Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant–soil–microbe interactions

Deciphering the root exudate-driven interplay between plantsand the rhizosphere microbiota is essential for understanding plant adaptationto the environment and future-proofing crop production. However, sampling rootexudates and rhizosphere soil remains challenging due to the low throughput anddestructive nature of the process.

We used the staple crop barley (Hordeum vulgare L.)as a model to benchmark different sampling approaches for simultaneousexudation and microbiota profiling of soil-grown plants.

Exudate profiles and total dissolved organic carbonexudation rates were consistent across different sampling approaches, whereasroot biomass, root morphology measurements, and organic nitrogen exudationvaried. High-throughput amplicon sequencing and quantitative PCR (qPCR) ofphylogenetic markers and nitrogen cycle-selected genes revealed aprotocol-specific footprint in the composition and abundance of rhizospherebacterial and fungal microbiota. Yet, on average, 75% of microbes enriched inand differentiating between barley rhizosphere and unplanted soil controls wererecovered across all the sampling approaches evaluated.

Our results demonstrated that, under the tested conditions,different sampling approaches produced comparable microbiota and exudationpatterns, enabling the integrated study of root exudation and microbialprofiles from the same plant. The observed differences across samplingapproaches must be considered according to the experimental scope.