Illuminating reactive microbial transport in saturated porous media: demonstration of a visualization method and conceptual transport model

We demonstrate a method to study reactive microbial transport in saturated translucent porous media using the bacteria Pseudomonas fluorescens 5RL genetically engineered to carry a plasmid with bioluminescence genes inducible by salicylate. Induced bacteria were injected into a cryolite grain filled chamber saturated with a sterile non-growth-promoting (phosphorus limited) chemical mixture containing salicylate as an aromatic hydrocarbon analogue. The amount of light produced by the bacteria serves as an estimator of the relative efficiency of aerobic biodegradation since bioluminescence is dependent on both salicylate and oxygen but only consumes oxygen. Bioluminescence was captured with a digital camera and analyzed to study the evolving spatial pattern of the bulk oxygen consuming reactions. As fluid flow transported the bacteria through the chamber, bioluminescence was observed to initially increase until an oxygen depletion zone developed behind the advective front. Bacterial transport was modeled with the advection dispersion equation and oxygen concentration was modeled assuming bacterial consumption via Monod kinetics with consideration of additional effects of rate-limited mass transfer from residual gas bubbles. Consistent with previous measurements, bioluminescence was considered proportional to oxygen consumed. Using the observed bioluminescence, model parameters were fit that were consistent with literature values and produced results in good agreement with the experimental data. These findings demonstrate potential for using this method to investigate the complex spatial and temporal dynamics of reactive microbial transport in saturated porous media.     

A reaction-based paradigm to model reactive chemical transport in groundwater with general kinetic and equilibrium reactions

This paper presents a reaction-based water quality transport model in subsurface flow systems. Transport of chemical species with a variety of chemical and physical processes is mathematically described by M partial differential equations (PDEs). Decomposition via Gauss-Jordan column reduction of the reaction network transforms M species reactive transport equations into two sets of equations: a set of thermodynamic equilibrium equations representing N(E) equilibrium reactions and a set of reactive transport equations of M-N(E) kinetic-variables involving no equilibrium reactions (a kinetic-variable is a linear combination of species). The elimination of equilibrium reactions from reactive transport equations allows robust and efficient numerical integration. The model solves the PDEs of kinetic-variables rather than individual chemical species, which reduces the number of reactive transport equations and simplifies the reaction terms in the equations. A variety of numerical methods are investigated for solving the coupled transport and reaction equations. Simulation comparisons with exact solutions were performed to verify numerical accuracy and assess the effectiveness of various numerical strategies to deal with different application circumstances. Two validation examples involving simulations of uranium transport in soil columns are presented to evaluate the ability of the model to simulate reactive transport with complex reaction networks involving both kinetic and equilibrium reactions.     

Estimating spatially-variable first-order rate constants in groundwater reactive transport systems

Numerical reactive transport models are often used as tools to assess aquifers contaminated with reactive groundwater solutes as well as investigating mitigation scenarios. The ability to accurately simulate the fate and transport of solutes, however, is often impeded by a lack of information regarding the parameters that define chemical reactions. In this study, we employ a steady-state Ensemble Kalman Filter (EnKF), a data assimilation algorithm, to provide improved estimates of a spatially-variable first-order rate constant λ through assimilation of solute concentration measurement data into reactive transport simulation results. The methodology is applied in a steady-state, synthetic aquifer system in which a contaminant is leached to the saturated zone and undergoes first-order decay. Multiple sources of uncertainty are investigated, including hydraulic conductivity of the aquifer and the statistical parameters that define the spatial structure of the parameter field. For the latter scenario, an iterative method is employed to identify the statistical mean of λ of the reference system. Results from all simulations show that the filter scheme is successful in conditioning the λ ensemble to the reference λ field. Sensitivity analyses demonstrate that the estimation of the λ values is dependent on the number of concentration measurements assimilated, the locations from which the measurement data are collected, the error assigned to the measurement values, and the correlation length of the λ fields.     

