A DNA Tracer System for Hydrological Environment Investigations

Encapsulating Fe3O4 Nanoparticles and Carbon Dots in a Metal-Organic Framework for Magnetic Fluorescent Taggants

Magnetic fluorescent composite nanomaterials have broad application prospects in the fields of biological imaging, anticounterfeiting identification, suspicious object tracking, and identification of latent fingerprints in forensic medicine. For an effective taggant, a clearly visible identifying mark is necessary to enable observers to capture labeling information quickly and accurately, even from a distance. The preparation method of magnetic fluorescent composite materials is complicated and usually needs different surface modification and assembly processes. The limited loading capacity of fluorescent materials also limits the fluorescence properties of the composite, so it is difficult to produce obvious fluorescence as a taggant to meet the requirements of visible labeling. In this study, a core-shell structure of a magnetic fluorescent composite was prepared by using the metal-organic framework ZIF-8 as the host of fluorescent materials and an encapsulation shell coated on the Fe3O4 nanoparticles. The porous ZIF-8 is beneficial for increasing the loading capacity of fluorescent materials to ensure the fluorescence performance of the composite materials. Further modification of the composite surface prevented the desorption of fluorescent materials from the pores of ZIF-8, enabling the samples to maintain good fluorescence properties even after multiple washing cycles. The preparation method is simple, rapid, and cost-effective, and the prepared magnetic fluorescent composite nanomaterial has high magnetic separation performance and fluorescence performance, making it a promising material for identification, marking, and tracking.

Microfluidic encapsulation of DNAs in liquid beads for digital PCR application

Droplet-based microfluidics and digital polymerase chain reaction (PCR) hold significant promise for accurately detecting and quantifying pathogens. However, existing droplet-based digital PCR (ddPCR) applications have been relying exclusively on single emulsion droplets. Single emulsion droplets may not be suitable for applications such as identifying the source and pathways of water contamination where the templates must be protected against harsh environmental conditions. In this study, we developed a core-shell particle to serve as a protective framework for DNAs, with potential applications in digital PCR. We employed a high-throughput and facile flow-focusing microfluidic device to generate liquid beads, core-shell particles with liquid cores, which provided precise control over process parameters and consequently particle characteristics. Notably, the interfacial interaction between the core and shell liquids could be adjusted without adding surfactants to either phase. As maintaining stability is essential for ensuring the accuracy of digital PCR (dPCR), we investigated parameters that affect the stability of core-shell droplets, including surfactants in the continuous phase and core density. As a proof of concept, we encapsulated a series of human faecal DNA samples in the core-shell droplets and the subsequent liquid beads. The core-shell particles ensure contamination-free encapsulation of DNA in the core. The volume of the core droplets containing the PCR mixture is only 0.12 nL. Our experimental results indicate that the liquid beads formulated using our technique can amplify the encapsulated DNA and be used for digital PCR without interfering with the fluorescence signal. We successfully demonstrated the ability to detect and quantify DNA under varying concentrations. These findings provide new insights and a step change in digital PCR that could benefit various applications, including the detection and tracking of environmental pollution.

Degradation and adsorption of synthetic DNA water tracers in environmental matrices

