Land-use differences shape soil fungal communities, with pathogen enrichment in agricultural soils and ectomycorrhizal fungi in remnant vegetation

High-throughput sequencing (HTS) has enabled detailed characterization of soil microbiomes; however, the trophic roles, functional guilds, and pathogenic potential of soil fungi in long-term agricultural systems remain incompletely resolved. Here, we used HTS to investigate how brassica–legume–cereal crop rotations shape soil mycobiomes by comparing two agricultural soils with an adjacent remnant vegetation soil in Kojonup, Western Australia. Fungal community composition differed significantly between land-use systems. Agricultural soils harbored higher relative abundances of fungal taxa with reported plant-pathogenic lifestyles, whereas the remnant vegetation soil was enriched in ectomycorrhizal fungi, indicating a clear shift in dominant fungal functional guilds. Fungal taxa reported as pathogens of brassica, legume, and cereal crops, as well as of hosts not cultivated in the study area, were detected. Diverse beneficial fungi, including taxa with reported antagonistic activity against plant pathogens, were also present. Bioassays demonstrated cross-antagonistic interactions among selected fungal plant pathogens detected in the soil community. In addition, multiple antagonistic taxa isolated from the soils were confirmed to inhibit the broad host-range pathogen Sclerotinia sclerotiorum , including taxa not previously reported in this context. Overall, intensively managed agricultural soils were associated with increased abundance of disease-related fungal taxa, while the presence of antagonistic fungi with demonstrated antifungal activity suggests potential for disease suppression, supporting the contribution of soil microbiomes to sustainable disease management.