National-scale biogeography and function of river and stream bacterial biofilm communities

Biofilm-dwelling microorganisms coat the surfaces of stones in river and stream ecosystems, forming diverse communities that are fundamental to biogeochemical processes and ecosystem functioning ^1,2 . Flowing water (lotic) ecosystems are under pressure from a wide range of interacting stressors including changes in land use, chemical pollution, and climate ³ . Despite their ecological importance, the taxonomic and functional diversity of river biofilms and their responses to environmental change are limited by a lack of understanding of their taxonomic composition and physicochemical drivers across large spatial scales. We conducted a national-scale assessment of bacterial diversity and function using metagenomic sequencing from rivers and streams across England, analogous to other large-scale efforts to understand microbial biogeography across diverse environments ^4,5,6,7 . We recovered 1,014 metagenome-assembled genomes (MAGs) from 450 biofilms collected across England’s extensive river network, revealing substantial taxonomic novelty, with ∼20% of the MAGs representing novel genera. We demonstrated that biofilm communities, dominated by generalist bacteria, exhibit remarkable functional diversity and metabolic versatility, and play a significant role in nutrient cycling with the potential for contaminant transformation. Environmental drivers, most notably geology, land cover, and nutrients, explained up to 90% of the variation in community composition. These findings highlight the importance of river biofilms and establish a foundation for future research on the roles of biofilms in ecosystem health and resilience to environmental change.