Biodegradation during contaminant transport in porous media: 4. Impact of microbial lag and bacterial cell growth

Miscible-displacement experiments were conducted to examine the impact of microbial lag and bacterial cell growth on the transport of salicylate, a model hydrocarbon compound. The impacts of these processes were examined separately, as well as jointly, to determine their relative effects on biodegradation dynamics. For each experiment, a column was packed with porous medium that was first inoculated with bacteria that contained the NAH plasmid encoding genes for the degradation of naphthalene and salicylate, and then subjected to a step input of salicylate solution. The transport behavior of salicylate was non-steady for all cases examined, and was clearly influenced by a delay (lag) in the onset of biodegradation. This microbial lag, which was consistent with the results of batch experiments, is attributed to the induction and synthesis of the enzymes required for biodegradation of salicylate. The effect of microbial lag on salicylate transport was eliminated by exposing the column to two successive pulses of salicylate, thereby allowing the cells to acclimate to the carbon source during the first pulse. Elimination of microbial lag effects allowed the impact of bacterial growth on salicylate transport to be quantified, which was accomplished by determining a cell mass balance. Conversely, the impact of microbial lag was further investigated by performing a similar double-pulse experiment under no-growth conditions. Significant cell elution was observed and quantified for all conditions/systems. The results of these experiments allowed us to differentiate the effects associated with microbial lag and growth, two coupled processes whose impacts on the biodegradation and transport of contaminants can be difficult to distinguish.     

The influence of substrate and electron acceptor availability on bioactive zone dynamics in porous media

Two approaches were used to investigate the influence of dissolved oxygen (DO) and substrate availability on the formation and dynamics of "bioactive zones" in a water-saturated porous medium. A bioactive zone is defined as a region where a microbial community is sufficiently active to metabolize bioavailable substrates. In the first approach, microbial activity was characterized by monitoring the spatial and temporal variability of DO and aqueous substrate (salicylate and naphthalene) concentrations during miscible-displacement experiments. In the second approach, microbial activity was monitored using multiple fiber optics emplaced in the porous medium to detect luminescence produced by Pseudomonas putida RB1353, a bioluminescent reporter organism that produces light when salicylate (an intermediate of naphthalene degradation) is present. The results of both approaches show that the location and size of the bioactive zones were influenced by in situ DO and substrate availability. When DO was not a limiting factor (i.e., lower substrate input concentrations), the bioactive zone encompassed the entire column, with the majority of the microbial activity occurring between the inlet and midpoint. However, as the availability of DO became limiting for the higher substrate input experiments, the size of the bioactive zone shrank and was ultimately limited to the proximity of the column inlet.     

Interaction between water flow and spatial distribution of microbial growth in a two-dimensional flow field in saturated porous media

Bacterial growth and its interaction with water flow was investigated in a two-dimensional flow field in a saturated porous medium. A flow cell (56 x 44 x 1 cm) was filled with glass beads and operated under a continuous flow of a mineral medium containing nitrate as electron acceptor. A glucose solution was injected through an injection port, simulating a point source contamination. Visible light transmission was used to observe the distribution of the growing biomass and water flow during the experiment. At the end of the experiment (on day 31), porous medium samples were destructively collected and analyzed for abundance of total and active bacterial cells, bacterial cell volume and concentration of polysaccharides and proteins. Microbial growth was observed in two stripes along the length of the flow cell, starting at the glucose injection port, where highest biomass concentrations were obtained. The spatial distribution of biomass indicated that microbial activity was limited by transverse mixing between glucose and nitrate media, as only in the mixing zone between the media high biological activities were achieved. The ability of the biomass to change the flow pattern in the flow cell was observed, indicating that the biomass was locally reducing the hydraulic conductivity of the porous medium. This bioclogging effect became evident when the injection of the glucose solution was turned off and water flow still bypassed the area around the glucose injection port, preserving the flow pattern as it was during the injection of the glucose solution. As flow bypass was possible in this system, the average hydraulic properties of the flow cell were not affected by the produced biomass. Even in the vicinity of the injection port, the total volume of the bacterial cells remained below 0.01% of the pore space and was unlikely to be responsible for the bioclogging. However, the bacteria produced large amounts of extracellular polymeric substances (EPS), which likely caused the observed bioclogging effects.     

