Divergent biofilm and free-living microbial communities on Phragmites australis and in plankton across an eutrophication gradient in the Great Masurian Lakes (Poland)

Biofilms are key components of freshwater microbial communities, contributing critically to ecosystem functioning. Composed of both bacteria and protists, biofilm communities are shaped by environmental conditions and the lifestyle traits of their constituent organisms. Although biofilm and planktonic communities may share some taxa, the extent of the overlap and the factors driving community differentiation remain poorly understood. Here, we used high-throughput metabarcoding of 16S and 18S rRNA genes to investigate bacterial and protist communities associated with Phragmites australis stem biofilms and planktonic fractions across five lakes spanning an eutrophication gradient in the Masurian Lake District, northeastern Poland. The biofilm communities on reed stems were highly distinct from planktonic ones, sharing only a small core microbiome. The biofilm core not only exceeded that of planktonic communities but also contained characteristic taxa, identified via machine learning, that were distinct from planktonic assemblages, including several with potential roles in bioremediation and as bioindicators. Planktonic communities were strongly influenced by environmental factors, whereas Phragmites australis-associated epiphytic biofilm communities appeared more uniform across lakes, consistent with host-associated selection and potentially with lifestyle-related buffering. Moreover, biofilm suspensions exhibited higher apparent physiological activity per inoculum volume and broader substrate use under our assay conditions than the free-living communities. Altogether, our findings demonstrate the ecological significance of biofilms in freshwater systems and underscore the need to integrate both biofilm and planktonic fractions of prokaryotic and eukaryotic organisms to fully capture microbial diversity, function, and ecosystem resilience.