Plant, pathogen and microbiome, the cry for help under the prism of omics investigations – MicroHelp

The "Cry for help" concept suggests that plants, when subjected to abiotic or biotic stress, recruit a specific microbiome, i.e. a community of micro-organisms, to combat this stress. The hypothesis is based on the plant's ability to structure a favourable microbiome by modulating its production of root metabolites. The aim of this project is to test and extend this concept by analysing variations in the primary and secondary root metabolites of rice and the evolution of its microbiome when subjected to different pathogens. Using an experimental evolution approach, we will impose selection pressure on the plant in successive cycles by inoculating bacterial, fungal or viral foliar pathogens. At each cycle, we will characterise the root microbiome and the primary and secondary metabolites found in the rhizosphere. By comparing chemical annotations with databases, we will be able to determine which compounds are preferentially involved in microbiome recruitment. Metagenomic analysis will enable us to target the microbial taxa and/or functions selected by the plant to provide better resistance to the pathogen. Comparisons between pathosystems will enable us to distinguish between general and specific responses to each pathogen. Using a transcriptomics approach, we will decipher the plant's response in the presence of evolved or non-evolved microbiomes, in order to determine which genes and functions are involved in the plant's interaction and resistance. Machine learning approaches will enable us to search for links between the very large datasets that we will generate, and a field validation of the molecules involved will be initiated in Cambodia. This project opens the door to potential applications in disease biocontrol.