Non-standard numerical methods applied to subsurface biobarrier formation models in porous media

Biofilm forming microbes have complex effects on the flow properties of natural porous media. Subsurface biofilms have the potential for the formation of biobarriers to inhibit contaminant migration in groundwater. Another example of beneficial microbial effects is the biotransformation of organic contaminants to less harmful forms, thereby providing an in situ method for treatment of contaminated groundwater supplies. Mathematical models that describe contaminant transport with biodegradation involve a set of coupled convection-dispersion equations with non-linear reactions. The reactive solute transport equation is one for which numerical solution procedures continue to exhibit significant limitations for certain problems of groundwater hydrology interest. Accurate numerical simulations are crucial to the development of contaminant remediation strategies. A new numerical method is developed for simulation of reactive bacterial transport in porous media. The non-standard numerical approach is based on the ideas of the ‘exact’ time-stepping scheme. It leads to solutions free from the numerical instabilities that arise from incorrect modeling of derivatives and reaction terms. Applications to different biofilm models are examined and numerical results are presented to demonstrate the performance of the proposed new method.     

Effect of fluorochromes on bacterial surface properties and interaction with granular media.

Simple, efficient, and safe tagging methods are desired in short-term microbial transport studies such as in the study of filtration systems for water and wastewater treatment. Suitability of selected fluorochromes as bacterial tagging agents in transport studies was evaluated on the basis of stability of stained cells and the effect of staining on bacterial surface characteristics and interaction with granular media. Surface properties were characterized by zeta potential and microbial adhesion to hydrocarbons. The effect of staining on interactions between bacteria and porous media was evaluated in terms of removal of bacteria in batch adsorption tests using sand coated with aluminum hydroxide to enhance adsorption. The DNA-specific fluorochrome 4',6-diamidino-2-phenylindole (DAPI) had generally negligible effects on bacterial surface properties and interaction with sand, as indicated in batch adsorption tests using pure cultures (Escherichia coli or Acinetobacter sp.) and wastewater bacteria. Cells stained with DAPI were stable for 48 h at 4 or 20 degrees C. Other nucleic acid fluorochromes tested had different but significant effects on bacterial cells and produced less stable fluorescence. Since transport through porous media is modulated by surface properties, it may be concluded based on these results that the choice of fluorochromes is critical in microbial transport studies. DAPI appeared to be a promising tagging agent. Time dependence of fluorescence of stained cells may limit the use of fluorochrome-tagged cells in long-term transport studies.     

Influence of the Gas-Water Interface on Transport of Microorganisms through Unsaturated Porous Media

In this article, a new mechanism influencing the transport of microorganisms through unsaturated porous media is examined, and a new method for directly visualizing bacterial behavior within a porous medium under controlled chemical and flow conditions is introduced. Resting cells of hydrophilic and relatively hydrophobic bacterial strains isolated from groundwater were used as model microorganisms. The degree of hydrophobicity was determined by contact-angle measurements. Glass micromodels allowed the direct observation of bacterial behavior on a pore scale, and three types of sand columns with different gas saturations provided quantitative measurements of the observed phenomena on a porous medium scale. The reproducibility of each break-through curve was established in three to five repeated experiments. The data collected from the column experiments can be explained by phenomena directly observed in the micromodel experiments. The retention rate of bacteria is proportional to the gas saturation in porous media because of the preferential sorption of bacteria onto the gas-water interface over the solid-water interface. The degree of sorption is controlled mainly by cell surface hydrophobicity under the simulated groundwater conditions because of hydrophobic forces between the organisms and the interfaces. The sorption onto the gas-water interface is essentially irreversible because of capillary forces. This preferential and irreversible sorption at the gas-water interface strongly influences the movement and spatial distribution of microorganisms.     

Monitoring bacterial transport by stable isotope enrichment of cells

Understanding the transport and behavior of bacteria in the environment has broad implications in diverse areas, ranging from agriculture to groundwater quality, risk assessment, and bioremediation. The ability to reliably track and enumerate specific bacterial populations in the context of native communities and environments is key to developing this understanding. We report a novel bacterial tracking approach, based on altering the stable carbon isotope value (delta(13)C) of bacterial cells, which provides specific and sensitive detection and quantification of those cells in environmental samples. This approach was applied to the study of bacterial transport in saturated porous media. The transport of introduced organisms was indicated by mass spectrometric analysis of groundwater samples, where the presence of (13)C-enriched bacteria resulted in increased delta(13)C values of the samples, allowing specific and sensitive detection and enumeration of the bacteria of interest. We demonstrate the ability to produce highly (13)C-enriched bacteria, present data indicating that results obtained with this approach accurately represent intact introduced bacteria, and include field data on the use of this stable isotope approach to monitor in situ bacterial transport. This detection strategy allows sensitive detection of an introduced, unmodified bacterial strain in the presence of the indigenous bacterial community, including itself in its unenriched form.     

