014

    • Author(s)
      飯田隆之、板倉学、伊沢剛、鮫島玲子、大久保卓、三井久幸、柿崎芳里、南澤究
    • Organizer
      第8回日本ゲノム微生物学会年会
    • Place of Presentation
      東京
    • Related Report
      2013 Annual Research Report
  • [Presentation] Analysis of symbiotic phenotypes of an effector gene unique to Bradyrhizobium japonicum USDA1222013

    • Author(s)
      Yuta Suzuki, Cristina Sa^^'nchez, Kaori Kakizaki-Chiba, Takakazu Kaneko, Shusei Sato, Takahiro Tsukui, Kiwamu Minamisawa
    • Organizer
      18th International Congress on Nitrogen Fixation
    • Place of Presentation
      Miyazaki, Japan
    • Related Report
      2013 Annual Research Report 2013 Final Research Report
  • [Presentation] Soybean symbiosis with Bradyrhizobium japonicum: Evolution and global warming2013

    • Author(s)
      Kiwamu Minamisawa
    • Organizer
      The 22th North American Conference on Symbiotic Nitrogen Fixation 北米窒素固定会議
    • Place of Presentation
      Minneapolis, USA
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] ダイズ根粒菌のゲノムバリエーション:マッピングによる挿入配列コピー数の推定2013

    • Author(s)
      飯田 隆之、柿崎 芳里、板倉 学、 南澤 究
    • Organizer
      日本土壌肥料学会2013年度名古屋大会
    • Place of Presentation
      名古屋
    • Related Report
      2013 Annual Research Report
  • [Presentation] Genome analysis suggests that the soil oligotrophic bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aeschynomene indica2013

    • Author(s)
      Takashi Okubo, Shohei Fukushima, Manabu Itakura, Kenshiro Oshima, Aphakorn Longtonglang, Neung Teaumroong, Hisayuki Mitsui, Masahira Hattori, Reiko Hattori, Tsutomu Hattori, Kiwamu Minamisawa
    • Organizer
      18th International Congress on Nitrogen Fixation
    • Place of Presentation
      Miyazaki, Japan
    • Related Report
      2013 Annual Research Report
  • [Presentation] Soil oligotrophic bacterium, Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is nitrogen-fixing symbiont of Aeschynomene indica as suggested by genome analysis2012

    • Author(s)
      Takashi Okubo, Shohei Fukusima, Manabu Itakura, Kenshiro Ohshima, Aphakorn Longtonlang, Neung Teaumroong, Hisayuki Mitsui, Masahira Hattori, Reiko Hattori, Tsutomu Hattori, and Kiwamu Minamisawa
    • Organizer
      The 2nd Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation
    • Place of Presentation
      Phuket, Thailand
    • Related Report
      2013 Final Research Report
  • [Presentation] ダイズ根粒菌Type III分泌系によるRj2 ダイズ共生不和合性の誘導2012

    • Author(s)
      津久井隆裕, 江田志磨, 金子貴一, 佐藤修正, 岡崎伸, 柿崎(千葉)芳里, 板倉学, 三井久幸, 南澤 究
    • Organizer
      植物微生物研究会第22回研究交流会
    • Place of Presentation
      神戸
    • Related Report
      2013 Final Research Report
  • [Presentation] 土壌低栄養細菌Agromonas oligotrophica S58^T のゲノム解析2012

    • Author(s)
      大久保卓, 大島健志朗, 三井久幸, 服部勉, 服部正平, 南澤 究
    • Organizer
      第6回日本ゲノム微生物学会年会
    • Place of Presentation
      東京
    • Related Report
      2013 Final Research Report
  • [Presentation] What does community analysis of plant-associated microbes tell us?2012

    • Author(s)
      Kiwamu Minamisawa
    • Organizer
      XV International Congress of Molecular Plant-Microbe Interactions (Invited speaker)
    • Place of Presentation
      Kyoto
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] N2O emission from soybean rhizosphere depends on denitrification by Bradyrhizobium japonicum and other soil microbes.2012