Synthetic DNA tracers are gaining interest as tools for tracking contamination pathways and hydraulic connections in surface water and groundwater systems. However, few quantitative data exist that describe DNA tracer degradation and adsorption in environmental matrices. We undertook laboratory experiments to quantify the degradation of multiple double-stranded DNA tracers in stream water, groundwater, and domestic and dairy-shed effluent, and adsorption to stream sediments, soils, coastal sand aquifer media and alluvial sandy gravel aquifer media. Faster DNA tracer degradation seemed to be associated with high bacterial concentrations in the liquid phase. Overall, the degradation of the 352 base pair (bp) DNA tracers in the aqueous phase was significantly (P = 0.018) slower than that of the 302 bp DNA tracers. Although the tracers' internal amplicon lengths were similar, the longer non-amplified flanking regions of the 352 bp tracers may better protect them from environmental degradation. Thermodynamic analysis suggests that longer flanking regions contribute to greater tracer stability. This finding may explain our previous field observations that 352 bp tracer mass reductions were often lower than 302 bp tracer mass reductions. The 2 sets of DNA tracers did not differ significantly regarding their adsorption to stream sediment-stream water or aquifer media-groundwater mixtures (P > 0.067), but the 352 bp tracers showed significantly less adsorption to soil-effluent mixtures than the 302 bp tracers (P = 0.005). The DNA tracers' adsorption to soil-effluent mixtures was comparatively less than their adsorption to the aquifer media-groundwater and stream sediment-stream water mixtures, suggesting that DNA tracers may compete with like-charged organic matter for adsorption sites. These findings provide insights into the fate of DNA tracers in the environment. The DNA tracers' degradation rate constants determined in this study for a range of environmental conditions could assist the design of future field investigations.

Simulation of experimental synthetic DNA tracer transport through the vadose zone

Although multiple experimental studies have proven the use of free synthetic DNA as tracers in hydrological systems, their quantitative fate and transport, especially through the vadose zone, is still not well understood. Here we simulate the water flow and breakthrough of deuterium (D) and one free synthetic DNA tracer from a 10-day experiment conducted in a transient variably saturated 1m³ 10° sloped lysimeter using the HYDRUS-2D software package. Recovery and breakthrough flux of D (97.78%) and the DNA tracer (1.05%) were captured well with the advection-dispersion equation (R² = 0.949, NSE = 0.937) and the Schijven and Šimůnek two-site kinetic sorption model recommended for virus transport modeling (R² = 0.824, NSE = 0.823), respectively. The degradation of the DNA tracer was very slow (estimated to be 10% in 10 days), because the "loamy sand" porous media in our lysimeter was freshly crushed basaltic tephra (i.e., crushed rocks) and the microbes and DNase that could potentially degrade DNA in regular soils were rare in our "loamy sand". The timing of the concentration peaks and the HYDRUS-2D simulated temporal and spatial distribution of DNA in the lysimeter both revealed the role of the solid-water-air contact lines in mobilizing and carrying DNA tracer under the experimental variably saturated transient flow condition. The free DNA was nearly non-selectively transported through the porous media, and showed a slightly early breakthrough, possibly due to a slight effect of anion exclusion or size exclusion. Our results indicate that free DNA have the potential to trace vadose zone water flow and solute/contaminant transport, and to serve as surrogates to trace viral pathogen pollution in soil-water systems. To our knowledge, this study is the first to simulate transport mechanisms of free synthetic DNA tracers through real soil textured porous media under variably saturated transient flow condition.

Preferential interactions of surface-bound engineered single stranded DNA with highly aromatic natural organic matter: Mechanistic insights and implications for optimizing practical aquatic applications

Engineered short-chain single stranded DNA (ssDNA) are emerging materials with various environmental applications, such as aptasensor, selective adsorbent, and hydrological tracer. However, the lack of fundamental understanding on the interactions of such materials with natural organic matter (NOM) hinders the improvement of their application performance in terms of sensitivity, selectivity, and stability. In this study, we investigated the interactions of ssDNA (four strands with systematically varied length and sequence) with two humic acids (Suwannee River humic acid (SRHA) and Aldrich humic acid (AHA)) and two humic-like NOM present in local aquatic matrices (ROM in river water and WOM in wastewater). Detailed, molecular level interaction mechanisms were obtained by probing the colloidal stability of the ssDNA-coated gold nanoparticles, coupled with product characterization using a suite of microscopic and spectroscopic techniques. Our study revealed that π-π interactions and divalent cation bridging were the major mechanisms for ssDNA-NOM interactions. ssDNA preferentially interacted with NOM with high aromaticity (AHA > SRHA/WOM/ROM). With divalent cations present (especially Ca²⁺), even a small amount of AHA could completely shield ssDNA, whereas the extent of shielding by SRHA/WOM/ROM depended on the relative content of ssDNA and NOM and whether bridges formed. The extent of shielding of ssDNA by NOM provides a potential answer to the reported conflicting effects of natural water matrices on the performance of DNA-based sensors. Taken together, our findings provide insights into the transformations of engineered ssDNA under environmentally relevant conditions as well as implications for their performance optimization in practical aquatic applications (e.g., from DNA design to pretreatment strategy).

