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.
