Waste stabilization ponds (WSPs) are widely used as cost-effective, nature-based systems for municipal wastewater treatment, particularly in developing countries. However, the structure, diversity, and fate of viral communities in these systems remain poorly understood. This study presents the first shotgun metagenomic analysis of DNA viral communities in a full-scale WSP system in Giza, Egypt, focusing on two key treatment stages (inlet and facultative pond) over four seasons. A total of 346 DNA viruses were identified. Taxonomic profiling revealed that the virome was dominated by bacteriophages, particularly members of the Class Caudoviricetes, with lower representation of eukaryotic viruses. The alpha diversity of viral communities, as measured by the Shannon index, declined from approximately 3.2–4.0 at the inlet to below 2.8 in the facultative pond, indicating a substantial reduction in both viral richness and evenness across the treatment process. Principal coordinate analysis (PCoA) and Cluster analysis revealed a clear separation between inlet and facultative samples. Distance-based redundancy analysis (db-RDA) showed that viral community shifts were driven by physicochemical gradients, with ammonium-nitrogen and biological oxygen demand associated with inlet samples, and total dissolved solids and electrical conductivity linked to facultative pond samples. Specific taxa such as P1virus and P2virus were strongly correlated with organic-rich influent conditions and may serve as potential viral bioindicators for wastewater treatment monitoring. Importantly, several human-associated viruses (e.g., Adenoviridae) were detected in the influent but were undetectable in the facultative effluent, suggesting efficient wastewater treatment processes. This study provides novel insights into viral community dynamics and removal, highlighting the value of integrating virome profiling into wastewater surveillance and water reuse frameworks.
Rizk et al. (Mon,) studied this question.