Exploring Endophytic Fungi from Humulus lupulus L. for Biocontrol of Phytopathogenic Fungi

Humulus lupulus L. (hop) is a crucial crop within the brewing industry and a rich source of bioactive compounds. Traditionally concentrated in northeast regions of Europe, hop cultivation has expanded towards southern territories such as Italy over recent decades. Managing phytosanitary threats in Mediterranean climates poses challenges due to limited knowledge and registered agrochemicals. In pursuit of eco-friendly alternatives for disease management, we isolated 262 endophytic fungal strains from wild hop roots, stems, leaves, and flowers. Through phylogenetic analyses, we identified 51 operational taxonomic units. Dominant species such as Ilyonectria macrodidyma, Penicillium sp., Diaporthe columnaris, Plectosphaerella cucumerina, and Fusarium oxysporum were exclusive to roots. In contrast, Alternaria spp. and Epicoccum spp. were prevalent in other tissues, and Botrytis cinerea was exclusively detected in female flowers. We tested seven isolates—Epicoccum sp., Aureobasidium pullulans, Plectosphaerella cucumerina, Stemphylium vesicarium, Periconia byssoides, Talaromyces wortmannii, and Nigrospora sphaerica—against the four phytopathogenic fungi Alternaria sp., Fusarium oxysporum, Botrytis cinerea, and Sclerotinia sclerotiorum. All endophytes exhibited antagonistic effects against at least one pathogen, with Plectosphaerella cucumerina showing the strongest inhibition against Alternaria sp. This study marks the first exploration of endophytic fungi from various hop tissues. All isolated strains were ex situ conserved for future bioactivity assessments and biotechnological applications. Original data with a key relevance for the environmentally friendly management of plant diseases are provided.