Aromatic compounds such as dioxins and benzene are major soil contaminants. Due to its high chemical stability, it is resistant to microbial and chemical degradation, which leads to the accumulation of toxic substances in the soil.
Previous research has used genetic engineering to enhance the ability of microorganisms to degrade environmental pollutants. However, strict ecological regulations limit the use of genetically modified microorganisms (GEMs) in natural environments.
In a study published in Journal of Materials Chemistry A, Researchers at Nagoya University have demonstrated that treating native soil bacteria with decoy molecules can degrade foreign compounds, including persistent pollutants such as dioxins, without genetic modification.
In other words, it is possible to effectively give bacteria abilities that they do not have, while keeping them in their original state. ”
Lead author of the study, Professor Osumi Shoji
Shoji and doctoral students Fumiya Ito and Masayuki Karasawa from the Nagoya University Graduate School of Science studied the application of cytochrome P450, a widely distributed enzyme group that breaks down and transforms substances in living organisms.
Cytochrome P450BM3 derived from soil bacteria Pristia Megatheriumnaturally hydroxylates fatty acids, but does not interact with contaminants such as dioxins. This substrate selectivity results from a lock-and-key mechanism that allows only molecules with a specific shape to bind to the enzyme.
Unlike the GEM approach, which introduces mutations that change the enzyme-binding site of a target molecule, the researchers instead used a decoy molecule that mimics fatty acids and induces the enzyme to break down the pollutant.
“In our previous research, we succeeded in tricking enzymes with decoy molecules and causing impossible reactions,” says Professor Shoji.
Decoy molecules bind to enzymes in a manner similar to fatty acids. However, due to the short length of the chain, it cannot reach the active site. This configuration creates a confined reaction space that allows molecules to enter and undergo hydroxylation. Since the decoy molecule itself is not hydroxylated, it remains functional and continues to facilitate enzymatic reactions.
Evaluation of decoy molecules in soil bacteria
The researchers used a set of 76 decoy molecules to assess the biochemical responses of 10 bacterial strains, each carrying cytochrome P450BM3 or a closely related enzyme.
The results showed that benzene hydroxylation occurs only with certain strain and decoy combinations. Strains tested include: P. megatherium, This includes cytochrome P450BM3 and other common soil bacteria. Bacillus subtilishave closely related enzymes.
Gene knockout experiments further confirmed the involvement of cytochrome P450s in these bacteria.
These bacteria were also successful in hydroxylating other aromatic compounds such as toluene, xylene, and naphthalene.
Surprisingly, in the presence of decoy molecules, Bacillus subtilis Dioxin model compounds are completely degraded within 2 hours at 45 degrees Celsius. Computer simulations show that cytochrome P450 Bacillus subtilis has sufficient binding capacity to accommodate both the decoy molecule and dioxin, a larger pollutant than benzene.
This finding indicates that the hydroxylation activity induced by decoy molecules in these bacteria increases the solubility of pollutants and promotes their degradation. This mechanism may accelerate the removal of soil contaminants by supporting faster and more efficient microbial decomposition.
Conclusion and future prospects
By systematically screening various soil bacteria and combining them with various decoy molecules, it became possible to identify highly active combinations. Remarkably, multiple bacterial species responded to these molecules, suggesting that this approach is not limited to specific organisms but may be broadly applicable.
Professor Shoji concluded: “Our work provides a generalizable chemical strategy to unlock the catalytic potential of ubiquitous environmental microorganisms and establishes a new paradigm for scalable and compliant bioremediation technology.”
sauce:
Reference magazines:
Fumiya Ito (2026). Chemical activation of natural cytochrome P450 in soil-borne bacteria by external molecules enables the biodegradation of aromatic pollutants. Materials Chemistry Journal A. DOI: 10.1039/d5ta09218c. https://pubs.rsc.org/en/content/articlelanding/2026/ta/d5ta09218c
