Environmental Assessment Based on Synoptic Molecular Taxonomy of Soil Bacterial DNA

• Project/Area Number: 18310009
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Environmental dynamic analysis
• Research Institution: Yokohama National University
• Principal Investigator: ITOH Kiminori Yokohama National University, 大学院・工学研究院, 教授 (40114376)
• Co-Investigator(Kenkyū-buntansha): AMEMIYA Takashi 横浜国立大学, 大学院・工学研究院, 准教授 (60344149)
• Project Period (FY): 2006 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥14,560,000 (Direct Cost: ¥12,700,000、Indirect Cost: ¥1,860,000); Fiscal Year 2008: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000); Fiscal Year 2007: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000); Fiscal Year 2006: ¥6,500,000 (Direct Cost: ¥6,500,000)
• Keywords: 環境計測 / 土壌細菌 / 鎖長多形 / DGGE / SSCP / DNA二次元電気泳動 / 生態系 / 湖 / 複雑系 / 食物網 / レジームシフト / 多様性 / 二次元電気泳動 / ランク・アバンダンスプロット / 回復性

Research Abstract

環境中で重要な機能を担うにも関わらず、その詳細が不明な土壌細菌群集に関して、実験的・理論的な解析を行った。実験的には、DNA を高い分離能の検出できる二次元電気泳動法と、異なるDNA の集合を全体的に見るための総観的分子分類学に基づいて、新しい評価法を開発した。二次元電気泳動では、それぞれの細菌種を、1 つ1 つのスポットとして得ることができるため、全体の見通しが良い。理論的には、多様性が出現する機構を、「食う・食われる」の関係を表す食物網から検討すると共に、生態系中の非線形な相互作用による動態の解析を行い、典型的な湖汚染であるアオコ(シアノバクテリアの集団)の季節変動や日内変動などの挙動を明らかにした

Research Products

• [Journal Article] Identification and Validation of suitable Reference Genes for Quantitative Expression of xylA and xylE Genes in Pseudomonas putida mt-2 (2009)
  • Author(s): Qing Chang, Takashi Amemiya, Jianbo Liu, Xianjing Xu, and Kiminori Itoh
  • Journal Title: Journal of Bioscience and Bioengineering (印刷中)
  • NAID: 110007110257
  • Peer Reviewed
• [Journal Article] Noise-triggered regime shifts in a simple aquatic model (2009)
  • Author(s): H. Serizawa, T. Amemiya, K. Itoh
  • Journal Title: Ecological Complexity (印刷中)
  • Peer Reviewed
• [Journal Article] Patchiness and bistability in the comprehensive cyanobacterial model(CCM) (2009)
  • Author(s): Hiroshi Serizawa ; Takashi Amemiya ; Kiminori Itoh
  • Journal Title: Ecological Modelling 220 Pages: 764-773
  • Peer Reviewed
• [Journal Article] Identification and Validation of suitable Reference Genes for Quantitative Expression of xylA and xylE Genes in Pseudomonas putida mt-2 (2009)
  • Author(s): Qing Chang
  • Journal Title: Journal of Bioscience and Bioengineering Volumel07. ISSUE2 Pages: 210-214
  • Peer Reviewed
• [Journal Article] Patchiness and bistability in the comprehensive cyanobacterial model(CCM) (2009)
  • Author(s): Hiroshi Serizawa
  • Journal Title: Ecological Modelling 220 Pages: 764-773
  • Peer Reviewed
• [Journal Article] Noise-triggered regime shifts in a simple aquatic model (2009)
  • Author(s): Hiroshi Serizawa
  • Journal Title: Ecological Complexity in press
  • Peer Reviewed
• [Journal Article] The top-down mechanism for body mass -abundance scaling (2008)
  • Author(s): A. G. Rossberg, R. Ishii, T. Amemiya, and K. Itoh
  • Journal Title: Ecology 89(2) Pages: 567-580
  • Peer Reviewed
• [Journal Article] Two-Dimensional DNA Gel Electrophoresis Mapping (2008)
  • Author(s): Guohua Liu, Takashi Amemiya, and Kiminori Itoh
