Lessons learned from bacterial transport research at the South Oyster Site

This paper provides a review of bacterial transport experiments conducted by a multiinvestigator, multiinstitution, multidisciplinary team of researchers under the auspices of the U.S. Department of Energy (DOE). The experiments were conducted during the time period 1999-2001 at a field site near the town of Oyster, Virginia known as the South Oyster Site, and included four major experimental campaigns aimed at understanding and quantifying bacterial transport in the subsurface environment. Several key elements of the research are discussed here: (1) quantification of bacterial transport in physically, chemically, and biologically heterogeneous aquifers, (2) evaluation of the efficacy of conventional colloid filtration theory, (3) scale effects in bacterial transport, (4) development of new methods for microbial enumeration and screening for low adhesion strains, (5) application of novel hydrogeophysical techniques for aquifer characterization, and (6) experiences regarding management of a large field research effort. Lessons learned are summarized in each of these areas. The body of literature resulting from South Oyster Site research has been widely cited and continues to influence research into the controls exerted by aquifer heterogeneity on reactive transport (including microbial transport). It also served as a model (and provided valuable experience) for subsequent and ongoing highly-instrumented field research efforts conducted by DOE-sponsored investigators.     

Evaluation of Monod kinetic parameters in the subsurface using moment analysis: Theory and numerical testing

The spatial moments of a contaminant plume undergoing bio-attenuation are coupled to the moments of microbial populations effecting that attenuation. In this paper, a scalable inverse method is developed for estimating field-scale Monod parameters such as the maximum microbial growth rate (μ^max), the contaminant half saturation coefficient (K_s), and the contaminant yield coefficient (Y_s). The method uses spatial moments that characterize the distribution of dissolved contaminant and active microbial biomass in the aquifer. A finite element model is used to generate hypothetical field-scale data to test the method under both homogeneous and heterogeneous aquifer conditions. Two general cases are examined. In the first, Monod parameters are estimated where it is assumed a microbial population comprised of a single bacterial species is attenuating one contaminant (e.g., an electron donor and an electron acceptor). In a second case, contaminant attenuation is attributed to a microbial consortium comprised of two microbial species, and Monod parameters for both species are estimated. Results indicate the inverse method is only slightly sensitive to aquifer heterogeneity and that estimation errors decrease as the sampling time interval decreases with respect to the groundwater travel time between sample locations. Optimum conditions for applying the scalable inverse method in both space and time are investigated under both homogeneous and heterogeneous aquifer conditions.     

Geostatistical analysis and conditional simulation for estimating the spatial variability of hydraulic conductivity in the Choushui River alluvial fan,Taiwan

This work evaluated the spatial variability and distribution of heterogeneous hydraulic conductivity (K) in the Choushui River alluvial fan in Taiwan, using ordinary kriging (OK) and mean and individual sequential Gaussian simulations (SGS). A baseline flow model constructed by upscaling parameters was inversely calibrated to determine the pumping and recharge rates. Simulated heads using different K realizations were then compared with historically measured heads. A global/local simulated error between simulated and measured heads was analysed to assess the different spatial variabilities of various estimated K distributions. The results of a MODFLOW simulation indicate that the OK realization had the smallest sum of absolute mean simulation errors (SAMSE) and the SGS realizations preserved the spatial variability of the measured K fields. Moreover, the SAMSE increases as the spatial variability of the K field increases. The OK realization yields small local simulation errors in the measured K field of moderate magnitude, whereas the SGS realizations have small local simulation errors in the measured K fields, with high and low values. The OK realization of K can be applied to perform a deterministic inverse calibration. The mean SGS method is suggested for constructing a K field when the application focuses on extreme values of estimated parameters and small calibration errors, such as in a simulation of contaminant transport in heterogeneous aquifers. The individual SGS realization is useful in stochastically assessing the spatial uncertainty of highly heterogeneous aquifers. Copyright © 2004 John Wiley & Sons, Ltd.     

