Distinguishing the effects of micro- and macro-habitats on plant-associated microbiomes in the Qinghai-Tibetan Qaidam Basin

Although microbiomes associated with plants and the environment are intricately intertwined, it remains unclear how various environmental scales affect these relationships differently. We employed high-throughput amplicon sequencing to examine the plant-associated bacterial and fungal communities across three different micro-habitats (leaf, root, and root zone soil) in 16 shrubs distributed across a >500 km transect of the eastern Qinghai-Tibetan Qaidam Basin. Among the three microhabitats, the diversity and composition of plant-associated bacterial and fungal communities differed significantly. Although micro-habitats play a crucial role in shaping plant-associated microbial communities, geographic and climatic variables largely influenced the community compositions across the three micro-habitats. Notably, the microbial communities in all three micro-habitats showed significant distance-decay patterns. Furthermore, fungi exhibited less variation across the three microenvironments, and were more sensitive to environmental changes than bacteria. Moreover, microbiome complexity and stochasticity gradually increased from soils to roots and finally to leaves. The microbial communities in soils and epiphytes (leaves and roots) were predominantly shaped by determinism and stochasticity, respectively. These results highlight that plant-associated microbiomes are primarily shaped by the microenvironments associated with plants; however, their compositions, dynamics, and assembly are further influenced by geographic and climatic factors. Overall, our findings greatly increase our understanding of the intricate dynamics between plant-associated microbiomes and their surrounding environment in drylands. This knowledge contributes to ongoing research on microbial ecology and provides substantial supports for the precise evaluation of desert ecosystem function. The findings are helpful for biodiversity conservation and sustainable management of desert shrublands.