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Role of bacteriophage communities in paddy soils and their gene diversity and uniqueness

Research Project

Project/Area Number 21380046
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Plant nutrition/Soil science
Research InstitutionNagoya University

Principal Investigator

KIMURA Makoto  名古屋大学, 生命農学研究科, 教授 (20092190)

Co-Investigator(Kenkyū-buntansha) MURASE Jun  名古屋大学, 大学院・生命農学研究科, 講師 (30285241)
Project Period (FY) 2009 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥17,550,000 (Direct Cost: ¥13,500,000、Indirect Cost: ¥4,050,000)
Fiscal Year 2011: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2010: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Fiscal Year 2009: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Keywordsg23遺伝子 / g20遺伝子 / psbA遺伝子 / T4型ファージ / DNA-SIP / 多様性 / 微生物循環 / 水田土壌 / SIP法 / 水田 / 根冠細胞 / ファージ / 細菌 / 感染率 / ^<13>C標識カルス / 安定同位体標識法(SIP) / 変性剤濃度勾配ゲル電気泳動(DGGE) / 死亡率 / カプシド遺伝子g20 / ウイルス / カプシド遺伝子g23
Research Abstract

The role of bacteriophage(phage) communities in paddy soils was studied from the phage contribution to bio-element cycling in this study, and the frequency of phage infection to their hosts and the carbon flow of plant residue to phage DNA were evaluated. Fresh and dried^13C-labelled callus cells were used as the model materials of root cap cells and plant residue, respectively. The gene diversity and uniqueness of phage communities in soils were examined from the phage g23, g20 and psbA sequences in comparison with those in marine and freshwater environments. The frequency of virulent phage infection to bacteria in soils was markedly higher than those reported from marine and freshwater environments. The recovery of 13C-labelled g23 and g20 clones indicated that the phage communities are important in bio-element cycling as the drivers of the microbial loop. The diversity of g23 clones was significantly higher than those in marine and freshwater environments, and their sequences were mostly soil-specific and different from those of marine and freshwater origins. In addition, it was known that g20 and psbA gene sequences in the floodwater of paddy fields were more similar to the sequences in the freshwater environment than to those in the marine environments and that g20 sequences in paddy field soils were different from those not only of marine and freshwater origins but also in the floodwaters overlying.

Report

(4 results)
  • 2011 Annual Research Report   Final Research Report ( PDF )
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (30 results)

All 2011 2010 2009

All Journal Article (20 results) (of which Peer Reviewed: 20 results) Presentation (6 results) Book (4 results)

  • [Journal Article] Heterotrophic growth of cyanobacteria and phage-mediated microbial loop in soil2011

    • Author(s)
      Chol Gyu Lee, Takeshi Watanabe, Yuichi Fujita, Susumu Asakawa, and Makoto Kimura
    • Journal Title

      Soil Science and Plant Nutrition

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Spatial and temporal changes of cyanophage communities in paddy field soils as revealed by capsid assembly protein gene g20.2011

    • Author(s)
      Guanghua Wang, Susumu Asakawa, and Makoto Kimura
    • Journal Title

      FEMS Microbiology Ecology

      Volume: 76(2) Pages: 352-359

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] High frequency of phage-infected bacterial cells in a rice field soil in Japan2011

    • Author(s)
      Ryu Takahashi, Saman Bowatte, Katsutoshi Taki, Yoshinori Ohashi, Nanako Yoshikawa, Susumu Asakawa, and Makoto Kimura
    • Journal Title

      Soil Science and Plant Nutrition

      Volume: 57(1) Pages: 35-39

    • NAID

      110008897262

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular analysis of the major capsid genes(g23) of T4-type bacteriophages in an upland black soil in Northeast China2011

    • Author(s)
      Guanghua Wang, Zhenhua Yu, Junjie Liu, Jian Jin, Xiaobing Liu, and Makoto Kimura
    • Journal Title

      Biology and Fertility of Soils

      Volume: 47(3) Pages: 273-282

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular analysis of the major capsid genes (g23) of T4-type bacteriophages in an upland black soil in Northeast China2011

