The microbiota of plants is composed of a large diversity of microbes, engaging with their host various types of interactions from beneficial to detrimental. Consequently, the study of how plants perceive mutualistic from pathogenic microbes and which molecular pathways drive the outcome of the interaction (partnership or defense) are critical questions for the understanding of plant-microbe interactions. In this study, we evaluated rice transcriptional response to a diversity of bacteria spanning from root pathogens to plant-growth-promoting rhizobacteria (PGPR) in hydroponic conditions. A transcriptomic analysis of rice leaf and root tissues was performed to identify common and specific transcriptional signatures during interaction with non-plant-isolated (Escherichia coli & Stenotrophomonas maltophilia), plant-isolated (Pseudomonas defensor & Bradyrhizobium sp. ORS278), or rice-isolated bacteria (Azospirillum sp. B510, & Burkholderia plantarii). Among all tested groups, the pools of differentially expressed genes (DEGs) modulated by all bacteria or by the PGPR represented only a fraction of total DEGs, highlighting the specificity of response to each bacterium. However, plant-isolated bacteria induced a stronger response than non-plant-isolated bacteria. Rice response to PGPR, pertaining to growth induction and stress mitigation, allowed us to identify putative marker genes of beneficial interaction. Ten genes (such as OsPR1b, rNBS41, related to defense response) were oppositely regulated: repressed upon pathogenic and induced upon PGPR interactions. These genes could be pivotal to trigger mutualism or immunity signals. These transcriptomic clues to bacterial mitigation of rice health were confirmed in a greenhouse experiment, in which PGPR demonstrated strong biocontrol potential against a foliar phytopathogen.
Guigard et al. (Fri,) studied this question.