Specific suppression of vascular wilt disease of onion is linked with fungal soil community structure

The soil microbiome plays an important role in plant health and is therefore being investigated as a target to develop new approaches for sustainable crop protection. Here, we aimed to investigate the roles of bacterial and fungal communities in suppression of vascular wilt disease caused by Fusarium oxysporum in soils used for the cropping of onion (Allium cepae). We used pot experiments to assess impacts of disease in suppressive and conducive soils, and in a mixture of the two, and profiled the microbiomes of bulk field soil and pot soils using high-throughput sequencing. The incidence of vascular wilt disease in onions grown in the pot experiment reflected the incidence previously observed in the field, with disease significantly higher in conducive than suppressive field soil. However, disease incidence remained low when conducive and suppressive soils were mixed. Beta diversity analysis revealed clear separation of suppressive and conducive soils and indicated that fungal community structures were more closely linked to suppressiveness than were bacterial communities. Major fungal taxa that differentiated suppressive and conducive soils included species from the genera Gibellulopsis, Penicillium, Acremonium and Pseudallescheria. We conclude that the reduced incidence of onion vascular wilt disease is an example of specific suppression, brought about by the elevated abundance of several fungal taxa, whereas bacterial communities play a less important role. Differences in abundance of beneficial fungal species may be linked to different crop rotations employed in the two fields. Our results may contribute to the adoption of improved soil management regimes that protect beneficial microorganisms, or to the development of microbial consortia for biological control of onion vascular wilt disease.