TRACKING THE SOURCES AND PATHWAYS OF GROUNDWATER
CONTAMINATION USING SYNTHETIC DNA TRACERS
Pang L1, Robson B1, Gillot L1,2, Varsani A3, Farkas K1,3, Abraham P1, Humphries B1
1
Institute of Environmental Science & Research Ltd (ESR)
Intern MSc student from Aix Marseille University
3
University of Canterbury
2
Background
With an expansion of animal farming and urbanisation in New Zealand, groundwater resources
(often used for drinking water) are increasingly exposed to pollution from animal and human
faecal wastes. This has resulted in an increased need for investigating the contamination sources
and their pathways in groundwater using effective tracing techniques.
Synthetic DNAs can be used as a robust investigation tool for this purpose. DNA tracers are
unique, highly sensitive for detection, harmless, and inexpensive. DNA tracers can be reproduced
by PCR amplification and sample analysis by qPCR is rapid. Unlimited number of DNA tracers
can be designed using random sequence generator software. The use of multiple DNA tracers
allows simultaneously identifying and characterising different contamination sources and
pathways.
DNA tracers have been applied in field groundwater tracing studies overseas 1-3. These
applications included establishing hydraulic connection between wells and between groundwatersurface water, delineating preferential flow-paths, and identifying contamination sources. DNA
tracers were traceable as far as 300 m in karst groundwater.
Method
The previous DNA tracer studies employed single-stranded DNAs, which are less stable than
double-stranded DNAs in environmental conditions. In this study, linear, double-stranded 302
base-pair DNAs were used. These synthetic DNAs were developed in a Marsden project for
DNA-labelling of virus surrogates (protein-coated silica particles)4. Our previous study
demonstrated that these DNA tracers were stable and readily detectable in a number of
environmental waters, treated domestic effluent, and solutions of stream sediment, beach sand
and pumice sand. Compared with previous published DNA tracer studies, our DNA tracers have
much lower detection limits.
To examine the usefulness of double-stranded DNA tracers for groundwater investigations, field
experiments were conducted with undiluted domestic effluent collected from an oxidation pond.
These included a groundwater experiment in an alluvial gravel aquifer at Burnham near
Christchurch and lysimeter studies with an intact core of sandy gravel vadose zone media. The
groundwater velocity passing through the sampling wells was 60-100 m/day. A non-reactive
solute tracer, bromide (Br-), was also used for validation. In the groundwater experiment, we
injected 400 g Br- but only 36 µg DNA, 8-orders of magnitude less mass than the Br- tracer.
Results
In the Burnham experiment, DNA concentrations in the last sampling well 37 m down-gradient
were still very high with a peak concentration of 3,710 copies/L, far above the detection limit of 3
copies/L. Compared to Br-, the DNA tracer showed slightly earlier breakthrough due to sizeexclusion as DNAs are the smallest colloids. DNA mass recovery relative to Br- was 100% at 12
m, 46% at 21 m and 56% at 37 m. The reduction is probably due to adsorption of DNA to the
aquifer media and degradation in groundwater. However the overall transport was quite similar to
Br- (Fig.1).
In the lysimeter studies, transport of DNAs was significantly less dispersive than Br - (Fig. 2). This
is a typical pattern that we have frequently observed for colloid transport in intact soil cores.
DNA4 tracer peaked 3.3 times earlier than Br and its mass recovery was 74% of Br. DNA2 tracer
peaked 2 times earlier than Br with mass recovery 20% of Br. The normalised peak DNA
concentrations were higher than that of Br. These results suggest that DNA tracers were
transported largely through preferential flow paths in the intact core, which had a higher
permeability than the matrix.
Our field studies suggest that the double-stranded DNA tracers that we have developed are
indeed useful for groundwater tracing purposes and characterising preferential flow-paths. We
believe that, when multiple DNA tracers are used at the same time, DNA tracer technology can
provide the answers to some groundwater contamination problems that the traditional tracers
would be unable to resolve. This information obtained could help a development of contamination
mitigation strategies.
Concentration C/Co
1.0e-2
1.5e-2
Br
DNA
8.0e-3
3.0e-2
2.5e-2
1.2e-2
2.0e-2
6.0e-3
9.0e-3
Well 3
Well 13
Well 5
1.5e-2
4.0e-3
6.0e-3
2.0e-3
3.0e-3
1.0e-2
0.0
5.0e-3
0.0
0
10
20
30
40
50
0.0
0
10
20
30
40
50
0
10
20
30
40
50
Hours since injection
Fig. 1. Field groundwater tracing experiment in alluvial gravel aquifer at Burnham injected with
domestic oxidation pond effluent. Well distance from the injection well was 12, 21 and 37 m,
respectively.
Normolised concentration (C/Co)
0.4
DNA tracers and Bromide
0.3
DNA tracer 2
DNA tracer 4
Br
0.2
0.1
0.0
0
100
200
300
400
500
Minute since injection
Fig. 2. Field lysimeter study injected with domestic oxidation pond effluent spiked with Br and two
different DNA tracers. The intact soil core (0.5 m diameter and 0.7 m long) includes 0.3 m of silt loam
and 0.4 m of sandy gravel vadose zone material.
References
1.
2.
3.
4.
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Ptak, T., Piepenbrink, M., & Martac, E. (2004). Tracer tests for the investigation of heterogeneous
porous media and stochastic modelling of flow and transport—a review of some recent developments.
Journal of Hydrology, 294(1), 122-163.
Aquilanti, L., Clementi, F., Landolfo, S., Nanni, T., Palpacelli, S., & Tazioli, A. (2013). A DNA tracer used
in column tests for hydrogeology applications. Environmental earth sciences, 70(7), 3143-3154.
Pang, L., Farkas, K., Bennett, G., Varsani, A., Easingwood, R., Tilley, R., Nowostawska, U., & Lin, S.
(2014). Mimicking filtration and transport of rotavirus and adenovirus in sand media using DNA-labeled,
protein-coated silica nanoparticles. Water research, 62, 167-179