2005 Fiscal Year Final Research Report Summary
Phylogenetic study on microbial communities at various habitats in paddy field ecosystem
| Project/Area Number |
15380051
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Plant nutrition/Soil science
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| Research Institution | Nagoya University |
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Principal Investigator |
KIMURA Makoto Nagoya University, Graduate School of Bioagricultural Sciences, Professor, 大学院・生命農学研究科, 教授 (20092190)
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| Co-Investigator(Kenkyū-buntansha) |
ASAKAWA Susumu Nagoya University, Graduate School of Bioagricultural Sciences, Associate Professor, 大学院・生命農学研究科, 助教授 (50335014)
MURASE Jun Nagoya University, Graduate School of Bioagricultural Sciences, Assistant Professor, 大学院・生命農学研究科, 助手 (30285241)
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| Project Period (FY) |
2003 – 2005
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| Keywords | Paddy soil ecosystem / PCR-DGGE / Bacteria / Eukaryote / Methanogenic archaea / Methanotroph / Phylogenetic analysis / DNA sequence |
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| Research Abstract |
For elucidating the community structure of microorganisms in the paddy field ecosystem, DNA and RNA were extracted from the samples collected from various habitats such as floodwater, rice straw on and in the plow layer, and surface oxidized and reduced soil layers, and they were PCR-amplified with primers specific to eubacteria, eukaryotes, methanogens, methanotrophs, and ammonia oxidizers. PCR products were subjected to denaturing gradient gel electrophoresis (DGGE) to estimate the seasonal variations and the specificity of respective habitats with the subsequent determination of DNA sequence for characteristic DGGE bands.
In general, microbial communities estimated from PCR-DGGE patterns were phylogenetically endemic at respective habitats with relatively small seasonal variations. Sequence analysis of characteristic DGGE bands at each habitat indicated the presence of endemic microorganisms representing the community, and the microbial habitats were grouped into floodwater and percolating water (aquatic habitat), rice straw, rice straw compost and plant debris (plant residue habitat), rice roots and microcrustaceans (symbiotic habitat).
As eubacterial and methanogenic communities in the plow layer soil that were observed in DGGE analysis of extracted DNA were also detected in DGGE analysis of extracted RNA, all the eubacteria and methanogens were estimated to be active all the year round.
Interesting was the finding that microbial communities estimated from the PCR-DGGE analysis of environmental DNA was similar to those estimated from phospholipid fatty acid (PLFA) analysis.
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[Journal Article] Phylogenetic study on a bacterial community in the floodwater of a Japanese paddy field estimated by sequencing 16S rDNA fragments after denaturing gradient gel electrophoresis.2006
Author(s)
Shibagaki-Shimizu, T., Nakayama, N., Nakajima, Y., Matsuya, K., Kimura, M., Asakawa, S.
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Journal Title
Biology and Fertility of Soils (in press)
Description
「研究成果報告書概要(和文)」より
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[Journal Article] Effect of free-air CO_2 enrichment (FACE) on methanogenic archaeal communities inhabiting rice roots in a Japanese rice field.2005
Author(s)
Hashimoto-Yasuda, T., Ikenaga, M., Asakawa, S., Kim, H.Y., Okada, M., Kobayashi, K., Kimura, M.
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Journal Title
Soil Science and Plant Nutrition 51(1)
Pages: 91-100
Description
「研究成果報告書概要(和文)」より
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[Journal Article] Phylogenetic study on a bacterial community in the floodwater of a Japanese paddy field estimated by sequencing 16S rDNA fragments after denaturing gradient gel electrophoresis.
Author(s)
Shibagaki-Shimizu, T., Nakayama, N., Nakajima, Y., Matsuya, K., Kimura, M., Asakawa, S.
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Journal Title
Biology and Fertility of Soils (in press)
Description
「研究成果報告書概要(欧文)」より
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