An Adjustable Protocol to Analyze Chemical Profiles of Non-sterile Rhizosphere Soil

The analysis of chemical diversity in non-sterile rhizosphere soil has been a pressing methodological challenge for years. Rhizosphere-enriched chemicals (i.e., rhizochemicals) include root exudation chemicals, (microbial) breakdown products thereof, and de novo produced metabolites by rhizosphere-inhabiting microbes, all of which can play an important role in plant-soil interactions. The power and resolution of analytical methods and statistical analysis pipelines allow for better acquisition, separation and identification of rhizochemicals, thus providing unprecedented insight into the biochemistry underpinning plant-soil interactions. The current protocol describes a recently developed method to characterize rhizochemical profiles from plants, including crops, and is modular and customizable, allowing for application across a range of different plant-soil combinations. The protocol provides in-depth details about the experimental system for sample collection, data acquisition by liquid chromatography coupled to mass spectrometry, and analytical pipeline, which statistically selects for rhizochemicals by statistical comparison between metabolite profiles from plant-containing soil and plant-free soil. Moreover, the optional addition of chemical standards permits a semi-targeted approach, which improves the annotation of chemical signatures and identification of single rhizochemicals.