The influence of system complexity on bacterial transport in saturated porous media

A series of miscible-displacement column experiments were conducted under saturated flow conditions to systematically investigate the influence of physical and biological complexity on bacterial activity and fate in the presence and absence of a non-sorbing growth substrate, salicylate. Bacterial elution was monitored for three different systems; System I--a sterilized, inoculated, well-sorted sand, System II--a sterilized, inoculated, heterogeneous loamy sand (Hayhook), and System III--two different unsterilized loamy sands (Hayhook and Vinton) each with their associated indigenous microbial community. Results show that System I behaved ideally with respect to both cell and substrate transport, wherein: (1) growth occurred in response to substrate addition, (2) cell elution increased in response to the substrate pulse, and (3) breakthrough curves were reproducible for both substrate and cell elution. In contrast, System II showed ideal behavior with respect to substrate transport but showed variable behavior for cell transport. Further, there was no measurable growth in response to substrate addition and no increase in cell elution during the salicylate pulse. System III exhibited non-ideal behavior for both substrate and cell transport. Of particular interest is the fact that the indigenous communities of the two soils behaved differently. Specifically, for the Hayhook soil, an increased elution response was observed for the heterotrophic population while the salicylate-degrading community was preferentially retained in the column. In contrast for the Vinton soil, the substrate pulse did not elicit an elution response from either the heterotrophic or salicylate-degrading community from the culturable, indigenous Vinton microorganisms. For Systems II and III, the observed variability appears to be associated with the biological component of the system, since sterile controls were reproducible. This type of systematic study is critical for understanding cell and substrate transport behavior in complex, heterogeneous systems, and illustrates the potential uncertainty associated with measurements in such systems.     

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.     

A high-resolution non-invasive approach to quantify oxygen transport across the capillary fringe and within the underlying groundwater

Oxygen transport across the capillary fringe is relevant for many biogeochemical processes. We present a non-invasive technique, based on optode technology, to measure high-resolution concentration profiles of oxygen across the unsaturated/saturated interface. By conducting a series of quasi two-dimensional flow-through laboratory experiments, we show that vertical hydrodynamic dispersion in the water-saturated part of the capillary fringe is the process limiting the mass transfer of oxygen. A number of experimental conditions were tested in order to investigate the influence of grain size and horizontal flow velocity on transverse vertical dispersion in the capillary fringe. In the same setup, analogous experiments were simultaneously carried out in the fully water-saturated zone, therefore allowing a direct comparison with oxygen transfer across the capillary fringe. The outcomes of the experiments under various conditions show that oxygen transport in the two zones of interest (i.e., the unsaturated/saturated interface and the saturated zone) is characterized by very similar transverse dispersion coefficients. An influence of the capillary fringe morphology on oxygen transport has not been observed. These results may be explained by the narrow grain size distribution used in the experiments, leading to a steep decline in water saturation at the unsaturated/saturated interface and to the absence of trapped gas in this transition zone. We also modeled flow (applying the van Genuchten and the Brooks-Corey relationships) and two-dimensional transport across the capillary fringe, obtaining simulated profiles of equivalent aqueous oxygen concentration that were in good agreement with the observations.     

Stochastic-convective transport with nonlinear reaction and mixing: application to intermediate-scale experiments in aerobic biodegradation in saturated porous media

Aerobic biodegradation of benzoate by Pseudomonas cepacia sp. in a saturated heterogeneous porous medium was simulated using the stochastic-convective reaction (SCR) approach. A laboratory flow cell was randomly packed with low permeability silt-size inclusions in a high permeability sand matrix. In the SCR upscaling approach, the characteristics of the flow field are determined by the breakthrough of a conservative tracer. Spatial information on the actual location of the heterogeneities is not used. The mass balance equations governing the nonlinear and multicomponent reactive transport are recast in terms of reactive transports in each of a finite number of discrete streamtubes. The streamtube ensemble members represent transport via a steady constant average velocity per streamtube and a conventional Fickian dispersion term, and their contributions to the observed breakthroughs are determined by flux-averaging the streamtube solute concentrations. The resulting simulations were compared to those from a high-resolution deterministic simulation of the reactive transport, and to alternative ensemble representations involving (i) effective Fickian travel time distribution function, (ii) purely convective streamtube transport, and (iii) streamtube ensemble subset simulations. The results of the SCR simulation compare favorably to that of a sophisticated high-resolution deterministic approach.     

Straining phenomena in bacteria transport through natural porous media

Background, aim, and scope  

Transport of bacteria through natural porous media is an issue of increasing concern arising in several very important environmental processes. These include the percolation of bacteria from fecal waste to drinking water reservoirs, thus leading to a risk for human health, or the bioremediation of contaminated soils in which the bacteria are expected to travel long distances underground in order to reach contaminated areas and degrade chemicals originating from accidental spills. An understanding of bacterial retention and transport mechanisms in porous media would be of great help in the development of models able to predict the distance covered by bacterial suspensions in these situations.     

