The core metabolome and root exudation dynamics of three phylogenetically distinct plant species

Root exudates are plant-derived, exported metabolites likely shaping root-associated microbiomes by acting as nutrients and signals. However, root exudation dynamics are unclear and thus also, if changes in exudation are reflected in changes in microbiome structure. Here, we assess commonalities and differences between exudates of different plant species, diurnal exudation dynamics, as well as the accompanying methodological aspects of exudate sampling. We find that exudates should be collected for hours rather than days as many metabolite abundances saturate over time. Plant growth in sterile, nonsterile, or sugar-supplemented environments significantly alters exudate profiles. A comparison of Arabidopsis thaliana, Brachypodium distachyon, and Medicago truncatula shoot, root, and root exudate metabolite profiles reveals clear differences between these species, but also a core metabolome for tissues and exudates. Exudate profiles also exhibit a diurnal signature. These findings add to the methodological and conceptual groundwork for future exudate studies to improve understanding of plant-microbe interactions. Root exudates display a diurnal signature, change with growth environment, and can be divided into a core metabolome common to multiple plant species, and specialized exudates produced by distinct species.

Automated summary

Root exudates, plant-derived metabolites, play a crucial role in shaping root-associated microbiomes as nutrients and signals. This study investigates the dynamics of exudation and its correlation with changes in microbiome structure. The research suggests that collections of exudates should be conducted for hours rather than days, as some metabolite abundances saturate over time. Plant growth in different environments alters exudate profiles significantly. Moreover, different plant species exhibit distinct exudate metabolite profiles, but also share a core metabolome for tissues and exudates. Furthermore, exudate profiles show diurnal patterns. These findings provide important insights for future studies on plant-microbe interactions.