Multi-substrate, multi-option groundwater transport model

A user friendly, finite-difference groundwater transport model, called “Multi-substrate, Multi-option Groundwater Transport Model (MMGTM)”, has been developed to afford users several options in defining a transport sequence. In addition to advective-dispersive transport, the model incorporates a variety of adsorption and biological decay mechanisms. Adsorption can be simulated for linear, Langmuir, or Freundlich isotherms coupled with equilibrium or non-equilibrium mass transfer. Biological decay can be simulated for first-order or Monod-type approaches, and can be linked to oxygen consumption and transport. Aqueous and sorbed phase decay can be simulated.Further, the transport of two substrates and oxygen can be simulated concurrently and the interaction between them can be described as competitive, diauxic-like or simultaneous. The growth of biomass and its effect as an adsorbent can also be simulated by means of a stoichiometric yield coefficient and a biomass/adsorbent conversion factor. Continuous or pulse input of solute in conjunction with either constant-mass-flux or constant-concentration boundaries can be selected. Menu screens allow the user to configure each problem while parameters can be input individually or called from a separate data file. The input data can be viewed, modified or saved before simulation. Output is visually displayed of the screen as breakthrough and profile curves, while also being saved to an ASCII file on a disk for subsequent processing.     

地下水环境中甲基叔丁基醚运移过程的动力学模型

建立了地下水环境中甲基叔丁基醚(MTBE)运移过程的变系数动力学模型,并对模型进行了验证和参数灵敏度分析.模拟结果表明,地下水流速和阻滞系数对于MTBE的运移过程影响最为显著,而水动力弥散系数的影响较小,忽略其变化不会对预测地下水环境中污染物运移的环境动力学行为造成太大误差.由此得到的结论可定量研究MTBE在地下水环境中的对流.扩散特征,还可为MTBE污染地下水的预测预报、修复治理等研究提供科学依据.     

The reactive transport of trichloroethene is influenced by residence time and microbial numbers

The dechlorination rate in a flow-through porous matrix can be described by the species specific dechlorination rate observed in a liquid batch unless mass transport limitations prevail. This hypothesis was examined by comparing dechlorination rates in liquid batch with that in column experiments at various flow rates (3-9-12 cm day(-1)). Columns were loaded with an inoculated sand and eluted with a medium containing 1mM trichloroethene (TCE) for 247 days. Dechlorination in the column treatments increased with decreasing flow rate, illustrating the effect of the longer residence time. Zeroth order TCE or cis-DCE degradation rates were 4-7 folds larger in columns than in corresponding batch systems which could be explained by the higher measured Geobacter and Dehalococcoides numbers per unit pore volume in the columns. The microbial numbers also explained the variability in dechlorination rate among flow rate treatments marked by a large elution of the dechlorinating species' yield as flow increased. Stop flow events did not reveal mass transport limitations for dechlorination. We conclude that flow rate effects on reactive transport of TCE in this coarse sand are explained by residence time and by microbial transport and that mass transport limitations in this porous matrix are limited.     

Sequential coupling of bio-augmented permeable reactive barriers for remediation of 1,1,1-trichloroethane contaminated groundwater

Sequential coupling of high-density luffa sponge (HDLS) immobilized microorganism and permeable reactive barriers (IM Bio-PRBs) was superior to intimate coupling of free microorganism and permeable reactive barriers (FM Bio-PRBs) for remediation of 1,1,1-trichloroethane contaminated groundwater. IM Bio-PRBs had much better performance to removal 1,1,1-trichloroethane (1,1,1-TCA) and prevent the transport of 1,1,1-TCA and inorganic ions (NO₃^?, PO₄^3?, and SO₄^2?). The majority of them were prevented and accumulated in upgradient of IM Bio-PRBs. 1,1,1-TCA and inorganic ions in there contributed to the much faster growth of microorganism in upgradient aquifer. Therefore, the removal of 1,1,1-TCA and consumption of inorganic ions in upgradient of Bio-PRBs played a constructive role in reducing the processing load of following zero-valent iron (ZVI) PRBs and the negative effect of free microorganism cells (biological clogging) and inorganic ions (chemical clogging) on Bio-PRB permeability. In addition, IM Bio-PRBs were more conducive to accelerate the removal of 1,1,1-TCA in long-term remediation and 1,1,1-TCA residual concentration significantly lower than the safety standard of 0.2 mg L^?1. The change of terminal by-products of 1,1,1-TCA contaminated groundwater in Bio-PRBs showed that 1,1,1-TCA could be effectively de-chlorinated and mineralized in Bio-PRBs. The reductant H₂S (prolong the service life of ZVI-PRBs) was much more produced and utilized in IM Bio-PRBs. Taken together, sequentially coupled IM Bio-PRBs had a better overall performance, and its service life could be prolonged. It was a different design and idea to update conventional PRB remediation technology and theory.

