Wastewater treatment plants (WWTPs) contain a diverse array of microbes, underscoring the need for regular monitoring to ensure treatment efficacy and protect health. However, detailed studies on waste stabilization ponds (WSPs) are scarce. This study evaluates a full-scale WSP, located in Giza Governorate, Egypt, including anaerobic, facultative, and maturation ponds, examining an array of parameters such as enteric viruses, microeukaryotes (protozoa and algae), bacterial indicators, bacterial pathogens, and physicochemical characteristics. Utilizing multivariate statistical models, we identified significant distinctions in physicochemical parameters and microbial communities, primarily driven by treatment stages rather than temporal variations. In addition, seven viruses (human rotavirus, adenovirus, norovirus, astrovirus, hepatitis A virus, polyomavirus, and papillomavirus) were detected during the different stages (inlet, anaerobic, facultative, and outlet) of the WSP, except norovirus and papillomavirus were absent in the outlet stage. The viral log means reductions ranged from 1.24 to 5.94, depending on the stage and virus type. The removal efficiency of bacterial pathogens was more than 99%. High throughput 18S rRNA gene amplicon sequencing indicated the dominance of animal parasitic Apicomplexa species and Vermamoeba spp. in the WSP. Network analysis indicated significant roles for Ciliophora in virus reduction. Notably, the maturation pond's outlet was dominated by Spirulina maxima, whose mat-forming tendencies may inhibit pathogen removal by providing protective shelters. Although the WSP effectively reduced pathogen levels, the high initial loads resulted in considerable concentrations in the final effluent, posing ongoing public health concerns. This study highlights the imperative of including pathogen standards in national regulations for wastewater reuse.
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