Metagenomic insights into viral community restructuring and microbial interactions in waste stabilization ponds

Waste stabilization ponds (WSPs) operate as sequential ecological compartments in which physicochemical gradients, microbial succession, and trophic interactions increase toward the final polishing stage. Among these units, the maturation pond represents the terminal control point for pathogen attenuation and effluent quality; however, its role in shaping viral community structure remains insufficiently resolved. Here, we applied shotgun metagenomics to characterize DNA viral communities across the full treatment train of a full-scale WSP system in Giza, Egypt, with particular emphasis on maturation-stage restructuring. Viral community composition was strongly structured by treatment stage (PERMANOVA R² = 0.53, p < 0.05), with the most pronounced compositional turnover occurring between upstream ponds and the maturation pond. Relative abundance changes were highly taxon dependent. Human-associated viral families, including Adenoviridae and Poxviridae , were detected in the inlet but fell below detection in the maturation pond, whereas other groups such as Microviridae showed partial persistence. In contrast, several bacteriophage-associated signals increased in relative abundance in the maturation pond, suggesting stage-associated restructuring of viral DNA profiles that may be linked to host community shifts, environmental filtering, or particle-associated DNA dynamics. Notably, the maturation pond virome displayed differentiation from upstream stages, including the emergence of eukaryote-associated viral signals, consistent with potential co-variation with locally established microeukaryotic communities. Cross-domain network analysis further revealed that the maturation pond was characterized by tightly connected virus–bacteria–microeukaryote modules dominated by positive associations, indicative of coordinated responses to shared environmental filtering. Together, these findings position the maturation pond as a distinct ecological compartment associated with downstream virome restructuring under combined environmental filtering, treatment-stage conditions, and host-community-associated processes.