     

Evaluating the sensitivity of a subsurface multicomponent reactive transport model with respect to transport and reaction parameters.

The input variables for a numerical model of reactive solute transport in groundwater include both transport parameters, such as hydraulic conductivity and infiltration, and reaction parameters that describe the important chemical and biological processes in the system. These parameters are subject to uncertainty due to measurement error and due to the spatial variability of properties in the subsurface environment. This paper compares the relative effects of uncertainty in the transport and reaction parameters on the results of a solute transport model. This question is addressed by comparing the magnitudes of the local sensitivity coefficients for transport and reaction parameters. General sensitivity equations are presented for transport parameters, reaction parameters, and the initial (background) concentrations in the problem domain. Parameter sensitivity coefficients are then calculated for an example problem in which uranium(VI) hydrolysis species are transported through a two-dimensional domain with a spatially variable pattern of surface complexation sites. In this example, the reaction model includes equilibrium speciation reactions and mass transfer-limited non-electrostatic surface complexation reactions. The set of parameters to which the model is most sensitive includes the initial concentration of one of the surface sites, the formation constant (Kf) of one of the surface complexes and the hydraulic conductivity within the reactive zone. For this example problem, the sensitivity analysis demonstrates that transport and reaction parameters are equally important in terms of how their variability affects the model results.     

Multi-component reactive transport modeling of natural attenuation of an acid groundwater plume at a uranium mill tailings site

Natural attenuation of an acidic plume in the aquifer underneath a uranium mill tailings pond in Wyoming, USA was simulated using the multi-component reactive transport code PHREEQC. A one-dimensional model was constructed for the site and the model included advective-dispersive transport, aqueous speciation of 11 components, and precipitation-dissolution of six minerals. Transport simulation was performed for a reclamation scenario in which the source of acidic seepage will be terminated after 5 years and the plume will then be flushed by uncontaminated upgradient groundwater. Simulations show that successive pH buffer reactions with calcite, Al(OH)3(a), and Fe(OH)3(a) create distinct geochemical zones and most reactions occur at the boundaries of geochemical zones. The complex interplay of physical transport processes and chemical reactions produce multiple concentration waves. For SO4(2-) transport, the concentration waves are related to advection-dispersion, and gypsum precipitation and dissolution. Wave speeds from numerical simulations compare well to an analytical solution for wave propagation.     

A review on reactive transport model and porosity evolution in the porous media

Environmental Science and Pollution Research - This work comprehensively reviews the equations governing multicomponent flow and reactive transport in porous media on the pore-scale, mesoscale and...     

Analysis of a deep well recharge experiment by calibrating a reactive transport model with field data

This paper describes the modeling of the hydrogeochemical effects of deep well recharge of oxic water into an anoxic pyrite-bearing aquifer. Kinetic expressions have been used for mineral dissolution-precipitation rates and organic matter oxidation. Hydrological and chemical parameters of the model were calibrated to field measurements. The results showed that oxidation of pyrite (FeS(2)) and, to a lesser extent, organic matter dominate the changes in quality of the recharged water during its passage through the aquifer. The recharge leads to the consumption of oxygen and nitrate and the formation of sulfate and ferrihydrite. Complexation reactions, cation exchange and precipitation and dissolution of calcite, siderite and rhodochrosite were also identified through the modeling. Despite problems of non-uniqueness of the calibrated parameters, the model was used successfully to depict the geochemical processes occurring in the aquifer. Non-uniqueness can be avoided by constraining the model as much as possible to measurements and/or data from literature, although they cannot be considered always as fixed values and should be considered as stochastic variables instead.     

