Microbial life in preferential flow paths in subsurface clayey till revealed by metataxonomy and metagenomics.

BACKGROUND: Subsurface microorganisms contribute to important ecosystem services, yet little is known about how the composition of these communities is affected by small scale heterogeneity such as in preferential flow paths including biopores and fractures. This study aimed to provide a more complete characterization of microbial communities from preferential flow paths and matrix sediments of a clayey till to a depth of 400 cm by using 16S rRNA gene and fungal ITS2 amplicon sequencing of environmental DNA. Moreover, shotgun metagenomics was applied to samples from fractures located 150 cm below ground surface (bgs) to investigate the bacterial genomic adaptations resulting from fluctuating exposure to nutrients, oxygen and water. RESULTS: The microbial communities changed significantly with depth. In addition, the bacterial/archaeal communities in preferential flow paths were significantly different from those in the adjacent matrix sediments, which was not the case for fungal communities. Preferential flow paths contained higher abundances of 16S rRNA and ITS gene copies than the corresponding matrix sediments and more aerobic bacterial taxa than adjacent matrix sediments at 75 and 150 cm bgs. These findings were linked to higher organic carbon and the connectivity of the flow paths to the topsoil as demonstrated by previous dye tracer experiments. Moreover, bacteria, which were differentially more abundant in the fractures than in the matrix sediment at 150 cm bgs, had higher abundances of carbohydrate active enzymes, and a greater potential for mixotrophic growth. CONCLUSIONS: Our results demonstrate that the preferential flow paths in the subsurface are unique niches that are closely connected to water flow and the fluctuating ground water table. Although no difference in fungal communities were observed between these two niches, hydraulically active flow paths contained a significantly higher abundance in fungal, archaeal and bacterial taxa. Metagenomic analysis suggests that bacteria in tectonic fractures have the genetic potential to respond to fluctuating oxygen levels and can degrade organic carbon, which should result in their increased participation in subsurface carbon cycling. This increased microbial abundance and activity needs to be considered in future research and modelling efforts of the soil subsurface.

Estimation of Effective Fracture Aperture in Glacial Tills by Analysis of Dye Tracer Penetration.

This study advances a methodology to estimate effective apertures of fractures in glacial tills based on dye tracer infiltration tests and numerical simulations. The approach uses the visible penetration depth of the dye tracer along fracture flow paths as primary information to calculate effective fracture apertures. Further data used in the calculation are the dye tracer input concentration and retardation, the duration of the tracer injection, and the hydraulic gradient applied to control the infiltrating water fluxes. The method does not require measurement of hydraulic conductivity for the fractured till and enables direct observation of flow and transport patterns within the fractures (e.g., uniform flow and dye tracer distribution, channeling due to aperture variability, and presence of biogenic macropores in fractures). The approach was successfully verified by using the estimated effective fracture aperture values in Large Undisturbed Columns (LUCs) to consistently simulate both the observed LUC effluent breakthrough of a conservative bromide tracer and the water fluxes with the hydraulic gradient applied in the experiments. Sensitivity analyses revealed that estimation of small effective fracture apertures (<10 µm) required accurate determination of the dye tracer retardation factor. By contrast, in the case of larger effective apertures (>20 µm), the sensitivity of the estimated effective fracture aperture to variations in the porous material and solute transport parameters was low compared to the dominant sensitivity to the water flow through the fractures (cubic relation between flow and aperture). The proposed approach may be extended beyond laboratory applications and assist in characterizing field-scale fracture networks.

A Large Undisturbed Column Method to Study Flow and Transport in Macropores and Fractured Media.

Intact soil columns can bridge the gap between field studies and idealized laboratory investigations of flow and transport in macropores and fractured media. However, the value of intact column studies is often hampered by shortcomings such as lack of column intactness, small column size, and column rim flow, which can cause serious artifacts and hamper system understanding. The flexible-wall pressurized large undisturbed column (LUC) method overcomes these limitations and is a valuable approach to analyze fluid flow and solute transport in macroporous and fractured geological formations. The method investigates subsurface processes in complex media, mimicking in situ conditions and facilitating the control of system boundary conditions including effective stress. In recent years, considerable experience has been gained through different applications of the LUC approach. Modeling tools have also been developed for a detailed interpretation of flow and transport processes in LUC systems. This paper describes the steps of the LUC method from column excavation in the field to experimental setup in the laboratory. The description encompasses the key features of the sampling of LUCs in field excavations, the laboratory setup, the procedure for hydraulic and transport experiments, as well as practical challenges and potential issues during operation of an LUC system. Application examples with a fully three-dimensional numerical model of LUC tracer experiments are also presented to illustrate the quantitative interpretation of transport processes in macroporous clayey tills.

Comparing discrete fracture and continuum models to predict contaminant transport in fractured porous media.

