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

Numerical analysis of MICP treated sand based on bio-chemo-hydro model

Microbially Induced Calcite Precipitation (MICP) represents an environmentally friendly and innovative soil grouting technology. Involving intricate biochemical processes, it poses challenges for a thorough investigation of factors influencing microbial grouting effectiveness through experimentation alone. Consequently, A three-dimensional numerical model was developed to predict the permeability of bio-grouting in porous media. The numerical model is validated by comparing its results with test results available in the literature. The validated model is then used to investigate the effects of variation bacterial solution concentration, cementation solution concentration, grouting rate and grouting time on grouting effectiveness. It was founded that the remediation effect was positively correlated with the bacterial solution concentration and the number of grouting. An increased grouting rate enhanced the transport efficiency of reactants. Additionally, the concentration of cementation solution exhibited no significant effect on the reduction of calcium carbonate yield and permeability.

Investigation of the transport and metabolic patterns of oil-displacing bacterium FY-07-G in the microcosm model using X-CT technology

AIMS

Microbial enhanced oil recovery (MEOR) is dedicated to enhancing oil recovery by harnessing microbial metabolic activities and their byproducts within reservoir rocks and fluids. Therefore, the investigation of microbial mobility and their extensive distribution within crude oil is of paramount importance in MEOR. While microscale models have been valuable for studying bacterial strain behavior in reservoirs, they are typically limited to 2D representations of porous media, making them inadequate for simulating actual reservoir conditions. Consequently, there is a critical need for 3D models and dependable visualization methods to observe bacterial transport and metabolism within these complex reservoir environments.

METHODS AND RESULTS

Bacterial cellulose (bc) is a water-insoluble polysaccharide produced by bacteria that exhibits biocompatibility and biodegradability. It holds significant potential for applications in the field of MEOR as an effective means for selective plugging and spill prevention during oil displacement processes. Conditionally cellulose-producing strain, FY-07-G, with green fluorescent labeling, was engineered for enhanced oil recovery. 3D micro-visualization model was constructed to directly observe the metabolic activities of the target bacterial strain within porous media and to assess the plugging interactions between cellulose and the medium. Additionally, X-ray computed tomography (X-CT) technology was employed for a comprehensive analysis of the transport patterns of the target strain in oil reservoirs with varying permeabilities. The results indicated that FY-07-G, as a microorganism employing biopolymer-based plugging principles to enhance oil recovery, selectively targets and seals regions characterized by lower permeability and smaller pore spaces.

CONCLUSIONS

This work provided valuable insights into the transport and metabolic behavior of MEOR strains and tackled the limitation of 2D models in faithfully replicating oil reservoir conditions, offering essential theoretical guidance and insights for the further application of oil-displacing bacterial strains in MEOR processes.

Clogging index: A tool to quantify filter bed clogging in horizontal subsurface flow macrophyte-assisted vermifilter

This study aimed to develop a mathematical index for quantifying filter bed clogging in horizontal subsurface flow macrophyte-assisted vermifilter (HSSF-MAVF). The developed clogging index (CI) simulates the porosity reduction in the HSSF-MAVF bed due to the combined actions of deposition of suspended solids, biofilm generation, and plant growth. A series of experiments based on HSSF-MAVF were conducted to examine the key parameters related to clogging of the vermifilter such as hydraulic loading rates (HLR), organic strength (COD), and total suspended solid (TSS) at different operating conditions for the treatment of synthetic dairy wastewaters. The index was then validated using the data collected from the experiments. The predicted CI was observed to be highly capable of replicating the clogging phenomenon, as observed in this experimental study within the error range of 2-8%. Based on the visual observation and value of CI, filter beds can be grouped as unclogged (CI < 25), partially clogged (25 < CI < 40), and clogged (40 < CI). Clogged filter beds with higher CI resulted in a 5-15% reduction in the COD removal performance of HSSF-MAVFs. Moreover, the CI also envisages one to understand the individual contributions of biofilm growth, suspended solid deposition, and plant roots growth on the filter bed clogging during the operation of vermifilter and thus helps in deciding the proper setting of operational conditions to prolong the time of HSSF-MAVF operations within the acceptable range of bed materials clogging. PRACTITIONER POINTS: A mathematical index was developed to quantify clogging of the HSSF-MAVF. Flow is the most sensitive parameter based upon the sensitivity analysis. Dairy wastewater was used for the validation of CI.