  • Journal Title: a Novel Approach to Diversity Analysis of Bacterial Communities in Environmental Soil J. Bioscience and Bioengineering 105 Pages: 127-133
  • Peer Reviewed
• [Journal Article] Mathematical modeling of colony formation in algal blooms (2008)
  • Author(s): H. Serizawa, T. Amemiya, T. Enomoto, A. G. Rossberg, and K. Itoh
  • Journal Title: phenotypic plasticity in cyanobacteria, Ecological Research 23 Pages: 841-850
  • Peer Reviewed
• [Journal Article] Computer simulations of seasonal outbreak and diurnal vertical migration of cyanobacteria (2008)
  • Author(s): Hiroshi Serizawa, Takashi Amemiya, Axel G. Rossberg, and Kiminori Itoh
  • Journal Title: Limnology 9 Pages: 185-194
  • NAID: 10025404591
  • Peer Reviewed
• [Journal Article] Spatial distribution of phytoplankton in a mathematical model (2008)
  • Author(s): Hiroshi Serizawa, Takashi Amemiya, and Kiminori Itoh
  • Journal Title: Journal of Biosciences 33 Pages: 391-403
  • Peer Reviewed
• [Journal Article] Two-Dimensional DNA Gel Electrophoresis Mapping : a Novel Approach to Diversity Analysis of Bacterial Communities in Environmental Soil (2008)
  • Author(s): Guohua Liu
  • Journal Title: J. Bioscience and Bioengineering 105 Pages: 127-133
  • Peer Reviewed
• [Journal Article] The top-down mechanism for body-mass-abundance scaling (2008)
  • Author(s): Axel G. Rossberg
  • Journal Title: Ecology 89 Pages: 567-580
  • Peer Reviewed
• [Journal Article] Mathematical modeling of colony formation in algal blooms : phenotypic plasticity in cyanobacteria (2008)
  • Author(s): Hiroshi Serizawa
  • Journal Title: Ecological Research 23 Pages: 841-850
  • Peer Reviewed
• [Journal Article] Computer simulations of seasonal outbreak and diurnal vertical migration of cyanobacteria (2008)
  • Author(s): Hiroshi Serizawa
  • Journal Title: Limnology 9 Pages: 185-194
  • Peer Reviewed
• [Journal Article] Spatial distribution of phytoplankton in a mathematical model (2008)
  • Author(s): Hiroshi Serizawa
  • Journal Title: Journal of Biosciences 33 Pages: 391-403
  • Peer Reviewed
• [Journal Article] The top-down mechanism for body mass-abundance scaling (2008)
  • Author(s): A.G. Rossberg
  • Journal Title: Ecology 89 Pages: 567-580
  • Peer Reviewed
• [Journal Article] Two-Dimentional DNA Gel Electrophoresis Mapping: a Novel Approach to Diversity Analysis of Bacterial Communities in Environmental Soil (2008)
  • Author(s): Guohua Liu
  • Journal Title: J. Bioscience and Bioengineering 105 Pages: 127-133
  • Peer Reviewed
• [Journal Article] Stability and dynamical behavior in a lake-model and implications for regime shifts in real lakes ecological modeling (2007)
  • Author(s): T. Amemiya, T. Enomoto, A. G. Rossberg, T. Yamamoto, Y. Inamori, and K. Itoh
  • Journal Title: Ecological Modelling 206 Pages: 54-62
  • Peer Reviewed
• [Journal Article] Stability and dynamical behavior in a lake-model and implications for regime shifts in real lakes ecological modeling. (2007)
  • Author(s): T. Amemiya
  • Journal Title: Ecological Modelling 206 Pages: 54-62
  • Peer Reviewed