A novel two-dimensional model for colloid transport in physically and geochemically heterogeneous porous media

A two-dimensional model for colloid transport in geochemically and physically heterogeneous porous media is presented. The model considers patchwise geochemical heterogeneity, which is suitable to describe the chemical variability of many surficial aquifers with ferric oxyhydroxide-coated porous matrix, as well as spatial variability of hydraulic conductivity, which results in heterogeneous flow field. The model is comprised of a transient fluid flow equation, a transient colloid transport equation, and an equation for the dynamics of colloid deposition and release. Numerical simulations were carried out with the model to investigate the colloid transport behavior in layered and randomly heterogeneous porous media. Results demonstrate that physical and geochemical heterogeneities markedly affect the colloid transport behavior. Layered physical or geochemical heterogeneity can result in distinct preferential flow paths of colloidal particles. Furthermore, the combined effect of layered physical and geochemical heterogeneity may result in enhanced or reduced preferential flow of colloids. Random distribution of physical heterogeneity (hydraulic conductivity) results in a random flow field and an irregularly distributed colloid concentration profile in the porous medium. Contrary to random physical heterogeneity, the effect of random patchwise geochemical heterogeneity on colloid transport behavior is not significant. It is mostly the mean value of geochemical heterogeneity rather than its distribution that governs the colloid transport behavior.     

Microbial growth and transport in porous media under denitrification conditions: experiments and simulations

Soil column experiments were conducted to study bacterial growth and transport in porous media under denitrifying conditions. The study used a denitrifying microbial consortium isolated from aquifer sediments sampled at the U.S. Department of Energy's Hanford site. One-dimensional, packed-column transport studies were conducted under two substrate loading conditions. A detailed numerical model was developed to predict the measured effluent cell and substrate concentration profiles. First-order attachment and detachment models described the interphase exchange processes between suspended and attached biomass. Insignificantly different detachment coefficient values of 0.32 and 0.43 day⁻¹, respectively, were estimated for the high and low nitrate loading conditions (48 and 5 mg l⁻¹ NO₃, respectively). Comparison of these values with those calculated from published data for aerobically growing organisms shows that the denitrifying consortium had lower detachment rate coefficients. This suggests that, similar to detachment rates in reactor-grown biofilms, detachment in porous media may increase with microbial growth rate. However, available literature data are not sufficient to confirm a specific analytical model for predicting this growth dependence.     

Effects of pH and ionic strength on sulfamethoxazole and ciprofloxacin transport in saturated porous media

Many antibiotics regarded as emerging contaminants have been frequently detected in soils and groundwater; however, their transport behaviors in soils remain largely unknown. This study examined the transport of two antibiotics, sulfamethoxazole (SMZ) and ciprofloxacin (CIP), in saturated porous media. Laboratory columns packed with quartz sand was used to test the effects of solution pH and ionic strength (IS) on their retention and transport. The results showed that these two antibiotics behaved differently in the saturated sand columns. In general, SMZ manifested a much higher mobility than CIP for all experimental conditions tested. Almost all SMZ transported through the columns within one pore volume in deionized water (i.e., pH=5.6, IS=0), but no CIP was detected in the effluents under the same condition after extended column flushing. Perturbations in solution pH (5.6 and 9.5) and IS (0 and 0.1M) showed no effect on SMZ transport in the saturated columns. When pH increased to 9.5, however, ~93% of CIP was eluted from the sand columns. Increase of IS from 0 to 0.1M also slightly changed the distribution of adsorbed CIP within the sand column at pH 5.6, but still no CIP was detected in the effluents. A mathematical model based on advection-dispersion equation coupled with equilibrium and kinetic reactions successfully simulated the transport of the antibiotics in water-saturated porous media with R(2)=0.99.     

