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Molecular Ecology of Non-Extremophilic Archaea in Deep Ocean

Research Project

Project/Area Number 18201003
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Environmental dynamic analysis
Research InstitutionThe University of Tokyo

Principal Investigator

KOGURE Kazuhiro  The University of Tokyo, 海洋研究所, 教授 (10161895)

Co-Investigator(Kenkyū-buntansha) OGAWA Hiroshi  東京大学, 海洋研究所, 准教授 (50260518)
SUNAMURA Michinari  東京大学, 大学院・理学系研究科, 助教 (90360867)
KAWARABAYASHI Hiroshi  独立行政法人産業技術総合研究所, セルエンジニアリング研究部門, 主任研究員 (90195165)
HAMASAKI Kouji  東京大学, 海洋研究所, 准教授 (80277871)
TSUNEDA Satoshi  早稲田大学, 先進理工学部, 教授 (30281645)
NISHIMURA Masahiko  東京大学, 海洋研究所, 助教 (10242174)
浦川 秀敏  東京大学, 海洋研究所, 准教授 (90370262)
千浦 博  国際基督教大学, 教養学部, 教授 (00103698)
Research Collaborator 井上 健太郎  東京大学, 海洋研究所, 大学院学生
Project Period (FY) 2006 – 2008
Project Status Completed (Fiscal Year 2008)
Budget Amount *help
¥52,650,000 (Direct Cost: ¥40,500,000、Indirect Cost: ¥12,150,000)
Fiscal Year 2008: ¥12,220,000 (Direct Cost: ¥9,400,000、Indirect Cost: ¥2,820,000)
Fiscal Year 2007: ¥11,700,000 (Direct Cost: ¥9,000,000、Indirect Cost: ¥2,700,000)
Fiscal Year 2006: ¥28,730,000 (Direct Cost: ¥22,100,000、Indirect Cost: ¥6,630,000)
Keywords海洋中深層 / 古細菌 / ゲノム解析 / 窒素代謝 / 有機物代謝
Research Abstract

近年の研究から、海洋の中心層には古細菌が広く分布することが分かってきた。1000m以深では、数的には原核生物のうちの半数近くを占めることが見出されてきたが、今のところ分離株が全くなく、その生態、系統、物質循環に対する寄与などについては殆ど未知の状況である。これらの環境は低温、高圧、貧栄養で特徴付けられるが、こうした環境は従来から知られていた古細菌の好熱性、好塩性、嫌気性などの性質からはずれがある。従ってこれらを非極限性の古細菌と呼ぶことにする。本研究はこの一群を中心とした古細菌に対する学際的研究である。
本研究では様々な課題を扱ったが、最大の成果は外洋域中心層から複数の古細菌を分離し、その系統的位置づけおよび性情等についての検討を開始できたことである。これは我々の知る限り、世界で初めてのことである。さらに、それが系統的には好塩性の古細菌に近縁であることが分かったことから、非極限性古細菌群集の起源や古細菌の進化上の広がりなどについて新たな仮説を提示できる段階に至った。

Report

(4 results)
  • 2008 Annual Research Report   Final Research Report ( PDF )
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • Research Products

    (42 results)

All 2009 2008 2007 2006

All Journal Article (30 results) (of which Peer Reviewed: 23 results) Presentation (10 results) Book (2 results)

  • [Journal Article] Hollow-Fiber Membrane Chamber as a Device for In Situ Environmental Cultivation2009

    • Author(s)
      Aoi Y, Kinoshita T, Hata T, Ohta H, Obokata H, Tsuneda S
    • Journal Title

      Applied and Environmental Microbiology 75

      Pages: 3826-3833

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific2008

    • Author(s)
      Taniguchi, A, Hamasaki, K
    • Journal Title

      Environmental Microbiology 10

      Pages: 1007-1017

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] First cultivation and ecological investigation of a bacterium affiliated with the candidate phylum OP5 from hot springs2008

    • Author(s)
      Mori K, Sunamura M, Yanagawa K, Ishibashi J, Miyoshi Y, Iino T, Suzuki K, Urabe T
    • Journal Title

