INTEVINE: Multi-omics data Integration to understand the grapevine holobiont

Soil bacteria and fungi are fundamental to plant health, engaging in complex interactions that influence and are influenced by the soil's physical and chemical properties. In this study, we utilized a multi-omics approach to investigate how variations in soil properties shape grapevine holobiont dynamics. This allowed us to uncover diverse and interconnected influences that would have remained hidden with a single-method analysis. Soil type (sand, peat, or peat enriched with manure) emerged as a dominant factor, significantly affecting bacterial and fungal community composition. Shifts in microbial taxa were observed, including those associated with nitrogen fixation, biocontrol, and pathogenicity. The multi-omics framework provided critical insights beyond the scope of individual analyses. For example, while peat enriched with manure exhibited fewer pathogenic fungi and supported plants with enhanced chlorophyll activity, as suggested by multispectral imaging, it also harboured the highest presence of pathogenic viruses. This underscores the importance of integrating multiple data to capture the full complexity of the plant-soilmicrobiome system, as focusing on one perspective alone would present only a fragment of the complete picture. Autoclaving the soil before planting grapevine cuttings had limited but persistent effects on bacterial diversity and composition, whereas its impact on fungal communities and on root transcriptome was comparatively limited. Conversely, root thermal treatment had minimal influence on the rhizosphere bacterial and fungal microbiome but induced transcriptomic changes in grapevine roots even 11 months after treatment. While environmental perturbations are often considered transient, our findings demonstrate their potential for lasting impacts on the holobiont. These effects were evident in microbial composition, plant gene expression, and nutrient dynamics.