Evaluation of Synthetic DNA Tracers for Tracking Water Flow Paths Using Droplet Digital PCR

Tracer tests are commonly used for determining the flow pathways of contaminants in surface and groundwater systems. However, limited options for conventional tracers such as chemical dyes, elements or streamflow gain and loss measurements as well as toxicity and watershed memory hinder their effectiveness in the characterization of complex hydrogeological regimes with numerous possible flow paths. To overcome these limitations, a study was conducted to develop and evaluate novel synthetic DNA-based tracers. Synthetic DNA tracers are advantageous because they have a low detection limit and have thousands of possibilities for unique tracers which can be used to identify multiple flow pathways simultaneously. Five unique DNA sequences were designed using an online random sequence generator, and checked for similarity to naturally occurring sequences using NCBI BLAST. A microcosm study was performed to evaluate the durability of the synthetic DNA tracers. A series of column experiments were conducted to determine how the tracers behaved in different types of media and to generate a breakthrough curve. Once the tracers were recovered and quantified using droplet digital PCR (ddPCR) for the laboratory-scale experiments, a set of field experiments was conducted whereby one of the synthetic DNA tracers was deployed in the southern reach of Helotes Creek. Water samples were collected and transported back to the laboratory for quantification using ddPCR. The results of this study demonstrate the feasibility of an engineered DNA tracer system and the effectiveness of droplet digital PCR in quantifying the tracers.