Phylogeny and Functions of Bacterial Communities Associated with Field-Grown Rice Shoots

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.