Unveiling the mycobiome of healthy and Esca diseased grapevines: fungal community dynamics across different microhabitats, seasons, years, and cultivars

Grapevines host diverse microbial communities, including fungal pathogens associated with grapevine trunk diseases (GTDs), which pose a major challenge in viticulture. Despite extensive research, the ecological drivers shaping fungal community composition across different grapevine microhabitats remain insufficiently understood. Using ITS2 metabarcoding, we characterized fungal communities in bark, wood, and soil from Esca symptomatic and asymptomatic vines, and evaluated the effects of season, year, cultivar, microhabitat, and plant health on key functional groups.

Seasonal variation had limited effects on fungal richness, whereas interannual differences had a strong impact on functional group diversity. Microhabitat played a key role: plant pathogens, particularly GTD-associated taxa, were most prominent in bark and wood; mycoparasites were dominant in bark; generalist saprotrophs prevailed in soil and bark; and GTD-related wood saprotrophs were most abundant in bark. Soil harbored the highest overall fungal diversity. Plant health status significantly affected only GTD pathogens, which showed higher abundance and diversity in symptomatic vines. Cultivar influenced only the richness of GTD-related wood saprotrophs.

Year (vintage) emerged as a major driver of fungal community composition across plant tissues and soil, driving the most pronounced shifts in the mycobiome. Abiotic factors (year and season) were most strongly associated with soil fungal communities, whereas biotic factors (cultivar and plant health) exerted a greater influence on fungi associated with grapevine tissues. These findings underscore the central role of microhabitat and temporal variation in structuring the grapevine mycobiome.