Plant-associated microorganisms are vital in nutrient uptake, disease suppression, and enhancing plant resilience to extreme environmental conditions. While soil microbial communities are known to influence plant development, the processes governing seed microbiome assembly remain poorly understood. Specifically, it is unclear whether stochastic or deterministic processes dominate this assembly. We hypothesized that reduced soil microbial diversity would negatively impact plant productivity and the composition of associated microbiota, but the functional diversity of seed-endophytes would not be affected (deterministic influence from the host plant). To test this hypothesis, a microbial diversity gradient was established using agriculture and corresponding γ-irradiated soils, and surface sterilized Setaria viridis seeds were grown for a full life cycle. 16S rRNA gene amplicon sequencing confirmed a clear gradient in soil microbial diversity, with α-diversity (Richness, Shannon, Phylogenetic diversity) and β-diversity showing distinct patterns across dilutions. Reduced soil microbial diversity significantly decreased plant height, biomass, chlorophyll content, photosynthetic efficiency, and seed yield. Root biomass, length, volume, and tiller number declined threefold under low-diversity conditions. These physiological reductions were accompanied by elevated stress markers, including malondialdehyde (MDA), proline, and anthocyanins, suggesting that soil microbial diversity decline acts as an environmental stress factor. Despite these effects, seed nutrient content and microbial functional diversity remained stable, indicating resilience that may safeguard reproductive success. Moreover, our statistical analysis supports the hypothesis that deterministic processes largely govern seed microbial assembly, highlighting the critical role of soil microbiomes in promoting plant vigor, enhancing stress tolerance, and potentially buffering against environmental stresses.
