Aromatic compounds, such as dioxins and benzene, are major soil pollutants. Their high chemical stability makes them resistant to microbial and chemical degradation, leading to toxic accumulation in the soil.
Previous studies have used genetic engineering to enhance the capacity of microorganisms to degrade environmental pollutants. However, strict ecological regulations restrict the use of genetically engineered microorganisms (GEMs) in natural environments.
In a study published in the Journal of Materials Chemistry A , Nagoya University researchers demonstrated that native soil bacteria, when treated with decoy molecules, can degrade non-native compounds, including persistent pollutants such as dioxins, without genetic modification.
"In other words, we can effectively give these bacteria capabilities they do not naturally have, while keeping them in their original state," said Professor Osami Shoji , the study's lead author.
Shoji and doctoral students Fumiya Ito and Masayuki Karasawa at Nagoya University's Graduate School of Science investigated the application of cytochrome P450, a widely distributed group of enzymes that degrade and convert substances in living organisms.
Cytochrome P450BM3, derived from the soil bacterium Priestia megaterium, naturally hydroxylates fatty acids but does not interact with pollutants such as dioxins. This substrate selectivity arises from the lock-and-key mechanism, which allows only molecules with a specific shape to bind to the enzyme.
While the GEM approach introduces mutations to alter enzyme binding sites for target molecules, the team instead used decoy molecules that mimic fatty acids to induce the enzyme to degrade pollutants.
"In our previous research, we successfully induced otherwise unlikely reactions by deceiving enzymes with decoy molecules," said Shoji.
Decoy molecules bind to enzymes in a manner similar to fatty acids; however, their shorter chain length prevents them from reaching the active site. This configuration creates a confined reaction space that allows molecules to enter and undergo hydroxylation. Because decoy molecules are not themselves hydroxylated, they maintain their function and continue to facilitate the enzymatic reaction.
Assessment of decoy molecules in soil bacteria
Researchers evaluated the biochemical responses of 10 bacterial strains, each harboring cytochrome P450BM3 or closely related enzymes, using a set of 76 decoy molecules.
The results showed that benzene hydroxylation occurred only with particular strain-decoy combinations. The tested strains included P. megaterium, which contains cytochrome P450BM3, as well as other common soil bacteria, such as Bacillus subtilis, which possess closely related enzymes.
Gene-knockout experiments further confirmed the involvement of cytochrome P450 in these bacteria.
These bacteria also successfully hydroxylated other aromatic compounds, including toluene, xylene and naphthalene.
Surprisingly, in the presence of decoy molecules, B. subtilis completely degraded dioxin model compounds within two hours at 45 degrees Celsius. Computational simulations demonstrated that cytochrome P450 in B. subtilis has sufficient binding capacity to accommodate both a decoy molecule and dioxin, which is a larger pollutant than benzene.
The findings indicate that the decoy molecule-induced hydroxylation activity in these bacteria increases the solubility of pollutants and facilitates their degradation. This mechanism could accelerate the removal of soil pollutants by supporting faster and more efficient microbial degradation.
Conclusion and future perspectives
Systematic screening of diverse soil bacteria, combined with various decoy molecules, enabled the identification of highly active combinations. Notably, multiple bacterial species responded to these molecules, suggesting that this approach could be broadly applicable rather than limited to a specific organism.
Shoji concluded, "Our study provides a generalizable chemical strategy to unlock latent catalytic potential in ubiquitous environmental microbes, establishing a new paradigm for scalable, regulation-compatible bioremediation technologies."
Paper information:
Fumiya Ito, Masayuki Karasawa, and Osami Shoji (2026). Chemical activation of native cytochrome P450s in soil-derived bacteria by external molecules enables biodegradation of aromatic pollutants, Journal of Materials Chemistry A. DOI: 10.1039/d5ta09218c
