Development of evaluation technique for soil quality using ITS-DNA microarray of indicator microorganisms.

• Project/Area Number: 23710091
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Environmental technology/Environmental materials
• Research Institution: Toyohashi University of Technology
• Principal Investigator: OKAMURA KEIKO 豊橋技術科学大学, エレクトロニクス先端融合研究所, 研究員 (10570533)
• Project Period (FY): 2011 – 2012
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000); Fiscal Year 2012: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2011: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: 強酸性茶園土壌 / AOA / AOB / amoA遺伝子 / PNR / 定量PCR / T-RFLP解析 / クローンライブラリー解析 / アンモニア酸化バクテリア / アンモニア酸化アーキア / T-RFLP / アンモニア酸化活性 / 茶園土壌 / マイクロアレイ / ITS / 土壌環境モニタリング / 指標微生物

Research Abstract

Ammonia oxidation is the important step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). In tea orchard soil, we must employ available means to inhibition incomplete nitrification by ammonia oxidizing microorganisms and to prevent denitrification by ammonia oxidizing bacteria. The aim of this study is to reveal activity and diversity of AOA and AOB in acidic tea orchard soil to develop agricultural management technologies.
Archaeal amoA genes are more abundant than bacterial amoA genes in soil samples, and qPCR suggested that ammonia oxidization is driven by AOA in acidic tea orchard soil. The result of the phylogenetic analyses showed that all clones in clone libraries for tea orchard soils can distinguished from those for unplanted soil. These results suggest the specific AOA populations dominate as ammonia oxidizers in acidic soils, particularly acidic tea orchard soils, as a result of the adaptation to specific ecological niches.

