Genome-centric metagenomes unveiling microbial functional potential in a glacier river in the Mount everest.

High-altitude rivers constitute ideal model systems for studying microbial roles in elemental cycling within complex ecosystems. Previous studies primarily addressed microbial community assembly, specific taxonomic groups, or antibiotic resistance gene risks, resulting in limited understanding of biogeochemical cycling profiles. Here, shotgun metagenomic sequencing was employed to profile the metabolic potential of planktonic and benthic microbiomes in the glacial-fed Rongbu River. We sequenced nine water and nine sediment samples along an altitudinal gradient, reconstructing 279 medium-to-high-quality metagenome-assembled genomes (MAGs), with 246 representing unclassified MAGs. Functional analyses revealed divergent niche specialization between habitats: (i) water MAGs encoded multifunctional carbohydrate-active enzymes (CAZymes), targeting labile polysaccharides while coupling nitrogen-sulfur metabolism to enhance nitrogen assimilation; and (ii) sediment MAGs specialized in complex polysaccharide degradation, exhibiting enriched denitrification and sulfide oxidation genes. Notably, a total of 13 plastic degradation genes (PDGs) were identified, which indicated altitudinal partitioning: high-elevation communities showed PBAT-degrading potential, while low-elevation MAGs harbored PVA-degrading genes. These findings indicated that altitude governed the spatial distribution of distinct biogeochemical potentials in high-altitude rivers. This study advances our understanding of elemental cycling processes in alpine river ecosystems.