• [Journal Article] Learning and recalling of phase patterns in coupled BVP oscillators with time delay (2007)
  • Author(s): T. Yamamoto
  • Journal Title: International Journal of Bifurcation and Chaos 17 Pages: 1-5
  • Peer Reviewed
• [Journal Article] Stability and dynamical behavior in a lake-model and implications for regime shifts in real lakes ecological modeling (2007)
  • Author(s): T.Amemiya, T.Enomoto, A.G.Rossberg, T.Yamamoto, Y.Inamori, K.Itoh
  • Journal Title: Ecological Modeling (印刷中)
• [Journal Article] Some properties of the speciation model for foodweb structure Mechanisms for degree distributions and intervality (2006)
  • Author(s): A.G. Rossberg, H. Matsuda, T. Amemiya, K. Itoh
  • Journal Title: Journal of Theoretical Biology 238 Pages: 401-415
  • Peer Reviewed
• [Journal Article] Food Webs : Experts Consuming Families of Experts (2006)
  • Author(s): Axel G. Rossberg ; Hiroyuki Matsuda ; Takashi Amemiya ; Kiminori Itoh
  • Journal Title: Food webs : Experts consuming families of experts, J. Theoretical Biology 241(3) Pages: 552-563
  • Peer Reviewed
• [Journal Article] Estimating trophic link density from quantitative but incomplete diet data (2006)
  • Author(s): Axel G. Rossberg, K Yanagi, Takashi Amemiya, Kiminori Itoh
  • Journal Title: Journal of Theoretical Biology 243 Pages: 261-272
  • Peer Reviewed
• [Journal Article] Development of a two-dimensional electrophoresis method to study soil bacterial diversity (2006)
  • Author(s): Takumi Isshi, Rajendran Narasimmalu, Takashi Amemiya and Kiminori Itoh
  • Journal Title: Soil Science and Plant Nutrition 52 Pages: 601-609
  • NAID: 110006251067
  • Peer Reviewed
• [Journal Article] Food Webs : Experts Consuming Families of Experts (2006)
  • Author(s): A.G.Rossberg, H.Matsuda, T.Amemiya, K.Itoh
  • Journal Title: J.Theoretical Biology Vol.241 Pages: 552-563
• [Journal Article] Estimating trophic link density from quantitative but incomplete diet data (2006)
  • Author(s): A.G.Rossberg, K.Yanagi, T.Amemiya, K.Itoh
  • Journal Title: Journal of Theoretical Biology Vol.243 Pages: 261-272
• [Journal Article] Development of a two-dimensional electrophoresis method to study soil bacterial diversity (2006)
  • Author(s): T.Isshi, N.Rajendran, T.Amemiya, K.Itoh
  • Journal Title: Soil Science and Plant Nutrition Vol.52 Pages: 601-609
  • NAID: 110006251067
• [Journal Article] Some properities of the speciation model for food-web structure - Mechanisms for degree distributions and intervality (2006)
  • Author(s): A.G.Rossberg, H.Matsuda, T.Amemiya, K.Itoh
  • Journal Title: Journal of Theoretical Biology 238 Pages: 401-415
• [Journal Article] 複雑性の科学が捉えた生態環境問題-予測と解決への展望- (2006)
  • Author(s): 雨宮 隆
  • Journal Title: 科学 Vol.76,No.10 Pages: 1047-1052
• [Presentation] キチン培地による殺藻細菌の単離-スキムミルク培地との比較- (2009)
  • Author(s): 柴田賢一, 雨宮隆, 伊藤公紀
  • Organizer: H21 年度日本水産学会春季大会
  • Place of Presentation: 東京海洋大学(東京)
  • Year and Date: 2009-03-29
• [Presentation] Understanding nonlinearity in ecosystems for benefitting sustainable ecosystem services (2009)
  • Author(s): Amemiya T