Monitoring Bacterial Transport by Stable Isotope Enrichment of Cells

Understanding the transport and behavior of bacteria in the environment has broad implications in diverse areas, ranging from agriculture to groundwater quality, risk assessment, and bioremediation. The ability to reliably track and enumerate specific bacterial populations in the context of native communities and environments is key to developing this understanding. We report a novel bacterial tracking approach, based on altering the stable carbon isotope value (δ¹³C) of bacterial cells, which provides specific and sensitive detection and quantification of those cells in environmental samples. This approach was applied to the study of bacterial transport in saturated porous media. The transport of introduced organisms was indicated by mass spectrometric analysis of groundwater samples, where the presence of ¹³C-enriched bacteria resulted in increased δ¹³C values of the samples, allowing specific and sensitive detection and enumeration of the bacteria of interest. We demonstrate the ability to produce highly ¹³C-enriched bacteria, present data indicating that results obtained with this approach accurately represent intact introduced bacteria, and include field data on the use of this stable isotope approach to monitor in situ bacterial transport. This detection strategy allows sensitive detection of an introduced, unmodified bacterial strain in the presence of the indigenous bacterial community, including itself in its unenriched form.     

A microscale model of bacterial and biofilm dynamics in porous media

A microscale model for the transport and coupled reaction of microbes and chemicals in an idealized two-dimensional porous media has been developed. This model includes the flow, transport, and bioreaction of nutrients, electron acceptors, and microbial cells in a saturated granular porous media. The fluid and chemicals are represented as a continuum, but the bacterial cells and solid granular particles are represented discretely. Bacterial cells can attach to the particle surfaces or be advected in the bulk fluid. The bacterial cells can also be motile and move preferentially via a run and tumble mechanism toward a chemoattractant. The bacteria consume oxygen and nutrients and alter the profiles of these chemicals. Attachment of bacterial cells to the soil matrix and growth of bacteria can change the local permeability. The coupling of mass transport and bioreaction can produce spatial gradients of nutrients and electron acceptor concentrations. We describe a numerical method for the microscale model, show results of a convergence study, and present example simulations of the model system.     

多孔介质中的微生物迁移行为与影响因素研究进展

微生物在地下水和土壤环境中的迁移与地下水资源保护、地下水污染修复及土壤污染防治等息息相关。自然界中多孔介质具有结构复杂性和空间异质性。这导致微生物在其中的迁移易受多重环境因素的影响。本文总结了几种典型多孔介质中微生物迁移模型、理论与研究方法,并对多孔介质中影响微生物迁移行为的3种因素——物理、化学和生物因素进行了梳理。其中物理因素的影响主要包括多孔介质的粒径、表面粗糙度、饱和度、环境温度、水体流速等相关;化学因素主要包含流体pH、离子种类与强度、可溶性有机物含量、多孔介质自身化学性质等;生物因素不但涉及微生物种类、细胞大小和细胞表面特性,还与胞外聚合物的分泌、鞭毛运动及趋化性等相关。本综述旨在总结近年来有关微生物在多孔介质中迁移的相关研究,深入理解微生物在多孔介质中的迁移行为,为其在地下水和土壤污染修复中的实际应用提供理论依据。     

Bacterial Enrichment at the Gas-Water Interface of a Laboratory Apparatus

The gas-water interface (GWI) is likely to have important effects on bacterial adsorption and transport in unsaturated porous media. A glass apparatus that isolated GWIs in ports above a flowthrough suspension of a groundwater bacterial isolate was used to represent unsaturated porous media. The surface microlayer was collected by placing a polycarbonate filter on the GWI. The filter was stained, and the bacteria were enumerated by direct count. The significance of five independent variables on the surface density of cells (s, in cells per square millimeter) was determined by nonlinear multiple regression. Three of the variables were shown to be significant: surfactant concentration (d), time (t), and bulk bacterial concentration (B). The surface density decreased with increasing d and increased with increasing t and B. When surfactant was absent, the GWI became highly enriched in bacteria. For example, when d = 0, 48 h < t < 72 h, and 5,000 cells mm(sup-3) < B < 10,000 cells mm(sup-3), s averaged 3.0 x 10(sup4) cells mm(sup-2). This surface density occupied about 6.0% of the GWI, and the surface microlayer concentration of cells was 190 times the bulk concentration. The other two variables: pH (p) and ionic strength (I) were shown to be insignificant. The strong effect of d and the lack of effect of I and p support the hypothesis that hydrophobic interaction dominates bacterial adsorption to the GWI.     

