Environmental impact of DNA-based tracer technology

In the framework of the Horizon 2020 project S4CE, ETH Zürich is developing a DNA-based tracer technology for surface and underground tracing. The DNA is adsorbed onto sub-micron silica particles and coated with a shell to increase the DNAs stability and applicability for tracing. Barcodes, as created with unique DNA sequences allow for multitracing applications in various tracing scenarios. ETH Zürichs role within S4CE is to assess the environmental impact of large-scale tracer use by establishing an ecotoxicological profile through acute and chronic ecotoxicity assays.

DNA is a biopolymer, which is made of a unique sequence of nucleotides (A, C, G, and T), storing the information of life in every living creature on earth. Actually, DNA is the largest data storage medium in the world, storing an amount of 150 trillion GB or 150 Zettabytes (1021 bytes) in just a single human body. The capability of synthetically writing a sequence of DNA (=synthesizing) gives us a powerful tool, using one of nature’s most fascinating creation as a purely technological platform for storing information.

Figure 1: Using DNA-based tracer to analyze aquifer connectivity

To create a unique barcode for each tracer batch, we synthesize a DNA strand of a length of 40 or more nucleotides, which theoretically allows us to create 404 = 256’000 combinations and the same number of distinguishable tracer batches. Imagine having 3 entry points into a connected aquifer and a single detection point; with 3 different DNA tracers, we would be able to quantify the contribution of each entry point at any position to better understand the connectivity of the aquifer (Fig. 1).

When employed as tracer, DNA is removed from its normal biological environment and is subjected to environmental stress. This stress damages and degrades DNA rendering the tracers unstable. Therefore, we are encapsulating the DNA in silica beads, similar to fossilization, protecting it from chemical and physical stress.

Figure 2: a) Images taken from zooplankton key Copyright © 2003-2013 Center for Freshwater Biology, Department of Biologcal Sciences, University of New Hampshire, Durham, NH 03824 USA b) Inhibition on mobility of Daphnia magna with varying concentrations of SPED c) Population growth of Ceriodaphnia dubia with varying concentrations of SPED

DNA and silica are both materials, which are naturally present in nature and are non-toxic. Silica is found in plants and water. It is also often used as a food additive in form of sub-micron particles. However, potential large scale use of this new tracer material requires an ecotoxicological assessment of the impact this material can have on relevant organisms. For this, we exposed two water crustacean species, Daphnia magna and Ceriodaphnia dubia (Fig. 2a) to the tracer material. The Daphnia magna immobilization test is conventionally used to assess the short-term acute effects of chemicals and effluents. The Ceriodaphnia dubnia test is a standard assay to evaluate chronic toxicity. We have found no adverse effects on these test organisms at relevant tracer concentrations (Fig 2b,c).

Based on the already established ecotoxicological profile of simple silica nanoparticles in the literature, showing no toxicity up to high concentrations (<100 ppm), we were able to establish an extended ecotoxicological profile which suggests low impact upon large scale application of the DNA silica tracer material. ETH Zurich will collaborate with S4CE partner Haelixa to plan a large scale field test of the tracer material. Additionally, the next step for ETH Zürich in the framework of S4CE is to develop a new type of DNA tracer material that is biodegradable in order to decrease the environmental footprint further.

Authors: Julian Koch, Robert Grass