News release

From: Flinders University

New way to help clean up environmental pollution

The ability of bacteria to remove pollutants from soil, water, mine waste and other environments could be supercharged by a ‘friendly’ compatible virus, according to a study led by Flinders University.

The new insights, published in Communications Biology, suggests phage virus ‘bioaugmentation’ offers a compelling new direction for environmental biotechnology, by harnessing the ecological roles of lysogenic phages to enhance microbial function in polluted soils.

Traditional bioaugmentation strategies, while cost-effective and sustainable, face challenges including slow degradation rates and environmental constraints on microbial efficacy.

Phage bioaugmentation using lysogenic bacteriophages – viruses that infect bacteria and integrate into their host’s genomes without immediately killing them – use pollutant-degrading genes to bolster the bacteria’s genetic capabilities for bioremediation.

Pollution of natural ecosystems is a global concern, with industrialisation contaminating millions of soil and water sites. These contaminants threaten human health, agricultural productivity, and ecological balance.

Pollutants such as arsenic, chromium, polychlorinated biphenyls, pesticides, petroleum hydrocarbons, and excess nutrients, disrupt ecosystem impair microbial communities essential for soil health and nutrient cycling. These impacts degrade groundwater quality, threatening drinking water resources.

Safeguarding soil microbiomes is critical for ecosystem resilience, the environment and public health.

Flinders University researcher Niki Romeo says it can take years for microbes to break down toxins and pollutants, with lysogenic phages able to integrate auxiliary metabolic genes (AMGs) into bacterial hosts to improve degradation – helping to address the cost and limitations of conventional in-situ methods.

The researchers say regulatory frameworks would need to evolve with such biotechnologies to assess ecological safety, genetic stability and long-term impacts of releasing engineered phages into natural environments.

“Issues such as gene transfer potential, persistence, containment, and unintended effects on non-target organisms will need to be addressed through biosafety protocols and environmental risk assessments before field-scale deployment,” says Flinders UniversityPhD candidate Niki Romeo.

In the meantime, the method warrants further investigation on field experiments to validate the most effective in-soil candidate phage and to develop tools to monitor phage integration and AMG expression.

“If used well, phage bioaugmentation could be used in controlled conditions to help restore polluted environments and promote microbial resilience,” she says.

The research accompanies a wealth of other bacteriophage studies led by the Flinders Accelerator for Microbiome Exploration and other research by the Restoration Ecology group at the College of Science and Engineering.

Matthew Flinders Professor Martin Breed, who co-supervises Ms Romeo’s PhD, says soil remediation and ecosystem restoration are critical elements in improving living conditions for humans and other life on Earth.

Urban soil biodiversity sustains critical ecosystem functions such as nutrient cycling and plant growth, while also supporting human health through pathogen suppression, soil remediation and human immune system training, he says.

The mini review article, ‘Phage bioaugmentation reveals the potential of lysogeny for soil bioremediation’ (2026) by Niki Romeo, Ernestina Hauptfeld (Utrecht University), Qi Yang (CSIRO) and James G Mitchell has been published in Communications Biology DOI: 10.1038/s42003-026-10106-1.

Acknowledgements: The research is supported by a Playford Memorial Trust and Thyne Reid Foundation PhD scholarship to NR and a European Research Council grant to EH. Thanks to the South Australian Environmental Protection Agency for support.