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

Abstract 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 low-molecular-weight, antimicrobial secondary metabolite- and 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, confirming hydrolysis as a critical control point for releasing short bioactive peptides and secondary metabolites. 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. 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 antimicrobial potential 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.