We used the FRAC3Dvs numerical model (Therrien and Sudicky 1996) to compare the dual-porosity (DP), equivalent porous medium (EPM), and discrete fracture matrix diffusion (DFMD) conceptual models to predict field-scale contaminant transport in a fractured clayey till aquitard. The simulations show that the DP, EPM, and DFMD models could be equally well calibrated to reproduce contaminant breakthrough in the till aquitard for a base case. In contrast, when groundwater velocity and degradation rates are modified with respect to the base case, the DP method simulated contaminant concentrations up to three orders of magnitude different from those calculated by the DFMD model. In previous simulations of well-characterized column experiments, the DFMD method reproduced observed changes in solute transport for a range of flow and transport conditions comparable to those of the field-scale simulations, while the DP and EPM models required extensive recalibration to avoid high magnitude errors in predicted mass transport. The lack of robustness with respect to variable flow and transport conditions suggests that DP models and effective porosity EPM models have limitations for predicting cause-effect relationships in environmental planning. The study underlines the importance of obtaining well-characterized experimental data for further studies and evaluation of model key process descriptions and model suitability.

A risk assessment tool for contaminated sites in low-permeability fractured media.

A risk assessment tool for contaminated sites in low-permeability fractured media is developed, based on simple transient and steady-state analytical solutions. The discrete fracture (DF) tool, which explicitly accounts for the transport along fractures, covers different source geometries and history (including secondary sources) and can be applied to a wide range of compounds. The tool successfully simulates published data from short duration column and field experiments. The use for risk assessment is illustrated by three typical risk assessment case studies, involving pesticides, chlorinated solvents, benzene and MTBE. The model is compared with field data and with results from a simpler approach based on an Equivalent Porous Media (EPM). Risk assessment conclusions of the DF and EPM approaches are very different due to the early breakthrough, long term tailing, and lower attenuation due to degradation associated with fractured media. While the DF tool simulates the field data, it is difficult to conclude that the DF model is superior to an EPM model because of a lack of long term monitoring data. However, better agreement with existing field data by the DF model using observed physical fracture parameters favors the use of this model over the EPM model for risk assessments.

Linking a one-dimensional pesticide fate model to a three-dimensional groundwater model to simulate pollution risks of shallow and deep groundwater underlying fractured till.

The one-dimensional pesticide fate model MACRO was loose-linked to the three-dimensional discrete fracture/matrix diffusion model FRAC3DVS to describe transport of the pesticide mecoprop in a fractured moraine till and local sand aquifer (5-5.5 m depth) overlying a regional limestone aquifer (16 m depth) at Havdrup, Denmark. Alternative approaches to describe the upper boundary in the groundwater model were examined. Field-scale simulations were run to compare a uniform upper boundary condition with a spatially variable upper boundary derived from Monte-Carlo simulations with MACRO. Plot-scale simulations were run to investigate the influence of the temporal resolution of the upper boundary conditions for fluxes in the groundwater model and the effects of different assumptions concerning the macropore/fracture connectivity between the two models. The influence of within-field variability of leaching on simulated mecoprop concentrations in the local aquifer was relatively small. A fully transient simulation with FRAC3DVS gave 20 times larger leaching to the regional aquifer compared to the case with steady-state water flow, assuming full connectivity with respect to macropores/fractures across the boundary between the two models. For fully transient simulations 'disconnecting' the macropores/fractures at the interface between the two models reduced leaching by a factor 24. A fully connected, transient simulation with FRAC3DVS, with spatially uniform upper boundary fluxes derived from a MACRO simulation with 'effective' parameters is therefore recommended for assessing leaching risks to the regional aquifer, at this, and similar sites.

Aquifer vulnerability to pesticide migration through till aquitards.

This study investigates the influence of key factors-mainly recharge rate and degradation half-life--on downward migration of the widely used pesticide mecoprop (MCPP) through a typical clayey till aquitard. The study uses the numerical model FRAC3Dvs, which is a three-dimensional discrete fracture/matrix diffusion (DFMD) numerical transport model. The model was calibrated with laboratory and field data from a site near Havdrup, Denmark, but the overall findings are expected to be relevant to many other sites in similar settings. Fracture flow and MCPP transport parameters for the model were obtained through calibration using well-characterized laboratory experiments with large (0.5 m diameter by 0.5 m high) undisturbed columns of the fractured till and a field experiment. A second level of upscaling and sensitivity analysis was then carried out using data on hydraulic head, fracture spacing, and water budget from the field site. The simulations of downward migration of MCPP show that MCPP concentration and mass flux into the underlying aquifer, and hence the aquifer vulnerability to this pesticide compound, is mainly dependent on the degradation rate of the pesticide, the overall aquitard water budget, and the ground water recharge rate into the aquifer. The influence of flow rate, matrix diffusion, and degradation rate are intertwined. This results in one to four orders of magnitude higher MCPP flux into the aquifer from aquifer recharge rates of 20 and 120 mm/yr, respectively, for no degradation and MCPP half-life of 0.5 yr. From a sensitivity analysis it was found that the range of MCPP flux into the aquifer varied less than one order of magnitude due to (1) changing fracture spacing from 1 to 10 m, or (2) preferential flow along inclined thin sand layers, which represent common conditions for the current and other settings of clayey till in Denmark and other glaciated areas in Europe and North America. The results indicate that for aquifers overlain by fractured clayey tills, the vulnerability to contamination with pesticides (pesticide flux into the aquifer) and other widespread agricultural contaminants is going to vary strongly in the watershed as a function of the distribution of aquitard water budget (flow rate) and aquitard redox environment (controlling contaminant degradation rates), even if the thickness of the till is relatively constant. DFMD modeling of cause-effect relationships within such systems has great potential to support decisions in planning, regulation, and contaminant remediation.

