Diversity and dynamics of unexplored marine microbiome described by massively parallel sequenceing

• Project/Area Number: 21200029
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research a proposed research project)
• Allocation Type: Single-year Grants
• Research Field: Environmental dynamic analysis; 基礎ゲノム科学
• Research Institution: The University of Tokyo
• Principal Investigator: HAMASAKI Koji 東京大学, 大気海洋研究所, 准教授 (80277871)
• Research Collaborator: MIKI Takeshi 国立台湾大学, 海洋研究所, 准教授
• Project Period (FY): 2009 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥31,980,000 (Direct Cost: ¥24,600,000、Indirect Cost: ¥7,380,000); Fiscal Year 2011: ¥10,270,000 (Direct Cost: ¥7,900,000、Indirect Cost: ¥2,370,000); Fiscal Year 2010: ¥10,400,000 (Direct Cost: ¥8,000,000、Indirect Cost: ¥2,400,000); Fiscal Year 2009: ¥11,310,000 (Direct Cost: ¥8,700,000、Indirect Cost: ¥2,610,000)
• Keywords: 微生物 / 多様性 / 西部北太平洋 / 細菌群集構造 / 時系列観測 / 454シーケンス / 国際生物センサス / 微生物多様性 / BrdU

Research Abstract

In this study, ocean basin-scale dynamics of microbial communities has been revealed with the use of 454 pyrosequencing technology and nucleoside tracer techniques. Although there are some caveats against insufficient read length and diversity inflation due to sequencing errors, deep sequencing of 16S rRNA genes shows the presence of diverse rare taxa and their active growth in seawater environments.

Research Products

• [Journal Article] Growth and succession patterns of major phylogenetic groups of marine bacteria during a mesocosm diatom bloom (2012)
  • Author(s): Tada, Y, Taniguchi, A., Sato-Takabe, Y. and Hamasaki, K.
  • Journal Title: J. Oceanoer. Volume: (In press)
• [Journal Article] 光エネルギーをめぐる複雑系:海洋における微生物群集の動態と光栄養 (2012)
  • Author(s): 浜崎恒二
  • Journal Title: 遺伝 Volume: 66巻第4号
• [Journal Article] メタゲノミクスで見る微生物多様性 (2011)
  • Author(s): 谷口亮人, 金子亮, 浜崎恒二
  • Journal Title: 遺伝 Volume: 65巻第3号 Pages: 61-67
• [Journal Article] Differing Growth Responses of Major Phylogenetic Groups of Marine Bacteria to Natural Phytoplankton Blooms in the Western North Pacific Ocean (2011)
  • Author(s): Tada, Y, A. Taniguchi, I. Nagao, T. Miki. M. Uematsu, A. Tsuda, and K. Hamasaki
  • Journal Title: Appl Environ Microbiol Volume: 77 Pages: 4055-4065
• [Journal Article] Seasonal variations in the community structure of actively growing bacteria in neritic waters of Hiroshima Bay, western Japan (2011)
  • Author(s): Taniguchi, A., Tada, Y and Hamasaki. K.
  • Journal Title: Microb. Environ. Volume: 26(4) Pages: 339-46
  • NAID: 10029978202
• [Journal Article] Community structure of ammonia-oxidizing marine archaea differs by depth of collection and temperature of cultivation (2011)
  • Author(s): Idichi, M. and Hamasaki K.
  • Journal Title: J. Oceanogr. Volume: 67 Pages: 739-745
  • NAID: 10030228172
• [Journal Article] Seasonal Variations in the Community Structure of Actively Growing Bacteria in Neritic Waters of Hiroshima Bay, Western Japan (2011)
  • Author(s): Akito Taniguchi, Yuya Tada, Koji Hamasaki
  • Journal Title: Microbes and Environments Volume: 26 Issue: 4 Pages: 339-346
  • DOI: 10.1264/jsme2.ME11212
  • NAID: 10029978202
  • ISSN: 1342-6311, 1347-4405
  • Peer Reviewed
• [Journal Article] Community structure of ammonia-oxidizing marine archaea differs by depth of collection and temperature of cultivation (2011)
  • Author(s): Minoru Idichi, Koji Hamasaid
  • Journal Title: J.Oceanogr. Volume: 67 Issue: 6 Pages: 739-745
  • DOI: 10.1007/s10872-011-0066-8
  • Peer Reviewed
• [Journal Article] Phylotype-specific growth rates of marine bacteria measured by bromodeoxyuridine immunocytochemistry and fluorescence in situ hybridization (2010)
  • Author(s): Tada, Y., A. Taniguchi, and K. Hamasaki
  • Journal Title: Aauat. Microb. Ecol. Volume: 59 Pages: 229-238
• [Journal Article] Psychrosphaera saromensis gen. nov., sp. Nov., within the family Pseudalteromonadaceae, isolated from Lake Saroma Japan (2010)
  • Author(s): Sanghwa Park, Susumu Yoshizawa, Koji Hamasaki. Kazuhiro Kogure, Akira Yokota
  • Journal Title: The Journal of General and Applied Microbiology Volume: 56 Pages: 475-480
• [Journal Article] Phylotype-specific growth rates of marine bacteria measured by bromodeoxyuridine immunocytochemistry and fluorescence in situ hybridization (2010)
  • Author(s): Tada, Y., A.Taniguchi, K.Hamasaki
  • Journal Title: Aquat.Microb.Ecol. Volume: 59 Pages: 229-238
  • Peer Reviewed
• [Journal Article] Phylotype-specific productivity of marine bacterial populations in eutrophic seawater, as revealed by bromodeoxyuridine immunocytochemistry combined with fluorescence in situ hybridization (2009)
  • Author(s): Tada, Y., Taniguchi, A. and Hamasaki, K.