Colloid transport in a geochemically heterogeneous porous medium: aquifer tank experiment and modeling

To examine colloid transport in geochemically heterogeneous porous media at a scale comparable to field experiments, we monitored the migration of silica-coated zirconia colloids in a two-dimensional layered porous media containing sand coated to three different extents by ferric oxyhydroxides. Transport of the colloids was measured over 1.65 m and 95 days. Colloid transport was modeled by an advection-dispersion-deposition equation incorporating geochemical heterogeneity and colloid deposition dynamics (blocking). Geochemical heterogeneity was represented as favorable (ferric oxyhydroxide-coated) and unfavorable (uncoated sand) deposition surface areas. Blocking was modeled as random sequential adsorption (RSA). Release of deposited colloids was negligible. The time to colloid breakthrough after the onset of blocking increased with increasing ferric oxyhydroxide-coated surface area. As the ferric oxyhydroxide surface area increased, the concentration of colloids in the breakthrough decreased. Model-fits to the experimental data were made by inverse solutions to determine the fraction of surface area favorable for deposition and the deposition rate coefficients for the favorable (ferric oxyhydroxide-coated) and unfavorable sites. The favorable deposition rate coefficient was also calculated by colloid filtration theory. The model described the time to colloid breakthrough and the blocking effect reasonably well and estimated the favorable surface area fraction very well for the two layers with more than 1% ferric oxyhydroxide coating. If mica edges in the uncoated sand were considered as favorable surface area in addition to the ferric oxyhydroxide coatings, the model predicted the favorable surface area fraction accurately for the layer with less than 1% ferric oxyhydroxide coating.     

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model

The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The modeling system is designed in such a way that constraint-based models targeting different microorganisms or competing organism communities can be easily plugged into the system. Constraint-based modeling is very costly given the size of a genome-scale reaction network. To save computation time, a binary tree is traversed to examine the concentration and solution pool generated during the simulation in order to decide whether the constraint-based model should be called. We also show preliminary results from the integrated model including a comparison of the direct and indirect coupling approaches and evaluated the ability of the approach to simulate field experiment.     

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...     

Consolidation of degraded ornamental porous limestone stone by calcium carbonate precipitation induced by the microbiota inhabiting the stone

Although it has already been shown that calcareous stone can be consolidated by using a bacterially inoculated culture medium, a more user-friendly method is the in situ application of a sterile culture medium that is able to activate, among the microbial community of the stone, those bacteria with a potential for calcium carbonate precipitation. In order to test this new method for stone consolidation, non-sterilized decayed porous limestone was immersed in sterile nutritional media. Results were compared to those of the runs in which stone sterilized prior to the treatment was used. The effects of the microbial community on stone consolidation were determined by recording the evolution of the culture media chemistry. The treated stone was tested for mechanical resistance and porosity. Results demonstrate that the tested media were able to activate bacteria from the microbial community of the stone. As a consequence of the growth of these bacteria, an alkalinization occurred that resulted in calcium carbonate precipitation. The new precipitate was compatible with the substrate and consolidated the stone without pore plugging. Therefore, a good candidate to in situ consolidate decayed porous limestone is the application of a sterile culture medium with the characteristics specified in the present study.     

Colloid transport in unsaturated porous media: the role of water content and ionic strength on particle straining

Packed column and mathematical modeling studies were conducted to explore the influence of water saturation, pore-water ionic strength, and grain size on the transport of latex microspheres (1.1 microm) in porous media. Experiments were carried out under chemically unfavorable conditions for colloid attachment to both solid-water interfaces (SWI) and air-water interfaces (AWI) using negatively charged and hydrophilic colloids and modifying the solution chemistry with a bicarbonate buffer to pH 10. Interaction energy calculations and complementary batch experiments were conducted and demonstrated that partitioning of colloids to the SWI and AWI was insignificant across the range of the ionic strengths considered. The breakthrough curve and final deposition profile were measured in each experiment indicating colloid retention was highly dependent on the suspension ionic strength, water content, and sand grain size. In contrast to conventional filtration theory, most colloids were found deposited close to the column inlet, and hyper-exponential deposition profiles were observed. A mathematical model, accounting for time- and depth-dependent straining, produced a reasonably good fit for both the breakthrough curves and final deposition profiles. Experimental and modeling results suggest that straining--the retention of colloids in low velocity regions of porous media such as grain junctions--was the primary mechanism of colloid retention under both saturated and unsaturated conditions. The extent of stagnant regions of flow within the pore structure is enhanced with decreasing water content, leading to a greater amount of retention. Ionic strength also contributes to straining, because the number of colloids that are held in the secondary energy minimum increases with ionic strength. These weakly associated colloids are prone to be translated to stagnation regions formed at grain-grain junctions, the solid-water-air triple point, and dead-end pores and then becoming trapped.     

