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.     

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.     

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.     

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 model of fluid-biofilm interaction using a Burger material law

A two-dimensional finite element model of the biofilm response to flow was developed. The numerical code sequentially coupled the fluid dynamics of turbulent, incompressible flow with the mechanical response of a single hemispherical biofilm cluster (approximately 100 microm) attached to the flow boundary. A non-linear Burger material law was used to represent the viscoelastic response of a representative microbial biofilm. This constitutive law was incorporated into the numerical model as a Prony series representation of the biofilm's relaxation modulus. Model simulations illuminated interesting details of this fluid-structure interaction. Simulations revealed that softer biofilms (characterized by lower elastic moduli) were highly susceptible to lift forces and consequently were subject to even greater drag forces found higher in the velocity field. A bimodal deformation path due to the two Burger relaxation times was also observed in several simulations. This suggested that interfacial biofilm may be most susceptible to hydrodynamically induced detachment during the initial relaxation time. This result may prove useful in developing removal strategies. Additionally, plots of lift versus drag suggested that the deformation paths taken by viscoelastic biofilms are largely insensitive to specific material coefficients. Softer biofilms merely seem to follow the same path (as a stiffer biofilm) at a faster rate. These relationships may be useful in estimating the hydrodynamic forces acting on an attached biofilm based on changes in scale and cataloged material properties.     

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.     

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.     

Silica‐modified luminescent LaPO4:Eu@LaPO4@SiO2 core/shell nanorods: Synthesis,structural and luminescent properties

Monoclinic‐type tetragonal LaPO₄:Eu (core) and LaPO₄:Eu@LaPO₄ (core/shell) nanorods (NRs) were successfully prepared using a urea‐based co‐precipitation process under ambient conditions. An amorphous silica layer was coated around the luminescent core/shell NRs via the sol–gel process to improve their solubility and colloidal stability in aqueous and non‐aqueous media. The prepared nano‐products were systematically characterized by X‐ray diffraction pattern, transmission electron microscopy, energy dispersive X‐ray analysis, and FTIR, UV/Vis, and photoluminescence spectroscopy to examine their phase purity, crystal phase, surface chemistry, solubility and luminescence characteristics. The length and diameter of the nano‐products were in the range 80–120 nm and 10–15 nm, respectively. High solubility of the silica‐modified core/shell/Si NRs was found for the aqueous medium. The luminescent core NRs exhibited characteristic excitation and emission transitions in the visible region that were greatly affected by surface growth of insulating LaPO₄ and silica layers due to the multiphonon relaxation rate. Our luminescence spectral results clearly show a distinct difference in intensities for core, core/shell, and core/shell/Si NRs. Highly luminescent NRs with good solubility could be useful candidates for a variety of photonic‐based biomedical applications.     

Using non‐invasive magnetic resonance imaging (MRI) to assess the reduction of Cr(VI) using a biofilm–palladium catalyst

Industrial waste streams may contain contaminants that are valuable like Pd(II) and/or toxic and mutagenic like Cr(VI). Using Serratia sp. biofilm the former was biomineralized to produce a supported nanocrystalline Pd(0) catalyst, and this biofilm–Pd heterogeneous catalyst was then used to reduce Cr(VI) to less dangerous Cr(III) at room temperature, with formate as the electron donor. Cr(VI)_(aq) is non‐paramagnetic while Cr(III)_(aq) is paramagnetic, which enabled spatial mapping of Cr species concentrations within the reactor cell using non‐invasive magnetic resonance (MR) imaging experiments. Spatial reactivity heterogeneities were thus examined. In batch reactions, these could be attributed primarily to heterogeneity of Pd(0) distribution and to the development of gas bubbles within the reactor. In continuous flow reactions, spatial reactivity heterogeneities resulted primarily from heterogeneity of Cr(VI) delivery. Biotechnol. Bioeng. 2010;107: 11–20. © 2010 Wiley Periodicals, Inc.     

