The natural ability of bacteria to clean up pollutants from soil, water and mine waste could be significantly enhanced through the use of a “friendly” compatible virus, according to new research led by Flinders University.
The study, published in Communications Biology, suggests that phage virus “bioaugmentation” represents a promising new direction for environmental biotechnology.
The approach works by harnessing the ecological roles of lysogenic phages to boost microbial function in polluted soils.
Traditional bioaugmentation methods, which involve introducing helpful microbes into contaminated environments, are cost-effective and sustainable but often face challenges such as slow degradation rates and environmental limits on microbial performance.
Phage bioaugmentation uses lysogenic bacteriophages, which are viruses that infect bacteria and integrate into their host’s genomes without immediately killing them.
These viruses can transfer pollutant-degrading genes, effectively bolstering the genetic capabilities of bacteria already working to break down contaminants.
Pollution remains a pressing global issue, with industrialisation having contaminated millions of soil and water sites worldwide.
These contaminants pose serious threats to human health, agricultural productivity and ecological balance.
Common pollutants including arsenic, chromium, polychlorinated biphenyls, pesticides, petroleum hydrocarbons and excess nutrients disrupt ecosystems and impair the microbial communities essential for healthy soil and nutrient cycling.
Such impacts can also degrade groundwater quality, putting drinking water resources at risk. Protecting soil microbiomes is therefore seen as critical for ecosystem resilience, environmental health and public wellbeing.
Flinders University researcher Niki Romeo stated that it can take years for microbes to naturally break down toxins and pollutants.
Lysogenic phages, however, are able to integrate auxiliary metabolic genes into bacterial hosts to improve degradation rates, helping to address the cost and limitations associated with conventional in-situ remediation methods.
The researchers note that regulatory frameworks will need to evolve alongside such biotechnologies to properly assess ecological safety, genetic stability and the 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,” stated Flinders University PhD candidate Niki Romeo.
In the meantime, the research team stated that the method warrants further investigation through field experiments to validate the most effective in-soil candidate phages and to develop tools capable of monitoring phage integration and gene expression.
“If used well, phage bioaugmentation could be used in controlled conditions to help restore polluted environments and promote microbial resilience,” she said.
The research builds on a broader body of bacteriophage studies led by the Flinders Accelerator for Microbiome Exploration, alongside related work from the Restoration Ecology group at the College of Science and Engineering.
Matthew Flinders Professor Martin Breed, who co-supervises Romeo’s PhD, stated that soil remediation and ecosystem restoration are vital to improving living conditions for humans and other life on Earth.
He noted that 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 immune system training.
