Cover crop identity determines root fungal community and arbuscular mycorrhiza colonization in following main crops

Cover crops (CC) can promote nutrient retention and recycling for main crops yet may also promote soilborne pathogens or suppress beneficial root symbionts such as arbuscular mycorrhizal fungi (AMF). We investigated how root fungal communities of main crop are affected by preceding CC monocultures and mixtures and by main crop identity. We expected that AMF abundance and diversity in main crops are promoted by AM-host CC, and suppressed by non-AM-host CC, and that mixtures of CC species can promote beneficial and suppress pathogenic root fungi. Our full-factorial field experiment comprised crop rotation in sand soil with different CC treatments (monocultures of radish [AM non-host], ryegrass, clover, vetch [AM hosts], mixtures of radish + vetch, ryegrass + clover and fallow) and two main crops (oat and endive). At peak crop growth, we investigated the root fungal communities in the main crops using microscopy and high throughput sequencing (Illumina MiSeq). Cover crop identity was of prime importance and CC legacy overruled main crop identity in determining root fungal communities in main crops. Compared with fallow, CC with ryegrass increased AMF colonization and richness in both main crops and of non-AMF in oat. Legacies of ryegrass, ryegrass + clover and vetch resulted in distinct root fungal communities in the main crops, while the legacy of CC with radish were similar to the legacy of fallow. Root fungal community in crops after clover had highest abundance of representative fungal pathogens in contrast with the other CC treatments that resulted in fungal communities where pathogens were scarce. Oppositely to expected, CC mixtures did not enhance fungal symbionts or suppressed pathogens. Overall, fungal communities in roots of the main crops in our field experiment were determined by the preceding CC species in monoculture, rather than by the CC AMF preference or functional group. This research highlights that the choice of CC determines the root fungal comm