      Applied and Environmental Microbiology 74

      Pages: 6223-6229

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Low temperature decreases the phylogenetic diversity of ammonia-oxidizing archaea and bacteria in aquarium biofiltration system2008

    • Author(s)
      Urakawa H, Tajima Y, Numata Y, Tsuneda S
    • Journal Title

      Applied and Environmental Microbiology 74

      Pages: 894-900

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Identification of the bacterial community involved in methane-dependent denitrification in activated sludge using DNA stable-isotope probing2008

    • Author(s)
      Osaka T, Ebie Y, Tsuneda S, Inamori Y
    • Journal Title

      FEMS Microbiology Ecology 64

      Pages: 494-506

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Retrieval of entire genes from environmental DNA by inverse PCR with pre-amplification of target genes using primers containing locked nucleic acids2008

    • Author(s)
      Yamada K, Terahara T, Kurata S, Yokomaku T, Tsuneda S, Harayama S
    • Journal Title

      Environmental Microbiology 10

      Pages: 978-987

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Rapid DNA chemical ligation for amplification of RNA and DNA signal2008

    • Author(s)
      Abe H, Kondo Y, Jinmei H, Abe N, Furukawa K, Uchiyama A, Tsuneda S, Aikawa K, Matsumoto I, Ito Y
    • Journal Title

      Bioconjugate Chemistry 19

      Pages: 327-333

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Production of dissolved and particulate organic matter by the reef-building corals Porites cylindrica and Acropora pulchra2008

    • Author(s)
      Tanaka Y, Miyajima T, Koike I, Hayashibara T, Ogawa H
    • Journal Title

      Bulletin of Marine Science 82

      Pages: 237-245

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Microbial activity and accumulation of organic matter in the burrow of the mud shrimp2008

    • Author(s)
      Kinoshita K, Wada M, Kogure K, Furota T
    • Journal Title

      Upogebia Major (Crustacea : Thalassinidea). Marine Biology 153

      Pages: 277-283

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Automatic counting of FISH-labeled microbes by an LED illuminated detecting apparatus2008

    • Author(s)
      Nishimura M, Shimakita T, Matsuzaki T, Tashiro Y, Kogure K
    • Journal Title

      Fisheries Science 74

      Pages: 405-410

    • NAID

      10020478363

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Automatic counting of FISH-labeled microbes by a LED illuminated detecting apparatus/2008

    • Author(s)
      Nishimura N, Shimakita T, Matsuzaki T, Tashiro Y, Kogure K.
    • Journal Title

      Fisheried Science 74

      Pages: 405-410

    • NAID

      10020478363

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Microbial activity and accumulation of organic matter in the burrow of the mud shrimp, Upogebia major (Crustancea:Thalassinidea)2008

    • Author(s)
      Kinishita K, Wada M, Kogure K, Furuta T
    • Journal Title

      Marine Biology 153

      Pages: 277-283

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] First cultivation and ecological investigation of a bacterium affiliated with the candidate phylum OP5 from hot springs2008

    • Author(s)
      Mori K, Sunamura M, others
    • Journal Title

      Applied and Environmental Microbiology 74

      Pages: 6223-6229

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] New Methodologies for Isolation and Cultivation of Unculturable Microorganisms:Hollow Fiber Membrane Chamber and Microbial Cell Chromatiguraphy2008

    • Author(s)
      Aoi Y, Kaneko Y, Obotaka H, Kinoshita T, Hata T, Tsuneda S
    • Journal Title

      Abstracts of the General Meeting of the American Society for Microbiology 108

      Pages: 338-339

    • Related Report
      2008 Annual Research Report
  • [Journal Article] Identification of the bacterial community involved in methae-dependent denitrification in activated slung using DNA stable-isotope probing2008

    • Author(s)
      Osaka T, Ebie Y, Tsuneda S, Inamori Y
    • Journal Title

      FEMS Microbiology Ecology 64

      Pages: 494-506

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Retrieval of entire genes from environmental DNA by inverse PCR with pre-amplification of Target genes using primers cintaining locked nucleic acids2008

    • Author(s)
      Yamada K, Terahara T, Kimata S, Yokomaku T, Tsuneda S, Harayama S
    • Journal Title