Life history of Daphnia galeata in a hypertrophic reservoir and consequences of non-consumptive mortality for the initiation of a midsummer decline

SUMMARY 1. Field and laboratory investigations were combined in a 2‐year study on the initiation of a midsummer decline of Daphnia galeata Sars in a hypertrophic reservoir. Quantitative field samples were taken twice a week, and, adult and juvenile mortality rates were calculated. Patterns of reproduction and survival of daphnids born during spring and early summer under fluctuating food conditions were determined in life‐table experiments. 2. The abundance of Daphnia increased strongly in early May and declined in June 1998 (midsummer decline). In 1999, Daphnia density increased only slowly in spring and remained constantly high throughout the summer. 3. Food conditions (concentrations of POC_{<30 μm}) for daphnids deteriorated in both years in response to increasing Daphnia densities, resulting in a clear‐water phase of about 4 weeks. When Daphnia abundance declined in 1998, POC_{<30 μm} concentrations increased greatly, whereas in 1999 food conditions improved only slightly and Secchi depth remained high. 4. Survival of daphnids in life‐table experiments decreased greatly after food became rare and was strongly reduced in those animals born during the clear‐water phase compared with those born later. In addition, age at first reproduction was retarded during the clear‐water phase, resulting in very low population growth rates. Survivorship patterns in life‐table experiments suggest a strong impact of non‐consumptive mortality on Daphnia population dynamics. 5. Field data of mortality point to differences in mortality patterns between years, probably resulting from different predation impacts of juvenile fish. In both years, however, adult mortality contributed substantially to overall mortality at the end of the clear‐water phase. As bottom‐up effects on D. galeata were very similar in both years, the significance of non‐consumptive mortality on the initiation of midsummer declines appears to depend largely on recruitment patterns before the clear‐water phase. A high impact can be expected when Daphnia populations are dominated by a peak cohort of nearly identical age during the clear‐water phase.     

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.     

Regulating the Catalytic Dynamics Through a Crystal Structure Modulation of Bimetallic Catalyst

The surface of solid catalysts is one of the most important factors where the interface with reaction products governs the reaction kinetics. Herein, the crystal phase of palladium–copper nanoparticles (PdCu NPs) is controlled to modulate their surface atomic arrangement, which will govern the growth dynamics of discharge products on their surfaces and thus the catalytic performances in non‐aqueous lithium–oxygen (Li‐O₂) batteries. First‐principles calculations and experimental validations reveal that homogeneous nucleation and distribution of discharge products are observed on the surface of body‐centered cubic PdCu NPs, promoting the oxygen reduction/evolution reaction (ORR/OER) activities in Li‐O₂ batteries. However, the agglomerates formed on the surface of its face‐centered cubic homologue deteriorates ORR/OER activities, which worsen the battery performances. For the first time, this work theoretically and experimentally demonstrates how the crystal phase modulation regulates the nucleation behaviors and growth dynamics of discharge products for ORR/OER.     

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.     

Structural and dynamics characterization of norovirus protease

Norovirus protease is an essential enzyme for proteolytic maturation of norovirus nonstructural proteins and has been implicated as a potential target for antiviral drug development. Although X‐ray structural studies of the protease give us wealth of structural information including interactions of the protease with its substrate and dimeric overall structure, the role of protein dynamics in the substrate recognition and the biological relevance of the protease dimer remain unclear. Here we determined the solution NMR structure of the 3C‐like protease from Norwalk virus (NV 3CLpro), a prototype strain of norovirus, and analyzed its backbone dynamics and hydrodynamic behavior in solution. ¹⁵N spin relaxation and analytical ultracentrifugation analyses demonstrate that NV 3CLpro is predominantly a monomer in solution. Solution structure of NV 3CLpro shows significant structural variation in C‐terminal domain compared with crystal structures and among lower energy structure ensembles. Also, ¹⁵N spin relaxation and Carr–Purcell–Meiboom–Gill (CPMG)‐based relaxation dispersion analyses reveal the dynamic properties of residues in the C‐terminal domain over a wide range of timescales. In particular, the long loop spanning residues T123–G133 show fast motion (ps‐ns), and the residues in the bII–cII region forming the large hydrophobic pocket (S2 site) undergo conformational exchanges on slower timescales (μs–ms), suggesting their important role in substrate recognition.     

Dynamic volume-averaged model of heat and mass transport within a compost biofilter: I. Model development

Successful, long-term operation of a biofilter system depends on maintaining a suitable biofilm environment within a porous medium reactor. In this article a mathematical study was conducted of the spatial and temporal changes of biofilter performance due to interphase heat and mass transport. The method of volume averaging was used to spatially smooth the three-phase (solid, liquid, and gas) conservation equations over the biofilter domain. The packing medium was assumed to be inert, removing the solid phase mass continuity equation from the system. The finite element method was used to integrate the resulting nonlinear-coupled partial differential equations, tracking eight state variables: temperature, water vapor, dry air, liquid water, biofilm, gas and liquid phase organic pollutant, and nutrient densities, through time and space. A multiphase, gas and liquid flow model was adapted to the biofilter model from previous studies of unsaturated groundwater flow. Newton's method accelerated by an LU direct solver was used to iterate the model for solutions. Effects of packing media on performance were investigated to illustrate the utility of the model. The moisture dynamics and nutrient cycling are presented in Part II of this article.     

