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

17 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 Sep 17
Externally published	Yes

Keywords

Metagenomics
Methanol
Plant hormone
Rice
Shoot

ASJC Scopus subject areas

Plant Science
Soil Science
Ecology, Evolution, Behavior and Systematics

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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, 29(3), 329-332. https://doi.org/10.1264/jsme2.ME14077

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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

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AU - Hattori, Masahira

AU - Sato, Tadashi

AU - Minamisawa, Kiwamu

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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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