  • Organizer: International Conference on Sustainability Science 2009 (ICSS2009)
  • Place of Presentation: The University of Tokyo (Tokyo)
  • Year and Date: 2009-02-05
• [Presentation] 湖沼の富栄養化によるアオコ(藍藻類)のパターン形成 (2009)
  • Author(s): 雨宮隆, 芹沢浩, 伊藤公紀
  • Organizer: 第18回非線形反応と協同現象研究会
  • Place of Presentation: 同志社大学(京都)
  • Year and Date: 2009-01-10
• [Presentation] A Rapid Analysis for Environmental Bacterial Community Structure based on Selective Primer Pairs-Two dimensional DNA Gel Electrophoresis Mapping (2009)
  • Author(s): G.-H. Liu, T. Amemiya, K. Itoh
  • Organizer: FEMS 2009-3rd Congress of European Microbiologists
  • Place of Presentation: Gothernborg(Sweden)(発表予定)
• [Presentation] Understanding nonlinearity in ecosystems for benefitting sustainable ecosystem services, The University of Tokyo (Tokyo). (2009)
  • Author(s): T. Amemiya
  • Organizer: International Conference on Sustainability Science 2009 (ICSS2009)
  • Place of Presentation: The University of Tokyo(Tokyo)
• [Presentation] キチン培地による殺藻細菌の単離-スキムミルク培地との比較-,東京海洋大学(東京) (2009)
  • Author(s): 柴田賢一
  • Organizer: H21年度日本水産学会春季大会
  • Place of Presentation: 東京海洋大学(東京)
• [Presentation] 細菌DNA の二次元電気泳動法の開発とその生態リスク評価への応用 (2008)
  • Author(s): 劉国華, 原田智幸, 雨宮隆, 伊藤公紀
  • Organizer: 日本微生物生態学会第24 回大会
  • Place of Presentation: 北海道大学(札幌)
  • Year and Date: 2008-11-26
• [Presentation] 顕微FT-IR によるアオコ(Microcystis 属)の生体内分子組成の解析 (2008)
  • Author(s): 安海日, 柴田賢一, 雨宮隆, 伊藤公紀
  • Organizer: 日本微生物生態学会第24 回大会
  • Place of Presentation: 北海道大学(札幌)
  • Year and Date: 2008-11-26
• [Presentation] 実下水処理場におけるリン除去への影響因子 : 微生物群集変化の長期モニタリングに着目して (2008)
  • Author(s): 砂田尚孝, 雨宮隆, 伊藤公紀
  • Organizer: 日本微生物生態学会第24回大会
  • Place of Presentation: 北海道大学(札幌)
  • Year and Date: 2008-11-26
• [Presentation] Desulfitobacterium sp. PCE1株によるテトラクロロエチレン分解の分子生物学的研究 (2008)
  • Author(s): 坪井隼, Narasimmalu Rajendran, 雨宮隆, 伊藤公紀
  • Organizer: 日本微生物生態学会第24回大会
  • Place of Presentation: 北海道大学(札幌)
  • Year and Date: 2008-11-26
• [Presentation] 大腸菌を用いたバイオアドソープションによる重金属除去 (2008)
  • Author(s): 濱島隆浩, 雨宮隆, 伊藤公紀
  • Organizer: 日本微生物生態学会第24回大会
  • Place of Presentation: 北海道大学(札幌)
  • Year and Date: 2008-11-26
• [Presentation] 細菌DNAの二次元電気泳動法の開発とその生態リスク評価への応用 (2008)
  • Author(s): 劉国華
  • Organizer: 日本微生物生態学会第24回大会
  • Place of Presentation: 北海道大学(札幌)
  • Year and Date: 2008-11-26
• [Presentation] 顕微FT-IRによるアオコ(Microcystis属)の生体内分子組成の解析 (2008)
  • Author(s): 安海日
  • Organizer: 日本微生物生態学会第24回大会
  • Place of Presentation: 北海道大学(札幌)
  • Year and Date: 2008-11-26
• [Presentation] 硫黄酸化細菌による硫黄系悪臭物質の分解の検討 (2008)
  • Author(s): 高木剛志
  • Organizer: 日本微生物生態学会第24回大会
  • Place of Presentation: 北海道大学(札幌)
  • Year and Date: 2008-11-26
• [Presentation] Influence of Organic Matter Sources on Bacterial Biomass in The Surface Sediments of Coastal Lagoon Environments-Stable Isotope and Quantitative PCR Analyses (2008)
  • Author(s): Shun Tsuboi
  • Organizer: The 12^<th> International Symposium on Microbial Ecology
  • Place of Presentation: Cairns, Australia
  • Year and Date: 2008-08-21
• [Presentation] Activities of algicidal bacteria and their influences on microbial communities (2008)
