Diversity and Biocontrol Potential of Fungi Associated with Cyst Nematodes and Soils in Swiss Potato Agroecosystems

Cyst nematodes are persistent soilborne pests that severely impact crop productivity worldwide. Their protective cysts enable long-term survival and host diverse fungal communities that remain largely unexplored as potential sources of biological control agents. In this study, we isolated culturable fungi from cysts of <i>Globodera</i>, <i>Heterodera</i>, and <i>Punctodera</i>, as well as from soils collected across Swiss potato fields between 2018 and 2024. Sequencing identified 78 fungal operational taxonomic units (OTUs), predominantly belonging to Ascomycota (73%), mainly Sordariomycetes (59%) and Eurotiomycetes (8%), with additional representatives from Mortierellomycota and Basidiomycota. <i>Fusarium</i> was the most abundant genus, followed by <i>Clonostachys</i>, <i>Chaetomium</i>, and <i>Pochonia</i>, while 28% of isolates remained unclassified, indicating potentially novel taxa. Selected fungi, including <i>Orbilia brochopaga</i> CH-02, <i>Clonostachys rosea</i> CH-04 and CH-15, and <i>Pochonia chlamydosporia</i> CH-51, significantly reduced motility, infection and root galling of <i>Meloidogyne incognita</i> in vitro and in planta. Notably, CH-02 reduced root galling by 63%, highlighting its strong mechanical and antagonistic activity. These results demonstrate that cyst nematodes harbor a rich and functionally diverse fungal community with substantial biocontrol potential, providing a foundation for developing sustainable and environmentally friendly alternatives to chemical nematicides in crop protection.