Selection of Bacteria with Favorable Transport Properties Through Porous Rock for the Application of Microbial-Enhanced Oil Recovery

This paper presents a bench-scale study on the transport in highly permeable porous rock of three bacterial species—Bacillus subtilis, Pseudomonas putida, and Clostridium acetobutylicum—potentially applicable in microbial-enhanced oil recovery processes. The transport of cells during the injection of bacterial suspension and nutrient medium was simulated by a deep bed filtration model. Deep bed filtration coefficients and the maximum capacity of cells in porous rock were measured. Low to intermediate (~10⁶/ml) injection concentrations of cellular suspensions are recommended because plugging of inlet surface is less likely to occur. In addition to their resistance to adverse environments, spores of clostridia are strongly recommended for use in microbial-enhanced oil recovery processes since they are easiest among the species tested to push through porous rock. After injection, further transport of bacteria during incubation can occur by growth and mobility through the stagnant nutrient medium which fills the porous rock. We have developed an apparatus to study the migration of bacteria through a Berea sandstone core containing nutrient medium.     

A novel approach to investigate biofilm accumulation and bacterial transport in porous matrices

Knowledge of bacterial transport through, and biofilm growth in, porous media is vitally important in numerous natural and engineered environments. Despite this, porous media systems are generally oversimplified and the local complexity of cell transport, biofilm formation and the effect of biofilm accumulation on flow patterns is lost. In this study, cells of the sulphate-reducing bacterium, Desulfovibrio sp. EX265, accumulated primarily on the leading faces of obstructions and developed into biofilm, which grew to narrow and block pore throats (at a rate of 12 micro m h(-1) in one instance). This pore blocking corresponded to a decrease in permeability from 9.9 to 4.9 Darcy. Biofilm processes were observed in detail and quantitative data were used to describe the rate of biofilm accumulation temporally and spatially. Accumulation in the inlet zone of the micromodel was 10% higher than in the outlet zone and a mean biofilm height of 28.4 micro m was measured in a micromodel with an average pore height of 34.9 microm. Backflow (flow reversal) of fluid was implemented on micromodels blocked with biofilm growth. Although biofilm surface area cover did immediately decrease (approximately 5%), the biofilm quickly re-established and permeability was not significantly affected (9.4 Darcy). These results demonstrate that the glass micromodel used here is an effective tool for in situ analysis and quantification of bacteria in porous media.     

An improved spectrophotometric method to study the transport, attachment, and breakthrough of bacteria through porous media

This study reports an improved spectrophotometric method for studying bacterial (Pseudomonas fluorescens UPER-1) transport and attachment in saturated porous media (silica sand). While studying the effect of ionic strength by the traditional packed-column spectrophotometric method, we encountered an artifact. The absorbance of a well-stirred bacterial suspension was found to decrease with time in the presence of high concentrations of sodium and potassium phosphate salts (> or = 10(-2) M) as the cells continued to age in a resting stage. Our results show that collision efficiency and a bed ripening index will be in error by as much as 20% if breakthrough is measured by the traditional spectrophotometric technique. We present an improved experimental technique that will minimize the artifact and should substantially advance the understanding of bacteria transport in porous media.     

Transport of vanadium (V) in saturated porous media: effects of pH,ionic-strength and clay mineral

Vanadium, a hazardous pollutant, has been frequently detected in soil and groundwater, however, its transport behavior in porous media were not clearly understood. In this study, the effects of solution pH, ionic strength (IS) and the effect of clay mineral on the transport of vanadium in saturated porous media were investigated. Laboratory experiments using a series of columns packed with quartz sand were carried out to explore the retention and transport of vanadium with a range of ionic-strength (0.001–0.1 M) and pH (4–8) and two different types of clay minerals montmorillonite and kaolinite. Results of the breakthrough experiments showed that vanadium was highly mobile in the saturated porous media. The increase in pH rendered a higher transport of vanadium in saturated porous media. The study also indicated an easier transfer of vanadium with an increase in IS. Montmorillonite enhanced the mobility of vanadium in the column when compared to kaolinite. A mathematical model based on advection-dispersion equation coupled with equilibrium and kinetic reactions was used to describe the retention and transport of vanadium in the columns very well.     

