Bacterial immune defenses persist through wastewater treatment

Bacteria are engaged in a constant battle with viruses, even in human-made environments. In a new study, researchers have mapped how bacterial defense systems against viruses behave in urban wastewater systems – from sewers and hospital wastewater to biological treatment plants.

According to Professor Søren J. Sørensen of the University of Copenhagen, senior author of the study, the findings provide new insight into microbial adaptation in human-engineered ecosystems:

- We can see that bacterial defenses against viruses do not simply disappear when bacteria are exposed to wastewater treatment. Instead, key defense genes are preserved on mobile genetic elements that can circulate between different bacteria, he says.

By analyzing DNA from wastewater collected in Denmark, Spain, and the United Kingdom, the researchers tracked bacteria, viruses, and their genetic defense mechanisms throughout the entire treatment process. The study provides the first comprehensive overview of how bacterial immune defenses are distributed and reshaped in wastewater environments. 

Treatment reduces bacteria – but not their genetic defenses

The results show that both the abundance and diversity of bacterial defense systems decline during biological wastewater treatment. However, this reduction is not directly linked to the number of bacteria present.

Professor Søren J. Sørensen explains:

- The explanation lies in plasmids – mobile genetic elements that bacteria can exchange with one another. We found that bacterial defense genes are far more concentrated on plasmids than on bacterial chromosomes, and that this distribution remains largely stable throughout the treatment process.

Mobile genetic elements act as genetic reservoirs

In particular, conjugative plasmids, which can actively transfer between bacteria, play a central role. These plasmids act as genetic reservoirs, allowing bacterial antiviral defenses to be preserved and disseminated even as bacterial community composition changes dramatically during wastewater treatment.

The study also reveals a close association between viral abundance and bacterial defense systems, pointing to ongoing evolutionary adaptation between bacteria and their viruses in wastewater environments.

Perspectives: implications for antibiotic resistance and phage therapy

Antibiotic resistance is a growing global health challenge, driven largely by mobile antibiotic resistance genes that spread between bacteria via plasmids and other mobile genetic elements.

In this context, phage therapy – the use of viruses to treat bacterial infections – has gained renewed attention as a potential alternative or complement to antibiotics. The present study provides important foundational knowledge by demonstrating that genes conferring resistance to bacteriophages are already widespread in the environment and are closely linked to the same mobile genetic mechanisms.

- Phage therapy is often highlighted as a promising alternative to antibiotics in the fight against resistant bacteria. But our study shows that bacteria already harbor substantial genetic preparedness to resist viral infection in the environment. In other words, we are not starting from zero – the bacteria are already prepared, says Søren J. Sørensen.

The study therefore underscores the importance of developing phage therapy with care and grounding it in a solid understanding of bacterial immune defenses – and of the dynamics created when resistance genes are linked to mobile genetic elements in the environment.

The results – which have just been published in the renowned journal Microbiome – could have implications for the development of future treatments against antibiotic-resistant infections. Read the results here.