Shrubs alter microbial community dynamics across various soil depths in alpine grassland ecosystems on the eastern Tibetan Plateau

• Shrub increased microbial diversity, but bacteria and fungi differed by soil depth. • Shrub enhanced the complexity of the microbial network. • Shrub reduced differences in the microbial network across soil depths. • Shrub elevated the importance of stochastic processes. • The importance of stochastic processes decreases with increasing soil depth. Shrub encroachment in alpine grassland ecosystems is intensifying because of climate change and human disturbance. While the effects of shrub encroachment on aboveground communities are well-documented, its impact on soil microbial community dynamics—especially in relation to soil depth—remains uncertain. Herein, we explored the impact of dominant shrubs on the diversity, composition, microbial networks, and community assembly of soil bacteria and fungi on the Qinghai-Tibet Plateau, examining the variations among different soil depths. We found that shrubs significantly increased bacterial and fungal diversity and altered their community composition. Notably, only the diversity of fungi in the topsoil was higher compared to the control grassland. Additionally, shrubs significantly enhanced the complexity of soil microbial networks. However, the complexity of microbial networks among different soil depths under shrubs did not significantly differ, unlike in the control grassland. This suggests that shrubs have a stronger ability to stabilize interspecific relationships among soil microorganisms. The normalized stochasticity ratio and neutral community models indicated that stochastic processes dominated the community assembly of bacteria and fungi, with the influence of these processes diminishing with increasing soil depth. Furthermore, the null model analysis showed that dispersal limitation and homogeneous selection dominated the bacterial assembly, while dispersal limitation dominated the fungal assembly. Our research has significantly advanced the understanding of how shrub encroachment influences soil microbial community interactions and ecological patterns in alpine grassland ecosystems.