An Improved Spectrophotometric Method To Study the Transport, Attachment, and Breakthrough of Bacteria through Porous Media

This study reports an improved spectrophotometric method for studying bacterial (Pseudomonas fluorescens UPER-1) transport and attachment in saturated porous media (silica sand). While studying the effect of ionic strength by the traditional packed-column spectrophotometric method, we encountered an artifact. The absorbance of a well-stirred bacterial suspension was found to decrease with time in the presence of high concentrations of sodium and potassium phosphate salts (≥10⁻² M) as the cells continued to age in a resting stage. Our results show that collision efficiency and a bed ripening index will be in error by as much as 20% if breakthrough is measured by the traditional spectrophotometric technique. We present an improved experimental technique that will minimize the artifact and should substantially advance the understanding of bacteria transport in porous media.     

Mathematical model for characterization of bacterial migration through sand cores

The migration of chemotactic bacteria in liquid media has previously been characterized in terms of two fundamental transport coefficients-the random motility coefficient and the chemotactic sensitivity coefficient. For modeling migration in porous media, we have shown that these coefficients which appear in macroscopic balance equations can be replaced by effective values that reflect the impact of the porous media on the swimming behavior of individual bacteria. Explicit relationships between values of the coefficients in porous and liquid media were derived. This type of quantitative analysis of bacterial migration is necessary for predicting bacterial population distributions in subsurface environments for applications such as in situ bioremediation in which bacteria respond chemotactically to the pollutants that they degrade.We analyzed bacterial penetration times through sand columns from two different experimental studies reported in the literature within the context of our mathematical model to evaluate the effective transport coefficients. Our results indicated that the presence of the porous medium reduced the random motility of the bacterial population by a factor comparable to the theoretical prediction. We were unable to determine the effect of the porous medium on the chemotactic sensitivity coefficient because no chemotactic response was observed in the experimental studies. However, the mathematical model was instrumental in developing a plausible explanation for why no chemotactic response was observed. The chemical gradients may have been too shallow over most of the sand core to elicit a measurable response. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 487-496, 1997.     

Physical and chemical factors influencing transport of microorganisms through porous media.

Resting-cell suspensions of bacteria isolated from groundwater were added as a pulse to the tops of columns of clean quartz sand. An artificial groundwater solution (AGW) was pumped through the columns, and bacterial breakthrough curves were established and compared to test the effects of ionic strength of the AGW, cell size (by using strains of similar cell surface hydrophobicity but different size), mineral grain size, and presence of heterogeneities within the porous media on transport of the bacteria. The proportion of cells recovered in the effluent ranged from nearly 90% for AGW of a higher ionic strength (I = 0.0089 versus 0.00089 m), small cells (0.75-micron-diameter spheres versus 0.75 by 1.8-micron rods), and coarse-grained sand (1.0 versus 0.33 mm) to less than 1% for AGW of lower ionic strength, large cells, and fine-grained sand. Differences in the widths of peaks (an indicator of dispersion) were significant only for the cell size treatment. For treatments containing heterogeneities (a vein of coarse sand in the center of a bed of fine sand), doubly peaked breakthrough curves were obtained. The first peak represents movement of bacteria through the transmissive coarse-grained vein. The second peak is thought to be dominated by cells which have moved (due to dispersion) from the fine-grained matrix to the coarse-grained vein near the top of the column and thus had been retarded, but not retained, by the column. Strength of effects tests indicated that grain size was the most important factor controlling transport of bacteria over the range of values tested for all of the factors examined.(ABSTRACT TRUNCATED AT 250 WORDS)     

Physical and chemical factors influencing transport of microorganisms through porous media.

Resting-cell suspensions of bacteria isolated from groundwater were added as a pulse to the tops of columns of clean quartz sand. An artificial groundwater solution (AGW) was pumped through the columns, and bacterial breakthrough curves were established and compared to test the effects of ionic strength of the AGW, cell size (by using strains of similar cell surface hydrophobicity but different size), mineral grain size, and presence of heterogeneities within the porous media on transport of the bacteria. The proportion of cells recovered in the effluent ranged from nearly 90% for AGW of a higher ionic strength (I = 0.0089 versus 0.00089 m), small cells (0.75-micron-diameter spheres versus 0.75 by 1.8-micron rods), and coarse-grained sand (1.0 versus 0.33 mm) to less than 1% for AGW of lower ionic strength, large cells, and fine-grained sand. Differences in the widths of peaks (an indicator of dispersion) were significant only for the cell size treatment. For treatments containing heterogeneities (a vein of coarse sand in the center of a bed of fine sand), doubly peaked breakthrough curves were obtained. The first peak represents movement of bacteria through the transmissive coarse-grained vein. The second peak is thought to be dominated by cells which have moved (due to dispersion) from the fine-grained matrix to the coarse-grained vein near the top of the column and thus had been retarded, but not retained, by the column. Strength of effects tests indicated that grain size was the most important factor controlling transport of bacteria over the range of values tested for all of the factors examined.(ABSTRACT TRUNCATED AT 250 WORDS)     

