Turnip mosaic virus drives selective filtering and community reassembly in the Arabidopsis thaliana root microbiome in a genotype-specific manner
Plant root microbiomes play a central role in plant health, yet their responses to viral infection remain poorly understood. Here, we investigated how Turnip mosaic virus (TuMV) alters root-associated bacterial and fungal communities in two Arabidopsis thaliana genotypes (Col-0 and Mar-12) grown in natural soils. Using 16S and ITS amplicon sequencing, we assessed changes in diversity, taxonomic composition, enriched microbial taxa, and co-occurrence network structure to distinguish between plant-mediated recruitment ("cry-for-help") and pathogen-induced dysbiosis. TuMV infection caused a pronounced reduction in bacterial diversity and a restructuring of bacterial community composition, whereas fungal communities remained largely stable. Viral infection also led to genotype-specific shifts in enriched bacterial genera, with opportunistic and stress-tolerant taxa proliferating differently in each genotype. Despite the initial perturbation, bacterial networks recovered connectivity and, in some cases, reached higher complexity than those of healthy plants, indicating strong microbial resilience. Together, these results reveal that TuMV infection acts as a selective filter on bacterial, but not fungal, root communities and that the surviving taxa can reorganize into functional networks. Our study provides one of the most comprehensive assessments of virus-induced microbiome restructuring and highlights the importance of host genotype in shaping microbial responses to biotic stress.