Microbial echoes of resistance: PIWI grapevine genotypes shape rhizosphere microbiomes beyond the graft line

The rhizosphere microbiome is a key determinant of grapevine health and productivity. PIWI varieties, bred for resistance to fungal pathogens, are increasingly adopted for sustainable viticulture. However, it remains unclear whether disease-resistance breeding influences rhizosphere microbial recruitment. This study assessed whether PIWI genotypes and susceptible parental lines differ in rhizosphere bacterial and fungal assemblages under pathogen pressure and contrasting nitrogen availability. We analyzed rhizosphere samples from four grapevine cultivars, including PIWI genotypes and their susceptible parental lines, grafted onto SO4 rootstock. Plants received two nitrogen levels and were either inoculated or not with Plasmopara viticola. Bacterial and fungal communities were characterized by 16S rRNA gene and ITS metabarcoding. Beta regression showed that resistant genotypes had lower disease severity and incidence than susceptible cultivars. Differences associated with resistant genotypes emerged mainly in fungal communities and under specific combinations of varietal background, pathogen inoculation, and nitrogen availability. Under 20 kg N ha− 1 and without pathogen inoculation, resistant genotypes showed distinct fungal assemblages compared with parental lines. Because all cultivars shared the same rootstock, these patterns point to a possible scion-associated effect on rhizosphere assembly. In red cultivars, pathogen inoculation altered bacterial (P-value = 0.03) and fungal communities (P-value = 0.001), whereas nitrogen fertilization primarily influenced bacterial assemblages (P-value = 0.001). Our findings suggest that disease-resistance breeding may be associated with a distinct, context-dependent belowground microbial signature. These results broaden the perspective on PIWI cultivars, indicating that their relevance may extend beyond foliar disease resistance to rhizosphere microbial interactions in sustainable viticulture