DNA-Based Tracers for the Characterization of Hydrogeological Systems—Recent Advances and New Frontiers

Abstract

Tracer technologies based on naturally occurring substances or intentionally introduced compounds have a broad spectrum of applications in hydrogeological research and subsurface resource management. DNA (deoxyribonucleic acid)-based tracers, with unlimited unique variations and exceptional specificity, could potentially map the complex intricacies of subsurface flow networks in greater detail than traditional tracer methods. Here, we review recent advances in DNA-based tracer research involving modern culture-independent (i.e., molecular) measurement techniques for subsurface/flowpath characterization purposes. The two broad categories of DNA-based tracers, i.e., synthetic and naturally occurring, are further classified into four specific types: “naked DNA”, “encapsulated DNA”, “barcoding microbial communities”, and “indicator microbial communities”. We summarize and compare the basic methodological workflows for each type of DNA-based tracer and provide an overview of research developments in the past two decades, covering both laboratory/field-scale experiments and data interpretation methods. Finally, we highlight remaining questions and challenges for each type of DNA-based tracer in terms of practicality. Future research directions are also identified, including the application of emerging DNA tracer methods to a wider range of geological formations. Fundamental characteristics of these novel tracers need to be better understood, and their applicability under a broader range of engineering scenarios requires further validation.

Artificial DNA in hydrology

“…Also, encDNA is not thought to take part in chemical reactions, or subject to enzymatic influences. Compared to dissolved artDNA, for encDNA additional work flow in the laboratory is required to encapsulate the DNA and to release DNA for quantification (Zhang & Huang, 2022). There are six types of DNA encapsulates for hydrological applications used in literature (Figure 2): The particle produced by Garnett et al (2009) was around 35 nm in size and was made of DNA that had been circumferentially wrapped in a condensed form.…”

“…The loss of DNA, either dissolved or encapsulated, in the experiments discussed above was attributed to several factors, with the most significant being instantaneous losses, adsorption or attachment, and decay [e.g., Zhang and Huang (2022)]. The following provides an overview of the processes underlying these sink and source terms in the DNA mass balance.…”

“…Secondly, one of the questions and challenges posed by Zhang and Huang (2022) with regard to dissolved artDNA and encDNA in groundwater environments was on resolving adsorption and degradation characteristics. Current review shows that progress has been made.…”

“…This review primarily focuses on the injection of artDNA in surface water, groundwater, and in laboratory set‐ups with the objective to understand artDNA transport behavior and demonstrate its potential and limitations in environmental applications. While Zhang and Huang (2022) recently reviewed the use of DNA based tracers for characterizing subsurface hydrogeological systems, this review concentrates on quantifying the mass balance of injected artDNA mass balance and elucidating the context‐specific and environment‐dependent mass balance terms of artificial DNA in both surface water and groundwater environments. This review begins by presenting and discussing the nomenclature related to DNA, followed by an evaluation of mass balance recoveries from injection experiments in Section 3.…”

Effect of channel bed sediment on the transport behaviour of superparamagnetic silica encapsulated DNA microparticles in open channel injection experiments

“…DNA tracers for hydrological investigations have received an increased interest over the past decade (Zhang & Huang, 2022). Synthetic DNA tracers enable multi‐tracing with virtually infinite numbers of unique DNA sequences which are distinguishable from the environmental background (Liao et al, 2018).…”