Upscaling hydraulic conductivity based on the topology of the sub-scale structure

The hydraulic conductivity of heterogeneous porous media depends on the distribution function and the geometry of local conductivities at the smaller scale. There are various approaches to estimate the effective conductivity K_eff at the larger scale based on information about the small scale heterogeneity. A critical geometric property in this ‘upscaling’ procedure is the spatial connectivity of the small-scale conductivities. We present an approach based on the Euler-number to quantify the topological properties of heterogeneous conductivity fields, and we derive two key parameters which are used to estimate K_eff. The required coefficients for the upscaling formula are obtained by regression based on numerical simulations of various heterogeneous fields. They are found to be generally valid for various different isotropic structures. The effective unsaturated conductivity function K_eff (ψ_m) could be predicted satisfactorily. We compare our approach with an alternative based on percolation theory and critical path analysis which yield the same type of topological parameters. An advantage of using the Euler-number in comparison to percolation theory is the fact that it can be obtained from local measurements without the need to analyze the entire structure. We found that for the heterogeneous field used in this study both methods are equivalent.     

Inter-comparison of seasonal variability and nonlinear trend between AERONET aerosol optical depth and PM10 mass concentrations in Hong Kong

Here we used Empirical Mode Decomposition(EMD) method to study seasonal variability and nonlinear trend of corrected AERONET Aerosol Optical Depth(AOD/Hi) and corrected PM10 mass concentrations(PM10×f(RH)) in Hong Kong during 2005–2011. AOD/Hi is highly correlated with PM10×f(RH) in semi-annual and annual time scales(with correlation coefficient 0.67 for semi-annual and 0.79 for annual components, 95% confidence interval). On the semi-annual scale, both AOD/Hi and PM10×f(RH) can capture the two maxima in March and October, respectively, with much stronger amplitude in March probably due to the long-range transport of dust storm. On the annual cycle, the AOD/Hi and PM10×f(RH), which are negatively correlated with the precipitation and solar radiation, vary coherently with the maxima in February. This annual peak occurs about one month earlier than the first peak of the semi-annual variability in March, but with only half amplitude. During 2005–2011, both AOD/Hi and PM10×f(RH) exhibit the pronounced decreasing trend with the mean rate of 14 μg m–3 per year for PM10×f(RH), which reflects the significant effects of the air pollution control policy in Hong Kong during the past decade. The nonlinear trend analysis indicates that the decreasing of PM10×f(RH) is slower than that of AOD/Hi when the AOD/Hi is less than 0.44 but becomes faster when the AOD/Hi exceeds 0.44. These results illustrate that the AERONET AOD can be used quantitatively to estimate local air-quality variability on the semi-annual, annual, and long-term trend time scales.     

Change of collision efficiency with distance in bacterial transport experiments

Understanding the mechanisms of bacterial transport in aquifers is important in developing bioremediation strategies. Collision efficiency (alpha) is one important parameter used in modeling bacterial transport. This study was undertaken to measure change in alpha with distance by performing a bacterial transport experiment in Oyster, Virginia. Following injection of a bacterium, Comamonas sp., into a well, water samples were collected at various distances along the flowpath and injected into columns packed with homogenized South Oyster focus area sediment. Zeta potentials of the bacteria in the samples were measured. Values of alpha were determined at various locations in the field in two ways: based on field breakthrough concentrations at the sampling points and based on column breakthrough concentrations. The alpha values estimated from field breakthrough decreased with distance, whereas those estimated from column breakthrough increased with distance. Bacterial cell surface charge became progressively more negative with distance in the field. We hypothesize that the apparent contradiction between field and column alpha values was caused by differences in the flow of the two systems. Flow in the columns was forced to occur through fine-grained zones of iron and aluminum hydroxide coatings that selectively removed the most negatively charged bacteria. In contrast, in the field, the injected cells did not come into contact with the positively charged coatings because the bulk solution bypassed them due to heterogeneous hydraulic properties. These results suggest that laboratory-based models may underestimate bacterial transport distance in the field. A more realistic approach may be necessary to capture the degree of heterogeneity.     