A review on reactive transport model and porosity evolution in the porous media

This work comprehensively reviews the equations governing multicomponent flow and reactive transport in porous media on the pore-scale, mesoscale and continuum scale. For each of these approaches, the different numerical schemes for solving the coupled advection-diffusion-reactions equations are presented. The parameters influenced by coupled biological and chemical reactions in evolving porous media are emphasised and defined from a pore-scale perspective. Recent pore-scale studies, which have enhanced the basic understanding of processes that affect and control porous media parameters, are discussed. Subsequently, a summary of the common methods used to describe the transport process, fluid flow, reactive surface area and reaction parameters such as porosity, permeability and tortuosity are reviewed.

Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation

Microhabitat conditions determine the magnitude and speed of microbial processes but have been challenging to investigate. In this study we used microfluidic devices to determine the effect of the spatial distortion of a pore space on fungal and bacterial growth, interactions, and substrate degradation. The devices contained channels differing in bending angles and order. Sharper angles reduced fungal and bacterial biomass, especially when angles were repeated in the same direction. Substrate degradation was only decreased by sharper angles when fungi and bacteria were grown together. Investigation at the cellular scale suggests that this was caused by fungal habitat modification, since hyphae branched in sharp and repeated turns, blocking the dispersal of bacteria and the substrate. Our results demonstrate how the geometry of microstructures can influence microbial activity. This can be transferable to soil pore spaces, where spatial occlusion and microbial feedback on microstructures is thought to explain organic matter stabilization.

Relationship Between Microbial Growth and Hydraulic Properties at the Sub-Pore Scale

Accumulation of microbial biomass and its influence on porous media flow were investigated under saturated flow conditions. Microfluidic experiments were performed with model organisms, and their accumulation was observed in the pore space and on the sub-pore scale. Time-lapse optical imaging revealed different modes of biomass accumulation through primary colonization, secondary growth, and filtration events, showing the formation of preferential flow pathways in the flooding domain as result of the increasing interstitial velocity. Navier–Stokes–Brinkmann flow simulations were performed on the segmented images—a digital-twin approach—considering locally accumulated biomass as impermeable or permeable based on optical biomass density. By comparing simulation results and the experimental responses, it was shown that accumulated biomass can be considered as a permeable medium. The average intra-biomass permeability was determined to be 500 ± 200 mD, which is more than a factor of 10 larger than previously assumed in modeling studies. These findings have substantial consequences: (1) a remaining interstitial permeability, as a result of the observed channel formation and the intra-biomass permeability, and (2) a potential advective nutrient supply, which can be considered more efficient than a purely diffusive supply. The second point may lead to higher metabolic activity and substrate conversion rates which is of particular interest for geobiotechnological applications.

Development of a novel microfluidic device to study metal geochemistry in situ using X-ray fluorescence microprobe spectroscopy

The study of in situ microscale biogeochemical processes represents a major challenge in the environmental sciences. The combination of microfluidic devices with X-ray fluorescence microprobe spectroscopy may address this need, but typical materials used in these devices attenuate the X-rays needed to analyze key elements of interest, such as Fe or As. In this work, a method is presented for fabricating an etched silicon microfluidic device that is sealed with a 30 µm thin glass window that is sufficiently transparent for X-ray fluorescence microprobe spectroscopy. The capabilities of these devices for X-ray microprobe spectroscopy are demonstrated using an Fe (hydr)oxide solid that is loaded with As and then infused with sulfide, on beamline 4-BM at NSLS-II, resulting in time-variant Fe precipitation reactions and As sorption. Key results include in situ X-ray fluorescence time-series maps of Fe, As and a Br flow tracer, as well as spot XANES at both the Fe K edge and As K edge. Additionally, multiple energy mapping is used to examine the spatial speciation of As over time. The results of this work clearly demonstrate the capabilities of this novel microfluidic system that can be analyzed using X-ray fluorescence microprobe spectroscopy and can be made to study a wide range of complex microscale geochemical systems.