  • Author(s): Shibata K, Amemiya T, Itoh K
  • Organizer: JST Presto Symposium on Mathematical Sciences towards Environmental Problems
  • Place of Presentation: Hokkaido University (Sapporo)
  • Year and Date: 2008-06-11
• [Presentation] 溶藻細菌の溶藻性発現条件 (2008)
  • Author(s): 柴田賢一
  • Organizer: 平成20年度日本水産学会春季大会
  • Place of Presentation: 東海大学(静岡)
  • Year and Date: 2008-03-30
• [Presentation] DNA-塩基ミスマッチの新規検出法 (2008)
  • Author(s): 菊池晋平
  • Organizer: 電気化学会第75回大会
  • Place of Presentation: 山梨大学
  • Year and Date: 2008-03-29
• [Presentation] Probe on Carrier型DNAチップの環境微生物解析への応用 (2008)
  • Author(s): 塚田結香
  • Organizer: 電気化学会第75回大会
  • Place of Presentation: 山梨大学
  • Year and Date: 2008-03-29
• [Presentation] DNA二次元電気泳動法による環境微生物の多様性解析 (2008)
  • Author(s): 原田知幸
  • Organizer: 電気化学会第75回大会
  • Place of Presentation: 山梨大学
  • Year and Date: 2008-03-29
• [Presentation] コケ植物による重金属イオン蓄積のメカニズム (2008)
  • Author(s): 中島啓光
  • Organizer: 電気化学会第75回大会
  • Place of Presentation: 山梨大学
  • Year and Date: 2008-03-29
• [Presentation] 抗原抗体反応に基づく光導波路センシング (2008)
  • Author(s): 中沢香里
  • Organizer: 電気化学会第75回大会
  • Place of Presentation: 山梨大学
  • Year and Date: 2008-03-29
• [Presentation] 微生物を用いた酸性土壌の改善-Paecilomyces lilacinusの中和作用 (2008)
  • Author(s): 高橋久美子
  • Organizer: 電気化学会第75回大会
  • Place of Presentation: 山梨大学
  • Year and Date: 2008-03-29
• [Presentation] 光導波路法に基づいたDNAセンシング (2008)
  • Author(s): 星野絵海
  • Organizer: 電気化学会第75回大会
  • Place of Presentation: 山梨大学
  • Year and Date: 2008-03-29
• [Presentation] 16S rDNAの二次元電気泳動法による土壌細菌の群集構造解析 (2008)
  • Author(s): 吉澤留莉子
  • Organizer: 電気化学会第75回大会
  • Place of Presentation: 山梨大学
  • Year and Date: 2008-03-29
• [Presentation] 溶藻細菌によるアオコの分解に関する研究 (2008)
  • Author(s): 柴田賢一
  • Organizer: 第42回日本水環境学会年会
  • Place of Presentation: 名古屋大学
  • Year and Date: 2008-03-21
• [Presentation] 有機塩素化合物による汚染土壌のDNA二次元電気泳動法による評価 (2008)
  • Author(s): 劉国華
  • Organizer: 第42回日本水環境学会年会
  • Place of Presentation: 名古屋大学
  • Year and Date: 2008-03-21
• [Presentation] 相模湖・津久井湖の藍藻類発生の数理モデル解析 (2008)
  • Author(s): 雨宮隆
  • Organizer: 第55回日本生態学会
  • Place of Presentation: 福岡国際会議場
  • Year and Date: 2008-03-17
• [Presentation] Relative Quantification of Gene Expression During Biodegradation to Select Reliable Reference Genes (2008)
  • Author(s): Qing Chang, Takashi Amemiya, Jianbo Liu and Kiminori Itoh
  • Organizer: 24^<th> Annual International Conference on Soils, Sediments and Water
  • Place of Presentation: University of Massachusetts in Amherst, (USA)
• [Presentation] Influence of Organic Matter Sources on Bacterial Biomass in The Surface Sediments of Coastal Lagoon Environments Stable Isotope and Quantitative PCR Analyses (2008)
  • Author(s): S. Tsuboi, Y. Urushigawa, K. Seto, Takashi Amemiya, Kiminori Itoh
  • Organizer: The 12^<th> International Symposium on Microbial Ecology、Cairns
  • Place of Presentation: Austraria
• [Presentation] Activities of algicidal bacteria and their influences on microbial communities (2008)
  • Author(s): K. Shibata
  • Organizer: JST Presto Symposium on Mathematical Sciences towards Environmental Problems