In silico nanosafety assessment tools and their ecosystem-level integration prospect

Engineered nanomaterials (ENMs) have tremendous potential in many fields, but their applications and commercialization are difficult to widely implement due to their safety concerns. Recently, in silico nanosafety assessment has become an important and necessary tool to realize the safer-by-design strategy of ENMs and at the same time to reduce animal tests and exposure experiments. Here, in silico nanosafety assessment tools are classified into three categories according to their methodologies and objectives, including (i) data-driven prediction for acute toxicity, (ii) fate modeling for environmental pollution, and (iii) nano-biological interaction modeling for long-term biological effects. Released ENMs may cross environmental boundaries and undergo a variety of transformations in biological and environmental media. Therefore, the potential impacts of ENMs must be assessed from a multimedia perspective and with integrated approaches considering environmental and biological effects. Ecosystems with biodiversity and an abiotic environment may be used as an excellent integration platform to assess the community- and ecosystem-level nanosafety. In this review, the advances and challenges of in silico nanosafety assessment tools are carefully discussed. Furthermore, their integration at the ecosystem level may provide more comprehensive and reliable nanosafety assessment by establishing a site-specific interactive system among ENMs, abiotic environment, and biological communities.

Ecotoxicological Assessment of DNA-Tagged Silica Particles for Environmental Tracing

Environmental tracers are chemical species that move with a fluid and allow us to understand its origin and material transport properties. DNA-based materials have been proposed and used for tracing due to their potential for multitracing with high specificity and sensitivity. For large-scale applications of this new material it is of interest to understand its impact on the environment. We therefore assessed the ecotoxicity of sub-micron silica particles with and without encapsulated DNA in the context of surface and underground tracing of natural waterflows using standard ecotoxicity assays according to ISO standards. Acute toxicity tests were performed with Daphnia magna (48 h), showing no effect on mobility at tracer concentrations below 300 ppm. Chronic ecotoxicological potential was tested with Raphidocelis subcapitata (green algae) (72 h) and Ceriodaphnia species (7 d) with no effect observed at realistic exposure scenario concentrations for both silica particles with and without encapsulated DNA. These results suggest that large-scale environmental tracing with DNA-tagged silica particles in the given exposure scenarios has a low impact on aquatic species with low trophic levels such as select algae and planktonic crustaceans.

Rapid Visual Authentication Based on DNA Strand Displacement

Novel ways to track and verify items of a high value or security is an ever-present need. Taggants made from deoxyribonucleic acid (DNA) have several advantageous properties, such as high information density and robust synthesis; however, existing methods require laboratory techniques to verify, limiting applications. Here, we leverage DNA nanotechnology to create DNA taggants that can be validated in the field in seconds to minutes with a simple equipment. The system is driven by toehold-mediated strand-displacement reactions where matching oligonucleotide sequences drive the generation of a fluorescent signal through the potential energy of base pairing. By pooling different "input" oligonucleotide sequences in a taggant and spatially separating "reporter" oligonucleotide sequences on a paper ticket, unique, sequence-driven patterns emerge for different taggant formulations. Algorithmically generated oligonucleotide sequences show no crosstalk and ink-embedded taggants maintain activity for at least 99 days at 60 °C (equivalent to nearly 2 years at room temperature). The resulting fluorescent signals can be analyzed by the eye or a smartphone when paired with a UV flashlight and filtered glasses.

