UTCHEM BIODEGRADATION MODEL

DESCRIPTION AND CAPABILITIES

Phillip C. deBlanc, Daene C. McKinney, Gerald E. Speitel, Jr.

Center for Research in Water Resources

Mojdeh Delshad, Gary A. Pope, Kamy Sepehrnoori

Center for Petroleum and Geosystems Engineering

University of Texas at Austin

April 5, 1996

1.0 INTRODUCTION


UTCHEM is a multi-phase, multi-component, three-dimensional, numerical model that simulates the fate and transport of both dissolved and non-aqueous phase organic contaminants in porous media. The model can be used to simulate spills of either lighter-than-water NAPLs (LNAPLs) or denser-than-water NAPLs (DNAPLs). The NAPL phase can contain up to five organic constituents. The transfer of organic contaminants from the NAPL to the aqueous phase is described through either equilibrium partitioning or a linear driving force non-equilibrium mass transfer model. Adsorption of organic constituents is modeled through equilibrium partitioning. An arbitrary number of injection and pumping wells can be specified so that bioremediation schemes can be modeled and bioremediation designs can be optimized. The previous version of the UTCHEM model is described in detail by Delshad et al. (1996).

Advanced biodegradation capabilities have recently been incorporated into UTCHEM. The biodegradation option allows an entirely new class of problems to be simulated with UTCHEM, such as surfactant remediation followed by biodegradation of the residual surfactant and contaminant. This document describes the biodegradation model capabilities, presents and explains the biodegradation equations, and provides examples of UTCHEM biodegradation simulations.

2.0 CURRENT MODEL CAPABILITIES


UTCHEM simulates the biodegradation of chemical compounds that can serve as substrates (carbon and/or energy sources) for microorganisms. The model simulates the destruction of substrates, the consumption of electron acceptors (e.g. oxygen, nitrate, etc.), and the growth of biomass. Substrates can be biodegraded by free-floating microorganisms in the aqueous phase or by attached biomass present as microcolonies in the manner of Molz et al. (1986). Multiple substrates, electron acceptors and biological species are accommodated by the model. Important assumptions for the biodegradation model are:
  1. Biodegradation reactions occur only in the aqueous phase.

  2. Microcolonies are fully penetrated; i.e., there is no internal resistance to mass transport within the attached biomass.

  3. Biomass is initially uniformly distributed throughout the porous medium.

  4. Biomass is prevented from decaying below a lower limit by metabolism of naturally occurring organic matter unless cometabolic reactions act to reduce the active biomass concentrations below natural levels.

  5. The area available for transport of organic constituents into attached biomass is directly proportional to the quantity of biomass present.

The biodegradation model includes the following features:

Examples of how these features are used in biodegradation modeling are provided below.

Example 1 - Biodegradation of benzene, toluene, ethylbenzene, and xylene (BTEX) from a gasoline spill


UTCHEM can simulate the biodegradation of each BTEX compound individually or as a pseudo-component using average biodegradation kinetic parameters. The model simulates the aerobic destruction of the BTEX, the development of an oxygen-deficient zone downgradient of the spill, and the dissolution of the BTEX compounds from any free-phase gasoline present. If nitrate is assumed to be present in the water, then the model can use electron acceptor inhibition functions to "switch off" aerobic biodegradation and "switch on" anaerobic biodegradation of toluene, ethylbenzene and xylene where oxygen concentrations are sufficiently low. Low concentrations of nutrients, such as nitrogen and phosphorous, also limit biodegradation reactions through nutrient Monod terms.

Example 2 - Aerobic biodegradation of trichloroethene (TCE)


TCE can be biodegraded with oxygen as the electron acceptor by methanotrophs that use methane as the primary carbon and energy source (McCarty, 1993). UTCHEM can model the mineralization of TCE under aerobic conditions. Methane competes with TCE for the enzyme that degrades the two compounds, resulting in lower rates of TCE biodegradation that might otherwise be anticipated. UTCHEM includes enzyme competition kinetics to take this competitive inhibition of TCE into account. Where methane is not present to act as a growth substrate, the biomass is deactivated by cometabolic reactions which "drain" reducing power from the microorganisms. The model also simulates the reduction in active biomass caused by highly reactive reaction intermediates through finite transformation capacities.

