Metagenomic and viromic data mining reveals viral threats in biologically treated domestic wastewater

Activated sludge (AS), a common biological secondary treatment process in wastewater treatment plants (WWTPs), is known to remove a large spectrum of microorganisms. Yet little is known about its effect on the entire viral community. After compiling 3 Tbp of next-generation sequencing (NGS) metagenomic/ viromic datasets consisted of 119 sub-datasets of influent, effluent, and AS samples from 27 WWTPs, viral removal efficacy is evaluated through data mining. The normalized abundance of viruses suggests effluents exhibit the highest viral prevalence (3.21 +/- 3.26%, n = 13) followed by the AS (0.48 +/- 0.25%, n = 57) and influents (0.23 +/- 0.17%, n = 17). In contrast, plasmids, representing genetic element of bacteria, show higher average prevalence (0.73 +/- 0.82%, n = 17) in influents than those of the AS (0.63 +/- 0.26%, n = 57) and effluents (0.35 +/- 0.42%, n = 13). Furthermore, the abundance-occupancy analysis identifies 142 core phage viruses and 17 non-phages core viruses, including several pathogenic viruses in the AS virome. The persistent occurrence of pathogenic viruses, coupled with nonfavorable virus removal by the AS treatment, reveals the hidden virus threats in biologically treated domestic wastewater. The mechanisms for why viruses persist and the possibility that WWTPs are potential hotspots for viral survival deserve attention. (C) 2021 The Author(s). Published by Elsevier B.V.

Automated summary

Activated sludge treatment process effectively removes a large spectrum of microorganisms, but its impact on the entire viral community remains unclear. Research showed that viral removal efficacy in wastewater treatment plants is suboptimal, highlighting potential viral threats in biologically treated domestic wastewater.