By Maya Suzuki, Summer Intern in Dr. Claudia Gunsch’s Lab
A single microbe cell cannot clean up a pollutant, but a community of microbes can! This is the promising collective power of organisms used in bioaugmentation.
Let’s start with a few definitions. Bioaugmentation is a technique that involves implanting a pollutant-degrading organism into a contaminated environment to speed up the break down of contaminants. Bioremediation, which is the use of natural or introduced microorganisms to clean up environmental contaminants, includes bioaugmentation and other similar strategies.
Bioaugmentation is a simple idea that holds a lot of promise to clean up polluted environments quickly and cheaply. But, there are still some shortcomings. When you insert a pollutant-degrading microbe into contaminated soil: remediation can occur initially, but won’t necessarily continue long-term. This is because the useful microbe may not survive in that environment and end up dying off a few days after. Here is where the “augmented” part of the term comes in. In genetic bioaugmentation, we introduce microbes that hold pollutant-degrading genes, with the goal of transferring those genes to the native microbes that are better equipped at surviving in that setting. Genetic bioaugmentation is additionally anticipated to overcome ethical barriers genetically engineering microbes might have.
Enough background – this summer I had the opportunity to work on my dream project. I worked in Dr. Claudia Gunsch’s lab, where we use genetic bioaugmentation to remediate polycyclic aromatic hydrocarbons (PAHs). We are studying how ecological growth strategies, such as fast-growing r-strategists, vs. slow-growing K-strategists, impact how effectively the PAH-degrading gene can be transferred and how effectively the PAH is degraded.
My work this summer helps us to begin answering some of these big questions. I have been performing multiplex qPCR reactions with various human-designed microbe communities, optimizing these for later conjugation (plasmid transfer) experiments. Even this rather preliminary process of running qPCR cycles has been a learning experience for me. For one, it is a rare chance to refine a laboratory technique that I will need further down the line, perhaps as I continue working in the Gunsch lab. In preparing a qPCR plate, precision is needed wherever possible. One must not forget to add all reagents to the master mixes. When plating the gene fragments and master mixes, one must be extraordinarily wary of potential contamination. As a result, I can confidently say that my pipette skills have gotten really good!
In addition to qPCR, I have also practiced growing liquid cultures, running many DNA extractions and quantifying DNA with Qubit. These skills will come in extremely handy for when we start running experiments with each microbe community. I am very excited that I got to take part in my mentor, Paige Varner’s PhD research project.
The work continues. I cannot wait to continue working with the conjugation experiments in the fall, where we will observe whether the naphthalene-degrading gene got transferred and the naphthalene degraded.