Distinct taxonomic signatures in the rhizobiome of two native plants from the polyextreme Salar de Huasco ecosystem

Global food security faces mounting pressure from population growth, climate change, and deteriorating soil conditions. Rhizospheric microbial communities (rhizobiomes) play a key role in plant physiology, enhancing growth and tolerance to abiotic stress. To explore their potential contribution to plant resilience in extreme environments, we characterized the rhizobiomes of Deyeuxia curvula and Werneria incisa across the Salar de Huasco (SH) in the Chilean Altiplano (~ 3800 masl), a polyextreme ecosystem characterized by high UV radiation, salinity gradients, water scarcity, and high metal concentrations. Our objectives were to identify microbial taxa associated with plant adaptation and to infer functional traits linked to survival under these conditions. We generated 16S rRNA amplicon sequencing data from 200 rhizosphere samples. Both host plant identity and geographic location significantly shaped microbial community composition, with site explaining a larger proportion of variance than plant identity alone. Actinomycetota dominated both rhizobiomes, with genera such as Modestobacter and Blastococcus (known for UV resistance, desiccation tolerance, and genomic plasticity) contributing to species-specific profiles. At the genus level, Ilumatobacter, Nesterenkonia, Tropicimonas, and Nitriliruptor were enriched in D. curvula, whereas Pseudarthrobacter, Kocuria, Crossiella, and Blastococcus were more abundant in W. incisa. Network analysis revealed greater complexity and functional redundancy in D. curvula, while W. incisa harbored a more generalist network. Functional predictions indicated that chemoheterotrophy dominates both rhizobiomes, while denitrification, methylotrophy, and ureolysis were enriched in W. incisa, and osmotic stress-tolerance functions such as glycine betaine cycling were enriched in D. curvula. The two plants follow contrasting ecological strategies: D. curvula relies on a specialization and resilience strategy supported by a diverse, stress-adapted rhizobiome, while W. incisa employs a nutritional versatility strategy through a generalist, metabolically flexible community. These findings highlight the value of high-altitude Andean rhizobiomes as reservoirs of great biodiversity with relevant functions for future biotechnological applications particularly for agriculture under arid and saline conditions. This underscores the importance of extending conservation policies to native microbial communities in protected areas such as the Salar de Huasco.