DNA-labeled clay: A sensitive new method for tracing particle transport

Abstract

The behavior of mobile colloids and sediment in most natural environments remains poorly understood, in part because characteristics of existing sediment tracers limit their widespread use. Here we describe the development of a new approach that uses a DNA-labeled montmorillonite clay as a highly sensitive and selective sediment tracer that can potentially characterize sediment and colloid transport in a wide variety of environments, including marine, wetland, groundwater , and atmospheric systems. Characteristics of DNA in natural systems render it unsuitable as an aqueous tracer but admirably suited as a label for tracing particulates. The DNA-labeled-clay approach, using techniques developed from molecular biology, has extremely low detection limits, very specific detection, and a virtually infinite number of tracer signatures. Furthermore, DNA-labeled clay has the same physical characteristics as the particles it is designed to trace, it is environmentally benign, and it can be relatively inexpensively produced and detected. Our initial results show that short (500 base pair) strands of synthetically produced DNA reversibly adsorb to both Na-montmorillonite and powdered silica surfaces via a magnesium bridge. The DNA-montmorillonite surface complexes are stable in calciumbicarbonate spring waters for periods of up to 18 days and only slowly desorb to the aqueous phase, whereas the silica surface complex is stable only in distilled water. Both materials readily release the adsorbed DNA in dilute EDTA solutions for amplification by the polymerase chain reaction (PCR) and quantification. The stability of the DNA-labeled clay complex suggests that this material would be appropriate for use as an extremely sensitive sediment tracer for flow periods of as long as 2 weeks, and possibly longer.

The development of rare earth element-labelled potassium-depleted clays for use as cohesive sediment tracers in aquatic environments

“…Such tracer particles have been labelled with DNA (Maher et al 1998a), iridium (Yin et al 1993) and rare earth elements (REEs) (Krezoski 1988(Krezoski , 1989Maher et al 1998b;Matisoff et al 2001), all with some degree of success. The use of labelled clays as sediment tracers has the added attraction that these materials are likely to exhibit the same physical behaviour as the natural cohesive clayrich sediments that they are intended to mimic and hence offer significant advantages over synthetic alternatives.…”

Using concurrent DNA tracer injections to infer glacial flow pathways

“…In contrast to these studies that applied DNA in its ‘free’ or unprotected form (i.e. DNA not attached to particles or encapsulated by a protective shell), Mahler et al () tested DNA attached to montmorillonite clay in a laboratory experiment for potential groundwater tracing. Their research showed that unique DNA‐labelled particles could be used as a highly sensitive and selective particulate transport tracer while providing some improved stability (i.e.…”

“…Mass loss of the free DNA tracers was attributed to adsorption onto sediment particles, decay and/or biological uptake by microorganisms. Free DNA has been shown to easily adsorb onto clay and other minerals (Greaves and Wilson, ; Mahler et al , ; Knippers, ) whereby adsorption increases with decreasing pH and the presence of divalent cations (Greaves and Wilson, ). While free DNA shows some potential as a tracer, it remains unsolved how degradation of the DNA when exposed to ultraviolet (UV) light and/or bacterial activity can be prevented (Pietramellara et al , ).…”

Dynamic interactions between cohesive sediment tracers and natural mud

“…Adams 1998). Natural clays have been labelled with DNA (Mahler et al 1998a), iridium (Yin et al 1993) and rare earth elements (REEs; Krezoski 1985;Mahler et al 1998b;Spencer et al 2007) and used to measure fine sediment transport pathways in a number of aquatic environments including estuaries, lakes, groundwater, shallow seas and karst systems. However, none of these techniques have been widely used by the regulatory authorities for the management of fine sediment for a number of reasons.…”