Environmental filtering shapes microbial mat community assembly across interconnected high-altitude hypersaline...

High-altitude saline ecosystems of the Atacama-Puna Plateau represent natural laboratories for investigating microbial adaptation and community assembly under polyextreme conditions. Despite their ecological importance, integrated assessments of microbial diversity across contrasting Andean systems remain scarce. Here, we characterized microbial mats, sediments, and saline crusts across three high-altitude sub-basins of northern Chile, including the Maricunga Salt Flat-Laguna Santa Rosa hydrological system, Laguna del Negro Francisco, and Laguna Verde. Microbial communities were analyzed using 16S rRNA gene amplicon sequencing, environmental characterization, predicted metabolic profiling, and co-occurrence network analyses. Salinity was the only environmental variable significantly associated with microbial community composition, although site identity explained a greater proportion of variation, highlighting the influence of local environmental conditions. Across ecosystems, communities were dominated by Pseudomonadota and Bacteroidota, whereas hypersaline habitats were enriched in halophilic archaeal lineages and brackish environments exhibited greater representation of photosynthetic and nitrogen-related functions. Only 15% of ASVs were shared between brackish and hypersaline habitats, indicating strong habitat specialization. Nevertheless, co-occurrence networks revealed a small set of highly connected keystone taxa shared among ecosystems, forming a regional core microbiome. Together, these findings demonstrate that salinity promotes taxonomic and functional specialization, while hydrological connectivity maintains ecological cohesion across interconnected ecosystems. By integrating lagoons, wetlands, saline crusts, and geothermal habitats within a regional framework, this study provides the first regional-scale assessment of microbial diversity, community assembly, and ecological connectivity across the southern Atacama-Puna Plateau.