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Isolation and characterization of oligotrophic denitrifying bacteria in surface and subsurface upland soil.

Research Project

Project/Area Number 14360042
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Plant nutrition/Soil science
Research InstitutionNational Agricultural Research Organization

Principal Investigator

HASHIMOTO Tomoyoshi  National Agricultural Research Organization, National Agricultural Research Center for Kyushu Okinawa Region, Department of Agro-Environmental Research, Head of Laboratory, 九州沖縄農業研究センター環境資源研究部, 室長 (90343946)

Co-Investigator(Kenkyū-buntansha) YAMANE Tsuyosi  National Agricultural Research Organization, Researcher, 研究員 (80414853)
Project Period (FY) 2002 – 2005
Project Status Completed (Fiscal Year 2005)
Budget Amount *help
¥12,600,000 (Direct Cost: ¥12,600,000)
Fiscal Year 2005: ¥2,700,000 (Direct Cost: ¥2,700,000)
Fiscal Year 2004: ¥2,900,000 (Direct Cost: ¥2,900,000)
Fiscal Year 2003: ¥3,200,000 (Direct Cost: ¥3,200,000)
Fiscal Year 2002: ¥3,800,000 (Direct Cost: ¥3,800,000)
KeywordsDenitrification / Oligotrophic denitrifying bacteria / Slurry / Nitrogen dynamics / Subsurface soil / N_2O / International research cooperation / South Korea
Research Abstract

This is the first investigation to show that oligotrophic denitrifying bacteria are dominant denitrifying bacteria in subsurface upland soil. We examined the vertical distribution of denitrifying bacterial populations in upland soil using two kinds of enumeration media. The number of denitrifying bacteria, enumerated in subsurface soil layers by a 100-fold diluted nutrient broth (DNB) medium with NO_<3^->, was two to three orders of magnitude greater than those enumerated by a conventional nutrient broth medium with NO_<3^-> suggesting the dominance of oligotrophic denitrifying bacteria. Seventy-four percent of the total denitrifying bacterial isolates were DNB organisms of the oligotrophic type, which did not show appreciable growth on conventional nutrient broth medium. The isolates were heterogeneous and were categorized as alpha (35 strains) and beta (19 strains) subdivisions of proteobacteria and high G+C gram-positive bacteria (7 strains) by 16S rRNA gene sequence analysis (AB118811-AB118817,AB162052-AB162105). The 35 alpha-subdivision of proteobacterial isolates were of oligotrophic type and widely distributed from the surface to subsurface soil layers. Phylogenetic analysis indicated that some isolates belonged to groups with few or no cultivated representatives and that one isolate may be a member of a new genus. This isolation procedure using a diluted media is valuable in detecting diverse and novel denitrifying bacteria in the subsurface soil.
We held International symposium on identification and use of microbial resources for sustainable agriculture on July 28 2004 at Kumamoto, Japan (See the URL http://konarc.naro.affrc.go.jp/photo/symp2004/repo/index-e.htm).

Report

(5 results)
  • 2005 Annual Research Report   Final Research Report Summary
  • 2004 Annual Research Report
  • 2003 Annual Research Report
  • 2002 Annual Research Report
  • Research Products

    (44 results)

All 2006 2005 2004 2003 2002 Other

All Journal Article (37 results) Book (1 results) Publications (6 results)

  • [Journal Article] A Quantitative evaluation and Phylogenetic Characterization of Oligotrophic Denitrifying Bacteria Harbored in Subsurface Upland Soil Using Improved Culturability.2006

    • Author(s)
      Hashimoto T., Whang, K., Nagaoka K.
    • Journal Title

      Biology and Fertility of Soils 42

      Pages: 179-185

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] A Quantitative Evaluation and Phylogenetic Characterization of Oligotrophic Denitrifying Bacteria Harbored in Subsurface Upland Soil Using Improved Culturability.2006

    • Author(s)
      Hashimoto T., Whang, K., Nagaoka K.
    • Journal Title

      Biology and Fertility of Soils 42

      Pages: 179-185

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] Accumulation of denitrifying bacteria and enhancement of denitrification activity in deep subsurface soil in relation to the geological profile.2005