  • Journal Title: Microb. Environ. Volume: 24 Pages: 315-321
  • NAID: 10025921246
• [Journal Article] Analysis of nanoplankton community structure using flow sorting and molecular techniques (2009)
  • Author(s): Yoshida, N, Nishimura, M., Inoue, K., Yoshizawa, S, Kamiya, E., Taniguchi, A., Hamasaki, K. and Kogure, K.
  • Journal Title: Microb. Environ Volume: 24 Pages: 297-304
  • NAID: 10025921150
• [Presentation] Bacterial community structures in relation to multiple environmental factors in the Kuroshio-Oyashio transition of the western North Pacific (2012)
  • Author(s): Hamasaki, K., K. Watanabe, Y. Tada, K. Takahashi, H. Saito, T. Miki
  • Organizer: ASLO aquatic science meeting
  • Place of Presentation: Shiga
  • Year and Date: 2012-07-12
• [Presentation] 西部北太平洋の生態系/物質循環南北比較研究 : 観測定点K2、S1の中深層における細菌群集の季節変動 (2012)
  • Author(s): 金子亮・内宮万里央・福田秀樹・鈴木翔太郎・渡辺敬吾・小川浩史・永田俊・本多牧生・濱崎恒二
  • Organizer: 日本海洋学会春季大会
  • Place of Presentation: つくば
  • Year and Date: 2012-03-29
• [Presentation] 黒潮続流域における細菌群集構造 (2012)
  • Author(s): 渡辺敬吾・多田雄哉・神谷英里子・西部悠太・古谷研・高橋一生・斎藤宏明・浜崎恒二
  • Organizer: 日本海洋学会春季大会
  • Place of Presentation: つくば
  • Year and Date: 2012-03-29
• [Presentation] 西部北太平洋の生態系/物質循環南北比較研究:観測定点K2、S1の中深層における細菌群集の季節変動 (2012)
  • Author(s): 金子亮・内宮万里央・福田秀樹・鈴木翔太郎・渡辺敬吾・小川浩史・永田俊・本多牧生・〓崎恒二
  • Organizer: 日本海洋学会春季大会
  • Place of Presentation: つくば
  • Year and Date: 2012-03-29
• [Presentation] 黒潮続流域における微生物群集の動態(1)-微生物現存量と有機物量- (2011)
  • Author(s): 浜崎恒二・多田雄哉・神谷英里子・西部悠太・古谷研・高橋一生・一宮睦雄・中町美和・筧茂穂・斎藤宏明
  • Organizer: 日本水産学会秋季大会
  • Place of Presentation: 長崎
  • Year and Date: 2011-09-30
• [Presentation] 黒潮続流域における微生物群集の動態(2)-細菌生産と被捕食速度- (2011)
  • Author(s): 浜崎恒二・多田雄哉・神谷英里子・西部悠太・古谷研・高橋一生・一宮睦雄・中町美和・筧茂穂・斎藤宏明
  • Organizer: 日本水産学会秋季大会
  • Place of Presentation: 長崎
  • Year and Date: 2011-09-30
• [Presentation] 海洋における微生物群集の動態と光栄養 (2011)
  • Author(s): 浜崎恒二, 佐藤由季, 谷口亮人
  • Organizer: 日本地球惑星科学連合大会
  • Place of Presentation: 幕張
  • Year and Date: 2011-05-26
• [Presentation] Phylogenetic Position of Oceanic Nitrifiers Demonstrated by Enrichment Cultures (2011)
  • Author(s): Ijichi, M. and K. Hamasaki
  • Organizer: Korea-Japan Symposium on Microbial Ecology
  • Place of Presentation: Gwandju
  • Year and Date: 2011-05-12
• [Presentation] Bacterial community response to the supply of dimethylsulfoniopropionate (DMSP) in the Southern Ocean (2011)
  • Author(s): Okamoto, A., Y. Tada, N. Kasamatsu-Takasawa, R. Kaneko, K. Hamasaki
  • Organizer: Korea-Japan Symposium on Microbial Ecology
  • Place of Presentation: Gwandju
  • Year and Date: 2011-05-12
• [Presentation] 「超並列シーケンスによる海洋微生物の多様性解析」CBDポスト2010年に向けた微生物多様性研究 (2011)
  • Author(s): 浜崎恒二
  • Organizer: 第58回日本生態学会企画集会
  • Place of Presentation: 札幌
  • Year and Date: 2011-03-12
• [Presentation] 超並列シーケンスによる海洋微生物の多様性解析 (2011)
  • Author(s): 浜崎恒二
  • Organizer: 第58回日本生態学会札幌大会企画集会「微生物の多様性」
