Unprecedented urban freshwater microviral survey highlights shift from sewage to river water communities

Microviruses are abundant yet still poorly resolved components of virosphere, particularly across urban freshwater continua. Here, we investigated complete microvirus genomes recovered from sewage water (SW), treated wastewater (TW), and river water (RW) along an urban SW TW RW continuum, providing an extensive genomic dataset of 18,449 complete genomes grouped into 825 genera. This catalog enabled a high-resolution assessment of microvirus diversity, taxonomy, and ecological distribution across anthropized aquatic compartments. All currently described microvirus orders were detected, with Gokushovirales dominating the dataset and Betagokushoviridae emerging as the most prevalent family in TW and RW samples. In contrast, Alpavirales were enriched in SW but strongly depleted after treatment, consistent with their association with gut-related bacterial hosts. Alpha- and beta-diversity analyses showed that water type was the main driver of microvirus community structure, whereas seasonal effects were weak and not robust under the hydrological conditions of the sampling year. Wastewater treatment plants thus acted as strong biological filters, reshaping viral assemblages and selecting compartment-specific microvirus populations. Finally, the pronounced and reproducible shifts observed across the continuum suggest that selected microvirus groups may serve as promising bioindicators of anthropogenic influence in freshwater systems.