    • Author(s)
      Hashimoto T., Furue K., Kubota T.
    • Journal Title

      Soil Science and Plant Nutrition 51

      Pages: 899-903

    • NAID

      110004704834

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] Biodiversity of oligotrophic denitrifying bacteria in subsurface soil.2005

    • Author(s)
      Whang, K., Hashimoto, T.
    • Journal Title

      Abstracts of the 2005 International meeting of the federation of Korean microbiological societies

      Pages: 136-137

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] 畑地下層土の低栄養性脱窒菌群の多様性評価2005

    • Author(s)
      黄敬淑, 山根剛, 趙眠彗, 李鐘和, 橋本知義
    • Journal Title

      微生物生態学会21回講演要旨集

      Pages: 211-211

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] nirK遺伝子を標的としたdirect in situ PCR法による土壌中の脱窒菌の可視化および定量2005

    • Author(s)
      森山典子, Gong Chunming, 橋本知義, 井上興一, 染谷孝
    • Journal Title

      微生物生態学会21回講演要旨集

      Pages: 52-52

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] 家畜スラリー施用履歴の違いが土壌中脱窒関連遺伝子(nirK)の類縁・系統関係に及ぼす影響2005

    • Author(s)
      山根剛, 黄敬淑, 橋本知義
    • Journal Title

      土壌肥料学会講演要旨集 51

      Pages: 37-37

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Biodiversity of oligotrophic denitrifying bacterial community in subsurface soil (in Japanese).2005

    • Author(s)
      Whang, K., Yamane, T., Cho, M., Lee, J., Hashimoto, T.
    • Journal Title

      Proceedings of the 21^<st> meeting of Japanese society of microbial ecology

      Pages: 211-211

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Visualization and enumeration of denitrifying bacteria in soil by nirK gene targeted direct in situ PCR (in Japanese).2005

    • Author(s)
      Moriyama, N., Gong, C., Hashimoto, T., Inoue, K., Someya, T.
    • Journal Title

      Proceedings of the 21^<st> meeting of Japanese society of microbial ecology

      Pages: 52-52

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Effect of slurry application on phylogenetic characteristics of denitrification gene (nirK) in upland soil (in Japanese).2005

    • Author(s)
      Yamane, T., Whang, K., Hashimoto, T.
    • Journal Title

      Abstracts of the annual meeting of the Japanese society of soil science and plant nutrition 51

      Pages: 37-37

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Direct in situ PCR法による土壌における脱窒菌の高感度迅速検出法の開発2005

    • Author(s)
      森山典子, Gong Chunming, 井上興一, 橋本知義, 染谷孝
    • Journal Title

      日本土壌肥料学会九州支部春季例会講演要旨集

      Pages: 17-17

    • Related Report
      2005 Annual Research Report
  • [Journal Article] 家畜スラリー施用履歴の違いが土壌中脱窒関連遺伝子(nirK)の類縁・系統関係に及ぼす影響2005

    • Author(s)
      山根剛, 橋本知義
    • Journal Title

      日本土壌肥料学会講演要旨集 51

      Pages: 37-37

    • Related Report
      2005 Annual Research Report
  • [Journal Article] 畑地下層土の低栄養性脱窒菌群の多様性評価2005

    • Author(s)
      黄敬淑, 山根剛, 趙眠彗, 李鐘和, 橋本知義
    • Journal Title

      日本微生物生態学会2005年度大会講演要旨集

      Pages: 211-211

    • Related Report
      2005 Annual Research Report
  • [Journal Article] nirK遺伝子を標的としたdirect in situ PCR法による土壌中の脱窒菌の可視化および定量2005

    • Author(s)
      森山典子, Gong Chun-ming, 橋本知義, 井上興一, 染谷孝
    • Journal Title

      日本微生物生態学会2005年度大会講演要旨集

      Pages: 52-52

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Biodiversity of barely culturable oligotrophic bacteria harbored in soil.2004

    • Author(s)
      Whang, K., Hattori, T.
    • Journal Title

      Proceedings of the tenth international congress for culture collections

      Pages: 147-150

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Biodiversity of oligotrophic denitrifying bacteria in layers of a subsurface upland soil.2004

