Material cycling in plant-associated bacteria by metagenome analysis
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 |
|
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
|
Project Status |
Completed (Fiscal Year 2013)
|
Budget Amount *help |
¥50,700,000 (Direct Cost: ¥39,000,000、Indirect Cost: ¥11,700,000)
Fiscal Year 2013: ¥13,130,000 (Direct Cost: ¥10,100,000、Indirect Cost: ¥3,030,000)
Fiscal Year 2012: ¥13,130,000 (Direct Cost: ¥10,100,000、Indirect Cost: ¥3,030,000)
Fiscal Year 2011: ¥24,440,000 (Direct Cost: ¥18,800,000、Indirect Cost: ¥5,640,000)
|
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 / 植物マイクロビオーム / 根圏微生物 |
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.
|
Report
(4 results)
Research Products
(143 results)
-
[Journal Article] A rice gene for microbial symbiosis, Oryza sativa CCaMK, reduces CH4 flux in a paddy field with low nitrogen input2014
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
Related Report
Peer Reviewed
-
[Journal Article] Low nitrogen fertilization adapts rice root microbiome to low nutrient environment by changing biogeochemical functions2014
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
NAID
URL
Related Report
Peer Reviewed
-
[Journal Article] Effects of elevated carbon dioxide, elevated temperature, and rice growth stage on the community structure of rice root-associated bacteria2014
Author(s)
Takashi Okubo, Takeshi Tokida, Seishi Ikeda, Zhihua Bao, Kanako Tago, Masahito Hayatsu, Hirofumi Nakamura, Hidemitsu Sakai, Yasuhiro Usui, Kentaro Hayashi, Toshihiro Hasegawa, and Kiwamu Minamisawa
-
Journal Title
Microbes Environ.
Volume: in press
NAID
Related Report
Peer Reviewed
-
-
[Journal Article] Arsenic alters uptake and distribution of sulphur in Ptreis vittata2014
Author(s)
Watanabe, T., Kouho, R., Katayose, T., Kitajima, N., Sakamoto, N., Yamaguchi, N., Shinano, T., Yurimoto, H. and Osaki, M.
-
Journal Title
Plant, Cell and Environment
Volume: 37(1)
Issue: 1
Pages: 45-53
DOI
Related Report
Peer Reviewed
-
-
-
[Journal Article] Genome anlaysis suggests that the soil oligotrophic bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aeschynomene indica2013
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
Related Report
Peer Reviewed
-
[Journal Article] Impact of <i>Azospirillum</i> sp. B510 Inoculation on Rice-Associated Bacterial Communities in a Paddy Field2013
Author(s)
Bao, Z., K. Sasaki, T. Okubo, S. Ikeda, M. Anda, E. Hanzawa, K. Kakizaki, T. Sato, H. Mitsui, and K. Minamisawa.
-
Journal Title
Microbes and Environments
Volume: 28
Issue: 4
Pages: 487-490
DOI
NAID
ISSN
1342-6311, 1347-4405
Related Report
Peer Reviewed
-
[Journal Article] Mitigation of nitrous oxide emissions from soils by Bradyrhizobium japonicum inoculation.2013
Author(s)
Itakura M, Uchida Y, Akiyama H, Takada-Hoshino Y, Shimomura Y, Morimoto S, Tago K, Wang Y, Hayakawa C, Uetake Y, Sanchez C, EdaS, Hayatsu M, Minamisawa K.
-
Journal Title
Nature Climate Change
Volume: 3
Issue: 3
Pages: 208-212
DOI
Related Report
Peer Reviewed
-
[Journal Article] The type III Secretion System of Bradyrhizobium japonicum USDA122 mediates symbiotic incompatibility with Rj2 soybean plants2013
Author(s)
Tsukui T, Eda S, Kaneko T, Sato S,Okazaki S, Kakizaki-Chiba K, Itakura M,Mitsui H, Yamashita A, Terasawa K,Minamisawa K
-
Journal Title
Appl Environ Microbiol
Volume: 79
Issue: 3
Pages: 1048-1051
DOI
Related Report
Peer Reviewed
-
-
-
[Journal Article] Identification of Important Volatiles in Fresh and Processing Carrot Varieties: Using Kuroda and Flakee Types2013
Author(s)
Fukuda, T., Tanaka, H., Ihori, H., Okazaki, K., Shinano, T. and Fukumori, Y.
