Effect of intercropping and plant genotype on fungal communities in pea and barley roots

Intercropping, or mixed cropping, is the simultaneous cultivation of more than one plant species. Intercropping is a promising approach to improve yield stability and resource use efficiency in agricultural systems. Despite increasing efforts to better understand interactions of species mixtures, little is known about effects of intercropping on root microbial diversity and composition and whether these effects are genotype-dependent. We performed a two-year field experiment with five pea varieties, grown either in pure stand or mixed with barley. We measured standard agronomic parameters and sampled the roots of both pea and barley and characterized fungal communities via metabarcoding. We found lower shoot length and higher pea root rot disease scores in mixed compared to pure stands. For fungal alpha diversity in pea, we found an interaction of plant genotype with intercropping. Fungal Shannon diversity was higher in mixtures compared to pure stands for the pea variety Vitra, while fungal richness was higher in pure stands for Alvesta. For beta diversity, intercropping, but not plant genotype, significantly shaped fungal root community composition with 12 operational taxonomic units (OTUs) differentially abundant. Fusarium equiseti, a known antagonistic endophyte, was more abundant in pure stands while Rhizoctonia solani, a known pathogen in pea and barley, was more abundant in mixed stands. In conclusion, neighboring plants influenced root fungal diversity associated with pea but not barley. Changes in relative abundances of OTUs could explain the observed reduced health in mixed stands. The observed genotype dependency for changes in alpha diversity ask for further investigations of functional relationships and might provide new insights on how to optimise mixing ability, in the context of cultivar choice and breeding.