Discovering of emerging pathogens belonging to Fusarium spp. in Italian wheat kernels

Wheat is one of the most cultivated cereal crops in the Mediterranean basin area, with both durum and soft wheat representing strategic resources for food security (1). As consequence of climate change, globalization and trade, adaptation, resistance to pesticides, monocultures and migration of insect vectors, the emergence of phytopathogenic fungal pathogens has been increasing for several years (2), posing a potentially devastating threat to critical crops to food safety and security. In this context, being Italy a geographical quadrivium and one of the most important European countries for durum wheat production it is essential to monitor the spread of wheat pathogens to find possible strategies in preventing their spread. Two parallel methods for fungal identification have been explored in this work, one by fungal metabarcoding, using the MinION sequencing platform (ONT), and one exploiting the in vitro cultivation of endophytic fungi from superficially sterilized kernels. The two methodologies showed complementary results, and although the in vitro isolation was much more time consuming, it allowed the isolation species that could not be identified by metabarcoding, including potential pathogens emerging in Europe such as Fusarium bothii and Fusarium elaeagni. Fusarium bothii is a phytopathogenic fungal species that is part of the Fusarium graminearum species complex (FGSC), normally restricted to other geographical areas in the world. It has been previously reported in the USA, Mexico and South Africa (3) in different agriproducts. Recent works from 2025 reports its emergence also in Ethiopia (3) and Serbia (4). Fusarium elaeagni is part of the F. fujikuroi species complex and there are currently no reports of its detection in Italy. These two species were preliminarily identified by Sanger sequencing of the ITS1-4 regions and subsequently performed whole genome sequencing on both. The isolates were also tested for their ability to produce mycotoxins on wheat matrices. This work highlights the importance of monitoring crop microbiomes in a changing environment to support early management strategies.