Biomass evolution in porous media and its effects on permeability under starvation conditions

The purpose of this study was to understand bacteria profile modification and its applications in subsurface biological operations such as biobarrier formation, in situ bioremediation, and microbial-enhanced oil recovery. Biomass accumulation and evolution in porous media were investigated both experimentally and theoretically. To study both nutrient-rich and carbon-source-depleted conditions, Leuconostoc mesenteroides was chosen because of its rapid growth rate and exopolymer production rate. Porous micromodels were used to study the effects of biomass evolution on the permeability of a porous medium. Bacterial starvation was initiated by switching the feed from a nutrient solution to a buffer solution in order to examine biofilm stability under nutrient-poor conditions. Four different evolution patterns were identified during the nutrient-rich and nutrient-depleted conditions used in the micromodel experiments. In phase I, the permeability of the porous micromodel decreased as a result of biomass accumulation in pore bodies and pore throats. In phase II, starvation conditions were initiated. The depletion of nutrient in the phase II resulted in slower growth of the biofilm causing the permeability to reach a minimum as all the remaining nutrients were consumed. In phase III, permeability began to increase due to biofilm sloughing caused by shear stress. In phase IV, shear stress remained below the critical shear stress for sloughing and the biofilm remained stable for long periods of time during starvation. The critical shear stress for biofilm sloughing provided an indication of biofilm strength. Shear removal of biofilms occurred when shear stress exceeded critical shear stress. A network model was used to describe the biofilm formation phenomenon and the existence of a critical shear stress. Simulations were in qualitative agreement with the experimental results, and demonstrate the existence of a critical shear stress.     

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.     

Biofilm development and the dynamics of preferential flow paths in porous media

A two-dimensional pore-scale numerical model was developed to evaluate the dynamics of preferential flow paths in porous media caused by bioclogging. The liquid flow and solute transport through the pore network were coupled with a biofilm model including biomass attachment, growth, decay, lysis, and detachment. Blocking of all but one flow path was obtained under constant liquid inlet flow rate and biomass detachment caused by shear forces only. The stable flow path formed when biofilm detachment balances growth, even with biomass weakened by decay. However, shear forces combined with biomass lysis upon starvation could produce an intermittently shifting location of flow channels. Dynamic flow pathways may also occur when combined liquid shear and pressure forces act on the biofilm. In spite of repeated clogging and unclogging of interconnected pore spaces, the average permeability reached a quasi-constant value. Oscillations in the medium permeability were more pronounced for weaker biofilms.     

Flowing biofilms as a transport mechanism for biomass through porous media under laminar and turbulent conditions in a laboratory reactor system

Fluid flow has been shown to be important in influencing biofilm morphology and causing biofilms to flow over surfaces in flow cell experiments. However, it is not known whether similar effects may occur in porous media. Generally, it is assumed that the primary transport mechanism for biomass in porous media is through convection, as suspended particulates (cells and flocs) carried by fluid flowing through the interstices. However, the flow of biofilms over the surfaces of soils and sediment particles, may represent an important flux of biomass, and subsequently affect both biological activity and permeability. Mixed species bacterial biofilms were grown in glass flow cells packed with 1 mm diameter glass beads, under laminar or turbulent flow (porous media Reynolds number = 20 and 200 respectively). The morphology and dynamic behavior reflected those of biofilms grown in the open flow cells. The laminar biofilm was relatively uniform and after 23 d had inundated the majority of the pore spaces. Under turbulent flow the biofilm accumulated primarily in protected regions at contact points between the beads and formed streamers that trailed from the leeward face. Both biofilms caused a 2 to 3-fold increase in friction factor and in both cases there were sudden reductions in friction factor followed by rapid recovery, suggesting periodic sloughing and regrowth events. Time-lapse microscopy revealed that under both laminar and turbulent conditions biofilms flowed over the surface of the porous media. In some instances ripple structures formed. The velocity of biofilm flow was on the order of 10 mum h(-1) in the turbulent flow cell and 1.0 mum h(-1) in the laminar flow cell.     

The effect of biofilm permeability on bio-clogging of porous media

A 3D Biofilm model, appropriate for complex porous media support structures, is successfully modified such that non‐zero permeability of biofilms structures is enabled. A systematic study is then conducted into the influence of biofilm permeability on overall biomass growth rate. This reveals a significant influence at large biofilm concentrations; even when the permeability of the biomass is 1.25% of that of the free pore space, biomass accumulation increased by a factor of ～3 over 40 h. The effect is shown to be retained when allowing for biomass detachment or erosion as a consequence of adjacent velocity shear. We conclude that biofilm permeability should be included in biofilm models and that further experimental work is required to better describe the link between biofilm permeability and local microstructure. Biotechnol. Bioeng. 2012; 109:1031–1042. © 2011 Wiley Periodicals, Inc.     

