A Pan‐European Whole‐Microbiome Study of Wastewater Influent: Prokaryotes, Protists, Fungi, and Metazoa

Abstract

Microbial communities entering wastewater treatment plants (WWTPs) through untreated sewage represent an important interface between human, environmental, and treatment‐associated microbiomes, yet our understanding of their biogeography remains poorly resolved, particularly for microbial eukaryotes. Using shotgun metagenomic time‐series data from influent samples of seven WWTPs across a European latitudinal gradient, we analyzed the taxonomic composition and dynamics of bacteria, protists, fungi, and microscopic metazoa. Influent community composition varied with geographic location and season, with a pronounced north–south divergence driven by dominant taxa and stronger seasonal shifts observed at higher latitudes. Cross‐domain associations were pervasive, suggesting that co‐varying bacterial and eukaryotic components structure the incoming microbial pool. Our findings provide a pan‐European baseline for whole‐microbiome wastewater surveillance and highlight that influent communities differ regionally and seasonally. These patterns may be relevant for downstream treatment‐stage microbiomes, but direct effects on reactor community assembly and treatment performance require targeted sampling across treatment stages.