Biogeoclimatic regions and land-use structure bacterial biodiversity and nitrogen cycling in headwater stream sediments

Microbial communities in freshwater ecosystems are structured by both natural environmental variation and anthropogenic pressures, yet how these drivers interact to shape biodiversity and ecosystem functioning remains poorly understood. Here, we assessed how biogeoclimatic regions and land-use pressures jointly structure bacterial diversity and inferred nitrogen-cycling potential in stream sediments along a broad environmental gradient across the Iberian Peninsula. We used 16S rRNA metabarcoding and functional inference across samples spanning three biogeoclimatic regions and four land-use types. Bacterial community composition and diversity showed strong regional differentiation, with pronounced taxonomic turnover and distinct alpha-diversity patterns, whereas differences among land-use types were weaker, less spatially coherent, and primarily reflected shifts in specific community components. Despite this variation, a consistent core microbiome was observed across samples, suggesting the presence of taxa shared across contrasting conditions. Inferred nitrogen-cycling functional potential partially mirrored taxonomic patterns, with contrasting regional dominance of nitrification, denitrification, nitrogen fixation and dissimilatory nitrate reduction to ammonium, while land-use effects were subtle and nested within regional patterns. These results indicate that bacterial diversity and nitrogen-cycling potential are hierarchically structured, with biogeoclimatic conditions acting as primary ecological filters and land-use as a secondary, context-dependent driver. The relationship between taxonomic composition and inferred functional potential was more evident at the regional than at the local scale, where functional redundancy may buffer ecosystem processes. Our findings highlight the importance of incorporating regional baselines into biomonitoring frameworks and support the integration of taxonomic and functional approaches to improve ecological status assessments in freshwater ecosystems.