Divergent biofilm and free-living microbial communities on Phragmites australis and in plankton across an eutrophication gradient in the Great Masurian Lakes (Poland)
Biofilms, consisting of bacteria and protists, are key components of freshwater microbial communities and contribute to ecosystem functioning. Although biofilm and planktonic communities may share taxa, the extent of their overlap and the drivers of differentiation are not fully understood. We used 16S and 18S rRNA gene metabarcoding to examine bacterial and protist communities in Phragmites australis stem biofilms and planktonic fractions across lakes with differing trophic states in the Great Masurian Lakes (NE Poland). Biofilm communities on reed stems were compositionally distinct from planktonic ones, sharing only a limited core microbiome. The biofilm core was larger than that of planktonic communities and included taxa identified by machine learning as characteristic of biofilm assemblages. Planktonic communities varied among lakes, whereas P. australis-associated biofilms were comparatively similar, which may reflect host association and lifestyle-related buffering. Additionally, biofilm suspensions showed higher physiological activity per inoculum volume and broader substrate use under the assay conditions than free-living communities. These results highlight the distinct nature of freshwater biofilms and underscore the importance of jointly examining biofilm and planktonic fractions of prokaryotic and eukaryotic communities in studies of microbial diversity and function in lake ecosystems.