Meta-omics profiling of full-scale groundwater rapid sand filters explains stratification of iron, ammonium and manganese removals

•Single dual- and consecutive single-media filters are eco- and operationally equivalent.•Both systems exhibited comparable performances and process compartmentalization.•Media coating and genome-based composition were homogeneous in each compartment.•Only protein abundances reflected stratification in activity.•Backwash shapes microbial community distribution in rapid sand filters.