    • Author(s)
      Guanghua Wang, Zhenhua Yu, Junjie Liu, Jian Jin, Xiaobing Liu, Makoto Kimura
    • Journal Title

      Biology and Fertility of Soils

      Volume: 47 Pages: 273-282

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High frequency of phage-infected bacterial cells in a rice field soil in Japan2011

    • Author(s)
      Ryu Takahashi, Saman Bowatte, Katsutoshi Taki, Yoshinori Ohashi, Nanako Yoshikawa, Susumu Asakawa, Makoto Kimura
    • Journal Title

      Soil Science and Plant Nutrition

      Volume: 57 Pages: 35-39

    • NAID

      110008897262

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Spatial and temporal changes of cyanophage communities in paddy field soils as revealed by capsid assembly protein gene g202011

    • Author(s)
      Guanghua Wang, Susumu Asakawa, Makoto Kimura
    • Journal Title

      FEMS Microbiology Ecology

      Volume: 76 Pages: 352-359

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genetic diversity of major capsid genes (g23) of T4-type bacteriophages in natural environments-a review (中国語)2011

    • Author(s)
      Guanghua Wang, Junjie Liu, Makoto Kimura
    • Journal Title

      Acta Microbiologica Sinica

      Volume: 51 Pages: 732-739

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Low diversity of T4-type bacteriophages in applied rice straw, plant residues and rice roots in Japanese rice soils2010

    • Author(s)
      Shun Fujihara, Jun Murase, Cho Cho Tun, Tomoya Matsuyama, Makoto Ikenaga, Susumu Asakawa, and Makoto Kimura
    • Journal Title

      Soil Science and Plant Nutrition

      Volume: 56(6) Pages: 800-812

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] High frequency of virus-infected bacterial cells in a sheep grazed pasture soil in New Zealand2010

    • Author(s)
      Saman Bowatte, Paul C. D. Newton, Ryu Takahashi, and Makoto Kimura
    • Journal Title

      Soil Biology and Biochemistry

      Volume: 42(5) Pages: 708-712

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Unique viral capsid assembly protein gene(g20) of cyanophages in the floodwater of a Japanese rice field2010

    • Author(s)
      Guanghua Wang, Jun Murase, Susumu Asakawa, and Makoto Kimura
    • Journal Title

      Biology and Fertility of Soils

      Volume: 46(2) Pages: 93-102

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Low diversity of T4-type bacteriophages in applied rice straw, plant residues and rice roots in Japanese rice soils : Estimation from major capsid gene (g23) composition2010

    • Author(s)
      Shun Fujihara
    • Journal Title

      Soil Science and Plant Nutrition

      Volume: 56 Pages: 800-812

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The unique cyanophage community in the floodwater of a Japanese rice field revealed by molecular analysis of the capsid assembly protein gene (g20)2010

    • Author(s)
      Guanghua Wang
    • Journal Title

      Biology and Fertility of Soils 46

      Pages: 93-102

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High frequency of virus-infected bacterial cells in a sheep grazed New Zealand pasture soil2010

    • Author(s)
      Saman Bowatte
    • Journal Title

      Soil Biology and Biochemistry 42

      Pages: 708-712

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Novel cyanophage photosynthetic gene psbA in the floodwater of a Japanese rice field2009

    • Author(s)
      Guanghua Wang, Jun Murase, Susumu Asakawa, and Makoto Kimura
    • Journal Title

      FEMS Microbiology Ecology

      Volume: 70(1) Pages: 79-86

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Change in T4-type bacteriophage communities during the composting process of rice straw2009

    • Author(s)
      Vita Ratri Cahyani, Jun Murase, Susumu Asakawa, and Makoto Kimura
    • Journal Title

      Soil Science and Plant Nutrition

      Volume: 55(4) Pages: 468-477

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Changes in major capsid genes(g23) of T4-type bacteriophages with soil depth in two Japanese rice fields2009

    • Author(s)
      Guanghua Wang, Jun Murase, Katsutoshi Taki, Yoshinori Ohashi, Nanako Yoshikawa, Susumu Asakawa, and Makoto Kimura
    • Journal Title

      Biology and Fertility of Soils

      Volume: 45(5) Pages: 521-529

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Changes in major capsid genes (g23) of T4-type bacteriophages with soil depth in two Japanese rice fields2009