Pore-scale investigation of biomass plug development and propagation in porous media.

Biomass plugging of porous media finds application in enhanced oil recovery and bioremediation. An understanding of biomass plugging of porous media was sought by using a porous glass micromodel through which biomass and nutrient were passed. This study describes the pore-scale physics of biomass plug propagation of Leuconostoc mesenteroides under nutrient-rich conditions. It was found that, as the nutrient flowed through the micromodel, the initial biomass plug occurred at the nutrient-inoculum interface due to growth in the larger pore throats. As growth proceeded, biomass filled and closed these larger pore throats, until only isolated groupings of pore throats with smaller radii remained empty. As nutrient flow continued, a maximum pressure drop was reached. At the maximum pressure drop, the biomass yielded in a manner similar to a Bingham plastic to form a breakthrough channel consisting of a path of interconnected pore throats. The channel incorporated the isolated groupings of empty pore throats that had been present before breakthrough. As the nutrient flow continued, subsequent plugs developed as breakthrough channels refilled with biomass and in situ growth was stimulated in the region just downstream of the previous plug. The downstream plugs had a higher fraction of isolated groupings of empty pore throats, which can be attributed to depletion of nutrient downstream. When the next breakthrough channel formed, it incorporated these isolated groupings, causing the breakthrough channels to be branched. It was observed that the newly formed plug could be less stable with this higher fraction of empty pore throats and that the location of breakthrough channels changed in subsequent plugs. This change in breakthrough channel location could be attributed to the redistribution of nutrient flow and the changes in flowrate in the pore throats.     

Flowing biofilms as a transport mechanism for biomass through porous media under laminar and turbulent conditions in a laboratory reactor system

Abstract

Fluid flow has been shown to be important in influencing biofilm morphology and causing biofilms to flow over surfaces in flow cell experiments. However, it is not known whether similar effects may occur in porous media. Generally, it is assumed that the primary transport mechanism for biomass in porous media is through convection, as suspended particulates (cells and flocs) carried by fluid flowing through the interstices. However, the flow of biofilms over the surfaces of soils and sediment particles, may represent an important flux of biomass, and subsequently affect both biological activity and permeability. Mixed species bacterial biofilms were grown in glass flow cells packed with 1 mm diameter glass beads, under laminar or turbulent flow (porous media Reynolds number = 20 and 200 respectively). The morphology and dynamic behavior reflected those of biofilms grown in the open flow cells. The laminar biofilm was relatively uniform and after 23 d had inundated the majority of the pore spaces. Under turbulent flow the biofilm accumulated primarily in protected regions at contact points between the beads and formed streamers that trailed from the leeward face. Both biofilms caused a 2 to 3-fold increase in friction factor and in both cases there were sudden reductions in friction factor followed by rapid recovery, suggesting periodic sloughing and regrowth events. Time-lapse microscopy revealed that under both laminar and turbulent conditions biofilms flowed over the surface of the porous media. In some instances ripple structures formed. The velocity of biofilm flow was on the order of 10 μm h^?1 in the turbulent flow cell and 1.0 μm h^?1 in the laminar flow cell.     

A new approach to model the spatiotemporal development of biofilm phase in porous media

Bacteria can exist within biofilms that are attached to the solid matrix of a porous medium. Under certain conditions, the biomass can fully occupy the pore space leading to reduced hydraulic conductivity and mass transport. Here, by treating biofilm as a growing, high-viscosity phase, a novel macroscopic approach to model biofilm spatial expansion and its corresponding effects on porous medium hydraulic properties is presented. The separate yet coupled flow of the water and biofilm phases is handled by using relative permeability curves that allow for biofilm movement within the porous medium and bioclogging effects. Fluid flow is governed by Darcy's law and component transport is set by the convection-diffusion equation reaction terms for each component. Here, the system of governing equations is solved by using a commercial multiphase flow reservoir simulator, which is used to validate the model against published laboratory experiments. A comparison of the model and experimental observations reveal that the model provides a reasonable means to predict biomass development in the porous medium. The results reveal that coupled flow of water and movement of biofilm, as described by relative permeability curves, is complex and has a large impact on the development of biomass and consequent bioclogging in the porous medium.     

