Community Analysis of Seed-Associated Microbes in Forage Crops using Culture-Independent Methods

Seishi Ikeda, Shin Ichi Fuji, Toshiro Sato, Nozomi Ytow, Hiroshi Ezura, Kiwamu Minamisawa, Tatsuhito Fujimura

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21 Citations (Scopus)


Microbial diversity in forage crop seeds was examined using culture-independent methods. Environmental DNA samples were extracted from the surface of the seeds, and the intergenic spacer region between small sub-unit and large subunit RNA genes was then amplified by ribosomal intergenic spacer analysis (RISA) for the profiling of microbial community structures. The results suggested the presence of stable microbial communities in seeds and sequencing of the RISA amplicons identified a total of 33 unique microbial sequences in 1.6 g of seed material from Italian ryegrass (Lolium multiflorum) and timothy (Phleum pretense). These included several sequences showing high similarity to known plant-associated microbes, such as Pseudomonas fluorescens and Clavibacter michiganensis, the Cladosporium and Dioszegia group of fungi, and also several uncultured bacteria.

Original languageEnglish
Pages (from-to)112-121
Number of pages10
JournalMicrobes and Environments
Issue number2
Publication statusPublished - 2006


  • environmental DNA
  • forage crop seed
  • Italian ryegrass
  • ribosomal intergenic spacer analysis
  • timothy


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