Host–virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier

Glaciers are retreating rapidly, altering ecosystem dynamics and increasing meltwater outflow into populated areas. Understanding microbial-virome interactions is crucial for predicting the consequences of this release. We sampled ice from four shallow pits in the weathering crust of the Rhonegletscher, Swiss Alps, and found a microbiome dominated by bacteria and microeukaryotes, alongside a metavirome infecting both groups. Viruses exhibited variable host specificity, with some targeting particular taxa and others showing a broader infectivity range. Variable genomic regions, including metagenomic and metaviromic islands, were enriched in genes related to replication, recombination, repair and transposable elements. Detected auxiliary metabolic genes were primarily involved in host coenzyme biosynthesis, uptake or utilization and in altering bacterial methylation patterns to evade detection. These findings underscore the major role of viruses in regulating microbial dynamics in glaciers and their potential downstream environmental impacts.