Modelling biofilm‐induced formation damage and biocide treatment in subsurface geosystems

Biofilm growth in subsurface porous media, and its treatment with biocides (antimicrobial agents), involves a complex interaction of biogeochemical processes which provide non‐trivial mathematical modelling challenges. Although there are literature reports of mathematical models to evaluate biofilm tolerance to biocides, none of these models have investigated biocide treatment of biofilms growing in interconnected porous media with flow. In this paper, we present a numerical investigation using a pore network model of biofilm growth, formation damage and biocide treatment. The model includes three phases (aqueous, adsorbed biofilm, and solid matrix), a single growth‐limiting nutrient and a single biocide dissolved in the water. Biofilm is assumed to contain a single species of microbe, in which each cell can be a viable persister, a viable non‐persister, or non‐viable (dead). Persisters describe small subpopulation of cells which are tolerant to biocide treatment. Biofilm tolerance to biocide treatment is regulated by persister cells and includes ‘innate’ and ‘biocide‐induced’ factors. Simulations demonstrate that biofilm tolerance to biocides can increase with biofilm maturity, and that biocide treatment alone does not reverse biofilm‐induced formation damage. Also, a successful application of biological permeability conformance treatment involving geologic layers with flow communication is more complicated than simply engineering the attachment of biofilm‐forming cells at desired sites.     

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.     

Mathematical Modeling of Chemotactic Bacterial Transport through a Two-Dimensional Heterogeneous Porous Medium

The impact of bacterial chemotaxis on in situ ground-water bioremediation remains an unanswered question. Although bacteria respond to chemical gradients in aqueous environments and under no-flow conditions, it is unclear whether they can also respond in porous media with advective flow to improve overall contaminant degradation. The effect of chemotaxis is most profound in regions with sharp chemical gradients, most notably around residual nonaqueous phase liquid (NAPL) ganglia and surrounding clay lenses or aquitards with trapped contamination. The purpose of this study is to simulate bacterial transport through a two-dimensional subsurface environment, containing one region of low permeability with trapped contaminant surrounded above and below by two regions of higher permeability. Using mathematical predictions of the effect of pore size on measured bacterial transport parameters, the authors observe a 50% decrease in both motility and chemotaxis in the finer-grained, low-permeability porous medium. The authors simulate how chemotaxis affects bacterial migration to the contaminated region under various flow and initial conditions. Results indicate that bacteria traveling through a high-permeability region with advective flow can successfully migrate toward and accumulate around a contaminant diffusing from a lower permeability region.     

Mathematical Modeling of Chemotactic Bacterial Transport through a Two-Dimensional Heterogeneous Porous Medium

The impact of bacterial chemotaxis on in situ ground-water bioremediation remains an unanswered question. Although bacteria respond to chemical gradients in aqueous environments and under no-flow conditions, it is unclear whether they can also respond in porous media with advective flow to improve overall contaminant degradation. The effect of chemotaxis is most profound in regions with sharp chemical gradients, most notably around residual nonaqueous phase liquid (NAPL) ganglia and surrounding clay lenses or aquitards with trapped contamination. The purpose of this study is to simulate bacterial transport through a two-dimensional subsurface environment, containing one region of low permeability with trapped contaminant surrounded above and below by two regions of higher permeability. Using mathematical predictions of the effect of pore size on measured bacterial transport parameters, the authors observe a 50% decrease in both motility and chemotaxis in the finer-grained, low-permeability porous medium. The authors simulate how chemotaxis affects bacterial migration to the contaminated region under various flow and initial conditions. Results indicate that bacteria traveling through a high-permeability region with advective flow can successfully migrate toward and accumulate around a contaminant diffusing from a lower permeability region.     

Biomass plug development and propagation in porous media

Exopolymer-producing bacteria can be used to modify soil profiles for enhanced oil recovery or bioremediation. Understanding the mechanisms associated with biomass plug development and propagation is needed for successful application of this technology. These mechanisms were determined from packed-bed and micromodel experiments that simulate plugging in porous media. Leuconostoc mesenteroides was used, because production of dextran, a water-insoluble exopolymer, can be controlled by using different carbon sources. As dextran was produced, the pressure drop across the porous media increased and began to oscillate. Three pressure phases were identified under exopolymer-producing conditions: the exopolymer-induction phase, the plugging phase, and the plug-propagation phase. The exopolymer-induction phase extended from the time that exopolymer-producing conditions were induced until there was a measurable increase in pressure drop across the porous media. The plugging phase extended from the first increase in pressure drop until a maximum pressure drop was reached. Changes in pressure drop in these two phases were directly related to biomass distribution. Specifically, flow channels within the porous media filled with biomass creating a plugged region where convective flow occurred only in water channels within the biofilm. These water channels were more restrictive to flow causing the pressure drop to increase. At a maximum pressure drop across the porous media, the biomass yielded much like a Bingham plastic, and a flow channel was formed. This behavior marked the onset of the plug-propagation phase which was characterized by sequential development and breakthrough of biomass plugs. This development and breakthrough propagated the biomass plug in the direction of nutrient flow. The dominant mechanism associated with all three phases of plugging in porous media was exopolymer production; yield stress is an additional mechanism in the plug-propagation phase.     

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.     

Xanthan degragation by biofilm in porous media

Biological activity in oil reservoirs can cause significant problems such as souring and plugging. This study focuses on the problem of polymer degradation and permeability reduction due to biofilm formation during polymer injection for improved oil recovery. Polymers are included in injection fluids to increase their viscosity. Results relating biological processes and polymer degradation to fluid‐dynamic conditions in a laboratory model porous medium are presented.