Example 3 - Anaerobic biodegradation of TCE by cometabolism


TCE can also be biodegraded anaerobically under methanogenic conditions to dichloroethene (DCE), which in turn can be biodegraded into vinyl chloride (VC) (Vogel, 1993). The entire process can be simulated by UTCHEM. UTCHEM can simulate the generation of DCE as a product of TCE biodegradation, and the production of VC as a by-product of DCE biodegradation. Biodegradation is repressed where oxygen is present through the electron acceptor inhibition functions. Reduced biodegradation rates near the TCE source, where high concentrations of TCE may be toxic to microorganisms, is modeled with a substrate inhibition term.

Example 4 - Anaerobic biodegradation of 1,1,1-trichloroethane (1,1,1-TCA)


As a final example, the anaerobic conversion of 1,1,1-TCA to 1,1-dichloroethane and then to chloroethane (CA) can be modeled by UTCHEM. CA can be converted abiotically into ethanol and chloride through hydrolysis reactions (McCarty, 1993). TCA can also be transformed directly into 1,1-DCE and acetic acid via abiotic reactions (McCarty, 1993). UTCHEM can simultaneously model both the biological reactions that convert 1,1,1-TCA to CA, the abiotic transformation of CA to ethanol and chloride, and the abiotic transformation of TCA to DCE and acetic acid.

3.0 BIODEGRADATION EQUATIONS AND SOLUTION PROCEDURE


The biodegradation model equations describe the transport of substrate and electron acceptor from the aqueous phase into attached biomass, the loss of substrate and electron acceptor through biodegradation reactions, and the resulting growth of the free-floating or attached biomass. The flow and biodegradation system is solved through operator splitting, in which the solution to the flow equations is used as the initial conditions for the biodegradation reactions. This approach is convenient because modifications can be made to the system of biodegradation equations without having to reformulate the partial differential equations that describe advection and dispersion.

The biodegradation equations comprise a system of ordinary differential equations that must be solved at each grid block and each time step after the advection and dispersion terms are calculated. Because the mass transfer terms can make the system of equations stiff, the system is solved using a Gear's method routine published by Kahaner et al. (1989). The characteristics and numerical solution of this system of equations is discussed by de Blanc et al. (1996).

The complete system of equations is presented in Table 1. A key to the symbols in these equations is included in Table 2.

Equation 1 describes the three mechanisms for loss of substrate in the aqueous phase. The first expression describes diffusion of substrate across a stagnant liquid into attached biomass. The second expression in Equation 1 describes the biodegradation of substrate by unattached microorganisms in the bulk liquid. The first Monod term in this expression accounts for substrate limitations on the reaction rate and incorporates substrate competition. The second Monod term accounts for reaction rate limitations by the electron acceptor. The third Monod term accounts for reducing power limitations on the reaction rate if cometabolism is causing a loss of reducing power in the biomass. The first product of Monod terms limits the reaction rate because of the concentration of any other compound needed for growth, such as nutrients like nitrogen or phosphorous. The second product term limits the reaction rate through inhibition. The inhibiting compound(s) can be another electron acceptor, a toxic reaction by-product, or the substrate itself. As many of these additional Monod terms as are needed can be specified in the model. The third expression accounts for abiotic loss of the substrate through first-order reactions.

One equation similar to Equation 1 is written for each substrate. One equation similar to Equation 1 is also written for each chemical constituent that appears in the biodegradation kinetic expression, including electron acceptors, nutrients, and inhibiting compounds, but not including NADH. Finally, one equation similar to Equation 1 is written for each product. The biodegradation expression for product generation, electron acceptor use and nutrient use are multiplied by a factor Eijk, which is the stoichiometric ratio of the mass of the other compound lost (or generated) per mass of substrate biodegraded.

Equation 2 is a mass balance equation written for a single microcolony in the manner of Molz et al. (1986) This equation describes the diffusion of substrate into the biomass and the biodegradation of the substrate within the biomass. Substrate competition and inhibition are incorporated into the biodegradation expression in the same manner as in the bulk liquid biodegradation expression. Equations similar to these are written for product generation, electron acceptor use, and nutrient use. One of these equations is required for each substrate, electron acceptor, nutrient, and inhibiting compound.

