Multi-omic characterization of microbial dynamics during spontaneous fermentation of sweet wine Picolit variety

Introduction – Spontaneous wine fermentation is driven by the ecological succession of vineyard-derived microorganisms, yet little is known about how this process unfolds in Picolit, a grape variety characterized by acinellatura (berry millerandage) and elevated sugar concentration. This study aimed to characterize the microbial and metabolic dynamics of spontaneous Picolit fermentation and to identify the ecological and functional transitions occurring throughout the process. Methods – An integrated multi-omic approach combining shotgun metagenomics and untargeted metabolomics was applied to spontaneous fermentations of Picolit grapes produced at Aquila del Torre, an organic and biodynamic winery located in Savorgnano del Torre (Friuli-Venezia Giulia, Italy), within the newly established “Friuli Colli Orientali Sottozona Savorgnano D.O.C.” Five fermentation stages were sampled and analyzed to investigate microbial succession, functional pathways and metabolomic changes. Results – The initial must displayed high microbial richness dominated by non-Saccharomyces yeasts, oxidative bacteria and Botrytis cinerea. An atypical persistence and increasing abundance of B. cinerea suggested a strong interaction between grape physiology and fungal activity. Early fermentation stages were characterized by diverse non-Saccharomyces taxa, including Lachancea, Pichia, Torulaspora and Schizosaccharomyces, which were associated with acid modulation, aromatic precursor release and phenolic turnover. From mid-fermentation onward, a multi-species Saccharomyces consortium established functional dominance, coinciding with a marked reduction in bacterial diversity and a transition from aroma-related metabolic pathways to stress adaptation functions. Multi-omic network analyses revealed a progressive loss of modularity as fermentation progressed and the system became more stable. Discussion – These findings demonstrate that spontaneous Picolit fermentation follows a distinctive ecological trajectory shaped by grape physiology, terroir and native microbial diversity. The persistence of B. cinerea, together with the succession of non-Saccharomyces and Saccharomyces populations, highlights unique microbial interactions that may contribute to wine identity. Overall, the results support the enological value of spontaneous fermentation and provide a microbial and functional framework for understanding and valorizing wines produced under the Savorgnano Bianco D.O.C.