Material cycling in plant-associated bacteria by metagenome analysis

2013 Fiscal Year Final Research Report

• Project/Area Number: 23248052
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Boundary agriculture
• Research Institution: Tohoku University
• Principal Investigator: MINAMISAWA Kiwamu 東北大学, 生命科学研究科, 教授 (70167667)
• Co-Investigator(Kenkyū-buntansha): SHINANO Takuro 独立行政法人農業・食品産業技術総合研究機構, 東北農業研究センター, 農業放射線研究センター長 (20235542) ; IKEDA Seishi 独立行政法人農業・食品産業技術総合研究機構, 北海道農業研究センター, 主任研究員 (20396609) ; YAMASHITA Akifumi 東北大学, 大学院生命科学研究科, 助教 (00573180) ; IKEDA Seishi 独立行政法人農業・食品産業技術総合研究機構, 北海道農業研究センター, 研究員 (40414750)
• Project Period (FY): 2011-04-01 – 2014-03-31
• Keywords: 植物共生微生物 / メタゲノム解析 / 物質代謝 / 植物マークロビオーム / メタン酸化 / 窒素施肥

Research Abstract

We investigated bacterial communities in paddy rice with low (LN), standard (SN) levels of N fertilizer application. Metagenome analysis suggested shifts of bacterial communities between LN and SN root microbiomes. The abundances of functional genes for methane oxidation were significantly increased in LN root microbiome. Plants have mutualistic symbiotic relationships with microorganisms by CCaMK. We examined the effect of an OsCCaMK mutant (NE1115). The CH4 flux of NE1115 in the LN field was significantly higher than that of WT, although no difference was observed in the SN field. qPCR and 13C/15N isotopic determinations suggested that CH4 oxidation and N2 fixation were simultaneously activated in the root of WT rice in the LN field, and both processes are likely controlled by OsCCaMK. Metaproteome and CARD-FISH analyses demonstrated that both processes are mediated by type II methanotrophs inhabiting the vascular bundles and epidermal cells of the rice roots.

Research Products

• [Journal Article] A rice gene for microbial symbiosis, Oryza sativa CCaMK, reduces CH4 flux in a paddy field with low nitrogen input (2014)
  • Author(s): Bao Z, Watanabe A, Sasaki K, Okubo T, Tokida T, Liu D, Ikeda S, Imaizumi-Anraku H, Asakawa S, Sato T, Mitsui H, and Minamisawa K
  • Journal Title: Appl. Environ. Microbiol. Volume: 80 Pages: 1995-2003
  • URL: http://www.ncbi.nlm.nih.gov/pubmed/24441161
  • Peer Reviewed
• [Journal Article] Low nitrogen fertilization adapts rice root microbiome to low nutrient environment by changing biogeochemical functions (2014)
  • Author(s): Ikeda, S., K. Sasaki, T. Okubo, A. Yamashita, K. Terasawa, Z. Bao, D. Liu, T. Watanabe, J. Murase, S. Asakawa, S. Eda, H. Mitsui, T. Sato, and K. Minamisawa
  • Journal Title: Microbes Environ. Volume: 29 Pages: 50-59
  • URL: http://www.ncbi.nlm.nih.gov/pubmed/24463575
  • Peer Reviewed
• [Journal Article] Effects of plant genotype and nitrogen level on bacterial communities (2013)
  • Author(s): Sasaki, K., S. Ikeda, T. Okubo, C. Kisara, T. Sato, and K. Minamisawa
  • Journal Title: Microbes Environ. Volume: 28 Pages: 391-395
  • URL: http://www.ncbi.nlm.nih.gov/pubmed/23979487
  • Peer Reviewed
• [Journal Article] Genome anlaysis suggests that the soil oligotrophic bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aeschynomene indica (2013)
  • Author(s): Okubo, T., S. Fukushima, M. Itakura, K. Oshima, A. Longtonglang, N. Teaumroong, H. Mitsui, M. Hattori, R. Hattori, T. Hattori, and K. Minamisawa
  • Journal Title: Appl. Environ. Microbiol. Volume: 79 Pages: 2542-2551
  • URL: http://www.ncbi.nlm.nih.gov/pubmed/23396330
  • Peer Reviewed
• [Journal Article] Pyrosequence read length of 16S rRNA gene affects phylogenetic assignment of plant-associated bacteria (2012)
  • Author(s): Okubo, T., S. Fukushima, and K. Minamisawa
  • Journal Title: MicrobesEnviron. Volume: 27 Pages: 204-208
  • URL: http://www.ncbi.nlm.nih.gov/pubmed/22791055
  • Peer Reviewed
• [Journal Article] The genotype of the calcium/calmodulin-dependent protein kinase gene (CCaMK) determines bacterial community diversity in rice roots under paddy and upland field conditions (2011)
  • Author(s): Ikeda S., T. Okubo, N. Takeda, M. Banba, K. Sasaki, H. Imaizumi-Anraku, S. Fujihara, Y. Ohwaki, K. Ohshima, Y. Fukuta, S. Eda, H. Mitsui, M. Hattori, T. Sato, T. Shinano, and K. Minamisawa
  • Journal Title: Appl. Environ. Microbiol. Volume: 77 Pages: 4399-4405
  • URL: http://www.ncbi.nlm.nih.gov/pubmed/21551283
  • Peer Reviewed
• [Presentation] 作物根圏における窒素と微生物の相互作用 (2013)
  • Author(s): 南澤究
  • Organizer: 土壌微生物学会2013年度大会
  • Place of Presentation: 東京
  • Year and Date: 20130620-21
  • Invited
• [Presentation] Nitrogen and plant-associated microbes (2012)
  • Author(s): Kiwamu Minamisawa
  • Organizer: The 2nd Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation
  • Place of Presentation: Phuket, Thailand
  • Year and Date: 20121028-1101
  • Invited
• [Presentation] Effects of rice genotype on methane flux and root-associatedmethanotrophs in paddy rice (2012)
  • Author(s): Zhihua Bao, Aya Watanabe, Takashi Okubo, Dongyan Liu, Seishi Ikeda, Kazuhiro Sasaki, Haruko Imaizumi-Anraku, Susumu Asagawa, Tadashi Sato, Hisayuki Mitsui, Kiwamu Minamisawa
  • Organizer: 第28回微生物生態学会
  • Place of Presentation: 豊橋
  • Year and Date: 20120919-22
• [Book] 作物根圏における窒素と微生物の相互作用,土と微生物 67(2) (2013)
  • Author(s): 南澤究、包智華、板倉学
  • Total Pages: 49-53
• [Book] 物質循環のミッシングリンクを解く微生物研究,遺伝、9月号, 67(5) (2013)
  • Author(s): 南澤究
  • Total Pages: 544-546