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Our lab investigates how bacteria rewire their metabolism to facilitate the process of “bioremediation” – using living organisms to clean up the environment. We’re most interested in the bioremediation of the toxic heavy metal chromium, Cr(VI). High levels of Cr(VI) are incompatible with most life. However, some bacteria are able to not only survive in its presence, but also reduce it to a much less hazardous form, Cr(III). A sort of biological "detox" if you will. This form of remediation is much more environmentally-friendly and sustainable than conventional chemical and physical methods.
Through screening of a public culture collection, we identified uncharacterized strains of the friendly soil bacterium Bacillus safensis with this Cr(VI)-resisting and reducing superpower. We uncovered this superpower using a DPC (1,5-diphenylcarbazide)-based assay. "Assay" is just a fancy word for an experiment where you're measuring something. And in this case, we were measuring Cr(VI) (that's the bad stuff, remember). DPC reacts with Cr(VI) (but not Cr(III)) to form a purple complex. If we add Cr(VI) to the media (broth) the bacteria is growing in, and test the broth with the DPC assay, we will see a purple color unless the bacteria were able to reduce the Cr(VI). In such a case, the purple color would "disappear." And this is what we found happen with many of the strains.
Now, we're starting to look under the hood (or I guess under the cell wall would be more precise) metabolically in order to figure out how these bacteria rewire their metabolism during the process.
The central focus of our investigation is the enzyme malate dehydrogenase (MDH), which plays a central role in central metabolism. It serves as a sort of coordinating hub whose activities and interactions can help direct carbon metabolism to meet the need for energy, the need for metal-chelating metabolites, and the need for reducing equivalents to counteract reactive oxygen species (ROS) generated by metal stress.
It can also directly produce oxaloacetate, which can be secreted and serve as a chelator (metal grabber) to precipitate metals, extracting them from the soil before they can do damage.
Through recombinant protein expression, we get E. coli cells to make a lot of the Bacillus safensis MDH protein, which we then purify.
Then we can test its activity using an MDH enzymatic assay. Having the pure protein lets us manipulate conditions to test its limits, how it's affected by its environment such as pH, temperature, even the presence of metals. We can even make changes to the protein's sequence to tease apart how it works.
In vitro is great for that sorts of things, but not very realistic. Therefore, back at the organismal level, we're comparing the metabolism of different strains and bacterial species in the presence of metals, using analytical methods like HPLC to measure metabolites.
We're also doing some genetic engineering.
With these in vivo experiments, we aim to help tease apart both conserved and unique metabolic adaptations.
Simultaneously, we are working to put this knowledge to practical use. We are optimizing the bioremediation potential of Bacillus safensis with hopes of using it to clean up heavy metal-contaminated environments and promote the growth of plants in once-barren landscapes.
Our work is undergraduate–driven and I’m so proud of the student researchers I have the privilege of working with!
Stay up to date with research from the Bibel lab through our YouTube playlist:
Stay up to date with research from the Bibel lab through our YouTube playlist:
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