Research Products

• [Journal Article] Defensive bacteriome symbiont with a drastically reduced genome (2013)
  • Author(s): Nakabachi, A., Ueoka, R., Oshima, K., Teta, R., Mangoni, A., Gurgui, M., Oldham, N.J., van Echten-Deckert, G., Okamura, K., Yamamoto, K., Inoue, H., Ohkuma, M., Hongoh, Y., Miyagishima, S.Y., Hattori, M., Piel, J., Fukatsu, T.
  • Journal Title: Curr. Biol. Volume: 23 Issue: 15 Pages: 1478-1484
  • DOI: 10.1016/j.cub.2013.06.027
  • Peer Reviewed
• [Journal Article] Community structure and population dynamics of ammonia oxidizers in composting processes of ammonia-rich livestock waste. (2013)
  • Author(s): Yamada, T., Araki, S., Ikeda-Ohtsubo, W., Okamura, K., Hiraishi, A., Ueda, H., Ueda, Y., Miyauchi, K., and Endo, G.
  • Journal Title: Systematic and Applied Microbiology Volume: in press Issue: 5 Pages: 359-67
  • DOI: 10.1016/j.syapm.2013.02.001
  • Peer Reviewed
• [Journal Article] Relationships between 16S-23S rRNA gene internal transcribed spacer DNA and genomic DNA similarities in the taxonomy of phototrophic bacteria (2013)
  • Author(s): Okamura, K., Hisada, T., Takata, K., and Hiraishi, A.
  • Journal Title: Journal of Physics : Conference Series Volume: 433 Pages: 12037-12037
  • Peer Reviewed
• [Journal Article] Relationships between 16S-23S rRNA gene internal transcribed spacer DNA and genomic DNA similarities in the taxonomy of phototrophic bacteria. (2013)
  • Author(s): Keiko Okamura, Takayoshi Hisada, Koji Takakata, and Akira Hiraishi
  • Journal Title: Journal of Physics: Conference Series Volume: 433 Pages: 1742-6596
  • DOI: 10.1088/1742-6596/433/1/012037
  • Peer Reviewed
• [Journal Article] Carotenoids in Rhodoplanes species: variation of compositions and substrate specificity of predicted carotenogenesis enzymes. (2012)
  • Author(s): Takaichi, S., Sasikala, C., Ramana, C.V., Okamura, K., and Hiraishi A.
  • Journal Title: Current Microbiology Volume: 65(2) Issue: 2 Pages: 150-155
  • DOI: 10.1007/s00284-012-0139-y
  • Peer Reviewed
• [Journal Article] Ammonia-oxidizing activity and microbial community structure in acid tea (Camellia sinensis) orchard soil (2012)
  • Author(s): Okamura, K., Takanashi, A., Yamada, T., and Hiraishi, A.
  • Journal Title: Journal of Physics : Conference Series Volume: 352 Pages: 12052-12052
  • Peer Reviewed
• [Journal Article] Ammonia-oxidizing activity and microbial community structure in acid tea (Camellia sinensis) orchard soil. (2012)
  • Author(s): Keiko Okamura, Aoi Takanashi, Takeshi Yamada, and Akira Hiraishi
  • Journal Title: Journal of Physics: Conference Series Volume: 352 Pages: 1742-6596
  • DOI: 10.1088/1742-6596/352/1/012052
  • Peer Reviewed
• [Presentation] Comparison of hybridization analyses of 16S-23S rRNA gene internal transcribed spacer DNA and of genomic DNA in phototrophic genera (2012)
  • Author(s): K. Okamura et al.
  • Organizer: The Irago Conference 2012
  • Place of Presentation: Irago Sea-Park & Spa
• [Presentation] Diversity analysis of ammonia-oxidizing archaea and bacteria in acidic tea orchard soil (2012)
  • Author(s): A. Takanashi et al.
  • Organizer: The Irago Conference 2012
  • Place of Presentation: Irago Sea-Park & Spa
• [Presentation] Analysis of ammonia-oxidizing microorganisms in acid tea orchard soil in terms of quantity, quality, and activity (2012)
  • Author(s): A. Takanashi et al.
  • Organizer: 第28回日本微生物生態学会大会
  • Place of Presentation: 豊橋技術科学大学
• [Presentation] 酸性茶園土壌におけるアンモニア酸化微生物の活性と多様性 (2012)
  • Author(s): 高梨藍生
  • Organizer: 環境バイオテクノロジー学会、2012年度大会
  • Place of Presentation: 京都大学宇治キャンパス宇治おうばくプラザ
• [Presentation] 強酸性茶園土壌におけるアンモニア酸化活性とアンモニア酸化微生物の群集構造解析 (2012)
  • Author(s): 高梨藍生
  • Organizer: 日本農芸化学会2012年度大会
  • Place of Presentation: 京都女子大学
• [Presentation] 酸性茶園土壌におけるアンモニア酸化微生物の活性と多様性 (2012)
  • Author(s): 髙梨藍生、岡村恵子、山田剛史、平石明
  • Organizer: 環境バイオテクノロジー学会2012年度大会
  • Place of Presentation: 京都大学 宇治キャンパス 宇治おうばくプラザ
• [Presentation] Analysis of ammonia-oxidizing microorganisms in orchard soil in terms of quantity, quality and activity (2012)
  • Author(s): Takanashi, A., Okamura, K., Yamada, T., and Hiraishi, A.
  • Organizer: The 28th Annual Meeting of the Japanese Society of Microbial Ecology
  • Place of Presentation: Toyohashi Univ. of Technol.
• [Presentation] Isolation and characterization of Acidiphilium iwatense sp. nov. and other acidophilic chemoorganotrophic bacteria from an acid mine drainage treatment process (2012)
  • Author(s): Okamura, K., Kawai, A., Yamada, T., Wakao, N., and Hiraishi, A.
  • Organizer: The 28th Annual Meeting of the Japanese Society of Microbial Ecology
  • Place of Presentation: Toyohashi Univ. of Technol.
• [Presentation] Diversity analysis of ammonia-oxidizing archaea and bacteria in acidic tea orchard soil (2012)
  • Author(s): Takanashi, A., Okamura, K., Yamada, T., and Hiraishi, A.
  • Organizer: The Asia-Pacific Interdiscliplinary Research Conference
  • Place of Presentation: Irago Sea-Park & Spa Hotel Tahara, Aichi, Japan
• [Presentation] Comparison of hybridization analyses of 16S-23S rRNA gene internal transcribed spacer DNA and of genomic DNA in phototrophic genera (2012)
  • Author(s): Okamura, K ., Hisada, T., Takata, K., and Hiraishi, A.
  • Organizer: The Asia-Pacific Interdiscliplinary Research Conference
  • Place of Presentation: Irago Sea-Park & Spa Hotel Tahara, Aichi, Japan
• [Presentation] 強酸性茶園土壌におけるアンモニア酸化活性とアンモニア酸化微生物の群集構造解析 (2012)
  • Author(s): 高梨藍生、岡村恵子、山田剛史、平石明
  • Organizer: 日本農芸化学会
  • Place of Presentation: 京都女子大
• [Presentation] Ammonia-oxidizing activity and community structure in hyper-acidic tea (Camellia sinensis) orchard soil (2011)
  • Author(s): K. Okamura et al.
  • Organizer: The Asia-Pacific Interdisciplinary Research Conference 2011
  • Place of Presentation: Toyohashi Univ. Technol.
• [Presentation] Ammonia-oxidizing activity and community structure in hyper-acidic tea (Camellia sinensis) orchard soil. (2011)
  • Author(s): Keiko Okamura, Aoi Takanashi, Takeshi Yamada, and Akira Hiraishi
  • Organizer: Asia-Pacific Interdisciplinary Research Conference 2011
  • Place of Presentation: Toyohashi University of Technology