Transport of kinetically sorbing solutes in heterogeneous sediments with multimodal conductivity and hierarchical organization across scales

Solute transport in subsurface environments is controlled by geological heterogeneity over multiple scales. In reactive transport characterized by a low Damköhler number, it is also controlled by the rate of kinetic mass transfer. A theory for addressing the impact of sedimentary texture on the transport of kinetically sorbing solutes in heterogeneous porous formations is derived using the Lagrangian-based stochastic methodology. The resulting model represents the hierarchical organization of sedimentary textures and associated modes of log conductivity (K) for sedimentary units through a hierarchical Markov Chain. The model characterizes kinetic sorption using a spatially uniform linear reversible rate expression. Our main interest is to investigate the effect of sorption kinetics relative to the effects of K heterogeneity on the dispersion of a reactive plume. We study the contribution of each scale of stratal architecture to the dispersion of kinetically sorbing solutes in the case of a low Damköhler number. Examples are used to demonstrate the time evolution and relative contributions of the auto- and cross-transition probability terms to dispersion. Our analysis is focused on the model sensitivity to the parameters defined at each hierarchical level (scale) including the integral scales of K spatial correlation, the anisotropy ratio, the indicator correlation scales, and the contrast in mean K between facies defined at different scales. The results show that the anisotropy ratio and integral scales of K have negligible effect upon the longitudinal dispersion of sorbing solutes. Furthermore, dispersion of sorbing solutes depends mostly on indicator correlation scales, and the contrast of the mean conductivity between units at different scales.     

A semi-analytical model of expected areal-average infiltration under spatial heterogeneity of rainfall and soil saturated hydraulic conductivity

A semi-analytical model for the estimate of expected areal-average infiltration rate at hillslope scale is presented. It accounts for spatial heterogeneity of the saturated hydraulic conductivity, K_s, and rainfall rate, r. The K_s field is characterized by a lognormal probability density function while the rainfall rate r is represented by a uniform distribution between two extreme values. The model formulation relies upon the use of cumulative infiltration as the independent variable which is then expressed as a function of an expected time for use in practical applications. The solution is applicable for those ranges of r and K_s that allow for neglecting the infiltration of surface water running downslope into pervious soils (run-on process). The model was tested by comparisons with Monte Carlo simulations carried out for a variety of coefficients of variation of r and K_s over a clay loam soil and a sandy loam soil. The model was found to be very reliable both with coupled spatial variability of r and K_s and when only one variable is characterized by spatial heterogeneity while the other is uniform.     

Equivalent diffusion coefficient of clay-rich geological formations: comparison between numerical and analytical estimates

Laboratory experiments in rock samples collected from clay-rich formations indicate that the effective molecular diffusion coefficient (D) is a heterogeneous and anisotropic property. Since laboratory measurements of D are representative of a very small volume, upscaling is necessary in order to incorporate these data in large-scale numerical models of diffusive transport. In this work we address the problem of the estimating the equivalent diffusion coefficient (D _eq ), in terms of total diffusive flux, in a three-dimensional domain characterized by a heterogeneous and anisotropic spatial distribution of D. D _eq was estimated from the results of steady-state diffusive transport simulations through several realizations of the D field. The ensemble averages of D _eq from fields with different degrees of heterogeneity and anisotropy were then compared with estimates from analytical upscaling expressions based on stochastic as well as power-averaging approaches. These expressions are largely based on similar expressions developed for calculating the effective hydraulic conductivity in heterogeneous and anisotropic domains. Comparisons showed that stochastic expressions provide accurate estimates of D _eq only for fields characterized by low heterogeneity. Within the range of heterogeneity and anisotropy considered, our results showed that a power-averaging expression is very accurate in predicting D _eq especially when the parameter p _i is estimated through fitting of the numerical results. Nonetheless, the relationship between this parameter and the anisotropy ratio is linear.     

Near Surface Electrical Characterization of Hydraulic Conductivity: From Petrophysical Properties to Aquifer Geometries—A Review

