Tracing groundwater flow paths in a contaminated fractured and karst aquifer using fluorescent dyes and silica-encapsulated DNA nanoparticles: challenges and insights

Reconstructing flow directions and velocities in highly heterogeneous contaminated aquifers, such as fractured and karstified systems, poses significant challenges. These arise from both the inherent complexity of the hydrogeological context and the technical and physicochemical interferences that contaminated sites can impose on the logistics and outcomes of tracer tests.

A short-term (14-day) tracer test was conducted under perturbed conditions in a fractured and karstified aquifer in Southern Italy, at a site contaminated by petroleum hydrocarbons and other pollutants. The objective was to gather critical insights into the dynamics of subsurface flow to inform subsequent contamination management and remediation strategies. Multiple tracers were used, including fluorescent dyes and silica-encapsulated DNA-labeled nanoparticles. Silica-encapsulated DNA nanoparticles hold significant potential as hydrogeological tracers due to their non-toxic nature, physicochemical stability, and exceptional detectability at extremely low concentrations via qPCR. However, their performance in real-world applications remains under investigation.

Three synthetic DNA nanotracers were injected into three wells, alongside two conservative dye tracers, Uranine and Tinopal. All three DNA tracers were successfully detected in groundwater samples collected from pumping wells at distances ranging from 30 to 160 meters from the injection point, indicating flow velocities between 7 and 130 m/day. While the fluorescent dyes traveled at comparable velocities, they covered shorter distances and exhibited delayed peak arrivals relative to the DNA tracers. Additionally, the detection of fluorescent dyes was sometimes hindered by the presence of hydrocarbons, a limitation that did not affect the DNA nanotracers. The tracer recovery results ultimately facilitated the identification of primary and secondary groundwater flow directions, some of which deviated from expectations based on the site’s preliminary conceptual groundwater flow model. Overall, the tracer test results underscored notable differences between the two tracer types, suggesting that DNA nanotracers and fluorescent dyes may navigate distinct porosity systems, offering complementary insights into the aquifer's structure and dynamics.

While the results are promising and demonstrate the potential of combining fluorescent dyes and DNA nanotracers for applications in highly heterogeneous contaminated aquifers, further research is needed to evaluate the versatility of DNA tracers in field applications. This includes addressing both field and analytical challenges, as well as better assessing their comparative utility relative to conventional dye tracers.