    • Author(s)
      Guanghua Wang
    • Journal Title

      Biology and Fertility of Soils 45

      Pages: 521-529

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Novel cyanophage photosynthetic gene psbA in the floodwater of a Japanese rice field2009

    • Author(s)
      Guanghua Wang
    • Journal Title

      FEMS Microbiology Ecology 70

      Pages: 79-86

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Change in T4-type bacteriophage communities during composting process of rice straw : estimation from major capsid gene (g23) sequences2009

    • Author(s)
      Vita Ratri Cahyani
    • Journal Title

      Soil Science and Plant Nutrition 55

      Pages: 468-477

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Presentation] ファージ感染が土壌細菌の計数に及ぼす影響2011

    • Author(s)
      高橋龍、浅川晋、木村偉人
    • Organizer
      日本土壌肥料学会
    • Place of Presentation
      つくば国際会議場
    • Year and Date
      2011-08-08
    • Related Report
      2011 Annual Research Report
  • [Presentation] Bacterial communities incorporating carbon of root cap cells under upland soil conditions2011

    • Author(s)
      Yong Li, Chol Gyu Lee, Takeshi Watanabe, Jun Murase, Susumu Asakawa, and Makoto Kimura
    • Organizer
      日本土壌肥料学会2011年度つくば大会
    • Place of Presentation
      つくば
    • Related Report
      2011 Final Research Report
  • [Presentation] ファージ感染が土壌細菌の計数に及ぼす影響2011

    • Author(s)
      高橋龍、浅川晋、木村眞人
    • Organizer
      日本土壌肥料学会2011年度つくば大会
    • Place of Presentation
      つくば
    • Related Report
      2011 Final Research Report
  • [Presentation] Ecology of viruses in rice fields.2010

    • Author(s)
      Makoto Kimura
    • Organizer
      19 World Congress of Soil Science
    • Place of Presentation
      Brisbane, Australia
    • Year and Date
      2010-08-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] Ecology of viruses in rice fields2010

    • Author(s)
      Makoto Kimura, Guanghua Wang, Natsuko Nakayama, and Susumu Asakawa
    • Organizer
      19th World Congress of Soil Science、Brisbane
    • Related Report
      2011 Final Research Report
  • [Presentation] 水田土壌中の植物遺体に存在するT4型バクテリオファージ群集のカプシド遺伝子g23による解析2009

    • Author(s)
      藤原俊、松山倫也、Tun Cho Cho,浅川晋、木村眞人
    • Organizer
      日本土壌微生物学会2009年度大会
    • Place of Presentation
      福岡
    • Year and Date
      2009-06-01
    • Related Report
      2011 Final Research Report
  • [Book] Ubiquitous bacteriophage hosts in rice paddy soilIn Guenther Witzany(ed.) Biocommunication of Soil Microorganisms.2010

    • Author(s)
      Makoto Kimura, Guanghua Wang, Natsuko Nakayama, and Susumu Asakawa
    • Publisher
      Springer Science+ Business Media. New York
    • Related Report
      2011 Final Research Report
  • [Book] Ubiquitous bacteriophage hosts in rice paddy soil. In Guenther Witzany (ed.) Biocommunication of Soil-Bacteria and Viruses.2010

    • Author(s)
      Makoto Kimura
    • Publisher
      Springer Science+Business Media
    • Related Report
      2010 Annual Research Report
  • [Book] Succession and phylogenetic composition of microbial communities responsible for the composting process of rice straw. In Joseph C. Pereira, and John L. Bolin(eds.), Composting : Processes, Materials and Approaches2009

    • Author(s)
      Vita Ratri Cahyani, Susumu Asakawa, and Makoto Kimura
    • Publisher
      Nova Science Publishers, Inc., New York, USA
    • Related Report
      2011 Final Research Report
  • [Book] Composting : Processes, Materials and Approaches2009

    • Author(s)
      Vita Ratri Cahyani
    • Total Pages
      316
    • Publisher
      Nova Science Publishers, Inc.
    • Related Report
      2009 Annual Research Report

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Published: 2009-04-01   Modified: 2016-04-21  

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