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

    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 Sept 17


    • Metagenomics
    • Methanol
    • Plant hormone
    • Rice
    • Shoot

    ASJC Scopus subject areas

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


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