White streams as microbial hotspots: taxonomic and functional insights from alpine river systems

Microbial communities living in extreme environments, such as in low pH alpine stream systems rich in heavy metals, provide a unique opportunity to study biological adaptation strategies. Recently, the appearance of high-alpine streams with white-colored stream sections, characterized by the precipitation of aluminum compounds, in European Alpine rivers has raised questions about the composition and functional capabilities of the associated microbiomes. In this study, we analyzed samples from two locations, Val Lavirun and Val Poschiavo (Engadine, Switzerland), using an integrated approach combining metabarcoding and shotgun metagenomic sequencing to examine both taxonomic diversity and functional microbial potential coping with these extreme environments.

Samples were collected along a defined environmental transect affected by aluminum precipitation, covering three distinct sections: the stream source (clear water), transitional phase (intermediate zone), and precipitation zone (marked by white-colored stream section). This progression alters the water's physicochemical properties and visibly affects its color and turbidity, creating an environmental stress gradient.

Metabarcoding analyses revealed marked differences in microbial community composition between sites  and sections (zones). Among prokaryotes, dominant phyla included Actinobacteriota, Bacteroidota, Pseudomonadota, and Planctomycetota, with significant shifts in relative abundance across sampling phases. Fungal communities were largely dominated by Ascomycota and Basidiomycota, while less abundant phyla such as Chytridiomycota and Rozellomycota were detected in specific ecological niches, suggesting functional specialization.

Shotgun metagenomic analysis provided insights into microbial functional potential. CAZy gene profiling highlighted the prevalence of Glycoside Hydrolases and Auxiliary Activities, particularly enzymes involved in lignin and cellulose degradation. NCyc gene analysis revealed distinct expression patterns in nitrogen cycling processes, including denitrification (nirK), nitrification (amoA), and nitrogen fixation (nifH), reflecting microbial adaptation to physicochemical gradients. EggNOG-based functional annotation showed significant variation in genes related to carbohydrate metabolism, energy production, stress response, and defense mechanisms.

This study contributes to a deeper understanding of microbial survival strategies in harsh high-alpine river systems and highlights the importance of integrating taxonomic and functional data to unravel the ecological roles of microorganisms in alpine freshwater habitats.