Molecular mechanisms underlying the microbiota-influenced host growth-defense coordination

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Plants live in intimate association with environmental microbes and, as sessile organisms, need to cope with changing biotic and abiotic conditions to ensure their survival. Plant-associated microbes, collectively called the plant microbiota, are able to manipulate host growth and immunity in various ways. We have shown that Rhizobiales commensal bacteria isolated from a variety of healthy plants promote Arabidopsis thaliana root growth and suppress immune responses triggered by elicitor peptides, such as flg22 and pep1. In this proposed research program, I aim to elucidate the molecular mechanisms underlying microbiota-influenced host growth-defense coordination using molecular genetics combined with systems biology and cell biological approaches. My goal is to build a comprehensive time- and space-resolved molecular model that describes how plants coordinate their growth and defense in the presence of complex microbial communities.My previous work showed that plant sulfated peptides are targeted by root-associated commensal bacteria to manipulate host root growth-defense coordination upon elicitor peptide treatments, suggesting the crosstalk between perception of growth-regulating sulfated peptides and immunity-regulating elicitor peptides and/or within the subsequent signaling processes. I will disentangle the molecular basis underlying this crosstalk analyzing the biochemical status of the receptors and signaling components, as well as the downstream gene expression profiles. I will also exploit a collection of plant-associated commensal bacterial strains, whose genomes have been sequenced, to identify bacterial genes that are responsible for the interference with host growth-defense coordination. To this end, I will perform multi-omics experiments using in vitro bacterial cultures cultivated in a system mimicking in planta conditions, which will be in turn used as an input for trans-omics-wide association study. Lastly, I will incorporate a large set of published and unpublished transcriptomic data of A. thaliana roots interacting with microbes engaged in different lifestyles to select potential key regulatory hub genes in a co-expressed gene network. Plant and bacterial reverse genetic approaches will be employed to experimentally validate the function of identified genes in influencing host growth-defense coordination as well as in root microbiota assembly.Overall, I will elucidate the genetic framework by which root-associated commensal bacteria interfere with host growth-defense coordination. This framework will form the basis for further exploration of the molecular dialog between plants and their associated microbiota and addressing the role of plant immunity in controlling the structure and functions of the root microbiota.