Sewer microbiomes shape microbial community composition and dynamics of wastewater treatment plants.

The link between the sewer microbiome and microbial communities in activated sludge wastewater treatment plants is currently poorly understood despite the systems being directly interconnected. Microbial immigration from wastewater has been identified as a key factor determining activated sludge community assembly. Here, we present the first comprehensive study of the sewer microbiome and hypothesize that the microbiome harbors process-critical activated sludge microbes and is thus critical for activated sludge community assembly and performance. We integrated species-level microbial analyses of biofilm, sediment, and sewer wastewater in domestic gravity and pressure sewers in Aalborg, Denmark, with samples from influent wastewater and activated sludge from two downstream wastewater treatment plants. By tracing the sources of incoming bacteria and determining their growth fate in the activated sludge, we confirmed that most activated sludge process-critical bacteria were part of the sewer microbiome. Within the sewer system, a gradient was observed, from dominance of gut bacteria in the wastewater upstream to the prevalence of biofilm and sediment bacteria downstream at the wastewater treatment plant inlet, with the relative ratio strongly affected by rain events. A holistic understanding of the sewer system and activated sludge is essential, as sewers hold massive amounts of active biomass serving as a major microbial source for community composition and dynamics in wastewater treatment plants. Sewer systems should be recognized as a crucial environmental filtration step, and the sewer microbiome as an important source for activated sludge, helping to explain the observed regional and global differences in activated sludge community structure.