  • Place of Presentation: Hokkaido University, Sapporo
• [Presentation] Relative Quantification of Gene Expression During Biodegradation to Select Reliable Reference Genes (2008)
  • Author(s): Qing Chang
  • Organizer: 24th Annual International Conference on Soils, Sediments and Water
  • Place of Presentation: University of Massachusetts in Amherst, USA
• [Presentation] Mathematical model of algal blooms with colony formation by phenotypic plasticity (2007)
  • Author(s): T. Amemiya
  • Organizer: Society for Mathematical Biology/Japanese Society for Mathematical Biology Joint Annual Meeting
  • Place of Presentation: San Jose, California, USA
  • Year and Date: 2007-07-31
• [Presentation] 二次元電気泳動法による環境細菌の多様性解析 (2007)
  • Author(s): 大木智行・原田知幸・雨宮隆・伊藤公紀
  • Organizer: 日本化学会第87春季年会
  • Place of Presentation: 関西大学(大阪)
• [Presentation] 藍藻類Microcyst is sp.の細胞内分子組成と生理生態の関連性 (2007)
  • Author(s): 渡辺悠介・榎本隆寿・雨宮隆・伊藤公紀
  • Organizer: 日本化学会第87春季年会
  • Place of Presentation: 関西大学(大阪)
• [Presentation] リアルタイムRT-PCR 法を用いたToluene 誘導下におけるtodC1遺伝子発現の相対定量 (2007)
  • Author(s): 劉建波, Narasimmalu Rajendran, 伊藤公紀, 雨宮隆
  • Organizer: 日本化学会第87春季年会
  • Place of Presentation: 関西大学(大阪)
• [Presentation] Two-Dimensional DNA Electrophoresis Mapping : Comparison of Dominant Bacteria in Trichloroethylene(TCE)-Contaminated Sites (2007)
  • Author(s): G.H. Liu, T. Amemiya, K. Itoh
  • Organizer: 日本化学会第87春季年会
  • Place of Presentation: 関西大学(大阪)
• [Book] Mathematical models for dynamics and management of algal blooms in aquatic ecosystems (2009)
  • Author(s): Amemiya T, Serizawa H, Ssakajo T, Itoh K
  • Publisher: in Aquatic Ecosystem Research Trends. Nova Scientific Publishers, Inc. (in press)
• [Book] よみがえれ! 研究者魂-研究はアイデア, 寄り道, セレンディピティだ- (2009)
  • Author(s): 雨宮隆, 他
  • Publisher: 丸全株式会社(印刷中)
• [Book] Mathematical models for dynamics and management of algal blooms in aquatic ecosystems. in Aquatic Ecosystem Research Trends. (in press) (2009)
  • Author(s): T. Amemiya
  • Publisher: Nova Scientific Publishers, Inc.
• [Book] 生態環境リスクマネジメントの基礎 (2007)
  • Author(s): 浦野紘平・松田裕之共編、伊藤公紀ら(17名)著
  • Publisher: オーム社
• [Book] 生態リスクマネジメントの基礎 (2007)
  • Author(s): 浦野 絋平, 編者
  • Total Pages: 209
  • Publisher: オーム社
• [Patent(Industrial Property Rights)] DNA 検出センサおよびDNA 検出方法 (2007)
  • Inventor(s): 伊藤公紀、菊池晋平
  • Industrial Property Rights Holder: 国立大学法人横浜国立大学
  • Industrial Property Number: 2007-212151
  • Filing Date: 2007-08-16
• [Patent(Industrial Property Rights)] DNA検出センサ (2007)
  • Inventor(s): 伊藤公紀
  • Industrial Property Rights Holder: よこはまTLO
  • Industrial Property Number: 2007-212151
  • Filing Date: 2007-08-25
• [Patent(Industrial Property Rights)] 光導波路型DNA センサおよびDNA 検出方法 (2006)
  • Inventor(s): 伊藤公紀、片岡淳司
  • Industrial Property Rights Holder: 国立大学法人横浜国立大学
  • Industrial Property Number: 2008-070214
  • Filing Date: 2006-09-13
• [Patent(Industrial Property Rights)] 光導波路型DNAセンサおよびDNA検出方法 (2006)
  • Inventor(s): 伊藤 公紀, 片岡 淳司
  • Industrial Property Rights Holder: 横浜国立大学
  • Industrial Property Number: 2006-248665
  • Filing Date: 2006-09-13