DNA tracer degradation and adsorption in environmental matrices

Synthetic DNA tracers are a promising tool for tracking water contamination pathways. However, quantitative data are lacking on their degradation and adsorption in environmental matrices. Laboratory experiments were conducted to exam the degradation of multiple DNA tracers in stream water, groundwater, and domestic and dairy-shed effluent, and adsorption to stream sediments, soils, coastal sand aquifer media and alluvial sandy gravel aquifer media. The selected DNA tracers were double stranded 302 base pair (bp) and 352 bp in lengths. Their internal amplicons used for qPCR detection were almost the same, but the 352 bp tracers had longer non-amplified flanking regions.

Overall, 352 bp tracer degradation was significantly slower than that of the 302 bp tracers (p = 0.018). Results of thermodynamic analysis indicated that the 352 bp tracers had greater tracer stability. These findings are consistent with our previous field observations that 352 bp tracer reductions were consistently lower than 302 bp tracer reductions in stream water, groundwater, and soils. These findings suggest that longer non-amplified flanking regions may better protect DNA tracers from environmental degradation. In general, the DNA tracers degraded more quickly in the stream water and effluent samples than in the groundwater samples, and fast DNA tracer degradation was associated with high bacterial concentrations.

The two sets of DNA tracers differed little in their adsorption to stream sediment-stream water or aquifer media-groundwater mixtures (p > 0.067). However, the 352 bp tracers adsorbed significantly less to soil-effluent mixtures than the 302 bp tracers (p = 0.005). Compared to their adsorption to the aquifer media-groundwater and stream sediment-stream water mixtures, DNA tracer adsorption to soil-effluent mixtures was relatively less. A plausible explanation is that DNA tracers may compete with like-charged organic matter for adsorption sites, thus were less adsorbed to environmental media in the presence of organic matter.

Our study findings provide insights into the fate of DNA tracers in the aquatic environment and may assist with the future design of DNA tracers for environmental studies. The DNA tracer degradation rates established in this study for a range of environmental conditions could be used to inform the design of future field investigations, such as injection concentrations, sampling distances and experimental durations.