Walder et al. 2017; Community Profiling of Fusarium in Combination with Other Plant-Associated Fungi in Different Crop Species Using SMRT Sequencing

The application of cover crops is a promissing tool for a sustainable intensification of current agricultural practices. However, cover crops might entail also phytopathological risks by acting as alternative hosts for noxious plant pathogens. Infections through fungi from the genus Fusarium frequently lead to Fusarium head blight, one of the most harmful cereal diseases, resulting not only in severe yield losses but also to contaminated grains with health-threatening mycotoxins. Up to now, molecular tools for the monitoring of Fusarium species' occurrence are limited to certain species. In the current study, we developed a sequencing-based community profiling methodology for crop-associated fungi with a focus on Fusarium species. By analysing a large 1600 bp amplicon spanning the highly variable segments ITS and D1-D2 of the ribosomal operon by SMRT sequencing, we were able to robustly quantify Fusarium fungi down to species level. The newly developed methodology was successfully validated in mock communities and provided similar results as the the culture-based assessment of Fusarium communities by seed health tests. Subsequently, we used the newly developed methodology to track Fusarium fungi along a wheat-maize crop sequence exhibiting different cover crop treatments under conventional or no-tillage regimes. The fungal communities along the wheat-cover crop-maize rotation varied highly and depended on the crop investigated. Different cover crops also harboured species specific fungal communities. By analysing wheat residues, cover crop shoots and maize grains, we revealed that the cover crop hairy vetch (Vicia villosa) acts as a potent alternative host for Fusarium (OTU F.ave/tri) showing an eightfold higher relative abundance compared to other cover crop treatments. Moreover, as the newly developed methodology allows also to track other crop-associated fungi, vetch and green fallow have been determined to host further fungal plant pathogens including Zymoseptoria triciti. The mean abundance of the Fusarium OTU F.ave/tri tended to be higher after vetch particularly under no tillage, which suggest that certain cover crops can act as alternative hosts for this plant pathogen. The newly developed sequencing based methodology is a powerful diagnostic tool of high resolution to track Fusarium species and other fungi associated to crops along a crop sequence.