Transport and reduction of nitrate in clayey till underneath forest and arable land.

Transport and reduction of nitrate in a typically macroporous clayey till were examined at variable flow rate and nitrate flux. The experiments were carried out using saturated, large diameter (0.5 m), undisturbed soil columns (LUC), from a forest and nearby agricultural sites. Transport of nitrate was controlled by flow along the macropores (fractures and biopores) in the columns. Nitrate reduction (denitrification) determined under active flow mainly followed first order reactions with half-lives (t(1/2)) increasing with depth (1.5-3.5 m) from 7 to 35 days at the forest site and 1-7 h at the agricultural site. Nitrate reduction was likely due to microbial degradation of accumulated organic matter coupled with successive consumption of O2 and NO3- in the macropore water followed by reductive dissolution of Fe and Mn from minerals along the macropores. Concentrations of total organic carbon measured in soil samples were near identical at the two study sites and consequently not useful as indicator for the observed differences in nitrate reduction. Instead the high reduction rates at the agricultural site were positively correlated with elevated concentration of water-soluble organic carbon and nitrate-removing bacteria relative to the forest site. After high concentrations of water-soluble organic carbon in the columns from the agricultural site were leached they lost their elevated reduction rates, which, however, was successfully re-established by infiltration of new reactive organics represented by pesticides. Simulations using a calibrated discrete fracture matrix diffusion (DFMD) model could reasonably reproduce the denitrification and resulting flux of nitrate observed during variable flow rate from the columns.

Modeling of non-reactive solute transport in fractured clayey till during variable flow rate and time.

Fractures and biopores can act as preferential flow paths in clay aquitards and may rapidly transmit contaminants into underlying aquifers. Reliable numerical models for assessment of groundwater contamination from such aquitards are needed for planning, regulatory and remediation purposes. In this investigation, high resolution preferential water-saturated flow and bromide transport data were used to evaluate the suitability of equivalent porous medium (EPM), dual porosity (DP) and discrete fracture/matrix diffusion (DFMD) numerical modeling approaches for assessment of flow and non-reactive solute transport in clayey till. The experimental data were obtained from four large undisturbed soil columns (taken from 1.5 to 3.5 m depth) in which biopores and channels along fractures controlled 96-99% of water-saturated flow. Simulating the transport data with the EPM effective porosity model (FRACTRAN in EPM mode) was not successful because calibrated effective porosity for the same column had to be varied up to 1 order of magnitude in order to simulate solute breakthrough for the applied flow rates between 11 and 49 mm/day. Attempts to simulate the same data with the DP models CXTFIT and MODFLOW/MT3D were also unsuccessful because fitted values for dispersion, mobile zone porosity, and mass transfer coefficient between mobile and immobile zones varied several orders of magnitude for the different flow rates, and because dispersion values were furthermore not physically realistic. Only the DFMD modeling approach (FRACTRAN in DFMD mode) was capable to simulate the observed changes in solute transport behavior during alternating flow rate without changing values of calibrated fracture spacing and fracture aperture to represent the macropores.

Monitoring well interception with fractures in clayey till.

When using monitoring wells for investigation of contaminant sources in clayey till, there is a high risk that fractures may cause mobile contaminants to bypass the monitoring wells. This paper indicates that the probability of interception between monitoring wells and hydraulic conductive fractures is often significantly less than 50%. Based on a field experiment and application of a calibrated discrete fracture matrix diffusion numerical model (FRAC3Dvs), the paper also evaluates pesticide-monitoring results for different positions of monitoring well screen relative to fractures. For well screens situated 0.25 and 2 m from a conductive fracture, the first concentrations of the pesticide metabolite (2,6 dichlorobenzamide, "BAM") would be measured two years and 18 years, respectively, after the contaminant had been transported into an underlying aquifer. In this way, underlying aquifers may be subjected to contamination by downward moving contamination without being observed in monitoring wells in the till.