Microbial community's shifts in an Andean glacier-fed watershed under anthropogenic pressures

Microorganisms play a crucial role in maintaining ecosystem functions by transforming matter and energy. The impact of environmental perturbations on the cycling and loss of aquatic microbial communities remains poorly characterized, particularly in the Southern Hemisphere. Here, we present the shifts in active microbial community and the maintenance of glacier-derived microbial core along the Aconcagua Basin, Central Chile. Through metabarcoding of the 16S rRNA transcripts and genes in water samples from 13 sites along the river continuum-including glacier-influenced headwaters, mining-proximal zones, agro-industrial reaches, and estuarine environments-distinct shifts in microbial community composition were observed. Glacier-fed waters harbored rich, cold-adapted microbial communities with elevated viral pressure, while mining and/or natural acid drainage promoted the dominance (up to 52% relative abundance) of sulfur-oxidizing bacteria (SOB) and reduced overall diversity. Among the SOB taxa, Thiovirga, Sulfuricurvum, and Thiobacillus-affiliated ASVs dominated together with minor taxa such as Thiomonas, Longilinea, Alishewenella, and Acidithiobacillus. Downstream, runoff and wastewater inputs from agricultural and urban areas altered microbial assemblages, introducing new taxa (e.g., C39 and Cellvibrio) and further diminishing glacier-derived core members. Estuarine sites exhibited pronounced eutrophication and significant loss of upstream microbial diversity. Along the basin, the virus-to-prokaryotes ratio gradually decreased (i.e., 95 to 5) from the glacier-fed lagoon with low prokaryotic biomass to the estuarine wetland with high virus and prokaryotic abundances. This study underscores the importance of integrating microbial diversity into water resource management and conservation policy to ensure ecosystem resilience amid climate change and intensifying human impacts.