Fungal Microbiome Indicators Are Associated with Genotypic Variation in Pea Root Rot Susceptibility when Intercropped with Barley

Intercropping of legume and cereal crop species shows potential to reduce root disease pressures by changing root-associated microbiomes and improving nitrogen (N) use via soil N-dependent fixation of atmospheric N2 by symbiotic rhizobia. A two-year field study was conducted to evaluate the effect of pea–barley association on crop performance and on the root fungal community. Five pea cultivars (Alvesta, Karpate, Mytic, Respect, and Vitra) were grown either in pure stands or mixed with one variety of barley (Atrika). We measured crop grain yield and root rot incidence and analyzed root fungal communities. In mixed stands, total grain yield was more stable compared with that in each pure stand, but pea root disease incidence was higher except for cultivars Vitra and Karpate. The effect of cropping system on fungal alpha diversity depended on the cultivar, with Vitra showing higher Shannon diversity and Alvesta showing lower richness in mixed compared with pure stands. All four operational taxonomic units (OTUs) belonging to the Didymellaceae family were positively associated with pea root rot, and another disease-associated OTU in pea, Neoascochyta exitialis, was found to be also part of the barley core microbiome. Eleven of twelve OTUs belonging to the Glomeraceae family were associated with healthy roots and abundant in cultivar Vitra. This study shows how the phenotype and fungal microbiome of different pea cultivars respond distinctly to intercropping. Furthermore, the identification of disease- and health-associated taxa in the pea root fungal community refines the characterization of different cultivar candidates for intercropping. [Graphic: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.