    • Author(s)
      Whang, K.
    • Journal Title

      Proceedings of International Symposium on Identification and Use of Microbial Resources for Sustainable Agriculture

      Pages: 8-14

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Vertical distribution and biodiversity of oligotrophic denitrifying bacteria in subsurface upland soil by using improved culturability.2004

    • Author(s)
      Whang, K., Hashimoto, T., Lee, J., Yang, H.
    • Journal Title

      Abstract of International Meeting of the Microbiological Society of Korea

      Pages: 24-24

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Biodiversity of nitrite reductase gene (nirK) fragments in a surface upland soil with slurry application.2004

    • Author(s)
      Yamane, T., Nagahara, S., Domon, E., Yang, H., Whang, K., Hashimoto, T.
    • Journal Title

      Proceedings of International Symposium on Identification and Use of Microbial Resources for Sustainable Agriculture

      Pages: 68-69

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] 地下水面に至る深層土壌における窒素代謝関連微生物群の動態解明-脱窒活性の増加とその要因の推定-2004

    • Author(s)
      橋本知義, 古江広治, 久保田富次郎
    • Journal Title

      九州農業研究 66

      Pages: 79-79

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Biodiversity of nitrite reductase gene (nirK) fragments in a surface upland soil with slurry application.2004

    • Author(s)
      Yamane, T., Nagahara, S., Domon, E., Yang, H., Whang, K, Hashimoto, T.
    • Journal Title

      Proceedings of International Symposium on Identification and Use of Microbial Resources for Sustainable Agriculture

      Pages: 68-69

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Flush increase of denitrification activity in deep subsurface soil (in Japanese).2004

    • Author(s)
      Hashimoto T., Furue K., Kubota T.
    • Journal Title

      Kyushu Nougyo Kenkyu 66

      Pages: 79-79

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Vertical distribution and biodiversity of oligotrophic denitrifying bacteria in subsurface upland soil by using improved culturability2004

    • Author(s)
      Whang Kyung-Sook et al.
    • Journal Title

      2004 International Meeting of Microbiological Society of Korea

      Pages: 24-24

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Biodiversity of Oligotrophic Denitrifying Bacteria in Layers of a Subsurface Upland Soil2004

    • Author(s)
      Whang Kyung-Sook
    • Journal Title

      Proceedings of International Symposium on Identification and Use of Microbial Resources for Sustainable Agriculture

      Pages: 8-14

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Biodiversity of nitrite reductase gene(nirK)fragments in a surface upland soil with slurry application2004

    • Author(s)
      Yamane T. et al.
    • Journal Title

      Proceedings of International Symposium on Identification and Use of Microbial Resources for Sustainable Agriculture

      Pages: 68-69

    • Related Report
      2004 Annual Research Report
  • [Journal Article] 家畜スラリー長期連用土壌から抽出したDNA由来の脱窒関連遺伝子(nirK)の類縁・系統関係2004

    • Author(s)
      山根剛
    • Journal Title

      日本土壌肥料学会講演要旨集 50

      Pages: 44-44

    • Related Report
      2004 Annual Research Report
  • [Journal Article] 南九州における脱窒菌の動態2004

    • Author(s)
      橋本知義
    • Journal Title

      九州・沖縄の農業と土壌肥料-自然と共存した食料供給基地を目指して-

      Pages: 134-137

    • Related Report
      2004 Annual Research Report
  • [Journal Article] PCR detection of genes encoding nitrate reductase in oligotrophic denitrifying bacteria.2003

    • Author(s)
      Whang, K., Hashimoto, T., Nagahara, S., Lee, J.
    • Journal Title

      土と微生物 57

      Pages: 150-150

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Vertical distribution of free-living and attached denitrifying bacteria in upland soil with slurry application.2003

    • Author(s)
      Hashimoto, T., Whang, K., Niimi, H.
    • Journal Title

      Abstract of 16^th International symposium on Environmental Biogeochemistry

      Pages: 140-140

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Denitrification in subsurface soil could save underground water from nitrogen leaching?2003