  • Place of Presentation: 札幌コンベンションセンター
  • Year and Date: 2011-03-12
• [Presentation] Active growth of rare microbes in the ocean (2010)
  • Author(s): Hamasaki, K.
  • Organizer: ISME meeting
  • Place of Presentation: Seattle
  • Year and Date: 2010-08-25
• [Presentation] Active growth of rare microbes in the ocean (2010)
  • Author(s): 浜崎恒二
  • Organizer: ISME2010 meeting
  • Place of Presentation: Seattle, USA
  • Year and Date: 2010-08-23
• [Presentation] Microbial degradation and the fate of salps carcasses in the western North Pacific (2010)
  • Author(s): Hamasaki, K., Sugimoto, Y., Tada Y. and J. Nishikawa
  • Organizer: Asia Oceania Geoscience Society 2010 meeting
  • Place of Presentation: Hyderabad
  • Year and Date: 2010-07-07
• [Presentation] Phylotype-specific productivity of marine bacteria in the western North Pacific, measured by bromodeoxyuridine immunocytochemistry and fluorescence in situ hybridization (2010)
  • Author(s): Tada, Y., A. Taniguchi, and K. Hamasaki
  • Organizer: Asia Oceania Geoscience Society 2010 meeting
  • Place of Presentation: Hyderabad
  • Year and Date: 2010-07-07
• [Presentation] 集積巻養で明らかになった海洋性アンモニア酸化古細菌の生理・生態的特徴 (2010)
  • Author(s): 伊知地稔・浜崎恒二
  • Organizer: 日本海洋学会春季大会
  • Place of Presentation: 東京
  • Year and Date: 2010-03-28
• [Presentation] 「海洋生態系における微生物の役割 : 微生物海洋学への展望」微生物群集と生態系をむすぶ : 微生物多様性と生態系の多様性の視点から (2010)
  • Author(s): 浜崎恒二
  • Organizer: 第57回日本生態学会企画集会
  • Place of Presentation: 東京
  • Year and Date: 2010-03-16
• [Presentation] 海洋生態系における微生物の役割:微生物海洋学への展望 (2010)
  • Author(s): 浜崎恒二
  • Organizer: 微生物群集と生態系をむすぶ:微生物多様性と生態系の多様性の視点から(第57回日本生態学会企画集会)
  • Place of Presentation: 東京大学
  • Year and Date: 2010-03-16
• [Presentation] 微生物多様性研究の新展開:稀少微生物圏の解析と群集形成の要因について (2009)
  • Author(s): 浜崎恒二
  • Organizer: 東京大学海洋研シンポジウム「新しい海洋区分の創設に向けた生物地球化学と生態学の統合研究」
  • Place of Presentation: 東京大学
  • Year and Date: 2009-12-22
• [Presentation] 「微生物多様性研究の新展開 : 稀少微生物圏の解析と群集形成の要因について」新しい海洋区分の創設に向けた生物地球化学と生態学の統合研究 (2009)
  • Author(s): 浜崎恒二
  • Place of Presentation: 東京
  • Year and Date: 2009-12-21
• [Presentation] 「超並列シーケンスが描く海洋微生物圏の多様性とダイナミクス」環境細菌の動態研究から見える新しい微生物機能 (2009)
  • Author(s): 浜崎恒二
  • Organizer: 東京大学生物生産工学研究センターシンポジウム
  • Place of Presentation: 東京
  • Year and Date: 2009-12-11
• [Presentation] 超並列シーケンスが描く海洋微生物圏の多様性とダイナミクス (2009)
  • Author(s): 浜崎恒二
  • Organizer: 東大生物生産工学センターシンポジウム「環境細菌の動態研究から見える新しい微生物機能」
  • Place of Presentation: 東京大学
  • Year and Date: 2009-12-11
• [Presentation] 南太平洋から南大洋における稀少微生物圏の多様性 (2009)
  • Author(s): 浜崎恒二
  • Organizer: 日本微生物生態学会秋季大会
  • Place of Presentation: 広島大学
  • Year and Date: 2009-11-25
• [Presentation] 南太平洋から南大洋における稀少微生物圏の多様性 (2009)
  • Author(s): 浜崎恒二, 谷口亮人
  • Organizer: 日本微生物生態学会
  • Place of Presentation: 広島
  • Year and Date: 2009-11-15
• [Presentation] 「ハロゲン化ヌクレオシドを用いた海洋微生物の生態研究」宇宙・地球化学と分析化学 (2009)
  • Author(s): 浜崎恒二