Coupled effects of solution chemistry and hydrodynamics on the mobility and transport of quantum dot nanomaterials in the vadose zone

To investigate the coupled effects of solution chemistry and hydrodynamics on the mobility of quantum dot (QD) nanoparticles in the vadose zone, laboratory scale transport experiments involving single and/or sequential infiltrations of QDs in unsaturated and saturated porous media, and computations of total interaction and capillary potential energies were performed. As ionic strength increased, QD retention in the unsaturated porous media increased; however, this retention was significantly suppressed in the presence of a non-ionic surfactant in the infiltration suspensions as indicated by surfactant enhanced transport of QDs. In the vadose zone, the non-ionic surfactant limited the formation of QD aggregates, enhanced QD mobility and transport, and lowered the solution surface tension, which resulted in a decrease in capillary forces that not only led to a reduction in the removal of QDs, but also impacted the vadose zone flow processes. When chemical transport conditions were favorable (ionic strength of 5 × 10(-4)M and 5 × 10(-3)M, or ionic strengths of 5 × 10(-2)M and 0.5M with surfactant), the dominating phenomena controlling the mobility and transport of QDs in the vadose zone were meso-scale processes, where infiltration by preferential flow results in the rapid transport of QDs. When chemical transport conditions were unfavorable (ionic strength of 5 × 10(-2)M and 0.5M) the dominating phenomena controlling the mobility and transport of QDs in the vadose zone were pore-scale processes governed by gas-water interfaces (GWI) that impact the mobility of QDs. The addition of surfactant enhanced the transport of QDs both in favorable and unfavorable chemical transport conditions. The mobility and retention of QDs was controlled by interaction and capillary forces, with the latter being the most influential. GWI were found to be the dominant mechanism and site for QD removal compared with solid-water interfaces (SWI) and pore straining. Additionally, ripening phenomena were demonstrated to enhance QDs removal or retention in porous media and to be attenuated by the presence of surfactant.     

Contaminant transport in groundwater in the presence of colloids and bacteria: Model development and verification

Colloids and bacteria (microorganisms) naturally exist in groundwater aquifers and can significantly impact contaminant migration rates. A conceptual model is first developed to account for the different physiochemical and biological processes, reaction kinetics, and different transport mechanisms of the combined system (contaminant–colloids–bacteria). All three constituents are assumed to be reactive with the reactions taking place between each constituent and the porous medium and also among the different constituents. A general linear kinetic reaction model is assumed for all reactive processes considered. The mathematical model is represented by fourteen coupled partial differential equations describing mass balance and reaction processes. Two of these equations describe colloid movement and reactions with the porous medium, four equations describe bacterial movement and reactions with colloids and the porous medium, and the remaining eight equations describe contaminant movement and its reactions with bacteria, colloids, and the porous medium. The mass balance equations are numerically solved for two-dimensional groundwater systems using a third-order, total variance-diminishing scheme (TVD) for the advection terms. Due to the complex coupling of the equations, they are solved iteratively each time step until a convergence criterion is met. The model is tested against experimental data and the results are favorable.     

Nitrogen as an indicator of mass transfer during in-situ gas sparging

Aiming at the stimulation of intrinsic microbial activity, pulses of pure oxygen or pressurized air were recurrently injected into groundwater polluted with chlorobenzene. To achieve well-controlled conditions and intensive sampling, a large, vertical underground tank was filled with the local unconfined sandy aquifer material. In the course of two individual gas injections, one using pure oxygen and one using pressurized air, the mass transfer of individual gas species between trapped gas phase and groundwater was studied. Field data on the dissolved gas composition in the groundwater were combined with a kinetic model on gas dissolution and transport in porous media. Phase mass transfer of individual gas components caused a temporary enrichment of nitrogen, and to a lower degree of methane, in trapped gas leading to the formation of excess dissolved nitrogen levels downgradient from the dissolving gas phase. By applying a novel gas sampling method for dissolved gases in groundwater it was shown that dissolved nitrogen can be used as a partitioning tracer to indicate complete gas dissolution in porous media.     

Development of the FMT chemical transport simulator: Coupling aqueous density and mineral volume fraction to phase compositions

The Fracture-Matrix Transport (FMT) code couples saturated porous medium advection and diffusion with mechanistic chemical models for speciation and interphase reactions. Previous versions of FMT simulated double-porosity transport in two dimensions on the continuum from advection- to diffusion-dominated, with a user-specified velocity field to allow double-porosity transport. However, aqueous density was assumed constant, and reactive minerals were assumed to occupy negligible volume. Both of these assumptions can be considered poor for evaporite systems, where large changes in porosity and aqueous density can result from high mineral solubilities. Further development of FMT has relaxed these restrictions, allowing aqueous density to vary with phase composition, and allowing void volume to change as minerals dissolve and precipitate. This paper describes the additional mathematical complexity and code modifications required to simulate such systems. The sensitivity of advection-dominated transport to these variables is explored briefly in a one-dimensional example.