Protecting water resource quality is a global concern, as both solute and colloidal contaminants from various sources can infiltrate into soil and eventually pollute groundwater. Understanding the fate and transport of colloidal contaminants- such as engineered nano- and micro-particles, as well as biological entities like bacteria and viruses- is crucial for mitigating their associated risks. The transport and deposition of the colloidal contaminants are complex and multiscale processes in porous media.
This dissertation explored the application of DNA-based particles as potential tracer agents. Advances in nanotechnology and molecular biology have enabled the development of synthetic DNA-based particles that synthetic DNA act as “barcodes”. These particles are highly detectable and quantifiable at low concentrations using qPCR techniques, making them ideal for mapping contamination pathways, determining aquifer hydraulic connectivity, tracking multiple sources simultaneously, and serving as surrogates for tracking the transport and pathways of colloidal contaminants.
DNA-based particles have recently been used as tracers in hydrological studies. The focus of the dissertation is on DNA-based particles with a core-shell structure made of silica encapsulating double-stranded DNA (referred to as DNAcol). Since DNA-based particles can be classified as colloidal particles, this research aims to better understand the mechanisms governing their transport and fate under varying physicochemical conditions. By examining its responses to different tested conditions, the study seeks to identify the environmental conditions in which this tracer can be most effectively applied.@en

In the terrestrial environment, interactions between natural organic matter (NOM) and colloids can lead to the formation of an environmental corona around colloids, influencing their transport behaviour and, ultimately, their ecotoxicity. We used a synthetically designed colloid tagged with DNA (DNAcol) as a surrogate for natural colloids and investigated its transport in saturated sand columns. We varied the concentrations of NOM and ionic strength (CaCl₂), to better understand the transport and release of DNAcol in porous media under both steady and transient porewater chemistry conditions. In addition, we aimed to understand the main factors that control deposition and release of DNAcol under tested conditions. To induce transient chemistry, we replaced the injection solution containing NOM and/or CaCl₂ with Milli-Q water. The results showed that the deposition rate of DNAcol was inversely proportional to the concentration of NOM. The deposition rate increased significantly even under low ionic strength (CaCl₂) conditions of tested conditions. Notably, the influence of NOM on the transport of DNAcol was most pronounced at the lowest range of [Ca²⁺]/DOC ratios, and the attachment of DNAcol to the sand grains was negligible. Moreover, the results showed while the DLVO theory captured the general trend of experimental results, it significantly underestimated the deposition of DNAcol in the presence of CaCl₂. Under transient porewater chemistry conditions, colloid remobilization was observed upon flushing the column with Milli-Q water, leading to a secondary peak in the breakthrough curves. We observed that under transient porewater chemistry conditions, when the ionic strength of the solution was 10 mM, the magnitude of the remobilization peak was more significant compared to conditions with 1 mM ionic strength. Our work emphasized the complex interplay between water quality on the one hand and deposition and release of colloidal matter in saturated porous media on the other hand.

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In recent years, DNA-tagged silica colloids have been used as an environmental tracer. A major advantage of this technique is that the DNA-coding provides an unlimited number of unique tracers without a background concentration. However, little is known about the effects of physio-chemical subsurface properties on the transport behavior of DNA-tagged silica tracers. We are the first to explore the deposition kinetics of this new DNA-tagged silica tracer for different pore water chemistries, flow rates, and sand grain size distributions in a series of saturated sand column experiments in order to predict environmental conditions for which the DNA-tagged silica tracer can best be employed. Our results indicated that the transport of DNA-tagged silica tracer can be well described by first order kinetic attachment and detachment. Because of massive re-entrainment under transient chemistry conditions, we inferred that attachment was primarily in the secondary energy minimum. Based on calculated sticking efficiencies of the DNA-tagged silica tracer to the sand grains, we concluded that a large fraction of the DNA-tagged silica tracer colliding with the sand grain surface did also stick to that surface, when the ionic strength of the system was higher. The experimental results revealed the sensitivity of DNA-tagged silica tracer to both physical and chemical factors. This reduces its applicability as a conservative hydrological tracer for studying subsurface flow paths. Based on our experiments, the DNA-tagged silica tracer is best applicable for studying flow routes and travel times in coarse grained aquifers, with a relatively high flow rate. DNA-tagged silica tracers may also be applied for simulating the transport of engineered or biological colloidal pollution, such as microplastics and pathogens.

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DNA-tagged particle tracers have been the subject of several researches as a new tracer for hydrological applica-tions. This tracer potentially permits the production of a large number of identically transported but distinguishabletracers. Such technique facilitates multi-point and multi-time tracer experiments in a specific location withoutconfounding the signal of the different tracers. All of those potential benefits of DNA-tagged particles can effec-tively improve our understanding on contamination flow origin and its pathways in the subsurface environment.@en