      Environmental Microbiology 10

      Pages: 978-987

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific2008

    • Author(s)
      Taniguchi A, hamasaki K
    • Journal Title

      Environmental Microbiology 10

      Pages: 1007-1017

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Production of dissolved and particulate organic matter by the reef-building corals Porites cylindrics and Acropora pulchra2008

    • Author(s)
      Tanaka Y, Miyajima T, Koike I, hayashibara T, Ogawa H
    • Journal Title

      Bulletin of marine Science 82

      Pages: 237-245

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Low temperature decreases the phylogenetic diversity of ammonia-oxidizing archaea and bacteria in aquarium biofiltration system2008

    • Author(s)
      Urakawa, H. Tajima, Y. Numata, Y .Tsuneda S.
    • Journal Title

      Applied and Environlhental Microbiology 74

      Pages: 894-900

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off Taketomi Island, Japan2007

    • Author(s)
      Hirayama H, Sunamura M, Takai K, Nunoura T, Noguchi T, Oida H, Furushima Y, Yamamoto H, Oomori T, Horikoshi K
    • Journal Title

      Applied and Environmental Microbiology 73

      Pages: 7642-7656

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Actively growing bacteria in the Inland Sea of Japan, identified by combined bromodeoxyuridine immunocapture and denaturing gradient gel electrophoresis2007

    • Author(s)
      Hamasaki K, Taniguchi A, Tada Y, Long RA, Azam F
    • Journal Title

      Applied and Environmental Microbiology 73

      Pages: 2787-2798

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Separation of marine bacteria according to buoyant density by use of the density-dependent cell sorting method2007

    • Author(s)
      Inoue K, Nishimura M, Nayak BB, Kogure K
    • Journal Title

      Applied and Environmental Microbiology 73

      Pages: 1049-1053

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Culture-dependent and-independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off TaketomiIsland,Japan2007

    • Author(s)
      Hirayama, H. Sunamura, M. and others(10authors)
    • Journal Title

      Applied and Environmental Microbiology 73

      Pages: 7642-7656

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Buoyant density of marine bacteria using the density-dependent cell sorting method2007

    • Author(s)
      Inoue, K. Nishimura, M. Nayak, B. B.Kogure, K.
    • Journal Title

      Applied and Environmental Microbiology 73

      Pages: 1049-1053

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Buoyant density of marine bacteria using density-dependent cell sorting method.2007

    • Author(s)
      Inoue K., M.Nishimura, B.B.Nayak, K.Kogure
    • Journal Title

      Applied and Enviornmental Microbiology 73

      Pages: 1049-1053

    • Related Report
      2006 Annual Research Report
  • [Journal Article] An automatic counter of marine bacteria with LED illumination.2006

    • Author(s)
      Nishimura, M., E.Kamiya, K.Kogure
    • Journal Title

      Fisheries Science 72

      Pages: 723-727

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Determination of picomolar levels of platinum in estuarine waters : A comparison of cathodic stripping voltammetry and isotope dilution-inductivity coupled plasma mass spectrometry.2006

    • Author(s)
      Obata, H, T.Yoshida, H.Ogawa
    • Journal Title

      Analytica Chimica Acta 580

      Pages: 32-38

    • Related Report
      2006 Annual Research Report
  • [Journal Article] MAolecular ecology of marine microorganisms.2006

    • Author(s)
      Urakawa, H.
    • Journal Title

      Nippon Suisan Gakkaishi 72

      Pages: 811-814

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Real-time quantitative LAMP (loop-mediated isothermal amplification of DNA) as a simple method for monitoring ammonia-0xidizing bacteria2006

    • Author(s)
      Aoi, Y., M.Hosogai, S.Tsuneda
    • Journal Title

      journal of Biotechnology 125

      Pages: 484-491

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Comparison of bromodeoxyuridine immunoassay with tritiated thymidine radioassay for measuring bacterial productivity in oceanic waters.2006

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

      Journal of Oceanography 62

      Pages: 793-799

    • NAID

      10018405641

    • Related Report
      2006 Annual Research Report
  • [Presentation] Diversity of active microbial communities in surface seawaters along a north-south transect in the 2009. Diversity of active microbial communities in surface seawaters along a north-south transect in the South Pacific Ocean2009