This paper reviews the recent geophysical literature addressing the estimation of saturated hydraulic conductivity (K) from static low frequency electrical measurements (electrical resistivity, induced polarization (IP) and spectral induced polarization (SIP)). In the first part of this paper, research describing how petrophysical relations between electrical properties and effective (i.e. controlling fluid transport) properties of (a) the interconnected pore volumes and interconnected pore surfaces, have been exploited to estimate K at both the core and field scale is reviewed. We start with electrical resistivity measurements, which are shown to be inherently limited in K estimation as, although resistivity is sensitive to both pore volume and pore surface area properties, the two contributions cannot be separated. Efforts to utilize the unique sensitivity of IP and SIP measurements to physical parameters that describe the interconnected pore surface area are subsequently introduced and the incorporation of such data into electrical based Kozeny–Carman type models of K estimation is reviewed. In the second part of this review, efforts to invert geophysical datasets for spatial patterns of K variability (e.g. aquifer geometries) at the field-scale are considered. Inversions, based on the conversion of an image of a geophysical property to a hydrological property assuming a valid petrophysical relationship, as well as joint/constrained inversion methods, whereby multiple geophysical and hydrological data are inverted simultaneously, are briefly covered. This review demonstrates that there currently exists an opportunity to link, (1) the petrophysics relating low frequency electrical measurements to effective hydraulic properties, with (2) the joint inversion strategies developed in recent years, in order to obtain more meaningful estimates of spatial patterns of K variability than previously reported.     

Field Study of Subsurface Heterogeneity with Steady‐State Hydraulic Tomography

Remediation of subsurface contamination requires an understanding of the contaminant (history, source location, plume extent and concentration, etc.), and, knowledge of the spatial distribution of hydraulic conductivity (K) that governs groundwater flow and solute transport. Many methods exist for characterizing K heterogeneity, but most if not all methods require the collection of a large number of small‐scale data and its interpolation. In this study, we conduct a hydraulic tomography survey at a highly heterogeneous glaciofluvial deposit at the North Campus Research Site (NCRS) located at the University of Waterloo, Waterloo, Ontario, Canada to sequentially interpret four pumping tests using the steady‐state form of the Sequential Successive Linear Estimator (SSLE) ( Yeh and Liu 2000 ). The resulting three‐dimensional (3D) K distribution (or K‐tomogram) is compared against: ( 1 ) K distributions obtained through the inverse modeling of individual pumping tests using SSLE, and ( 2 ) effective hydraulic conductivity (K_eff) estimates obtained by automatically calibrating a groundwater flow model while treating the medium to be homogeneous. Such a K_eff is often used for designing remediation operations, and thus is used as the basis for comparison with the K‐tomogram. Our results clearly show that hydraulic tomography is superior to the inversions of single pumping tests or K_eff estimates. This is particularly significant for contaminated sites where an accurate representation of the flow field is critical for simulating contaminant transport and injection of chemical and biological agents used for active remediation of contaminant source zones and plumes.     

On the effective hydraulic conductivity in mean vertical unsaturated steady flows

Water flow in partially saturated heterogeneous porous formations is modelled by regarding the hydraulic parameters as stationary random space functions (RSFs). As a consequence, the flow variables are also RSFs, and we aim to develop a procedure to derive the effective hydraulic conductivity (EHC). The methodology relies on a perturbation approach which regards the variances of the hydraulic parameters as small quantities. By using the Gardner’s [Gardner WR. Some steady state solutions of unsaturated moisture flow equations with application to evaporation from a water table. Soil Sci 1958;85:228–32] two-parameters (K_s, α) model for the local unsaturated conductivity, we obtain the EHC for any dimensionality d of the flow domain, and arbitrary correlation functions of the input RSFs. Unlike previous studies [e.g. Yeh T-CJ, Gelhar J, Gutjahr A. Stochastic analysis of unsaturated flow in heterogenous soils. 1. Statistically isotropic media. Water Resour Res 1985;21;447–56, Yeh T-CJ, Gelhar J, Gutjahr A. Stochastic analysis of unsaturated flow in heterogenous soils. 2. Statistically anisotropic media with variable α. Water Resour Res 1985:21:457–64], the EHC is represented here as product between the local scale conductivity valid for a domain of mean parameters, and a correction function κ¹ which depends on the medium heterogeneity structure and the mean pressure head.Generally, the correction function κ¹ is expressed by d-fold quadrature. These quadratures are further reduced after adopting specific (i.e. exponential and Gaussian) structure for the (cross) correlation functions involved in the computation of κ¹. We have also focused on some particular formation structures which are relevant for the applications, and permit simplification of the computational aspect, as well.We investigate effects of the heterogeneity formation properties as well as the mean head on the structure of κ¹. Overall, results suggest that, given the formation statistics, the impact of the heterogeneity upon κ¹ is enhanced as the medium becomes drier. This is particularly so when the variability of the fluctuation of Y = ln K_s is small compared with that of ζ = ln α. Conversely, when the heterogeneity of Y is prevalent upon that of ζ, κ¹ is influenced solely by the anisotropic structure of the formation unless the horizontal correlation scales are much greater than the vertical ones.     

