Phylogenetic and functional analysis of key denitrifiers in rice paddy soil : towards community genomics of soil microorganisms

2009 Fiscal Year Final Research Report

• Project/Area Number: 19380041
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Plant nutrition/Soil science
• Research Institution: The University of Tokyo
• Principal Investigator: SENOO Keishi The University of Tokyo, 大学院・農学生命科学研究科, 教授 (40206652)
• Co-Investigator(Kenkyū-buntansha): OTSUKA Shigeto 東京大学, 大学院・農学生命科学研究科, 准教授 (10313074)
• Project Period (FY): 2007 – 2009
• Keywords: 水田土壌 / 脱窒細菌 / 土壌核酸 / SIP解析 / FSC分離法 / クローンライブラリ解析 / 脱窒機能遺伝子 / 16S rRNA遺伝子

Research Abstract

Rice paddy soil has been shown to have strong denitrifying activity. However, the microbial populations responsible for denitrification have not been well characterized. We used multiple approaches, including stable isotope probing, large-scale 16S rRNA gene sequence analysis, nitrite reductase gene analysis, and a novel single-cell isolation procedure, to identify the key players in denitrification in rice paddy soil. Based on the culture-independent analyses, bacteria in the orders Burkholderiales and Rhodocyclales were identified as the key players in denitrification in rice paddy soil under both laboratory and field conditions. Based on 16S rRNA gene, nirS and nirK sequence, oligonucleotide probes for phylogenetic and functional microarray were successfully designed.

