Synthetic DNA Tracers Enable Ultra-High-Reproducibility Characterization of Aquifer Hydraulic Conductivity and Contaminant Transport

Abstract Reliable characterization of aquifer hydraulic conductivity (K) via tracer-based methods remains a major challenge due to environmental background noise. We report that synthetic DNA tracers, free of background-noise interference, enable highly reproducible tomographic inversion of K fields across six replicate experiments conducted in a heterogeneous laboratory sandbox measuring 180 cm (length) × 10 cm (width) × 90 cm (height) at a steady flow rate of approximately 177.4 cm3 min–1. The results demonstrate superior reproducibility of the DNA tracers relative to dye tracers across three evaluation levels: travel-time consistency, where the contrast is most pronounced (mean R2 = 0.84 for DNA tracers versus R2 = 0.10 for dye tracers), inverted lnK field coherence, and prediction-level robustness. Contaminant-transport forecasts under four scenarios, spanning pulse versus continuous releases and conservative versus decaying solutes, further indicate that DNA-derived K fields yield substantially more stable predictions than dye-derived K fields in nearly all cases. These advantages arise from the standardized molecular design of oligonucleotides and their sequence-specific quantitation via qPCR, which collectively mitigate background interference and tracer-specific transport artifacts. These findings show that synthetic DNA tracers constitute a promising tool for aquifer characterization, addressing a critical gap in tracer-based tomography for groundwater investigations.