Upscaling unsaturated hydraulic parameters for flow through heterogeneous anisotropic sediments

We compare two methods for determining the upscaled water characteristics and saturation-dependent anisotropy in unsaturated hydraulic conductivity from a field-scale injection test. In both approaches an effective medium approximation is used to reduce a porous medium of M textures to an equivalent homogenous medium. The first approach is a phenomenological approach based on homogenization and assumes that moisture-based Richards’ equation can be treated like the convective–dispersive equation (CDE). The gravity term, dK_z(θ)/d(θ), analogous to the vertical convective velocity in the CDE, is determined from the temporal evolution of the plume centroid along the vertical coordinate allowing calculation of an upscaled K_z(θ). As with the dispersion tensor in the CDE, the rate of change of the second spatial moment in 3D space is used to calculate the water diffusivity tensor, D(θ), from which an upscaled K(θ) is calculated. The second approach uses the combined parameter scale inverse technique (CPSIT). Parameter scaling is used first to reduce the number of parameters to be estimated by a factor M. Upscaled parameters are then optimized by inverse modeling to produce an upscaled K(θ) characterized by a pore tortuosity–connectivity tensor, L. Parameters for individual textures are finally determined from the optimized parameters by inverse scaling using scale factors determined a priori. Both methods produced upscaled K(θ) that showed evidence of saturation dependent anisotropy. Flow predictions with the STOMP simulator, parameterized with upscaled parameters, were compared with field observations. Predictions based on the homogenization method were able to capture the mean plume behavior but could not reproduce the asymmetry caused by heterogeneity and lateral spreading. The CPSIT method captured the effects of heterogeneity and anisotropy and reduced the mean squared residual by nearly 90% compared to local-scale and upscaled parameters from the homogenization method. The Pacific Northwest National Laboratory is operated for the US Department of Energy by Battelle under Contract DE-AC05-76RL01830.     

Continuum-scale convective mixing in geological CO2 sequestration in anisotropic and heterogeneous saline aquifers

Deep saline aquifers are important geological formations for CO₂ sequestration. It has been known that dissolution of CO₂ increases brine density, which results in downward density-driven convection and consequently greatly enhances CO₂ sequestration. In this study, a continuum-scale lattice Boltzmann model is used to investigate convective mixing of CO₂ in saline aquifers. It is found that increasing permeability in either the vertical or horizontal direction accelerates the development of convective mixing. In a heterogeneous aquifer, increasing heterogeneity hampers the onset of convective mixing, because the heterogeneous permeability field results in a large portion of low-velocity region which reduces the instability of the system. The critical time for the onset of instability depends mainly on the coefficient of variation (COV) of the permeability field, and is insensitive to the correlation length. This implies that within the scale of critical time, mass transport is dominated by diffusion, and thus depends mainly on fine-scale heterogeneity controlled by COV. We derived an empirical formula for estimating the critical time, which leads to good estimates for all combinations of COV and correlation length. Fingering, channeling, and dispersion are the three mechanisms for mass transport. In dispersion, dissolved mass is approximately proportional to the square root of time, while in fingering and channeling it is approximately proportional to time. Mass transport by channeling depends significantly on permeability structure, while by fingering it is controlled by gravitational instability. It is also found that larger volumes of CO₂ can be stored in heterogeneous aquifers because of higher mass dissolution rates.     