Equations 3 and 4 describe the growth and decay of unattached and attached biomass, respectively. If there is cometabolism, then the equations describe the growth and loss of active biomass rather than total biomass. The loss of biomass due to cometabolism is expressed through the transformation capacity, Tc, which is the ratio (cometabolite biodegraded/biomass consumed). The cometabolic model is based on the model of Chang and Alvarez-Cohen (1995). The third expression in these equations describes the loss of biomass through endogenous decay. One of each of these equations is written for each biological species.

Equations 5 and 6 describe the consumption of reducing power (NADH) by cometabolic reactions and the regeneration of reducing power by growth substrates. Inclusion of a reducing power limitation for cometabolism is optional in the program. One of each of these equations is required for each biological species that cometabolizes a substrate.

The effect of the Monod and inhibition terms, and the mass transfer limitations on the biodegradation kinetics is described in more detail by de Blanc et al. (1995). This complex system of ordinary differential equations is solved at each grid block and each time step by Gear's method using subroutine SDRIV2 published by Kahaner et al.

4.0 MODEL TESTING AND VALIDATION


The biodegradation component of UTCHEM has been extensively tested to ensure that correct solutions to the biodegradation equations are produced. The testing consisted of batch biodegradation simulations, in which the solutions to the equations provided by the model for simple systems were compared to solutions calculated in spreadsheets.

Complete biodegradation solutions were also compared against literature solutions to ensure that the simultaneous transport and biodegradation of substrates and electron acceptors produced reasonable results. One-dimensional, single-phase simulations have been compared to biodegradation model solutions published by Molz et al. (1986). Substrate profiles generated by the two models in one such comparison are shown in Figure 1. In this simulation, a single substrate is biodegraded by attached biomass using oxygen as the electron acceptor. The simulation results are very similar to the data of Molz et al. (1986), indicating that the UTCHEM biodegradation model is functioning properly. The model predictions are not exactly the same because of slightly different assumptions about endogenous decay and slightly different flow conditions.

5.0 EXAMPLE SIMULATIONS


The multi-phase flow and biodegradation capabilities of the model are demonstrated through the simulation of hypothetical LNAPL and DNAPL spills. In these simulations, the modeling domain consists of a confined aquifer that is 125 m long by 54 m wide by 6 m thick. The domain is simulated with 25 grid blocks in the x direction, 11 grid blocks in the y direction, and 5 grid blocks in the z direction. Groundwater is flowing from left to right with an average velocity of 0.1 m/day. The spills are modeled by injecting the NAPL into the center of grid block (5, 6, 1), which is approximately 22 meters from the left boundary in the center of the modeling grid. There is no air phase in these simulations; the top boundary is a no-flow boundary.

LNAPL Simulation Example


Sequential use of electron acceptors and partitioning of multiple components into the aqueous phase are illustrated with an example LNAPL simulation. The LNAPL example simulates a leak of 1,000 gallons of crude oil containing approximately 1% by volume of benzene and 6% by volume of toluene into a shallow, confined aquifer. The leak is assumed to occur over a four-day period.

Figure 2 shows the evolution of the oil lens in a vertical slice down the center of the aquifer in the x-z plane. As seen in Figure 2, the oil moves little once the oil lens is established. The oil lens gradually decreases in size as the organic constituents dissolve into the flowing groundwater.

As the benzene and toluene partition out of the crude oil into the aqueous phase, they become available to microorganisms as substrates. For simplicity, a single population of microorganisms capable of biodegrading the benzene and toluene is assumed to exist in the aquifer. This biological species biodegrades both benzene and toluene aerobically and biodegrades toluene anaerobically with nitrate as the electron acceptor. Biodegradation kinetic parameters used for the simulation were obtained from Chen et al. (1992).

