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

Amy C. Thorpe (), Susheel Bhanu Busi (), Jonathan Warren, Laura H. Hunt, Kerry Walsh and Daniel S. Read ()
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Amy C. Thorpe: Crowmarsh Gifford, UK Centre for Ecology & Hydrology, Benson Lane
Susheel Bhanu Busi: Crowmarsh Gifford, UK Centre for Ecology & Hydrology, Benson Lane
Jonathan Warren: Horizon House, Environment Agency
Laura H. Hunt: Horizon House, Environment Agency
Kerry Walsh: Horizon House, Environment Agency
Daniel S. Read: Crowmarsh Gifford, UK Centre for Ecology & Hydrology, Benson Lane

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract Biofilm-dwelling microorganisms coat the surfaces of stones in rivers and streams, forming diverse communities that are fundamental to biogeochemical processes and ecosystem functioning. Flowing water (lotic) ecosystems face mounting pressures from changes in land use, chemical pollution, and climate change. Despite their ecological importance, the taxonomic and functional diversity of river biofilms and their responses to environmental change are poorly understood at large spatial scales. We conducted a national-scale assessment of bacterial diversity and function using metagenomic sequencing from rivers and streams across England. We recovered 1,014 metagenome-assembled genomes (MAGs) from 450 biofilms collected across England’s extensive river network. Substantial taxonomic novelty was identified, with ~20% of the MAGs representing novel genera. Here we show that biofilm communities, dominated by generalist bacteria, exhibit remarkable functional diversity and metabolic versatility, and likely play a significant role in nutrient cycling with the potential for contaminant transformation. Measured environmental drivers collectively explained an average of 71% of variation in the relative abundance of bacterial MAGs, with geology and land cover contributing most strongly. 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.

Date: 2025
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DOI: 10.1038/s41467-025-65620-3

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