Journal of General Plant Pathology

, Volume 77, Issue 2, pp 121–131 | Cite as

Microbial community profiles in intercellular fluid of rice

  • Hideki TakahashiEmail author
  • Hiroyuki Sekiguchi
  • Toyoaki Ito
  • Masashi Sasahara
  • Noriko Hatanaka
  • Atsushi Ohba
  • Shu Hase
  • Sugihiro Ando
  • Hiroshi Hasegawa
  • Shigehito Takenaka
Disease Control


Plants harbor microorganisms that are thought to stimulate plant defense systems or promote plant growth. Individual species in these intercellular microbial communities are often not sufficiently abundant to be easily described, although some endophytic microorganisms amenable to culture have been characterized. To better understand the microbial population of plants, we collected intercellular fluid (IF) from leaf blades and sheaths of rice and subsequently isolated DNA from the IF. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S and 18S rDNA fragments amplified from IF DNA by PCR indicated that these band patterns were distinguishable from those of a leaf surface-wash fluid (SF). Analysis of a set of rDNA fragments amplified from IF DNA of rice with different genotypes, paddies or growth stages for the primary survey of overall microbial community in the IF suggested that this approach is suitable for analyzing microbial diversity in the IF from various plant samples. Actually, comparative analysis of amplified rDNA fragments of rice and other five plant species indicated that the microbial diversity in IF is likely to vary substantially among plant species. We can also use sequence analysis of 16S rDNA fragments amplified from rice IF DNA to identify species including unculturable bacteria and proteobacteria and Xanthomonas and 18S rDNA fragments to identify Tilletiaria anomala, Tilletia iowensis, Ustilago maydis and unculturable eukaryotes. Thus, IF DNA analysis seems to be a good tool to further study the microbial ecology of plants.


Endophyte Intercellular fluid Microbial community Unculturable microorganisms Rice (Oryza sativa



This work was supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan.

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Copyright information

© The Phytopathological Society of Japan and Springer 2010

Authors and Affiliations

  • Hideki Takahashi
    • 1
    Email author
  • Hiroyuki Sekiguchi
    • 2
  • Toyoaki Ito
    • 3
  • Masashi Sasahara
    • 4
  • Noriko Hatanaka
    • 4
  • Atsushi Ohba
    • 4
  • Shu Hase
    • 1
  • Sugihiro Ando
    • 1
  • Hiroshi Hasegawa
    • 5
  • Shigehito Takenaka
    • 2
  1. 1.Department of Life Science, Graduate School of Agricultural ScienceTohoku UniversitySendaiJapan
  2. 2.Rhizosphere Environment Research TeamNational Agricultural Research Center for Hokkaido Region, Shinsei, MemuroKasaiJapan
  3. 3.Environmental Crop Science, Graduate School of Agricultural ScienceTohoku UniversityOsakiJapan
  4. 4.Department of Crop ProtectionMiyagi Prefectural Furukawa Agricultural Experiment StationOsakiJapan
  5. 5.National Agricultural Research Center for Tohoku RegionNational Agricultural Research OrganizationFukushimaJapan

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