Geochemistry of high arsenic groundwater in Chia-Nan plain, Southwestern Taiwan: possible sources and reactive transport of arsenic

Major ion, trace element, and stable isotope analyses were performed on groundwater samples collected during November 2005 and 2006 in Chia-Nan plain of southwestern Taiwan to examine As mobilization in aquifers. The high concentrations of As, Fe and Mn in the groundwater is consistent with low Eh values (under moderately reduced state). Moreover, the observed Na/Cl and SO(4)/Cl molar ratios in groundwater demonstrate the influence of seawater intrusion. Seawater intrusion could provide required electron acceptors (i.e., SO(4)) for bacterial sulfate reduction and promote reducing conditions that are favorable for As mobilization. The concurrent increases in the concentrations of Fe and Mn from 2005 to 2006 may be caused by bacterial Fe(III) and Mn(IV) reduction. Geochemical modeling demonstrate that As(III) is the dominant As species and the presence of Fe-bearing carbonates, sulfides, and oxide phases may locally act as potential sinks for As. Mud volcano fluids were also collected and analyzed to assess the possible source of As in the Chia-Nan plain groundwater. The oxygen and hydrogen isotopic signatures indicate that the As-rich mud volcano fluids may have been modified by chemical exchange with (18)O-rich crustal rocks and possibly originated from mixing of deep brines with circulating meteoric water. Thus As in the Chia-Nan plain groundwater may have been evolved from deep crustal fluids or rock sources. The hydrogeochemistry and widespread As enrichment in groundwater of Chia-Nan plain result from multiple processes, e.g., de-watering of deep crustal fluids, seawater intrusion, and biogeochemical cycling of Fe, As, and S in alluvial sediments.     

Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: coupling transport, microbial metabolism and geochemistry

Microbial reactions play an important role in regulating pore water chemistry as well as secondary mineral distribution in many subsurface systems and, therefore, may directly impact radionuclide migration in those systems. This paper presents a general modeling approach to couple microbial metabolism, redox chemistry, and radionuclide transport in a subsurface environment. To account for the likely achievement of quasi-steady state biomass accumulations in subsurface environments, a modification to the traditional microbial growth kinetic equation is proposed. The conditions for using biogeochemical models with or without an explicit representation of biomass growth are clarified. Based on the general approach proposed in this paper, the couplings of uranium reactions with biogeochemical processes are incorporated into computer code BIORXNTRN Version 2.0. The code is then used to simulate a subsurface contaminant migration scenario, in which a water flow containing both uranium and a complexing organic ligand is recharged into an oxic carbonate aquifer. The model simulation shows that Mn and Fe oxyhydroxides may vary significantly along a flow path. The simulation also shows that uranium(VI) can be reduced and therefore immobilized in the anoxic zone created by microbial degradation.     

Database uncertainty as a limiting factor in reactive transport prognosis

The effect of uncertainties in thermodynamic databases on prediction performances of reactive transport modeling of uranium (VI) is investigated with a Monte Carlo approach using the transport code TReaC. TReaC couples the transport model to the speciation code PHREEQC by a particle tracking method. A speciation example is given to illustrate the effect of uncertainty in thermodynamic data on the predicted solution composition. The transport calculations consequently show the prediction uncertainty resulting from uncertainty in thermodynamic data. A conceptually simple scenario of elution of uranium from a sand column is used as an illustrating example. Two different cases are investigated: a carbonate-enriched drinking water and an acid mine water associated with uranium mine remediation problems. Due to the uncertainty in the relative amount of positively charged and neutral solution species, the uncertainty in the thermodynamic data also infers uncertainty in the retardation behavior. The carbonated water system shows the largest uncertainties in speciation calculation. Therefore, the model predictions of total uranium solubility have a broad range. The effect of data uncertainty in transport prediction is further illustrated by a prediction of the time when eluted uranium from the column exceeds a threshold value. All of these Monte Carlo transport calculations consume large amounts of computing time.     

Enhancement of gasworks groundwater remediation by coupling a bio-electrochemical and activated carbon system

Environmental Science and Pollution Research - Here, we show the electrical response, bacterial community, and remediation of hydrocarbon-contaminated groundwater from a gasworks site using a...     

