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Groundwater is one of the main sources of drinking water, thus, human enteric viruses in groundwater could pose safety risks. Many enteric viruses enter drinking water sources through irrigation or recharge of contaminated water. It is therefore advised to test the potential transport risk with harmless surrogates before wastewater or recycled water is used for irrigation or groundwater recharge. An ideal virus surrogate should be able to mimic the particle size, the surface properties and the inactivation rate of its target virus and should be easy to detect. Particle size should be the first consideration when selecting a suitable virus surrogate in soil and aquifer. The natural bacteriophages could only mimic the viruses that are inherently similar to themselves, and there is only a limited number of readily available bacteriophages. Therefore, once a certain bacteriophage is chosen for study, its particle size, surface properties and inactivation rate are set and unmodifiable for the experiment. Fluorescent microspheres <200 nm could surrogate target viruses in fast-flow subsurface systems, where inactivation can be neglected. However, the current detection limit of fluorescent nanospheres cannot support the detection of small-sized fluorescent microspheres (∼20 nm) through porous media without macropores. Newly emerging DNA tracers not only allow controlling the size and surface properties, but also offer a low detection limit (ideally 1 copy of DNA). Investigating new types of DNA tracers that could either simulate or mimic the inactivation rate of target viruses could widen the use of virus surrogates to study groundwater contamination and drinking water supply safety., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025 Elsevier B.V. All rights reserved.)

Groundwater aquifers worldwide experience unsustainable depletion, compounded by population growth, economic development, and climate forcing. Managed aquifer recharge provides one tool to alleviate flood risk and replenish groundwater. However, concerns grow that intentional flooding of farmland for groundwater recharge, a practice known as Ag-MAR, may increase the leaching of pesticides and other chemicals into groundwater. This study employs a physically based unsaturated flow model to determine the fate and transport of residues of four pesticide in three vadose zone profiles characterized by differing fractions of sand (41 %, 61 %, and 84 %) in California's Central Valley. Here, we show that the complex heterogeneity of alternating coarse and fine-grain hydrogeologic units controls the transit times of pesticides and their adsorption and degradation rates. Unsaturated zones that contain a higher fraction of sand are more prone to support preferential flow, higher recharge rates (+8 %), and faster (42 %) water flow and pesticide transport, more flooding-induced pesticide leaching (about 22 %), as well as more salt leaching correlating with increased risks of groundwater contamination. Interestingly, considering preferential flow predicted higher degradation and retention rates despite shorter travel times, attributed to the trapping of pesticides in immobile zones where they degrade more effectively. The findings underscore the importance of considering soil texture and structure in Ag-MAR practices to minimize environmental risks while enhancing groundwater recharge. The study also highlights that selecting less mobile pesticides can reduce leaching risks in sandy areas., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests/personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

It has been recently demonstrated that free DNA tracers have the potential in tracing water flow and contaminant transport through the vadose zone. However, whether the free DNA tracer can be used in flood irrigation area to track water flow and solute/contaminant transport is still unclear. To reveal the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation, we tested the fate and transport behavior of surface applied free DNA tracers through packed saturated sandy soil columns with a 10 cm water head mimicking flood irrigation. From the experimental breakthrough curves and by fitting a two-site kinetic sorption model (R 2  = 0.83-0.91 and NSE = 0.79-0.89), adsorption/desorption rates could be obtained and tracer retention profiles could be simulated. Together these results revealed that 1) the adsorption of free DNA was dominantly to clay particles in the soil, which took up 1.96 % by volume, but took up >97.5 % by surface area and densely cover the surface of sand particles; and 2) at a pore water pH of 8.0, excluding the 4.9 % passing through and 3.1 % degradation amount, the main retention mechanisms in the experimental soil were ligand exchange (42.0 %), Van der Waals interactions (mainly hydrogen bonds), electrostatic forces and straining (together 44.7 %), and cation bridge (5.3 %). To our knowledge, this study is the first to quantify the contribution of each of the main retention mechanisms of free synthetic DNA tracers passing through soil. Our findings could facilitate the application of free DNA tracer to trace vadose zone water flow and solute/contaminant transport under flood irrigation and other infiltration conditions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Agricultural managed aquifer recharge (Ag-MAR) is a promising approach to replenish groundwater resources using flood water and cropland as spreading grounds. However, site selection, particularly the layering of sediment deposits in the subsurface, can greatly influence Ag-MAR efficacy as it controls water flow and solute transport in the vadose zone. In this study, we use the HYDRUS-1D software to simulate water flow and solute transport from the land surface to the groundwater table in three vadose zone profiles (LS, MS, HS) characterized by differing fractions of sand (44 %, 47 %, and 64 %). For each profile, the single- and dual-porosity models (i.e., considering or not nonequilibrium water flow and solute transport) were calibrated using observed surface ponding, soil water content, and KBr breakthrough data. Water flow and bromide transport in the profile with the lowest sand fraction (LS) were best captured using the model that considered both preferential flow and nonequilibrium bromide transport. Water flow and bromide transport in the profile with the highest sand fraction (HS) was best simulated with the model that considered preferential flow and equilibrium bromide transport. Uniform water flow and nonequilibrium bromide transport provided the best fit for the third profile (MS). The degree of preferential flow was highest in the profile with the largest sand fraction (HS), which also showed the largest flow velocities compared to the profiles with lower sand amounts (LS and MS). Preferential flow did not significantly impact the overall water balance (within 3 %), but caused a significant decrease in vadose zone travel times (bromide) by up to 38 %, relative to a single-porosity model fit. Recharge efficiency varied between 88 % and 90 %, while the average travel times from the soil surface to groundwater varied up to 119 % (from 3.6 to 7.9 days) between the three sites. This study demonstrates that similar recharge efficiency can be achieved at sites with differing soil texture profiles, but subsurface heterogeneity can substantially affect contaminant transport processes and their travel times., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)

