The Rice Microbiome: A Model Platform for Crop Holobiome

Abstract

The plant microbiome, the consortium of microbes surrounding a plant, has potential for improving crop productivity and sustainability. Despite the necessity of agriculturally applicable microbiomes, plant microbiome studies have been conducted in noncrop plants because of the relative easiness of research. However, in order to make plant microbiomes useful for agriculture, a crop plant-based model is needed. In parallel, overlooked parts of microbiomes other than the bacteria-centered research need to be considered to expand our understandings on microbiomes to the ecosystem level. Beyond the microbial composition, functional properties of microbiomes over time and space will help us to select appropriate microbes that can support crop plants by providing stage-specific functions. Less explored communities such as fungi and protists also can provide novel insights on compositional and functional dynamics of each community, including interkingdom or multitrophic interactions. Finally, identification of host factors on functional microbiomes using genetic information of both the host and the microbiomes will shift host-centered breeding to parallel breeding of host and microbiome. This review will give basic and collective information on the rice microbiome and foster the establishment of a crop plant-based model to meet agricultural needs.