The rapid melting of mountain glaciers and the vanishing of their streams is emblematic of climate change1,2. Glacier-fed streams (GFSs) are cold, oligotrophic and unstable ecosystems in which life is dominated by microbial biofilms2,3. However, current knowledge on the GFS microbiome is scarce4,5, precluding an understanding of its response to glacier shrinkage. Here, by leveraging metabarcoding and metagenomics, we provide a comprehensive survey of bacteria in the benthic microbiome across 152 GFSs draining the Earth's major mountain ranges. We find that the GFS bacterial microbiome is taxonomically and functionally distinct from other cryospheric microbiomes. GFS bacteria are diverse, with more than half being specific to a given mountain range, some unique to single GFSs and a few cosmopolitan and abundant. We show how geographic isolation and environmental selection shape their biogeography, which is characterized by distinct compositional patterns between mountain ranges and hemispheres. Phylogenetic analyses furthermore uncovered microdiverse clades resulting from environmental selection, probably promoting functional resilience and contributing to GFS bacterial biodiversity and biogeography. Climate-induced glacier shrinkage puts this unique microbiome at risk. Our study provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem.

Biological and Environmental Science and Engineering Division King Abdullah University of Science and Technology Thuwal Kingdom of Saudi Arabia

Department of Ecology Faculty of Science Charles University Prague Czechia

Institut de Physique du Globe de Paris Paris France

MARBEC University of Montpellier CNRS IFREMER IRD Montpellier France

River Ecosystems Laboratory Alpine and Polar Environmental Research Center Ecole Polytechnique Fédérale de Lausanne Sion Switzerland

Systems Ecology Group Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch sur Alzette Luxembourg

UK Centre for Ecology and Hydrology Wallingford UK

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