Collection and Purification of Secondary Metabolites from Root Exudates for LC-MS/MS Analyses

Plants communicate with their environment through the production of root exudates. These contain a variety of secondary metabolites that mediate plant interactions in the rhizosphere. Collecting these exudates without altering root structure, the metabolites, and the environmental conditions is crucial to understanding real processes occurring in our studies, enabling time-course experiments and separate analysis of roots and exudates. The present chapter shows an easy and non-destructive method to collect root exudates from intact plants, as well as their purification and concentration using C18 solid-phase extraction (SPE) columns for subsequent liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses. Interestingly, this methodology allows for repeated exudate collection over time from the same plant to efficiently recover charged metabolites, including rhizosphere signaling molecules such as strigolactones and flavonoids. We show an easy, viable, and non-destructive method for quantifying low-abundance root exudate metabolites from intact plants.