Magnetic Nanoparticles to Unique DNA Tracers: Effect of Functionalization on Physico-chemical Properties

To monitor and manage hydrological systems such as brooks, streams, rivers, the use of tracers is a well-established process. Limited number of potential tracers such as salts, isotopes and dyes, make study of hydrological processes a challenge. Traditional tracers find limited use due to lack of multiplexed, multipoint tracing and background noise, among others. In this regard, DNA based tracers possess remarkable advantages including, environmentally friendly, stability, and high sensitivity in addition to showing great potential in the synthesis of ideally unlimited number of unique tracers capable of multipoint tracing. To prevent unintentional losses in the environment during application and easy recovery for analysis, we hereby report DNA encapsulation in silica containing magnetic cores (iron oxide) of two different shapes-spheres and cubes. The iron oxide nanoparticles having size range 10-20 nm, have been synthesized using co-precipitation of iron salts or thermal decomposition of iron oleate precursor in the presence of oleic acid or sodium oleate. Physico-chemical properties such as size, zeta potential, magnetism etc. of the iron oxide nanoparticles have been optimized using different ligands for effective binding of dsDNA, followed by silanization. We report for the first time the effect of surface coating on the magnetic properties of the iron oxide nanoparticles at each stage of functionalization, culminating in silica shells. Efficiency of encapsulation of three different dsDNA molecules has been studied using quantitative polymerase chain reaction (qPCR). Our results show that our DNA based magnetic tracers are excellent candidates for hydrological monitoring with easy recoverability and high signal amplification.

Water tracking in surface water, groundwater and soils using free and alginate-chitosan encapsulated synthetic DNA tracers

Investigating contamination pathways and hydraulic connections in complex hydrological systems will benefit greatly from multi-tracer approaches. The use of non-toxic synthetic DNA tracers is promising, because unlimited numbers of tracers, each with a unique DNA identifier, could be used concurrently and detected at extremely low concentrations. This study aimed to develop multiple synthetic DNA tracers as free molecules and encapsulated within microparticles of biocompatible and biodegradable alginate and chitosan, and to validate their field utility in different systems. Experiments encompassing a wide range of conditions and flow rates (19 cm/day-39 km/day) were conducted in a stream, an alluvial gravel aquifer, a fine coastal sand aquifer, and in lysimeters containing undisturbed silt loam over gravels. The DNA tracers were identifiable in all field conditions investigated, and they were directly detectable in the stream at a distance of at least 1 km. The DNA tracers showed promise at tracking fast-flowing water in the stream, gravel aquifer and permeable soils, but were unsatisfactory at tracking slow-moving groundwater in the fine sand aquifer. In the surface water experiments, the microencapsulated DNA tracers' concentrations and mass recoveries were 1-3 orders of magnitude greater than those of the free DNA tracers, because encapsulation protected them from environmental stressors and they were more negatively charged. The opposite was observed in the gravel aquifer, probably due to microparticle filtration by the aquifer media. Although these new DNA tracers showed promise in proof-of-concept field validations, further work is needed before they can be used for large-scale investigations.

Dosage effects of lincomycin mycelial residues on lincomycin resistance genes and soil microbial communities

Lincomycin mycelial residues (LMRs) are one kind of byproduct of the pharmaceutical industry. Hydrothermal treatment has been used to dispose of them and land application is an attractive way to reuse the treated LMRs. However, the safe dose for soil amendment remains unclear. In this study, a lab-scale incubation experiment was conducted to investigate the influence of the amendment dosage on lincomycin resistance genes and soil bacterial communities via quantitative PCR and 16S rRNA sequencing. The results showed that introduced lincomycin degraded quickly in soil and became undetectable after 50 days. Degradation rate of the high amendment amount (100 mg kg^-1) was almost 4 times faster than that of low amendment amount (10 mg kg^-1). Moreover, the introduced LMRs induced the increase of lincomycin resistance genes after incubation for 8 days, and two genes (lmrA and lnuB) showed a dosage-related increase. For example, the abundance of gene lmrA was 17.78, 74.13 and 128.82 copies g^-1 soil for lincomycin concentration of 10, 50 and 100 mg kg^-1, respectively. However, the abundance of lincomycin resistance genes recovered to the control level as the incubation period extended to 50 days, indicating a low persistence in soil. In addition, LMRs application markedly shifted the bacterial composition and significant difference was found between control soil, 10 mg kg^-1 and 50 mg kg^-1 lincomycin amended soil. Actually, several genera bacteria were significantly related to the elevation of lincomycin resistance genes. These results provided a comprehensive understanding of the effects of lincomycin dosage on the fate of resistance genes and microbial communities in LMRs applied soil.