A transparent flow cell with an etched two‐dimensional network of pores served as a model porous medium. A sterile xanthan polymer and natural sea water solution were continuously injected into the porous medium. A bacterial culture capable of xanthan degradation was introduced into the cell by a single injection. Some of the cells from this culture attached to the pore walls forming an immobile bacterial culture, termed biofilm. The development of this biofilm, its xanthan degradation and its effect on permeability were measured.

The effects of injection rate and rate transitions were analyzed. Injection fluid viscosity was reduced by 30% after 5 min flow through the porous medium at the maximum steady state degradation rate observed. Permeability was significantly reduced by the xanthan degrading biofilm, causing an increase in pressure drop through the porous medium of up to 80%. Polymer injection in oil reservoirs may, therefore, have negative effects on oil recovery, unless efficient biofouling control is applied. The methodology presented may serve as a tool in the development of biofouling control measures in porous media.     

Permeability of a growing biofilm in a porous media fluid flow analyzed by magnetic resonance displacement‐relaxation correlations

Biofilm growth in porous media is difficult to study non‐invasively due to the opaqueness and heterogeneity of the systems. Magnetic resonance is utilized to non‐invasively study water dynamics within porous media. Displacement‐relaxation correlation experiments were performed on fluid flow during biofilm growth in a model porous media of mono‐dispersed polystyrene beads. The spin–spin T₂ magnetic relaxation distinguishes between the biofilm phase and bulk fluid phase due to water–biopolymer interactions present in the biofilm, and the flow dynamics are measured using PGSE NMR experiments. By correlating these two measurements, the effects of biofilm growth on the fluid dynamics can be separated into a detailed analysis of both the biofilm phase and the fluid phase simultaneously within the same experiment. Within the displacement resolution of these experiments, no convective flow was measured through the biomass. An increased amount of longitudinal hydrodynamic dispersion indicates increased hydrodynamic mixing due to fluid channeling caused by biofilm growth. The effect of different biofilm growth conditions was measured by varying the strength of the bacterial growth medium. Biotechnol. Bioeng. 2013; 110: 1366–1375. © 2012 Wiley Periodicals, 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.     

Peristaltic transport in a channel with a porous peripheral layer: model of a flow in gastrointestinal tract

Peristaltic transport in a two dimensional channel, filled with a porous medium in the peripheral region and a Newtonian fluid in the core region, is studied under the assumptions of long wavelength and low Reynolds number. The fluid flow is investigated in the waveframe of reference moving with the velocity of the peristaltic wave. Brinkman extended Darcy equation is utilized to model the flow in the porous layer. The interface is determined as a part of the solution using the conservation of mass in both the porous and fluid regions independently. A shear-stress jump boundary condition is used at the interface. The physical quantities of importance in peristaltic transport like pumping, trapping, reflux and axial velocity are discussed for various parameters of interest governing the flow like Darcy number, porosity, permeability, effective viscosity etc. It is observed that the peristalsis works as a pump against greater pressure in two-layered model with a porous medium compared with a viscous fluid in the peripheral layer. Increasing Darcy number Da decreases the pumping and increasing shear stress jump constant beta results in increasing the pumping. The limits on the time averaged flux Q for trapping in the core layer are obtained. The discussion on pumping, trapping and reflux may be helpful in understanding some of the fluid dynamic aspects of the transport of chyme in gastrointestinal tract.     

Study of Displacement Efficiency and Flow Behavior of Foamed Gel in Non-Homogeneous Porous Media

Field trials have demonstrated that foamed gel is a very cost-effective technology for profile modification and water shut-off. However, the mechanisms of profile modification and flow behavior of foamed gel in non-homogeneous porous media are not yet well understood. In order to investigate these mechanisms and the interactions between foamed gel and oil in porous media, coreflooding and pore-scale visualization waterflooding experiments were performed in the laboratory. The results of the coreflooding experiment in non-homogeneous porous media showed that the displacement efficiency improved by approximately 30% after injecting a 0.3 pore volume of foamed gel, and was proportional to the pore volumes of the injected foamed gel. Additionally, the mid-high permeability zone can be selectively plugged by foamed gel, and then oil located in the low permeability zone will be displaced. The visualization images demonstrated that the amoeba effect and Jamin effect are the main mechanisms for enhancing oil recovery by foamed gel. Compared with conventional gel, a unique benefit of foamed gel is that it can pass through micropores by transforming into arbitrary shapes without rupturing, this phenomenon has been named the amoeba effect. Additionally, the stability of foam in the presence of crude oil also was investigated. Image and statistical analysis showed that these foams boast excellent oil resistance and elasticity, which allows them to work deep within formations.