-
Journal Title
Food Science and Technology Research
Volume: 19
Issue: 3
Pages: 497-504
DOI
NAID
ISSN
1344-6606, 1881-3984
Related Report
Peer Reviewed
-
[Journal Article] Mitigation of peroxidative stress for barley exposed to cadmium in the presence of water-extractable organic matter from compost-like materials2013
Author(s)
Tachibana, N., Nagasawa, K., Wang, B., Nishiya, K., Fukushima, M., Kanno, H., Shinano, T. and Okazaki, K.
-
Journal Title
Chemosphere
Volume: 93(4)
Issue: 4
Pages: 695-700
DOI
Related Report
Peer Reviewed
-
-
-
[Journal Article] Effect of phosphorus levels on the protein profiles of secreted protein and root surface protein of rice2013
Author(s)
Shinano, T., Yoshimura, T., Watanabe, T., Unno, Y., Osaki, M., Nanjo, Y. and Komatsu, S.
-
Journal Title
Journal of Proteome Research
Volume: 12(11)
Issue: 11
Pages: 4748-4756
DOI
Related Report
Peer Reviewed
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
[Journal Article] Effect of exogenous phosphatase and phytase activities on organic phosphate mobilization in soils with different phosphate adsorption capacities2012
Author(s)
Maruyama, H., Yamamura, T., Kaneko, Y., Matsui, H., Watanabe, T., Shinano, T., Osaki, M., Wasaki, J.
-
Journal Title
Soil Science and Plant Nutrition
Volume: 58
Issue: 1
Pages: 41-51
DOI
NAID
Related Report
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 conditions2011
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
Related Report
Peer Reviewed
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
[Presentation] N2O emission during nitrogen transformation in soybean rhizosphere2013
Author(s)
Kiwamu Minamisawa, Shoko Inaba, Makoto Moriuchi, Fumio Ikenishi, Yuko Takada-Hoshino, Masahito Hayatsu, Manabu Itakura, Yoko Shiina, Shima Eda, Naohiko Chiba, Chie Katsuyama, Yuichi Suwa, Hisayuki Mitsui
Organizer
3rd International Conference on Nitrification (ICoN3)
Place of Presentation
Tokyo, Japan
Related Report
-
-
-
[Presentation] Rice methanotrophic diazotrophs as non-leguminous rhizobia2013
Author(s)
Kiwamu Minamisawa, Zhihua Bao, Kenji Seki, Dongyan Liu, Susumu Asakawa, Haruko Imaizumi-Anraku, Kazuhiro Sasaki, Seishi Ikeda, Akio Tani, Sachiko Masuda, Ryoji Mitsui, Takashi Okubo
Organizer
18th International Congress on Nitrogen Fixation
Place of Presentation
Miyazaki, Japan
Related Report
-
[Presentation] Genome analysis suggests that the soil oligotrophic bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aeschynomene indica2013
Author(s)
Takashi Okubo, Shohei Fukushima, Manabu Itakura, Kenshiro Oshima, Aphakorn Longtonglang, Neung Teaumroong, Hisayuki Mitsui, Masahira Hattori, Reiko Hattori, Tsutomu Hattori, Kiwamu Minamisawa
Organizer
18th International Congress on Nitrogen Fixation
Place of Presentation
Miyazaki, Japan
Related Report
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
[Presentation] 植物共生微生物と農業2012
Author(s)
池田成志
Organizer
農の周辺講座、有機実業、大牧牧場、共催
Place of Presentation
とかちプラザ(帯広)(招待講演)
Year and Date
2012-03-02
Related Report
-
-
-
-
-
[Presentation] Effects of rice genotype on methane flux and root-associatedmethanotrophs in paddy rice2012
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
Related Report
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
[Presentation] 根の世界2011
Author(s)
信濃卓郎
Organizer
サッポロ農学校2011
Place of Presentation
北大農学部(札幌)
Year and Date
2011-09-15
Related Report
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-