Figure 3 compares the concentration of benzene in the aqueous phase at 500 days to the concentration of benzene that would exist if no biodegradation reactions were occurring. The figure shows that significant biodegradation of dissolved benzene has occurred. The toluene plume is also shown in Figure 3. Although toluene has a lower solubility than benzene, the maximum toluene concentration in the dissolved phase is higher than the maximum concentration of the benzene plume because its concentration in the crude oil is greater than the benzene crude oil concentration. Toluene concentrations are nearly as low as benzene concentrations at the fringes of the plume because toluene is biodegraded both aerobically and anaerobically, where oxygen is exhausted, but the benzene is not.

The concentrations of benzene, toluene, oxygen and nitrate at 500 days are compared in Figure 4. Oxygen immediately downgradient of the spill is practically exhausted. Nitrate is also nearly exhausted from the area immediately downgradient of the spill because sufficient time has elapsed since oxygen depletion to allow denitrification to occur. However, at the forward edge of the plume, relatively high nitrate concentrations still exist in areas where oxygen has been depleted, but not exhausted.

DNAPL Simulation Example


Different model capabilities are illustrated with a DNAPL simulation in which TCE is biodegraded through cometabolism. In this simulation, 7.5 gallons of TCE is spilled in a single day. The cometabolic process is illustrated by injecting water containing methane through five injection wells located approximately 24 meters downgradient of the spill. The water contains 20 mg/L methane and 8 mg/L oxygen. The water injection rate is 1.4 m3 per day per well.

A population of methanotrophic microorganisms capable of biodegrading TCE aerobically through cometabolism is assumed to exist in the aquifer. The methanotrophs use methane as the primary substrate and oxygen as the electron acceptor. TCE biodegradation is assumed to reduce the active biomass and consume reducing power of the methanotrophs, so that TCE biodegradation both reduces the active biomass concentration and reduces the active biomass's biodegradation effectiveness. Once biomass has become deactivated, it does not become active again. Biodegradation rate parameters were obtained from Chang and Alvarez-Cohen (1995).

The effect of the methane injection wells is illustrated in Figure 5, where concentrations of TCE, a hypothetical TCE tracer, oxygen and methane are shown at 170 days. The TCE tracer is simply TCE that is not allowed to biodegrade in the model so that the effects of biodegradation can be seen. Concentration contours of the different constituents are shown in the top 1.2-m layer of the aquifer. Oxygen is depleted downgradient of the plume, but only a small fraction of the oxygen is consumed upgradient of the methane injection wells. Most of the oxygen upgradient of the wells remains because the high TCE concentrations deactivate the biomass and consume reducing power, preventing the TCE from biodegrading and further depleting the oxygen.

Even with a small TCE spill, TCE concentrations in the aquifer are so high that most biomass immediately downgradient of the spill is deactivated. Significant TCE biodegradation occurs only where appreciable methane is present to regenerate the microorganism's reducing power and where TCE concentrations are low. These effects can be seen in Figure 5. The high concentration contours of the TCE and TCE tracer are nearly the same, but biodegradation of the TCE causes a slight retardation in the progress of the TCE plume at low concentrations.

5.0 FUTURE MODEL ENHANCEMENTS


The UTCHEM biodegradation model is continually being refined. The following capabilities are planned for inclusion in the model prior to its completion:

· Biomass transport;

· Biomass growth limitations to prevent unbridled biomass growth;

· Effects of biomass growth on porosity and permeability;

· Incorporation of lag times to account for biomass acclimation.

6.0 REFERENCES


Chang, H. and L. Alvarez-Cohen, Model for the cometabolic biodegradation of chlorinated organics, Environmental Science and Technology, 29(9): 2357-2367, 1995.

de Blanc, P., D. C. McKinney and G. E. Speitel, Jr., Modeling subsurface biodegradation of non-aqueous liquids: a literature review, Technical Report CRWR 257, University of Texas at Austin, February, 1995.

de Blanc, P. C., K. Sepehrnoori, G. E. Speitel Jr. and D. C. McKinney, Investigation of numerical solution techniques for biodegradation equations in a groundwater flow model, Proceedings of the XI International Conference on Computational Methods in Water Resources, Cancun, Mexico, July 22-26, 1996 (in press).

