Stochastic processes dominate bacterial and fungal community assembly in ultra-high-altitude areas of southeast Tibet

• This study provides new insights into microbial dynamics above 4000 m in extreme environments. • Dispersal limitation and drift dominate microbial community assembly in ultra-high-altitude regions. • Drift increases and dispersal limitation decreases with increasing vegetation richness. • Bacteria exhibit greater niche breadth and phenotypic plasticity than fungi. • Core bacterial genera contribute more significantly to community assembly than fungi. Microbial community assembly processes have gained increasing attention for addressing global biodiversity loss in recent years, especially their relations to different plant habitats succession. However, it remains scarce in the ultra-high-altitude regions of the plateau. This study explored the contribution of deterministic and stochastic processes in shaping bacterial and fungal communities as well as key factors influencing these processes across five habitats in the southeastern ultra-high-altitude area of the Qinghai-Tibet Plateau. The results indicated that stochastic processes, particularly dispersal limitation and drift, dominated microbial community assembly across all five successive habitats (talus slope, alpine meadow, alpine shrubland, deciduous broadleaf forest, and mixed needle-broadleaf forest) in this study. Their relative importance varied, with drift increasing (bacterial from 31.03% to 47.13% while fungal from 38.07% to 58.88%) and dispersal limitation decreasing (bacterial from 47.29% to 22.91% while fungal from 48.69% to 33.53%), as habitat succession progresses. Bacterial community exhibited wider niche width and higher phenotypic plasticity, making homogeneous selection more significant in bacterial community compared to fungal community. Core genera made more contributions to microbial community assembly, with bacterial core genera having a greater influence than fungal core genera. Our findings firstly provide insights into the distinctive interaction of microbial community assembly with plant habitats heterogeneity in the ultra-high-altitude mountainous ecosystems.