  • Organizer: 第58回日本分析化学会年会特別シンポジウム
  • Place of Presentation: 札幌
  • Year and Date: 2009-09-24
• [Presentation] ハロゲン化ヌクレオシドを用いた海洋微生物の生態研究 (2009)
  • Author(s): 浜崎恒二
  • Organizer: 日本分析化学会第58年会「特別シンポ1:宇宙・地球化学と分析化学」
  • Place of Presentation: 北海道大学
  • Year and Date: 2009-09-24
• [Presentation] Drastic change of the biomass and productivity of major subgroups of bacteria along a steep environmental gradient in the Southern Ocean frontal systems (2009)
  • Author(s): Tada, Y, Taniguchi A, Hamasaki, K
  • Organizer: SCAR Biology Symposium
  • Place of Presentation: Sapporo
  • Year and Date: 2009-07-27
• [Presentation] Identification of actively growing bacteria in seawater supplemented with dimethylsulfoniopropionate (DMSP) in the Southern Ocean (2009)
  • Author(s): Okamoto, A, Tada, Y, Kasamatsu, N, Hamasaki, K
  • Organizer: SCAR Biology Symposium
  • Place of Presentation: Sapporo
  • Year and Date: 2009-07-27
• [Presentation] Massively Parallel Sequencing of 16S rRNA V6 Regions Revealed the Diversity of Active-but-Rare Microbial Populations in Oceanic Pelagic Ecosystems (2009)
  • Author(s): Hamasaki, K, Taniguchi, A
  • Organizer: 1st Korea-Japan Symposium on Microbial Ecology
  • Place of Presentation: Jeju
  • Year and Date: 2009-05-29
• [Presentation] Massively Parallel Sequencing of 16S rRNA V6 Regions Revealed the Diversity of Active-but-Rare Microbial Populations in Oceanic Pelagic Ecosystems (2009)
  • Author(s): 浜崎恒二
  • Organizer: 1st Korea-Japan Symposium on Microbial Ecology
  • Place of Presentation: 済州島,大韓民国
  • Year and Date: 2009-05-29
• [Presentation] Diversity of active microbial communities in the South Pacific Ocean revealed by bromodeoxyuridine labeling and 454 tag sequencing technology (2009)
  • Author(s): Hamasaki, K, Taniguchi, A
  • Organizer: DNA Barcoding of Marine Biodiversity (MarBOL)
  • Place of Presentation: Tokyo
  • Year and Date: 2009-05-21
• [Presentation] Diversity of active microbial communities in the South Pacific Ocean revealed by bromodeoxyuridine labeling and 454 tag sequencing technology (2009)
  • Author(s): 浜崎恒二
  • Organizer: DNA Barcoding of Marine Biodiversity (MarBOL) Symposium
  • Place of Presentation: 東京大学
  • Year and Date: 2009-05-21
• [Presentation] Diversity of active microbial communities in surface seawaters along a north-south transect in the South Pacific Ocean (2009)
  • Author(s): 浜崎恒二
  • Organizer: International Census of Marine Microbes 454 Users Spring Meeting
  • Place of Presentation: Woods Hole Marine Biology Laboratory, USA
  • Year and Date: 2009-04-06
• [Presentation] Diversity of active microbial communities in surface seawaters along a north-south transect in the South Pacific Ocean (2009)
  • Author(s): Hamasaki, K, Taniguchi, A
  • Organizer: International Census of Marine Microbes 454 Users Spring Meeting
  • Place of Presentation: Woods Hole