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Biofilms play pivotal roles in fluvial ecosystems, yet virtually nothing is known about viruses in these communities. Leveraging an optimized sample-to-sequence pipeline, we studied the spatiotemporal turnover of dsDNA viruses associated with stream biofilms and found an astounding diversity to be structured by seasons and along the longitudinal gradient in the stream. While some vOTUs were region- or season-specific, we also identified a large group of permanent biofilm phages, taxonomically dominated by Myoviridae. Comparison of the observed viral distribution with predictions based on neutral community assembly indicated that chance and dispersal may be important for structuring stream biofilm viral communities. Deviation from neutral model predictions suggests that certain phages distribute efficiently across distant locations within the stream network. This dispersal capacity appears to be linked to EPS depolymerases that enable phages to efficiently overcome the biofilm barrier. Other phages, particularly vOTUs classified as Siphoviridae, appear locally overrepresented and to rely on a lysogenic life cycle, potentially to exploit the spatial distribution of bacterial populations in stream biofilms. Overall, biofilm viral and bacterial community turnover were significantly coupled. Yet, viral communities were linked to the presence of the most abundant bacterial community members. With this work, we provide a foundational ecological perspective on factors that structure viral diversity in stream biofilms and identify potentially important viral traits related to the biofilm mode of life.

Viral diversity is linked to bacterial community composition in alpine stream biofilms