Yeast-derived biomolecule mixtures from wine lees display antimicrobial activity: an integrated bioprocess approach against grapevine pathogens

Grapevine trunk diseases threaten sustainable viticulture, while wine lees remain an underexploited biocontrol-relevant by-product within the circular economy framework. An integrated bioprocess was developed to upgrade lees into high-molecular-weight biomolecule mixtures and low-molecular-weight peptide-enriched fractions through a defined sequence of unit operations: fermentation design by using Saccharomyces monocultures and sequential inoculations with non-Saccharomyces strains, ultrasound-assisted autolysis, enzymatic hydrolysis, and 3 kDa ultrafiltration. The antifungal activity of the products was tested in vitro and in vivo against Phaeomoniella chlamydospora and Phaeoacremonium minimum, the two main pathogens that cause Petri disease in grapevine. The results demonstrated that high-molecular-weight autolysates showed no inhibition. The post-hydrolysis fractions reduced mycelial growth of Phaeoacremonium minimum by 45%–75% and Phaeomoniella chlamydospora by 40%–57%, and decreased conidiation by up to 92% and 61%, respectively. They also reduced symptoms (wood discoloration) by 47%–52% and 35%–73% and endophytic fungal growth by 63%–84% and 80%–91% respectively. Those results indicate an association between hydrolysis and the appearance of antifungal activity. Untargeted metabolomics employing liquid chromatography–mass spectrometry (UHPLC–ESI–TIMS–QTOF) highlighted strain- and fermentation-dependent secondary metabolite signatures, with 448 features differentiating across fermentation conditions. Activity-based correlation fingerprinting identified 49 putative biomarkers negatively associated with pathogen growth. Overall, fermentation design functions as a controllable upstream quality parameter, offering a scalable circular economy pathway for the production of antifungal bioproducts derived from winery waste