A sensibility analysis of model selection in modeling the reactive transport of cesium in crushed granite

We performed a sensibility analysis of model selection in modeling the reactive transport of cesium in crushed granite through model calibration and validation. Based on some solid phase analysis data and kinetic batch experimental results, we hypothesized three two-site sorption models in the LEHGC reactive transport model to fit the breakthrough curves (BTCs) from the corresponding column experiments. The analysis of breakthrough curves shows that both the empirical two-site kinetic linear sorption model and the semi-mechanistic/semi-empirical two-site kinetic surface complexation model, regardless of their complexity, can match our experimental data fairly well under given test conditions. A numerical experiment to further compare the two models shows that they behave differently when the pore velocity is not of the same order of magnitude as our test velocities. This result indicates that further investigations to help determine a better model are needed. We suggest that a multistage column experiment, which tests over the whole range of practical flow velocities, should be conducted to help alleviate inadequate hypothesized models.     

Process-based reactive transport modeling of a permeable reactive barrier for the treatment of mine drainage

Reactive transport modeling of a permeable reactive barrier for the treatment of mine drainage was used to integrate a comprehensive data set including pore water chemistry and solid phase data from several sampling events over a >3-year time period. The simulations consider the reduction of sulfate by the organic carbon-based treatment material and the removal of sulfate and iron by precipitation of reduced mineral phases including iron monosulfides and siderite. Additional parameters constraining the model include dissolved H2S, alkalinity and pH, as well as a suite of solid phase S-fractions identified by extractions. Influences of spatial heterogeneity necessitated the use of a 2-dimensional modeling approach. Simulating observed seasonal fluctuations and long-term changes in barrier reactivity required the use of temperature dependent rate coefficients and a multimodal Monod-type rate expression accounting for the variable reactivity of different organic carbon fractions. Simulated dissolved concentrations of SO4, Fe, H2S, alkalinity and pH, as well as solid phase accumulations of reduced sulfur phases generally compare well to observed trends over 23 months. Spatial variations, seasonal fluctuations and the time-dependent decline in reactivity were also captured. The modeling results generally confirm, and further strengthen, the existing conceptual model for the site. Overall sulfate reduction and S-accumulation rates are constrained with confidence within a factor of 1.5.     

地下水中多环芳烃迁移转化研究

吸附和生物降解是受污染地下水中多环芳烃(PAHs)归宿的主要途径.论述了PAHs在含水层中吸附过程的特征、影响因素与研究方法,并比较各种研究方法的优缺点;分析了PAHs在含水层中生物降解过程机制以及研究进展;介绍了PAHs在地下水中迁移、转化数学模型与数值模拟的研究开发状况;指出了PAHs与固相介质的吸附机制和竞争吸附行为、高分子量PAHs的生物降解途径和机制及共存PAHs或与其他污染物在地下水中的迁移、转化、归宿与修复技术是深入研究的方向.     

An overview of uncertainties in modelling groundwater solute transport

Model predictions are uncertain because of uncertainties on future and/or anthropogenic stresses, parameter values and conceptual models. The first two groups of problems can be addressed through rather systematic methods (scenario analysis, error transmission techniques, automatic calibration algorithms, etc.). However, conceptual uncertainties are rarely given adequate attention. The objective of this paper is to synthesize conceptual difficulties associated with transport. These include: (1) processes that are significant at small scales may not be relevant at large scales; (2) inversely, new processes (e.g., dispersion) emerge in response to increase in scale and the way to represent them may depend on the assumed model structure; (3) the observed shapes of both breakthrough curves and pollutant plumes are not well represented by the classical transport equation; (4) porosities and dispersivities derived from field tracer tests often exhibit a directional dependence; etc. Though not directly related to solute transport, scale effects on hydraulic conductivity may also affect solute transport modelling. When these anomalies are examined, it is concluded that they are directly or indirectly caused by heterogeneity. Current approaches for dealing with heterogeneity can be divided into stochastic and deterministic. Stochastic methods have been successful in explaining qualitatively some anomalies of solute transport, but they appear to be far from reaching a stage at which they can be used routinely for solving realistic field problems. On the other hand, when applied with care, deterministic methods have been successfully used in actual problems. Yet, it can be argued that they fail to account for small-scale variability of concentrations so that they would become ineffective when dealing with nonlinear processes, such as chemical reactions. Relevance of on-going research for overcoming these difficulties is discussed.     

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.