    • Author(s)
      Hamasaki K, Taniguchi A
    • Organizer
      at International Census of Marine Microbes 454 User Spring Meeting
    • Place of Presentation
      At Woods Hole, USA
    • Year and Date
      2009-04-07
    • Related Report
      2008 Final Research Report
  • [Presentation] Biogeography, a case for microbes in marine environments2008

    • Author(s)
      Kogure, K
    • Organizer
      at Evolutionary Biology and Biodiversity Conservations
    • Place of Presentation
      Sao Paulo, Brazil
    • Year and Date
      2008-11-10
    • Related Report
      2008 Final Research Report
  • [Presentation] Biogeography, a case for microbes in marine environments2008

    • Author(s)
      小暮啓一
    • Organizer
      Evolutionary Biology and Biodiversity Conservation
    • Place of Presentation
      サンパウロ、ブラジル
    • Year and Date
      2008-11-10
    • Related Report
      2008 Annual Research Report
  • [Presentation] Biogeography, a case for microbes in marine environments2008

    • Author(s)
      小暮啓一
    • Organizer
      第12回国際微生物生態学シンポジウム
    • Place of Presentation
      ケアンズ、オーストラリア
    • Year and Date
      2008-08-19
    • Related Report
      2008 Annual Research Report
  • [Presentation] 海洋性古細菌の鉛直的な群集構造の変動と栄養特性2008

    • Author(s)
      井上健太郎、木暮一啓
    • Organizer
      第21 回 日本Archaea 研究会講演会
    • Place of Presentation
      沖縄
    • Year and Date
      2008-07-05
    • Related Report
      2008 Final Research Report
  • [Presentation] New methodologies for isolation and cultivation of unculturable microorganisms : Hollow fiber membrane chamber and microbial cell chromatography2008

    • Author(s)
      Aoi, Y. ; Kaneko, Y. ; Obokata, H. ; Kinoshita, T. ; Hata, T. ; Tsuneda, S.
    • Organizer
      at 108th General Meeting of the American Society for Microbiology
    • Place of Presentation
      Boston, USA
    • Year and Date
      2008-06-03
    • Related Report
      2008 Final Research Report
  • [Presentation] Biogeography, a case for microbes in marine environments2008

    • Author(s)
      小暮啓一
    • Organizer
      海洋微生物センサス[ICOMM(International Census of marine Microbes)]
    • Place of Presentation
      アムステルダム、オランダ
    • Year and Date
      2008-05-27
    • Related Report
      2008 Annual Research Report
  • [Presentation] Bactsphere, a new concept on bacterial surface2008

    • Author(s)
      Kogure, K
    • Organizer
      49th Microbial Society of Korea General Meeting
    • Place of Presentation
      Dejeon, Korea
    • Year and Date
      2008-05-16
    • Related Report
      2008 Final Research Report
  • [Presentation] Biogeography, a case for microbes in marine environments2008

    • Author(s)
      小暮啓一
    • Organizer
      第48回韓国微生物学会総会および2008年度微生物国際シンポジウム
    • Place of Presentation
      Daejeon、韓国
    • Year and Date
      2008-05-16
    • Related Report
      2008 Annual Research Report
  • [Presentation] New serial transducing particles-Are we still missing the Essentials2007

    • Author(s)
      Hiroshi X.Chiura and Branko Velimirov
    • Organizer
      International Symposium on Microbial Ecology, Asian 2007
    • Place of Presentation
      愛媛大学
    • Year and Date
      2007-09-16
    • Related Report
      2007 Annual Research Report
  • [Book] 海洋生物の連鎖2006

    • Author(s)
      木暮一啓
    • Total Pages
      340
    • Publisher
      東海大学出版会
    • Related Report
      2008 Final Research Report
  • [Book] 海洋生物の連鎖2006

    • Author(s)
      木暮一啓(編集)
    • Total Pages
      340
    • Publisher
      東海大学出版社
    • Related Report
      2006 Annual Research Report

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Published: 2006-04-01   Modified: 2016-04-21  

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