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

      Proceedings of 2003 International Symposium on Microbial Ecology & Resources

      Pages: 21-27

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] 家畜スラリー連用畑土壌における低栄養要求型脱窒菌群の垂直分布2003

    • Author(s)
      橋本知義, 安起弘, 金澤晋二郎
    • Journal Title

      九州農業研究 65

      Pages: 84-84

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] PCR detection of genes encoding nitrate reductase in oligotrophic denitrifying bacteria.2003

    • Author(s)
      Whang, K., Hashimoto, T., Nagahara, S., Lee, J.
    • Journal Title

      Soil Microorganisms 57

      Pages: 150-150

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Vertical distribution of free-living and attached denitrifying bacteria in upland soil with slurry application.2003

    • Author(s)
      Hashimoto, T., Whang, K., Niimi, H.
    • Journal Title

      Abstract of 16th International Symposium on Environmental Biogeochemistry

      Pages: 140-140

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Vertical distribution of oligotrophic denitrifying bacterial population in upland soil with slurry application.2003

    • Author(s)
      Hashimoto, T., An, G., Kanazawa, S.
    • Journal Title

      Kyushu Nougyo Kenkyu (in Japanese) 65

      Pages: 84-84

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Vertical changes of denitrification activity and denitrifying bacterial populations in Kuroboku upland soil with slurry application.2002

    • Author(s)
      Hashimoto, t., Niimi, H., Asanuma, S.
    • Journal Title

      Soil Science and Plant Nutrition 48

      Pages: 65-69

    • NAID

      110001717605

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] 家畜スラリー還元畑土壌から分離された低栄養性脱窒細菌新規菌株の分類学的位置づけ2002

    • Author(s)
      黄敬淑, 橋本知義, 金人基, 長岡一成, 浅川晋
    • Journal Title

      微生物生態学会第18回講演要旨集

      Pages: 170-170

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Vertical changes of denitrification activity and denitrifying bacterial populations in Kuroboku upland soil with slurry application.2002

    • Author(s)
      Hashimoto, T., Niimi, H., Asanuma, S.
    • Journal Title

      Soil Science and Plant Nutrition 48

      Pages: 65-69

    • NAID

      110001717605

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Isolation and characterization of oligotrophic denitrifying bacteria in upland soil with slurry application (in Japanese).2002

    • Author(s)
      Whang, K., Hashimoto, T., Kim, I., Nagaoka, K., Asakawa, S.
    • Journal Title

      Proceedings of the 18^<th> meeting of Japanese society of microbial ecology

      Pages: 170-170

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Book] Proceedings of International Symposium on Identification and Use of Microbial Resources for Sustainable Agriculture2004

    • Author(s)
      九州沖縄農業研究センター編
    • Total Pages
      170
    • Publisher
      九州沖縄農業研究センター
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Publications] Hashimoto, T. et al.: "Vertical Distribution of Free-living and Attached Denitrifying Bacteria in UPland Soil with Slurry Application"16th International Symposium on Environmental Biogeochemistry Abstracts. 140 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Hashimoto, T.: "Denitrification in Subsurface Soil Could Save Underground Water from Nitrogen Leaching"2003 International Symposium on Microbial Ecology & Resources, Forward Edges of Microbial Resources and Development. 21-27 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 橋本知義ら: "地下水面に至る深層土壌における窒素代謝関連微生物群の動態解明"九州農業研究. 66(印刷予定). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] 橋本知義: "家畜スラリー連用土壌における低栄養要求型脱窒菌群の垂直分布"九州農業研究. 65(印刷予定). (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] 黄敬淑: "家畜スラリー還元畑土壊中から分離された低栄養性脱窒細菌新基菌株の分類学的位置づけ"第18回日本微生物生態学会講演要旨集. 170-170 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 橋本知義: "乳牛スラリー連用畑下層土には多様な低栄養性脱窒菌が多数生息する"九州沖縄農業研究成果情報. 18・下巻(印刷予定). (2003)

    • Related Report
      2002 Annual Research Report

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Published: 2002-04-01   Modified: 2016-04-21  

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