Vegetation cover shapes community structure and metabolic genetic potential of high- alpine soil microbiomes

Background Alpine permafrost-affected soils, particularly in the European Alps, remain poorly understood despite rapid warming and projected vegetation increase at higher elevations. We investigated how vegetation cover and physicochemical soil properties structure microbial communities across ten high-altitude alpine permafrost-affected sites. Results Soil parameters (pH, soil water content, temperature, and total C and N contents) varied significantly between sites and revealed pH and C:N ratio as key drivers modulated by vegetation cover, highlighting its indirect role in shaping soil environments. Microbial community composition differed significantly across sites, and functional gene profiles mirrored taxonomic patterns, indicating strong coupling between community structure and functional gene potential, without functional redundancy. Microbial abundance increased with vegetation cover, whereas taxonomic and functional gene diversity plateaued at intermediate vegetation cover, suggesting that the presence of vegetation primarily enhances microbial abundance rather than diversity. Genome-resolved metagenomics revealed a shift from generalist-dominated communities in barren soils to increased prevalence of specialist taxa in vegetated soils. Functional gene abundances, particularly for C cycling, were higher in vegetated soils, while N and S cycling gene potentials were associated with soil temperature and water content. A microcosm experiment measuring ex situ CO₂ and CH₄ fluxes from incubated summer soils, identified vegetated soils as modest CO₂ sources. Vegetated soils exhibited lower, pH and C:N ratio, shaping a more abundant microbial community with more specialist members and higher C cycling gene potential. Conclusion Overall, our findings indicate that alpine greening reshapes microbial communities via vegetation-mediated changes in soil properties, with implications for biogeochemical cycling and C emissions under climate warming.