The last decade brought great progress in describing the repertoire of microbes associated with plants and identifying principles of their interactions. Metabolites exuded by plant roots have been considered candidates for the mechanisms by which plants shape their root microbiome. Here, we review the evidence for several plant metabolites affecting plant interaction with microbes belowground. We also discuss the development of new approaches to study the mechanisms of such interaction that will help to elucidate the metabolic networks in the rhizosphere.

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Plants exude secondary metabolites from the roots to shape the composition and function of their microbiome. Many of these compounds are known for their anti-microbial activity and are part of the plant immunity, such as the indole-derived phytoalexin camalexin. Here we studied the dynamics of camalexin synthesis and exudation upon induction of Arabidopsis thaliana with a plant growth promotion bacteria Pseudomonas sp. CH267 or a bacterial pathogen Burkholderia glumae PG1. We show that while the camalexin accumulation and exudation is more rapidly but transiently induced upon interaction with the growth promoting strain, the pathogen induces a higher and more stable camalexin levels. By combination of experiments with cut shoots and roots and grafting of wild type plant with mutants in camalexin synthesis we showed that while camalexin can be produced and released by both organs, in intact plant the exuded camalexin originates in the shoots. We also reveal that the root specific CYP71A27 affects specifically the outcome of interaction with plant growth promoting bacteria and that its transcript levels are controlled by a shoot derived signal. In conclusion, camalexin synthesis seems to be controlled on a whole plant level and coordinated between shoots and roots.