Metabolomics in plant-microbe interactions in the roots

In the last decade the importance of microbiota for plant performance has been over-whelmingly demonstrated. Plant microbiomes, both in roots and shoots, fulfill a plethora of functions that can strongly influence various plant traits. Metabolites are the main tools that plants use to actively shape their microbiome. Mechanistically, plants exude a complex mix of primary and secondary metabolites from roots, which serve as growth substrates for certain microbial strains, exert toxic effects on others, or act as signals in mediating the plant microbe interactions. Flavonoids and strigolactones have long been known to play important roles in enabling microbial symbiosis, even though their full complexity may not yet be fully elucidated. Recently, several other plant metabolites have also been implicated as important players mediating the interaction with the root microbiome, including molecules such as coumarins, camalexin and triterpenes. Because plants use such a wide range of chemical classes to shape their microbiome, mechanistic studies of plant-microbe interactions are increasingly applying high-throughput metabolomics techniques. In this review, we describe how metabolomics approaches have profiled the chemical complexity of plant rhizodeposits, and discuss how metabolomics can be utilized to functionally characterize specific metabolites that influence plant-microbe interactions. We will also discuss the advanced metabolite analyses that are needed to disentangle the complex metabolic interactions between plant hosts and their associated microbial communities.