Impacts of hydrodynamic conditions and microscale surface roughness on the critical shear stress to develop and thickness of early-stage Pseudomonas putida biofilms

Biofilms can increase pathogenic contamination of drinking water, cause biofilm-related diseases, alter the sediment erosion rate, and degrade contaminants in wastewater. Compared with mature biofilms, biofilms in the early-stage have been shown to be more susceptible to antimicrobials and easier to remove. Mechanistic understanding of physical factors controlling early-stage biofilm growth is critical to predict and control biofilm development, yet such understanding is currently incomplete. Here, we reveal the impacts of hydrodynamic conditions and microscale surface roughness on the development of early-stage Pseudomonas putida biofilm through a combination of microfluidic experiments, numerical simulations, and fluid mechanics theories. We demonstrate that early-stage biofilm growth is suppressed under high flow conditions and that the local velocity for early-stage P. putida biofilms (growth time < 14 h) to develop is about 50 μm/s, which is similar to P. putida's swimming speed. We further illustrate that microscale surface roughness promotes the growth of early-stage biofilms by increasing the area of the low-flow region. Furthermore, we show that the critical average shear stress, above which early-stage biofilms cease to form, is 0.9 Pa for rough surfaces, three times as large as the value for flat or smooth surfaces (0.3 Pa). The important control of flow conditions and microscale surface roughness on early-stage biofilm development, characterized in this study, will facilitate future predictions and managements of early-stage P. putida biofilm development on the surfaces of drinking water pipelines, bioreactors, and sediments in aquatic environments.     

Towards optimum permeability reduction in porous media using biofilm growth simulations

While biological clogging of porous systems can be problematic in numerous processes (e.g., microbial enhanced oil recovery—MEOR), it is targeted during bio‐barrier formation to control sub‐surface pollution plumes in ground water. In this simulation study, constant pressure drop (CPD) and constant volumetric flow rate (CVF) operational modes for nutrient provision for biofilm growth in a porous system are considered with respect to optimum (minimum energy requirement for nutrient provision) permeability reduction for bio‐barrier applications. Biofilm growth is simulated using a Lattice‐Boltzmann (LB) simulation platform complemented with an individual‐based biofilm model (IbM). A biomass detachment technique has been included using a fast marching level set (FMLS) method that models the propagation of the biofilm–liquid interface with a speed proportional to the adjacent velocity shear field. The porous medium permeability reduction is simulated for both operational modes using a range of biofilm strengths. For stronger biofilms, less biomass deposition and energy input are required to reduce the system permeability during CPD operation, whereas CVF is more efficient at reducing the permeability of systems containing weaker biofilms. Biotechnol. Bioeng. 2009;103: 767–779. © 2009 Wiley Periodicals, Inc.     

Functional,histological and biomechanical characterization of wheat water‐mutant leaves

A wheat (Triticum turgidum subsp. durum) mutant, generated with sodium azide from wild‐type (WT) cv. ‘Trinakria’, differs in its water affinity of dry leaves, and was designated as a water‐mutant. Compared with the WT, water‐mutant leaves have lower rates of water uptake, while stomatal and cuticular transpiration do not differ. The nuclear magnetic resonance proton signals used for image reconstruction of leaf cross sections showed differences between these genotypes for the T₁ proton spin–density and the T₂ proton spin–spin relaxation time. Structural and histochemical analyses at midrib level showed that the water‐mutant has thinner leaves, with more and smaller cells per unit area of mesophyll and sclerenchyma, and has altered staining patterns of lignin and pectin‐like substances. Stress–strain curves to examine the rheological properties of the leaves showed a biphasic trend, which reveals that the tensile strength at break load and the elastic modulus of the second phase of the water‐mutant are significantly higher than for the WT. These data support the proposal of interrelationships among local biophysical properties of the leaf, the microscopic water structure, the rheological properties and the water flux rate across the leaf. This water‐mutant can be used for analysis of the genetic basis of these differences, and for identification of gene(s) that govern these traits.     

Modelling epilithic biofilms combining hydrodynamics,invertebrate grazing and algal traits

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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.