Molecular and Dual-Isotopic Profiling of the Microbial Controls on Nitrogen Leaching in Agricultural Soils under Managed Aquifer Recharge.

Nitrate (NO3-) 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 NO3- leaching outcomes. We combine natural dual isotopes of NO3- (15N/14N and 18O/16O) 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 NO3- 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 15N-NO3- and 18O-NO3- 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 NO3- being leached. Metagenomic profiling and laboratory microcosm demonstrated that both nitrifying and denitrifying groups, responsible for controlling NO3- 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 NO3- changes (P < 0.05), respectively. Overall, our study provides new insight into specific depth limitations of microbial controls on soil NO3- leaching in agroecosystems.

Beyond Metrics? The Role of Hydrologic Baseline Archetypes in Environmental Water Management.

Balancing ecological and human water needs often requires characterizing key aspects of the natural flow regime and then predicting ecological response to flow alterations. Flow metrics are generally relied upon to characterize long-term average statistical properties of the natural flow regime (hydrologic baseline conditions). However, some key aspects of hydrologic baseline conditions may be better understood through more complete consideration of continuous patterns of daily, seasonal, and inter-annual variability than through summary metrics. Here we propose the additional use of high-resolution dimensionless archetypes of regional stream classes to improve understanding of baseline hydrologic conditions and inform regional environmental flows assessments. In an application to California, we describe the development and analysis of hydrologic baseline archetypes to characterize patterns of flow variability within and between stream classes. We then assess the utility of archetypes to provide context for common flow metrics and improve understanding of linkages between aquatic patterns and processes and their hydrologic controls. Results indicate that these archetypes may offer a distinct and complementary tool for researching mechanistic flow-ecology relationships, assessing regional patterns for streamflow management, or understanding impacts of changing climate.

Nitrogen fate during agricultural managed aquifer recharge: Linking plant response, hydrologic, and geochemical processes.

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 (NO3-) 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 NO3- 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 m3 m-2 of water. Hydrologic, geochemical, and microbial results indicate that NO3- leaching from the first 1 m of the vadose zone was the dominant N loss pathway during flooding. Based on pore water sample and N2O emission data, denitrification played a lesser role in decreasing NO3- 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.

Estimating the impact of vadose zone heterogeneity on agricultural managed aquifer recharge: A combined experimental and modeling study.

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.

Revealing the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation.

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 (R2 = 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.

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 Simunek 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.

Identifying climate change impacts on surface water supply in the southern Central Valley, California.

Mountain regions in arid and semi-arid climates, such as California, are considered particularly sensitive to climate change because global warming is expected to alter snowpack storage and related surface water supply. It is therefore important to accurately capture snowmelt processes in watershed models for climate change impact assessment. In this study we use the Soil and Water Assessment Tool (SWAT) to estimate projected changes in snowpack and streamflow in four alpine tributaries to the agriculturally important but less studied southern Central Valley, California. Watershed responses are evaluated for four CMIP5 climate models (HadGEM_ES, CNRM-CM5, CanESM2 and MIROC5) and two emission scenarios (RCP 4.5 and RCP 8.5) for 2020-2099. SWAT models are calibrated following a dual-objective, lumped calibration approach with an automatic calibration against observed streamflow (stage 1) and a manual calibration against reconstructed Parallel Energy Balance (ParBal) snow water equivalent (SWE) data (stage 2). Results indicate that under a warming climate, peak streamflow is expected to increase 0.5-4 times in magnitude in the coming decades and to arrive 2-4 months earlier in the year because of earlier snowmelt. In the foreseeable future, snow cover will reduce gradually in the lower elevations and diminish at higher rates at higher elevation towards the end of the 21st century. Surface water supply is predicted to increase in the southern Central Valley under the evaluated scenarios but increased temporal variability (wetter wet seasons and drier dry seasons) will create new challenges for managing supply. The study further highlights that the use of remote sensing based, reconstructed SWE data could fill the current gap of limited in-situ SWE observations to improve the snow calibration of SWAT to better predict climate change impacts in semi-arid, snow-dominated watersheds.

Fabrication, detection, and analysis of DNA-labeled PLGA particles for environmental transport studies.

Poly(lactic-co-glycolic acid) (PLGA) particle carriers of synthetic DNA have recently received increased attention for environmental applications due to their biodegradability, customizability, and nearly limitless number of uniquely identifiable "labels". In this paper, we present methodologies for the preparation of DNA-labeled particles, control of particle size, extraction of DNA-labels, and analysis via quantitative polymerase chain reaction (qPCR). Characterization and analysis of the DNA-labeled particles reveal spherical particles of diameters ranging from 60 to 1000 nm, with consistent zeta potentials around -45 mV, that are stable to aggregation, even in the presence of concentrated mono- and divalent cations. A highly correlated and consistent relationship between particle concentration and DNA-label count was observed, with a detection range spanning 7 orders of magnitude, from 0.01 to 10,000 mg/L (10-107 particles/µL). The results of two environmental applications of the DNA-labeled particles are also presented, highlighting their feasibility for use in environmental studies. Whether exploring size-dependent transport phenomena or identifying potential pathogen transport pathways, the DNA-labeled particle approach presented here provides a powerful tool for the identification of overlapping particle signals at a range of concentrations.

Explaining and modeling the concentration and loading of Escherichia coli in a stream-A case study.

Escherichia coli (E. coli) level in streams is a public health indicator. Therefore, being able to explain why E. coli levels are sometimes high and sometimes low is important. Using citizen science data from Fall Creek in central NY we found that complementarily using principal component analysis (PCA) and partial least squares (PLS) regression provided insights into the drivers of E. coli and a mechanism for predicting E. coli levels, respectively. We found that stormwater, temperature/season and shallow subsurface flow are the three dominant processes driving the fate and transport of E. coli. PLS regression modeling provided very good predictions under stormwater conditions (R2 = 0.85 for log (E. coli concentration) and R2 = 0.90 for log (E. coli loading)); predictions under baseflow conditions were less robust. But, in our case, both E. coli concentration and E. coli loading were significantly higher under stormwater condition, so it is probably more important to predict high-flow E. coli hazards than low-flow conditions. Besides previously reported good indicators of in-stream E. coli level, nitrate-/nitrite-nitrogen and soluble reactive phosphorus were also found to be good indicators of in-stream E. coli levels. These findings suggest management practices to reduce E. coli concentrations and loads in-streams and, eventually, reduce the risk of waterborne disease outbreak.