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 journalArticle

16 Citations (Scopus)

Abstract

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
Volume29
Issue number3
DOIs
Publication statusPublished - 2014 Sep 17
Externally publishedYes

Fingerprint

paddy field
bacterial communities
phylogeny
shoot
rice
shoots
metabolism
rhizosphere
cultivar
phyllosphere
salicylate
salicylates
beta-Proteobacteria
catabolism
gene
Actinobacteria
alpha-Proteobacteria
gamma-Proteobacteria
cultivars
nitrogen fixation

Keywords

  • Metagenomics
  • Methanol
  • Plant hormone
  • Rice
  • Shoot

ASJC Scopus subject areas

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

Cite this

Phylogeny and functions of bacterial communities associated with field-grown rice shoots. / Okubo, Takashi; Ikeda, Seishi; Sasaki, Kazuhiro; Ohshima, Kenshiro; Hattori, Masahira; Sato, Tadashi; Minamisawa, Kiwamu.

In: Microbes and Environments, Vol. 29, No. 3, 17.09.2014, p. 329-332.

Research output: Contribution to journalArticle

Okubo, T, Ikeda, S, Sasaki, K, Ohshima, K, Hattori, M, Sato, T & Minamisawa, K 2014, 'Phylogeny and functions of bacterial communities associated with field-grown rice shoots', Microbes and Environments, vol. 29, no. 3, pp. 329-332. https://doi.org/10.1264/jsme2.ME14077
Okubo, Takashi ; Ikeda, Seishi ; Sasaki, Kazuhiro ; Ohshima, Kenshiro ; Hattori, Masahira ; Sato, Tadashi ; Minamisawa, Kiwamu. / Phylogeny and functions of bacterial communities associated with field-grown rice shoots. In: Microbes and Environments. 2014 ; Vol. 29, No. 3. pp. 329-332.
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