Viral pathogen infection drives deterministic assembly of plant endophytic microbiomes: soil properties as divergent drivers and low-abundance taxa as primary responders

Understanding how viral pathogens reshape plant endophytic community assembly is essential for assessing soil biological health, given that soil is the primary microbial reservoir, but key knowledge gaps persist. Using 16S rRNA amplicon sequencing, we investigated potato virus Y (PVY) infection effects on the assembly processes in plant endophytic community and their associations with soil properties. PVY infection significantly affected β-diversity (but not α-diversity) of endophytes in roots, but had no significant impact on either α- or β-diversity in leaves and enhanced deterministic assembly by 17% in roots and 3% in leaves. In infected plant root, endophytic community exhibited increased significantly in the importance of heterogeneous selection (HeS) and homogeneous selection (HoS) alongside decreased significantly in dispersal limitation (DL). Conversely, the importance of drift (DR) significantly increased in endophytic community assembly for infected leaves. Such virus-induced deterministic assembly was significantly correlated with soil physicochemical properties. For example, pH negatively correlated with the importance of HeS in endophytic community of infected leaves ( ρ = −0.943), while that was reverse for infected roots ( ρ = 0.943). Available potassium (AK) positively correlated with HeS in leaves ( ρ = 0.986), while that was negative in roots ( ρ = −0.899). Furthermore, PVY infection influenced a subset of low-abundance taxa (≤5%) rather than reshaping the overall community structure, including Delftia (bin 17) and Allorhizobium (bin 5), which are known contributors to soil biological health. Taken together, these findings demonstrate that viral pathogens enhance deterministic assembly in plant endophytic community, which was greatly constrained by soil properties.