Nitrate (NO 3 - ) leaching is a serious health and ecological concern in global agroecosystems, particularly those under the application of agricultural-managed aquifer recharge (Ag-MAR); however, there is an absence of information on microbial controls affecting NO 3 - leaching outcomes. We combine natural dual isotopes of NO 3 - ( 15 N/ 14 N and 18 O/ 16 O) with metagenomics, quantitative polymerase chain reaction (PCR), and a threshold indicator taxa analysis (TITAN) to investigate the activities, taxon profiles, and environmental controls of soil microbiome associated with NO 3 - leaching at different depths from Californian vineyards under Ag-MAR application. The isotopic signatures demonstrated a significant priming effect ( P < 0.01) of Ag-MAR on denitrification activities in the topsoil (0-10 cm), with a 12-25-fold increase of 15 N-NO 3 - and 18 O-NO 3 - after the first 24 h of flooding, followed by a sharp decrease in the enrichment of both isotopes with ∼80% decline in denitrification activities thereafter. In contrast, deeper soils (60-100 cm) showed minimal or no denitrification activities over the course of Ag-MAR application, thus resulting in 10-20-fold of residual NO 3 - being leached. Metagenomic profiling and laboratory microcosm demonstrated that both nitrifying and denitrifying groups, responsible for controlling NO 3 - leaching, decreased in abundance and potential activity rates with soil depth. TITAN suggested that Nitrosocosmicus and Bradyrhizobium , as the major nitrifier and denitrifier, had the highest and lowest tipping points with regard to the NO 3 - changes ( P < 0.05), respectively. Overall, our study provides new insight into specific depth limitations of microbial controls on soil NO 3 - leaching in agroecosystems.

Agricultural managed aquifer recharge (Ag-MAR, on-farm recharge), where farmland is flooded with excess surface water to intentionally recharge groundwater, has received increasing attention by policy makers and researchers in recent years. However, there remain concerns about the potential for Ag-MAR to exacerbate nitrate (NO 3 - ) contamination of groundwater, and additional risks, such as greenhouse gas emissions and crop tolerance to prolonged flooding. Here, we conducted a large-scale, replicated winter groundwater recharge experiment to quantify the effect of Ag-MAR on soil N biogeochemical transformations, potential NO 3 - leaching to groundwater, soil physico-chemical conditions, and crop yield. The field experiment was conducted in two grapevine vineyards in the Central Valley of California, which were each flooded for 2 weeks and 4 weeks, respectively, with 1.31 and 1.32 m 3 m -2 of water. Hydrologic, geochemical, and microbial results indicate that NO 3 - leaching from the first 1 m of the vadose zone was the dominant N loss pathway during flooding. Based on pore water sample and N 2 O emission data, denitrification played a lesser role in decreasing NO 3 - in the root zone but prolonged anoxic conditions resulted in a significant 29 % yield decrease in the 4-week flooded vineyard. The results from this research, combined with data from previous studies, are summarized in a new conceptual model for integrated water-N dynamics under Ag-MAR. The proposed model can be used to determine best Ag-MAR management practices., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

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 1m 3 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 (R 2  = 0.949, NSE = 0.937) and the Schijven and Šimůnek two-site kinetic sorption model recommended for virus transport modeling (R 2  = 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., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. The authors declare the following financial interests/personal relationships which may be considered as potential competing interests, (Copyright © 2022. Published by Elsevier Ltd.)