Abstract Description

Viruses are the most abundant biological entities and are core constituents of wastewater treatment plant (WWTP) microbiomes. In these systems, viruses shape microbial community structure and regulate metabolic pathways through auxiliary metabolic genes (AMGs). However, the impact of wastewater pollutants on viral communities and their ecological functions remains largely unknown. Here, we characterize viral community composition, functional potential and virus-host interactions in WWTPs and adjacent river systems. From 23 metagenomes, we recovered 26, 519 viral operational taxonomic units (vOTUs). The results suggest distinct viral communities, with high relative diversity in both WWTPs and river samples. DNA viruses of the class Caudoviricetes (92-98 %) were dominant, with significantly higher richness observed in WWTPs compared with river samples. Human associated viruses, especially CrAssphages, were frequently detected in WWTP samples. We further reconstructed 1, 990 viral metagenome assembled genomes (vMAGs), from high quality viral contigs, which encoded 1200 AMGs. These AMGs were linked to functions related to carbohydrate, nitrogen and sulfur metabolism, highlighting the potential role of viruses in transforming key compounds. Host prediction linked these vMAGS to four putative bacterial hosts including Actinobacteriota, Bacteroidota, Firmicutes and Proteobacteria. Overall, our results provide new insights into the ecological role of viruses in WWTPs and river systems. In addition to shaping microbial dynamics, our data hint at the role played by viruses towards pollution degradation and nutrient cycling thereby influencing ecosystem function in human-impacted aquatic environments.