Habitat-Dependent Ecological Differentiation of Soil and Water Microbiomes in High-Altitude Alpine Meadow Ecosystems on the Qinghai–Tibetan Plateau

High-altitude ecosystems are characterized by extreme environmental conditions that strongly influence microbial community structure and function. However, whether soil and water microbiomes exhibit similar ecological responses to environmental variation in alpine meadow ecosystems on the Qinghai–Tibetan Plateau remains poorly understood. Here, we combined 16S rRNA gene amplicon sequencing and metagenomic sequencing to compare soil and water microbiomes across two regions (LZ and NQ) with distinct physicochemical profiles. Environmental heterogeneity was more pronounced in water habitats, where all measured parameters (pH, total nitrogen, total organic carbon, and chemical oxygen demand) varied significantly between sites (p < 0.001). Correspondingly, water microbiomes exhibited greater regional differentiation than soil microbiomes, evidenced by stronger beta-diversity separation (PERMANOVA, R2 = 0.667 vs. 0.376) and a lower proportion of shared ASVs (65.3% vs. 97.2%). Ecological assembly analysis revealed a sharp contrast: water communities were primarily governed by deterministic processes (accounting for >80% of assembly, with heterogeneous selection as the dominant driver), whereas soil microbiomes were dominated by stochastic processes (>50%). Furthermore, water microbiomes underwent more intense network restructuring, with interaction complexity increasing significantly from 70 nodes and 268 edges in the LZ region to 130 nodes and 577 edges in the NQ region, whereas soil networks remained relatively stable (146 nodes/368 edges to 128 nodes/391 edges). Functional profiling further indicated broader regional redistribution in water compared to the relatively conserved functional framework of soil communities. Resistome analysis identified distinct ARG structures between habitats while revealing 25 overlapping categories, suggesting potential ecological connectivity. Collectively, our findings demonstrate that water microbiomes are more sensitive to regional environmental variation than soil microbiomes, with aquatic communities responding through deterministic restructuring and heightened interaction complexity. These results provide quantitative evidence that high-altitude soil and water microbiomes adopt distinct ecological strategies, offering new insights into the mechanisms governing microbial adaptation and antibiotic resistance distribution.