Non-Invasive Measurement, Mathematical Simulation and In Situ Detection of Biofilm Evolution in Porous Media: A Review

The development of biofilms and the related changes in porous media in the subsurface cannot be directly observed and evaluated. The primary reason that the mechanism of biofilm clogging in porous media cannot be clearly demonstrated is due to the opacity and structural complexity of three-dimensional pore space. Interest in exploring methods to overcome this limitation has been increasing. In the first part of this review, we introduce the underlying characteristics of biofilm in porous media. Then, we summarize two approaches, non-invasive measurement methods and mathematical simulation strategies, for studying fluid–biofilm–porous medium interaction with spatiotemporal resolution. We also discuss the advantages and limitations of these approaches. Lastly, we provide a perspective on opportunities for in situ monitoring at the field site.

Studying key processes related to CO2 underground storage at the pore scale using high pressure micromodels

Micromodels experimentation for studying and understanding CO₂ geological storage mechanisms at the pore scale.

The State of the Art of Clogging in Vertical Flow Wetlands

Clogging in vertical flow (VF) wetlands is an important process influencing water purification processes. The main contributing factors are the growth of microorganisms within the filter media, the accumulation of suspended solids on top of the wetland, as well as within the filter media. Both processes lead to a decrease of the available pore space, hence changing the soil’s hydraulic properties. This will alter the water flow and cause malfunctioning of the system. This paper summarizes the state of the art of the prevailing physical, biological and chemical processes influencing clogging in VF wetlands. Different design and operational parameters are discussed to give a better understanding on their influence to prevent malfunctioning. Based on a literature review, a detailed overview on experimental as well as modelling studies carried out is presented. The main conclusions are that on the one hand, important insights on clogging processes in VF wetlands have been gained but, on the other hand, design parameters such as intermittent loading operation and the grain size of the filter media are not well represented in those studies. Clogging models use different conceptual approaches ranging from black box models to process based models.

The impact of biodegradable carbon sources on microbial clogging of vertical up-flow sand filters treating inorganic nitrogen wastewater

The addition of biodegradable carbon sources to sand filters can enhance microbial activity but may lead to substrate clogging, a major operational problem. In laboratory-scale soil columns emulating vertical up-flow filters, the clogging effect of two readily biodegradable organic substrates-sucrose as a sugar source and ethanol as an alcohol source-were examined with coarse sand as the substrate medium. Wastewater without the addition of supplemental organics and a 'control' treated with tap water were monitored as references. Changes in saturated hydraulic conductivity were measured for all treatments over time. Other parameters that can influence the clogging rate, including temperature, dissolved oxygen, chemical oxygen demand, protein, and polysaccharides, were measured in the influent and effluent wastewater on a weekly basis. At the end of the clogging experiment, the main layer of each filter bed was separated into three sections and saturated hydraulic conductivity, organic matter content, and protein and polysaccharide concentrations were measured in each section. The rate of clogging development in the columns depended on treatment, with ethanol-treated cores clogging more quickly than sucrose-treated cores. Wastewater-treated cores took far longer to clog and the tap water control did not clog, but the saturated hydraulic conductivity declined by 60% over a year. Saturated hydraulic conductivity within the treated cores declined far less than the calculated decline in saturated hydraulic conductivities for the entire cores at the end of the experiment, indicating that clogging in the vicinity of the inlet plate by microbial mats was a major factor influencing the reduction in flow through the columns. To reduce bio-clogging in inlet filters, it may be advantageous to inject organic amendments directly into the bed, rather than pass them through the filters, as is usually the case.

