Eliminating waste Genetic-engineered bacteria break down industrial contaminants Five clusters of genes from different organisms put into a single bacterial strain. John Timmer – May 7, 2025 4:50 pm | 2 Credit: Aldo Pavan Credit: Aldo Pavan Story text Size Small Standard Large Width * Standard Wide Links Standard Orange * Subscribers only   Learn more Over the last century or more, humanity has been developing an ever-growing list of chemicals that have never been seen by Earth's creatures. Many of these chemicals end up being toxic contaminants that we'd love to get rid of, but we struggle to purify them from the environment or break them down once we do. And microbes haven't had much chance to evolve the ability to break them down for us. Over the last few years, however, we've found a growing number of cases where bacteria have evolved the ability to break down industrial contaminants and plastics. Unfortunately, these bacteria are all different species, target different individual contaminants, and thrive in different environments. But now, researchers have developed a new way to take the genes from all these species and place them in a single bacterial strain that can decontaminate complex waste mixtures. Targeting contaminants The inspiration for this work was the fact that a lot of industrial contamination contains a mixture of toxic organic molecules, but is found in brackish or salty water. So, the research team, based in Shenzhen, China, started by simply testing a number of lab strains to determine the ability to survive these conditions. The one that seemed to do the best is called Vibrio natriegens. These bacteria were discovered in a salt marsh, and their primary claim to fame is an impressive growth rate, with a population being able to double about every 10 minutes. Unfortunately, Vibrio natriegens doesn't have the sophisticated molecular tools that are available in a species like E. coli. So, the researchers spent some time making Vibrio natriegens a bit more amenable to manipulations, making it more capable of taking up DNA and incorporating it into a specific location in the genome. Once that was done, the researchers started looking through the genomes of species that have been identified as breaking down industrial contaminants. The breakdown of complex molecules typically involves more than one enzyme, and the genes for these enzymes tend to end up clustered together, so that they can be produced as a single, large RNA that encodes all the proteins needed. This simplifies regulating their production, making it easy to ensure the bacteria only make the proteins if the molecule they break down is actually present. In this case, the clusters ranged from just three genes all the way up to 11. Once nine of these gene clusters were identified, the DNA that would encode them was ordered and assembled into a single DNA molecule in yeast. The researchers took some time while ordering this DNA to better optimize the genes to be active and produce proteins in Vibrio natriegens, as opposed to whatever species the genes were normally used by. From yeast, each of these individual gene clusters was inserted into Vibrio natriegens, creating different strains that could digest one of the following: benzene, toluene, phenol, naphthalene, biphenyl, DBF29, and dibenzothiophene (DBT). (Some of the nine clusters target the same contaminant.) Each of these bacterial strains was then put in a solution with the chemical they were engineered to digest. Five of the nine worked, giving researchers strains that could digest biphenyl, phenol, napthalene, DBF, and toluene. Good, but limited From there, the researchers developed a system that would enable them to iteratively insert a new gene cluster at the tail end of a previously inserted gene cluster. This allowed them to build up a cluster of clusters, eventually including all five of the ones that had shown activity in the earlier tests. Given two days, this single strain could remove about a quarter of the phenol, a third of the biphenyl, 30 percent of the DBF, all of the naphthalene, and nearly all of the toluene. All those contaminants came from a mixture created by the researchers specifically for the test. To get a better sense of its capabilities, the team got hold of two wastewater mixtures that also included some salt in the water. Here, the engineered Vibrio natriegens strain proved highly effective, eliminating over 95 percent of most chemicals, and about 80 percent of phenol. The strain also worked against contaminated soil. That said, this shouldn't be seen as the solution to contamination with organic chemicals. For starters, there were a number of chemical targets that weren't digested—not to mention a huge range of chemicals that weren't tested. In addition, Vibrio natriegens doesn't grow especially well when salt isn't present, so it can't just be unleashed on all of our contamination. But perhaps the biggest problem is that, unlike the bacteria that the gene clusters originated in, Vibrio natriegens has no way of using the broken-down products of these reactions. Other bacteria evolved these gene clusters because the clusters allowed them to incorporate the breakdown products as if they were food. In contrast, Vibrio natriegens lacks the enzymes that enable this sort of incorporation; instead, these chemical products just end up sitting around when the bacteria are done digesting. That means that, while this engineered strain gets rid of dangerous chemicals, it will leave a variety of less dangerous chemical contaminants. And, since the Vibrio natriegens can't use this material as food, there's no evolutionary selection going on for the activity of these engineered gene clusters. That means that there's no pressure to even keep the gene clusters around (though the researchers confirmed they weren't lost during these experiments). Also, no pressure that could improve their activity further. So, in the long term, it might be best to start plugging the pathways that break down contaminants into the cell's basic metabolism. Despite these limitations, though, the work is a clear demonstration of the potential of bacteria to help us clean up some of the messes we're making. Nature, 2025. DOI: 10.1038/s41586-025-08947-7  (About DOIs). John Timmer Senior Science Editor John Timmer Senior Science Editor John is Ars Technica's science editor. He has a Bachelor of Arts in Biochemistry from Columbia University, and a Ph.D. in Molecular and Cell Biology from the University of California, Berkeley. When physically separated from his keyboard, he tends to seek out a bicycle, or a scenic location for communing with his hiking boots. 2 Comments