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

doi:10.1264/jsme2.ME14077

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 journal › Article › peer-review

26 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 language	English
Pages (from-to)	329-332
Number of pages	4
Journal	Microbes and environments
Volume	29
Issue number	3
DOIs	https://doi.org/10.1264/jsme2.ME14077
Publication status	Published - 2014 Sept 17

Keywords

Metagenomics
Methanol
Plant hormone
Rice
Shoot

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Soil Science
Plant Science

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10.1264/jsme2.ME14077

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title = "Phylogeny and functions of bacterial communities associated with field-grown rice shoots",

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.",

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AU - Okubo, Takashi

AU - Ikeda, Seishi

AU - Sasaki, Kazuhiro

AU - Ohshima, Kenshiro

AU - Hattori, Masahira

AU - Sato, Tadashi

AU - Minamisawa, Kiwamu

PY - 2014/9/17

Y1 - 2014/9/17

N2 - 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.

AB - 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.

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KW - Methanol

KW - Plant hormone

KW - Rice

KW - Shoot

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

Abstract

Keywords

ASJC Scopus subject areas

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