Effect of anisotropy on solute transport in degraded fen peat soils

Peat soils are heterogeneous, anisotropic porous media. Compared to mineral soils, there is still limited understanding of physical and solute transport properties of fen peat soils. In this study, we aimed to explore the effect of soil anisotropy on solute transport in degraded fen peat. Undisturbed soil cores, taken in vertical and horizontal direction, were collected from one drained and one restored fen peatland both in a comparable state of soil degradation. Saturated hydraulic conductivity (K _s) and chemical properties of peat were determined for all soil cores. Miscible displacement experiments were conducted under saturated steady state conditions using potassium bromide as a conservative tracer. The results showed that (1) the K _s in vertical direction (K _sv) was significantly higher than that in horizontal direction (K_sh), indicating that K _s of degraded fen peat behaves anisotropically; (2) pronounced preferential flow occurred in vertical direction with a higher immobile water fraction and a higher pore water velocity; (3) the 5% arrival time (a proxy for the strength of preferential flow) was affected by soil anisotropy as well as study site. A strong correlation was found between 5% arrival time and dispersivity, K _s and mobile water fraction; (4) phosphate release was observed from drained peat only. The impact of soil heterogeneity on phosphate leaching was more pronounced than soil anisotropy. The soil core with the strongest preferential flow released the highest amount of phosphate. We conclude that soil anisotropy is crucial in peatland hydrology but additional research is required to fully understand anisotropy effects on solute transport.     

Multicomponent competitive monovalent cation exchange in hierarchical porous media with multimodal reactive mineral facies

This paper presents a stochastic model for multicomponent competitive monovalent cation exchange in hierarchical porous media. Reactive transport in porous media is highly sensitive to heterogeneities in physical and chemical properties, such as hydraulic conductivity (K), and cation exchange capacity (CEC). We use a conceptual model for multimodal reactive mineral facies and develop a Eulerian-based stochastic theory to analyze the transport of multiple cations in heterogeneous media with a hierarchical organization of reactive minerals. Numerical examples investigate the retardation factors and dispersivities in a chemical system made of three monovalent cations (Na⁺, K⁺, and Cs⁺). The results demonstrate how heterogeneity influences the transport of competitive monovalent cations, and highlight the importance of correlations between K and CEC. Further sensitivity analyses are presented investigating how the dispersion and retardation of each cation are affected by the means, variances, and integral scales of K and CEC. The volume fraction of organic matter is shown to be another important parameter. The Eulerian stochastic framework presented in this work clarifies the importance of each system parameters on the migration of cation plumes in formations with hierarchical organization of facies types. Our stochastic approach could be used as an alternative to numerical simulations for 3D reactive transport in hierarchical porous media, which become prohibitively expensive for the multicomponent applications considered in this work.     

Homogenization of the transport behavior of nonlinearly adsorbing pollutants in physically and chemically heterogeneous aquifers

This paper addresses the question of how spatial variability in the hydraulic and chemical properties of groundwater systems affects the transport and sorption behavior of pollutants at the field scale. In this paper, we limit our investigations on pollutants that adsorb according to an equilibrium controlled nonlinear Freundlich sorption isotherm. The new contribution of this paper is take into account not only spatially variable Freundlich distribution coefficients _KS$K_S$ but spatially variable Freundlich nonlinearity parameters p as well. Using a homogenization theory approach, we shortly review the impact of spatially variable hydraulic properties on the transport and extend the theory to spatially variable chemical properties. We show that spatially variable Freundlich exponents cause a very different field scale transport and sorption behavior than spatial variations in the distribution coefficients only since in the first case field scale Freundlich parameters and field scale dispersion coefficients become concentration dependent. In particular, field scale retardation is much larger than small-scale retardation.     

Effects of starvation on bacterial transport through porous media

A major problem preventing widespread implementation of microbial injection strategies for bioremediation and/or microbially enhanced oil recovery is the tendency of bacteria to strongly adhere to surfaces in the immediate vicinity of the injection point. Long term (weeks to months) nutrient starvation of bacteria prior to injection can decrease attachment and enhance transport through porous media. This paper summarizes results of starvation-enhanced transport experiments in sand columns of 30 cm, 3 m, and 16 m in length. The 16 m column experiments compared transport, breakthrough and distribution of adhered cells for starved and vegetative cultures of Klebsiella oxytoca, a copious biofilm producer. Results from these experiments were subsequently used to design and construct a field-scale biofilm barrier using starved Pseudomonas fluorescens. The 30 cm and 3 m sand columns experiments investigated starvation-enhanced transport of Shewanella algae BrY, a dissimilatory metal-reducing bacterium. In both cases the vegetative cells adsorbed onto the sand in higher numbers than the starved cells, especially near the entrance of the column. These results, taken together with studies cited in the literature, indicate that starved cells penetrate farther (i.e. higher breakthrough concentration) and adsorb more uniformly along the flow path than vegetative cells.