Research on soil moisture prediction model based on deep learning

Soil moisture is one of the main factors in agricultural production and hydrological cycles, and its precise prediction is important for the rational use and management of water resources. However, soil moisture involves complex structural characteristics and meteorological factors, and it is difficult to establish an ideal mathematical model for soil moisture prediction. Existing prediction models have problems such as prediction accuracy, generalization, and multi-feature processing capability, and prediction performance must improve. Based on this, taking the Beijing area as the research object, the deep learning regression network (DNNR) with big data fitting capability was proposed to construct a soil moisture prediction model. By integrating the dataset, analyzing the time series of the predictive variables, and clarifying the relationship between features and predictive variables through the Taylor diagram, selected meteorological parameters can provide effective weights for moisture prediction. Test results prove that the deep learning model is feasible and effective for soil moisture prediction. Its’ good data fitting and generalization capability can enrich the input characteristics while ensuring high accuracy in predicting the trends and values of soil moisture data and provides an effective theoretical basis for water-saving irrigation and drought control.

Tomographic Reservoir Imaging with DNA-Labeled Silica Nanotracers: The First Field Validation

This study presents the first field validation of using DNA-labeled silica nanoparticles as tracers to image subsurface reservoirs by travel time based tomography. During a field campaign in Switzerland, we performed short-pulse tracer tests under a forced hydraulic head gradient to conduct a multisource-multireceiver tracer test and tomographic inversion, determining the two-dimensional hydraulic conductivity field between two vertical wells. Together with three traditional solute dye tracers, we injected spherical silica nanotracers, encoded with synthetic DNA molecules, which are protected by a silica layer against damage due to chemicals, microorganisms, and enzymes. Temporal moment analyses of the recorded tracer concentration breakthrough curves (BTCs) indicate higher mass recovery, less mean residence time, and smaller dispersion of the DNA-labeled nanotracers, compared to solute dye tracers. Importantly, travel time based tomography, using nanotracer BTCs, yields a satisfactory hydraulic conductivity tomogram, validated by the dye tracer results and previous field investigations. These advantages of DNA-labeled nanotracers, in comparison to traditional solute dye tracers, make them well-suited for tomographic reservoir characterizations in fields such as hydrogeology, petroleum engineering, and geothermal energy, particularly with respect to resolving preferential flow paths or the heterogeneity of contact surfaces or by enabling source zone characterizations of dense nonaqueous phase liquids.

Silica-Encapsulated DNA-Based Tracers for Aquifer Characterization

Environmental tracing is a direct way to characterize aquifers, evaluate the solute transfer parameter in underground reservoirs, and track contamination. By performing multitracer tests, and translating the tracer breakthrough times into tomographic maps, key parameters such as a reservoir's effective porosity and permeability field may be obtained. DNA, with its modular design, allows the generation of a virtually unlimited number of distinguishable tracers. To overcome the insufficient DNA stability due to microbial activity, heat, and chemical stress, we present a method to encapsulated DNA into silica with control over the particle size. The reliability of DNA quantification is improved by the sample preservation with NaN₃ and particle redispersion strategies. In both sand column and unconsolidated aquifer experiments, DNA-based particle tracers exhibited slightly earlier and sharper breakthrough than the traditional solute tracer uranine. The reason behind this observation is the size exclusion effect, whereby larger tracer particles are excluded from small pores, and are therefore transported with higher average velocity, which is pore size-dependent. Identical surface properties, and thus flow behavior, makes the new material an attractive tracer to characterize sandy groundwater reservoirs or to track multiple sources of contaminants with high spatial resolution.