Metagenomics reveals overlooked viral risks in treated water

Viruses are everywhere in wastewater treatment plants, quietly interacting with bacteria as sewage is cleaned and reused. A new study reveals that these viral communities are far more complex and influential than previously recognized, with implications for water safety, antibiotic resistance, and how treatment performance is monitored.

In research published in Biocontaminant, scientists used advanced metagenomic sequencing to track viruses and their microbial hosts across full scale wastewater treatment plants in China and Singapore. By analyzing samples from influent to final effluent, the team uncovered persistent viral populations that survive treatment and interact closely with disease causing bacteria.

Wastewater treatment plants are designed to remove pollutants and known pathogens, but viruses have largely been overlooked. Our results show that viruses are not just passive passengers. They actively shape microbial processes and may influence both treatment efficiency and health risks."

Shu Hong Gao, corresponding author of Harbin Institute of Technology

The researchers identified 99 families of viruses across 28 wastewater and sludge samples. Two viral groups, Peduoviridae and Casjensviridae, were consistently abundant throughout all treatment stages, from raw sewage to treated effluent. Their persistence suggests they could serve as reliable biological indicators of treatment performance.

Traditionally, wastewater monitoring relies on bacterial indicators such as Escherichia coli. However, the study found that E. coli did not track viral dynamics well. Instead, the abundances of Pseudomonas aeruginosa and Aeromonas caviae, both opportunistic pathogens, closely mirrored the behavior of dominant viruses.

"This challenges the idea that one or two standard bacteria can represent overall biological risk," Gao said. "Our findings suggest that alternative indicators linked to viral populations may provide a more accurate picture of treatment effectiveness."

Beyond identifying viruses, the team explored what these viruses can do. Many carried auxiliary metabolic genes, which can alter the metabolism of their bacterial hosts. These genes were linked to carbohydrate metabolism, pollutant degradation, and xenobiotic breakdown, processes that may help wastewater systems remove contaminants more efficiently.

At the same time, the study uncovered a potential downside. Some viral genes may enhance the competitiveness of antibiotic resistant bacteria, indirectly promoting the spread of antibiotic resistance genes.

"These viral functions act like a double edged sword," Gao explained. "They may support pollutant removal, but they can also increase the risk of resistance spreading among pathogens."

Using machine learning to predict virus host relationships, the researchers found that most viruses targeted bacteria within the phylum Pseudomonadota, which includes many multidrug resistant pathogens commonly detected in wastewater. This highlights wastewater treatment plants as hotspots where viral host interactions could influence microbial evolution before water is released back into the environment.

Importantly, disinfection steps did not eliminate all viral functions. In some plants, viral metabolic genes persisted even after final treatment, suggesting that current processes may not fully address viral associated risks.

The authors say their work supports expanding wastewater surveillance beyond traditional indicators and incorporating viral monitoring into routine assessments.

"Understanding virus host networks gives us new tools to manage biological risks," Gao said. "With better monitoring and targeted process optimization, wastewater treatment can be made safer and more resilient in a world facing growing public health challenges."

The study provides a foundation for improving wastewater reuse safety and for developing next generation monitoring strategies that reflect the true biological complexity of engineered water systems.