Phylogeny and functions of bacterial communities associated with field-grown rice shoots

Takashi Okubo, Seishi Ikeda, Kazuhiro Sasaki, Kenshiro Ohshima, Masahira Hattori, Tadashi Sato, Kiwamu Minamisawa*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

26 Citations (Scopus)


Metagenomic analysis was applied to bacterial communities associated with the shoots of two field-grown rice cultivars, Nipponbare and Kasalath. In both cultivars, shoot microbiomes were dominated by Alphaproteobacteria (51-52%), Actinobacteria (11-15%), Gammaproteobacteria (9-10%), and Betaproteobacteria (4-10%). Compared with other rice microbiomes (root, rhizosphere, and phyllosphere) in public databases, the shoot microbiomes harbored abundant genes for C1 compound metabolism and 1-aminocyclopropane-1-carboxylate catabolism, but fewer genes for indole-3-acetic acid production and nitrogen fixation. Salicylate hydroxylase was detected in all microbiomes, except the rhizosphere. These genomic features facilitate understanding of plant-microbe interactions and biogeochemical metabolism in rice shoots.

Original languageEnglish
Pages (from-to)329-332
Number of pages4
JournalMicrobes and Environments
Issue number3
Publication statusPublished - 2014 Sep 17
Externally publishedYes


  • Metagenomics
  • Methanol
  • Plant hormone
  • Rice
  • Shoot

ASJC Scopus subject areas

  • Plant Science
  • Soil Science
  • Ecology, Evolution, Behavior and Systematics


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