Pore-Scale Hydrodynamics in a Progressively Bioclogged Three-Dimensional Porous Medium: 3-D Particle Tracking Experiments and Stochastic Transport Modeling

Biofilms are ubiquitous bacterial communities that grow in various porous media including soils, trickling, and sand filters. In these environments, they play a central role in services ranging from degradation of pollutants to water purification. Biofilms dynamically change the pore structure of the medium through selective clogging of pores, a process known as bioclogging. This affects how solutes are transported and spread through the porous matrix, but the temporal changes to transport behavior during bioclogging are not well understood. To address this uncertainty, we experimentally study the hydrodynamic changes of a transparent 3-D porous medium as it experiences progressive bioclogging. Statistical analyses of the system's hydrodynamics at four time points of bioclogging (0, 24, 36, and 48 h in the exponential growth phase) reveal exponential increases in both average and variance of the flow velocity, as well as its correlation length. Measurements for spreading, as mean-squared displacements, are found to be non-Fickian and more intensely superdiffusive with progressive bioclogging, indicating the formation of preferential flow pathways and stagnation zones. A gamma distribution describes well the Lagrangian velocity distributions and provides parameters that quantify changes to the flow, which evolves from a parallel pore arrangement under unclogged conditions, toward a more serial arrangement with increasing clogging. Exponentially evolving hydrodynamic metrics agree with an exponential bacterial growth phase and are used to parameterize a correlated continuous time random walk model with a stochastic velocity relaxation. The model accurately reproduces transport observations and can be used to resolve transport behavior at intermediate time points within the exponential growth phase considered.

Irreversible membrane fouling abatement through pre-deposited layer of hierarchical porous carbons

In this work, dual-templated hierarchical porous carbons (HPCs), produced from a coupled ice-hard templating approach, are shown to be a highly effective solution to the commonly occurring problem of irreversible fouling of low-pressure membranes used for pre-treatment in wastewater reuse. For the first time, dual-templated HPCs, along with their respective counterparts - single-templated meso-porous carbon (MPCs) (without macropores) - are tested in terms of their fouling reduction capacity and ability to remove different effluent organic matter fractions present in wastewater and compared with a commercially available powdered activated carbon (PAC). The synthesized HPCs provided exceptional fouling abatement, a 4-fold higher fouling reduction as compared to the previously reported best performing commercial PAC and ∼2.5-fold better fouling reduction than their respective mesoporous counterpart. Thus, it is shown that not only mesoporosity, but macroporosity is also necessary to achieve high fouling reduction, thus emphasizing the need for dual templating. In the case of HPCs, the pre-deposition technique is also found to outperform the traditional sorbent-feed mixing approach, mainly in terms of removal of fouling components. Based on their superior performance, a high permeability (ultra-low-pressure) membrane consisting of the synthesized HPC pre-deposited on a large pore size membrane support (0.45 μm membrane), is shown to give excellent pre-treatment performance for wastewater reuse application.

Applying a resting operation to alleviate bioclogging in vertical flow constructed wetlands: an experimental lab evaluation

The aim of this study is to evaluate the effects of and analyze the reasons for applying a resting operation to alleviate bioclogging in vertical flow constructed wetlands (VFCWs). In parallel, three groups of laboratory-scale VFCWs were continuously fed with prepared wastewater (BOD = 600 mg/L) at a relatively high hydraulic loading rate of 0.5 m(3)/m(2)·d until clogging. Parameters related to the clogging of the wetland substrate before and after resting were examined and measured. The results showed that the resting operation could effectively alleviate bioclogging because the hydraulic conductivity and effective porosity were improved after 3, 7 and 10 days of resting. In the upper 0-10 cm layer, the hydraulic conductivity increased 2.0, 2.6 and 3.5 times, respectively, for the three resting periods. The reduction of the extracellular polymeric substance (EPS), biofilm decay and the consequential change in the biofilm structure are the main reasons that the resting operation relieved clogging. In addition, the observed and theoretical resting times (approximately 7 days) agreed well. The results provide a theoretical basis and technical support for solving clogging problems.

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.

Sand box experiments with bioclogging of porous media: hydraulic conductivity reductions

Tracer experiments during clogging and de-clogging experiments in a 2D sand box were via an image analysis used to establish a data set on the relation between changes in hydraulic conductivity (K) and relative porosity (β). Clogging appears to create a finger-like tracer transport, which could be caused by an initial heterogeneous distribution of biomass in the sand box. De-clogging occurs at a slower rate possibly due to the presence of inert biomass that is not affected by the starvation conditions by sudden removal of the substrate source. The tracer front was observed to get disturbed closer and closer to the substrate source during the experiments suggesting that the zone of clogging moved upstream. Three clogging models, K(β), from the literature were tested for their ability to describe the temporal changes in clogging at the scale of the sand box; the model of Clement et al. (1996) that makes no assumption on biomass distribution, the plug formation model of Thullner et al. (2002a), and the biofilm-plug formation model of Vandevivere (1995). The plug formation and biofilm-plug formation models both match the observed changes between the hydraulic conductivity of the sand box and the relative porosity. Unfortunately our experiments did not reach low relative porosities where the two models predict different behaviors. The model by Clement et al. (1996) underestimates clogging.

