Botrytis cinerea infection reshapes the grape berry microbiome during noble rot

Abstract

Noble rot, caused by Botrytis cinerea, profoundly alters grape berry physiology and is essential to produce botrytized wines. In this study, we profiled bacterial and fungal communities associated with Vitis vinifera cv. Semillon berries across four stages of noble rot development and four consecutive vintages using 16S rRNA gene and ITS1 amplicon sequencing. Noble rot stage significantly impacted the structure of bacterial communities across vintages, while fungal communities showed more variable vintage-dependent responses. Bacterial alpha diversity increased consistently at advanced stages of infection (S3), coinciding with a marked shift from Pseudomonas-dominated communities toward acetic acid bacteria, particularly Gluconobacter, which was significantly enriched at S3 in all vintages. Fungal communities remained dominated by Sclerotiniaceae throughout infection, consistent with pervasive B. cinerea colonization, while non-Botrytis fungal taxa shifted from filamentous fungi such as Cladosporium and Alternaria toward fermentative yeasts including Hanseniaspora and Lachancea. Co-occurrence network analysis revealed a positive association between Gluconobacter and these fermentative yeasts, suggesting coordinated enrichment of oxidative and fermentative microorganisms at advanced noble rot stages. Together, these results reveal a reproducible stage-associated microbial succession during noble rot progression and identify acetic acid bacteria as consistent markers of advanced infection.