Transport of bacteria in porous media: II. A model for convective Transport and growth

A model is presented for the coupled processes of bacterial growth and convective transport of bacteria has been modeled using a fractional flow approach. The various mechanisms of bacteria retention can be incorporated into the model through selection of an appropriate shape of the fractional flow curve. Permeability reduction due to pore plugging by bacteria was simulated using the effective medium theory. In porous media, the rates of transport and growth of bacteria, the generation of metabolic products, and the consumption of nutrients are strongly coupled processes. Consequently, the set of governing conservation equations form a set of coupled, nonlinear partial differential equations that were solved numerically. Reasonably good agreement between the model and experimental data has been obtained indicating that the physical processes incorporated in the model are adequate. The model has been used to predict the in situ transport and growth of bacteria, nutrient consumption, and metabolite production. It can be particularly useful in simulating laboratory experiments and in scaling microbial-enhanced oil recovery or bioremediation processes to the field. (c) 1994 John Wiley & Sons, Inc.     

Real time monitoring of biofilm development under flow conditions in porous media

Biofilm growth can impact the effectiveness of industrial processes that involve porous media. To better understand and characterize how biofilms develop and affect hydraulic properties in porous media, both spatial and temporal development of biofilms under flow conditions was investigated in a translucent porous medium by using Pseudomonas fluorescens HK44, a bacterial strain genetically engineered to luminesce in the presence of an induction agent. Real-time visualization of luminescent biofilm growth patterns under constant pressure conditions was captured using a CCD camera. Images obtained over 8 days revealed that variations in bioluminescence intensity could be correlated to biofilm cell density and hydraulic conductivity. These results were used to develop a real-time imaging method to study the dynamic behavior of biofilm evolution in a porous medium, thereby providing a new tool to investigate the impact of biological fouling in porous media under flow conditions.     

Real time monitoring of biofilm development under flow conditions in porous media

Biofilm growth can impact the effectiveness of industrial processes that involve porous media. To better understand and characterize how biofilms develop and affect hydraulic properties in porous media, both spatial and temporal development of biofilms under flow conditions was investigated in a translucent porous medium by using Pseudomonas fluorescens HK44, a bacterial strain genetically engineered to luminesce in the presence of an induction agent. Real-time visualization of luminescent biofilm growth patterns under constant pressure conditions was captured using a CCD camera. Images obtained over 8 days revealed that variations in bioluminescence intensity could be correlated to biofilm cell density and hydraulic conductivity. These results were used to develop a real-time imaging method to study the dynamic behavior of biofilm evolution in a porous medium, thereby providing a new tool to investigate the impact of biological fouling in porous media under flow conditions.     

Pore‐network modeling of biofilm evolution in porous media

The influence of bacterial biomass on hydraulic properties of porous media (bioclogging) has been explored as a viable means for optimizing subsurface bioremediation and microbial enhanced oil recovery. In this study, we present a pore network simulator for modeling biofilm evolution in porous media including hydrodynamics and nutrient transport based on coupling of advection transport with Fickian diffusion and a reaction term to account for nutrient consumption. Biofilm has non‐zero permeability permitting liquid flow and transport through the biofilm itself. To handle simultaneous mass transfer in both liquid and biofilm in a pore element, a dual‐diffusion mass transfer model is introduced. The influence of nutrient limitation on predicted results is explored. Nutrient concentration in the network is affected by diffusion coefficient for nutrient transfer across biofilm (compared to water/water diffusion coefficient) under advection dominated transport, represented by mass transport Péclet number >1. The model correctly predicts a dependence of rate of biomass accumulation on inlet concentration. Poor network connectivity shows a significantly large reduction of permeability, for a small biomass pore volume. Biotechnol. Bioeng. 2011;108: 2413–2423. © 2011 Wiley Periodicals, Inc.