Delshad, M., G. A. Pope and K. Sepehrnoori, A compositional simulator for modeling surfactant enhanced aquifer remediation, In press, Journal of Contaminant Hydrology, 1996.

Kahaner, David, C. Moler and S. Nash, Numerical Methods and Software, Prentice Hall, Englewood Cliffs, NJ, 1989.

Molz, F. J., M. A. Widdowson and L. D. Benefield, Simulation of microbial growth dynamics coupled to nutrient and oxygen transport in porous media, Water Resources Research, 22(8): 1207-1216, August 1986.

McCarty, P. L. and L. Semprini, Ground-water treatment for chlorinated solvents, In: Handbook of Bioremediation, (J. E. Mathews project officer), Lewis Publishers, Boca Raton, FL, pp. 87-116, 1993.

Vogel, T. M., Natural bioremediation of chlorinated solvents, In: Handbook of Bioremediation, (J. E. Mathews project officer), Lewis Publishers, Boca Raton, FL, pp. 201-224, 1993.

TABLE 1

BIODEGRADATION EQUATIONS

Equation 1 Substrate loss in the bulk fluid:



Equation 2 Substrate loss in attached biomass:



Equation 3 Growth of unattached biomass:



Equation 4 Growth of attached biomass:



Equation 5 Reducing power (NADH) consumption and production in unattached biomass:



Equation 6 Reducing power (NADH) consumption and production in attached biomass:



TABLE 2

KEY TO SYMBOLS IN BIODEGRADATION EQUATIONS

Letters:

b Endogenous decay coefficient (T-1)

Ci concentration of species i in bulk liquid (mass C/volume of aqueous phase)

Ci concentration of species i within attached biomass (mass C/volume of biomass)

Eijk electron acceptor use coefficient of electron acceptor j for biodegradation of substrate i by bacterial species k (mass electron acceptor consumed/mass substrate consumed)

Iaijk electron acceptor inhibition constant for biodegradation of substrate i by bacterial species k using electron acceptor j (mass/volume of phase)

Isijk substrate self-inhibition constant for biodegradation of substrate i by bacterial species k using electron acceptor j (mass/volume of phase)

kabio first-order abiotic reaction coefficient

Kaijk Monod half-saturation constant for electron acceptor j under j-based metabolism of substrate i by bacterial species k (mass A/volume of phase)

Kr Monod half-saturation constant for NADH growth limitations (mass/volume of phase)

Ksijk Monod half-saturation constant for substrate i under j-based metabolism by bacterial species k (mass /volume of phase)

mk mass of a single bacterial colony (mass/colony)

t time (T)

Tc transformation capacity (mass of biomass deactiveated/mass of cometabolite biodegraded)

Vk volume of a single bacterial colony (volume/colony)

Xk concentration of attached biomass k (mass/volume of aqueous phase)

Xk concentration of free-floating biomass k (mass/volume of aqueous phase)

Yijk yield coefficient for component i under j-based metabolism by bacterial species k (dimensionless; mass of biomass produced/mass of substrate utilized)

Greek Letters:

i mass transfer coefficient of species i (L/T)

[[beta]] surface area of a single bacterial colony available for mass transfer (L2/colony)

uijkmax Monod maximum growth rate for component i under j-based metabolism by bacterial species k (T-1)

[[rho]]k biomass density (active biomass/volume of biomass)

TABLE 2

KEY TO SYMBOLS IN BIODEGRADATION EQUATIONS





Subscripts:



c cometabolite

i substrate

ih inhibiting compound

j electron acceptor

k biological species

m competing substrate

n nutrient

na number of electron acceptors

nb number of biological species

ncom number of cometabolites

ncs number of competing substrates

nih number of inhibiting compounds

nn number of nutrients

ns number of substrates

r reducing power (NADH)

Superscripts such as ijk refer to metabolic combinations of substrate, electron acceptor and biological species. Figure 1. Comparison of substrate profiles simulated by UTCHEM to column profiles simulated by the model of Molz et al. (1986) in a laboratory column.







Figure 4. Concentrations of benzene without biodegradation, benzene with biodegradation, toluene, oxygen, and nitrate in upper 1.2 m of aquifer along aquifer center line at 500 days.