Metagenomic insights into viral community restructuring and microbial interactions in waste stabilization ponds
Abstract
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.
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BibTeX
@article{rizk2026metagenomic,
title = {{Metagenomic insights into viral community restructuring and microbial interactions in waste stabilization ponds}},
author = {Neveen M. Rizk and Mohamed A. Marouf and Nehal Ismail Ahmed and Mona H. El-Gayar and Marwa A. Kamel and Mohamad A. El-Khateeb and Rehab Sedhom and Esmat M. S. Elfeky and Mohamed Azab El-Liethy and Mahmoud Gad},
journal = {Scientific Reports},
year = {2026},
month = oct,
doi = {10.1038/s41598-026-71071-7},
url = {https://www.nature.com/articles/s41598-026-71071-7},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Metagenomic insights into viral community restructuring and microbial interactions in waste stabilization ponds
AU - Neveen M. Rizk
AU - Mohamed A. Marouf
AU - Nehal Ismail Ahmed
AU - Mona H. El-Gayar
AU - Marwa A. Kamel
AU - Mohamad A. El-Khateeb
AU - Rehab Sedhom
AU - Esmat M. S. Elfeky
AU - Mohamed Azab El-Liethy
AU - Mahmoud Gad
PY - 2026
DA - 2026/10/02
JO - Scientific Reports
DO - 10.1038/s41598-026-71071-7
UR - https://www.nature.com/articles/s41598-026-71071-7
AB - 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.
SN - 2045-2322
ER -