    • Author(s)
      Kiwamu Minamisawa
    • Organizer
      14th International Symposium on Microbial Ecology
    • Place of Presentation
      Copenhagen, Denmark
    • Related Report
      2012 Research-status Report
  • [Presentation] Isolation and characterization of Aurantimonas species responded to legume nodulation genonotypes.2012

    • Author(s)
      Mizue Anda
    • Organizer
      14th International Symposium on Microbial Ecology
    • Place of Presentation
      Copenhagen, Denmark
    • Related Report
      2012 Research-status Report
  • [Presentation] Metagenome and microscopic analyses for plant-associated microbes towards sustainable agriculture2012

    • Author(s)
      Takashi Okubo
    • Organizer
      第28回微生物生態学会 (Invited speaker)
    • Place of Presentation
      豊橋
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] 光合成Bradyrhizobium とBurkholderia kururiensis のイネへの接種効果と組織局在性2012

    • Author(s)
      福島翔平
    • Organizer
      植物微生物研究会第22回研究交流会
    • Place of Presentation
      神戸
    • Related Report
      2012 Research-status Report
  • [Presentation] ダイズ根粒菌Type III 分泌系によるRj2 ダイズ共生不和合性の誘導2012

    • Author(s)
      津久井隆裕
    • Organizer
      植物微生物研究会第22回研究交流会
    • Place of Presentation
      神戸
    • Related Report
      2012 Research-status Report
  • [Presentation] Nitrogen and plant-associated microbes.2012

    • Author(s)
      Kiwamu Minamisawa
    • Organizer
      The 2nd Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation. (Invited oral speaker in plenary Lecture)
    • Place of Presentation
      Phuket, Thailand
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] Soil oligotrophic bacterium, Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is nitrogen-fixing symbiont of Aeschynomene indica as suggested by genome analysis.2012

    • Author(s)
      Takashi Okubo
    • Organizer
      The 2nd Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation
    • Place of Presentation
      Phuket, Thailand
    • Related Report
      2012 Research-status Report
  • [Presentation] Colonization of phyosynthetic Bradyshiobium and Burkholderia kururiensis in rice plant.2012

    • Author(s)
      Shohei Fukusima
    • Organizer
      The 2nd Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation
    • Place of Presentation
      Phuket, Thailand
    • Related Report
      2012 Research-status Report
  • [Presentation] 「植物共生微生物の多様性と機能」根粒菌とエンドファイトによる物質循環と宿主相互作用.2012

    • Author(s)
      南澤 究
    • Organizer
      (株)コンポン研究所 植物技術講演会(招待講演)
    • Place of Presentation
      (株)コンポン研究所 (名古屋)
    • Related Report
      2011 Research-status Report
  • [Presentation] 土壌低栄養細菌Agromonas oligotrophica S58Tのゲノム解析2012

    • Author(s)
      大久保 卓
    • Organizer
      第6回日本ゲノム日生物学会年会
    • Place of Presentation
      立教大学池袋キャンパス (東京)
    • Related Report
      2011 Research-status Report
  • [Presentation] 農耕地生態系における微生物群集構造の変動法則の理解から作物生産への貢献を目指して2011

    • Author(s)
      南澤 究
    • Organizer
      日本学術会議と土壌肥料学会共同シンポジウム 「作物生産に対する土壌微生物の貢献」(招待講演)
    • Place of Presentation
      エポカルつくば(つくば国際会議場)(つくば)
    • Related Report
      2011 Research-status Report
  • [Presentation] シンポジウム 植物共生微生物の多様性研究とその社会貢献.2011

    • Author(s)
      南澤 究
    • Organizer
      第27回日本微生物生態学会大会(招待講演)
    • Place of Presentation
      京都大学北部キャンパス農学部総合館(京都)
    • Related Report
      2011 Research-status Report

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Published: 2011-08-05   Modified: 2019-07-29  

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