Research Products

• [Journal Article] Isolation of Functional Single Cells from Environments Using a Micromanipulator : Application to Study Denitrifying Bacteria (2010)
  • Author(s): Ashida, N., Ishii, S., Hayano, S., Tago, K., Tsuji, T., Yoshimura, Y., Otsuka, S., Senoo, K.
  • Journal Title: Appl.Microbiol.Biotechnol. 85 Pages: 1211-1217
  • Peer Reviewed
• [Journal Article] The nirK-Harboring Denitrifiers Are More Responsive to the Denitrification Inducing Condition in a Rice Paddy Soil Than nirS-Harboring Bacteria (2010)
  • Author(s): Megumi Yoshida, Satoshi Ishii, Shigeto Otsuka, Keishi Senoo
  • Journal Title: Mcirobes and Environments 25 Pages: 45-48
  • Peer Reviewed
• [Journal Article] Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil (2009)
  • Author(s): Yoshida, M., Ishii, S., Otsuka, S., Senoo, K.
  • Journal Title: Soil Biol.Biochem. 41 Pages: 2044-2051
  • Peer Reviewed
• [Journal Article] Microbial populations responding to denitrification-inductive conditions in rice paddy soil, as revealed by comparative 16S rRNA gene analysis (2009)
  • Author(s): Ishii, S., M. Yamamoto, M. Kikuchi, K. Oshima, M. Hattori, S. Otsuka, K. Senoo
  • Journal Title: Appl.Environ.Microbiol. 75 Pages: 7070-7078
  • Peer Reviewed
• [Presentation] Functional single cell 分離法による水田土壌からの新規脱窒細菌株の取得 (2010)
  • Author(s): 石井聡, 芦田直明, 大塚重人, 妹尾啓史
  • Organizer: 第4回日本ゲノム微生物学会年会
  • Place of Presentation: 福岡
  • Year and Date: 2010-03-07
• [Presentation] Comparative Analysis of the 16S rRNA Gene Clone Libraries Identified Microbial Populations Responding to Environmental Changes in a Rice Paddy Soil (2009)
  • Author(s): Satoshi Ishii, Michihiro Yamamoto, Mami Kikuchi, Kenshiro Oshima, Masahira Hattori, Shigeto Otsuka, Keishi Senoo
  • Organizer: 10th International Symposium on Bacterial Genetics and Ecology
  • Place of Presentation: Uppsala, Sweden
  • Year and Date: 20090615-20090619
• [Presentation] Comparative 16S rRNA Gene Clone Library Analyses Can Identify Soil Microbial Population Responding to the Denitrification-Inductive Condition (2009)
  • Author(s): S. Ishii, M. Yamamoto, M. Kikuchi, K. Oshima, M. Hattori, S. Otsuka, K. Senoo
  • Organizer: 109th General Meeting of the American Society for Microbiology
  • Place of Presentation: Philadelphia, U.S.A.
  • Year and Date: 20090517-20090521
• [Presentation] 水田土壌で機能する脱窒細菌群集の特定と Single-Cell Isolation (2009)
  • Author(s): 妹尾啓史, 石井聡, 多胡香奈子, 吉田愛美, 大塚重人
  • Organizer: 第25回日本微生物生態学会広島大会
  • Place of Presentation: 広島
  • Year and Date: 2009-11-23
• [Presentation] 各地の水田土壌より分離した脱窒細菌の系統と機能の多様性 (2009)
  • Author(s): 多胡香奈子, 石井聡, 上井祐介, 大塚重人, 妹尾啓史
  • Organizer: 第25回日本微生物生態学会広島大会
  • Place of Presentation: 広島
  • Year and Date: 2009-11-23
• [Presentation] 水田土壌における脱窒機能遺伝子の発現解析 : 室内モデル系による解析 (2009)
  • Author(s): 吉田愛美, 石井聡, 多胡香奈子, 藤井大地, 大塚重人, 妹尾啓史
  • Organizer: 第25回日本微生物生態学会広島大会
  • Place of Presentation: 広島
  • Year and Date: 2009-11-22
• [Presentation] Phylogenetic and Functional Diversity of Denitrifying Bacteria Isolated from Rice Paddy Soil (2009)
  • Author(s): Kanako Tago, Satoshi Ishii, Yusuke Uei, Shigeto Otsuka, Keishi Senoo
  • Organizer: MARCO SYMPOSIUM 2009
  • Place of Presentation: つくば
  • Year and Date: 2009-10-06
• [Presentation] Temporal shifts in diversity and quantity of nitrite reductase genes, nirS and nirK, in a rice paddy field soil (2009)
  • Author(s): Megumi Yoshida, Satoshi Ishii, Shigeto Otsuka, Keishi Senoo
  • Organizer: MARCO SYMPOSIUM 2009
  • Place of Presentation: つくば
  • Year and Date: 2009-10-06
• [Presentation] Megumi Yoshida and Shigeto Otsuka, Multiple Approaches to Identify Key Players in Denitrification in Rice Paddy Soil (2009)
  • Author(s): Keishi Senoo, Satoshi Ishii, Kanako Tago
  • Organizer: MARCO SYMPOSIUM 2009
  • Place of Presentation: つくば
  • Year and Date: 2009-10-06
• [Presentation] Functional Single-Cell 分離法による水田土壌からの脱窒菌の分離と脱窒能の特徴 (2009)
  • Author(s): 多胡香奈子, 石井聡, 上井祐介, 大塚重人, 妹尾啓史
  • Organizer: 日本土壌微生物学会2009年度大会
  • Place of Presentation: 福岡
  • Year and Date: 2009-06-12
• [Presentation] 16S rRNA遺伝子の大量シーケンスによる水田土壌における脱窒細菌コミュニティの解析 (2009)
  • Author(s): 石井聡, 山本倫大, 菊池真美, 大島健志朗, 服部正平, 大塚重人, 妹尾啓史
  • Organizer: 第3回日本ゲノム微生物学会年会
  • Place of Presentation: 東京
  • Year and Date: 2009-03-06
• [Presentation] Denitrifying Community Structure in Rice Paddy Soil Investigated by Multiple Approaches (2008)
  • Author(s): K. Tago, S. Ishii, T. Saito, M. Yoshida, M. Yamamoto, S. Hayano, N. Ashida, T. Tsuji, Y. Yoshimura, S. Otsuka, K. Senoo
  • Organizer: 7th International Symposium of Subsurface Microbiology
  • Place of Presentation: 静岡
  • Year and Date: 20081116-20081121
• [Presentation] Seasonal Change in Diversity of Nitrate Reducing Genes in Rice Field Soil (2008)
  • Author(s): Megumi Yoshida, Takayuki Saito, Satoshi Ishii, Shigeto Otsuka, Keishi Senoo
  • Organizer: 12th International Symposium on Microbial Ecology
  • Place of Presentation: ケアンズ
  • Year and Date: 20080817-20080822
• [Presentation] Functional Single-Cell Isolation Method : Application to Study Denitrifying Community in Rice Paddy Soil (2008)
  • Author(s): Naoaki Ashida, Sadakazu Hayano, Satoshi Ishii, Takashi Tsuji, Yoshitaka Yoshimura, Shigeto Otsuka, Keishi Senoo
  • Organizer: 12th International Symposium on Microbial Ecology
  • Place of Presentation: ケアンズ
  • Year and Date: 20080817-20080822
• [Presentation] 水田土壌の窒素浄化機能に貢献する脱窒細菌群集構造の解析 (2008)
  • Author(s): 妹尾啓史, 石井聡
  • Organizer: 農業環境技術研究所公開セミナー「農業分野におけるメタゲノム解析技術の応用の可能性」
  • Place of Presentation: つくば
  • Year and Date: 2008-12-17
• [Presentation] 脱窒機能遺伝子 nirS, nirK 解析に基づく水田土壌の脱窒細菌群集構造 (2008)
  • Author(s): 吉田愛美, 石井聡, 斉藤貴之, 大塚重人, 妹尾啓史
  • Organizer: 第24回日本微生物生態学会札幌大会
  • Place of Presentation: 札幌
  • Year and Date: 2008-11-26
• [Book] 水田土壌で機能する脱窒細菌群集の土壌DNAに基づく特定と Single-Cell Isolation In 難培養微生物研究の最新技術II～ゲノム解析を中心とした最前線と将来展望～ (2010)
  • Author(s): 妹尾啓史・石井聡
  • Total Pages: 184-196
  • Publisher: シーエムシー出版