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.

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.

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.

Biofilm formation by strains of Leuconostoc citreum and L. mesenteroides

Although biofilms produced by various Leuconostoc sp. are economically important as contaminants of sugar processing plants, very few studies are available on these systems. Twelve strains of Leuconostoc citreum and L. mesenteroides that produce a variety of extracellular glucans were compared for their capacity to produce biofilms. 16s rRNA sequence analysis was used to confirm the species identity of these strains, which included four isolates of L. mesenteroides, five isolates of L. citreum, and three glucansucrase mutants of L. citreum strain NRRL B-1355. Strains identified as L. mesenteroides produce glucans that are generally similar to commercial dextran. Nevertheless, these strains differed widely in their capacity to form biofilms, with densities ranging from 2.7 to 6.1 log cfu/cm(2). L. citreum strains and their derivatives produce a variety of glucans. These strains exhibited biofilm densities ranging from 2.5 to 5.9 log cfu/cm(2). Thus, biofilm-forming capacity varied widely on a strain-specific basis in both species. The types of polysaccharides produced did not appear to affect the ability to form biofilms.

Biofilm formation in environmental bacteria is influenced by different macromolecules depending on genus and species

The formation of biofilms by diverse bacteria isolated from contaminated soil and groundwater on model substrata with different surface properties was assessed in a multifactorial screen. Diverse attachment phenotypes were observed as measured by crystal violet dye retention and confocal laser scanning microscopy (CLSM). Bulk measurements of cell hydrophobicity had little predictive ability in determining whether biofilms would develop on hydrophobic or hydrophilic substrata. Therefore selected pairs of bacteria from the genera Rhodococcus, Pseudomonas and Sphingomonas that exhibited different attachment phenotypes were examined in more detail using CLSM and the lipophilic dye, Nile Red. The association of Rhodococcus sp. cell membranes with lipids was shown to influence the attachment properties of these cells, but this approach was not informative for Pseudomonas and Sphingomonas sp. Confocal Raman Microspectroscopy of Rhodococcus biofilms confirmed the importance of lipids in their formation and indicated that in Pseudomonas and Sphingomonas biofilms, nucleic acids and proteins, respectively, were important in identifying the differences in attachment phenotypes of the selected strains. Treatment of biofilms with DNase I confirmed a determining role for nucleic acids as predicted for Pseudomonas. This work demonstrates that the attachment phenotypes of microbes from environmental samples to different substrata varies markedly, a diverse range of macromolecules may be involved and that these differ significantly between genera. A combination of CLSM and Raman spectroscopy distinguished between phenotypes and could be used to identify the key macromolecules involved in cell attachment to surfaces for the specific cases studied.

Effects of pore-scale heterogeneity and transverse mixing on bacterial growth in porous media

Microbial degradation of contaminants in the subsurface requires the availability of nutrients; this is impacted by porous media heterogeneity and the degree of transverse mixing. Two types of microfluidic pore structures etched into silicon wafers (i.e., micromodels), (i) a homogeneous distribution of cylindrical posts and (ii) aggregates of large and small cylindrical posts, were used to evaluate the impact of heterogeneity on growth of a pure culture (Delftia acidovorans) that degrades (R)-2-(2,4-dichlorophenoxy)propionate (R-2,4-DP). Following inoculation, dissolved O2 and R-2,4-DP were introduced as two parallel streams that mixed transverse to the direction of flow. In the homogeneous micromodel, biomass growth was uniform in pore bodies along the center mixing line, while in the aggregate micromodel, preferential growth occurred between aggregates and slower less dense growth occurred throughout aggregates along the center mixing line. The homogeneous micromodel had more rapid growth overall (2 times) and more R-2,4-DP degradation (9.5%) than the aggregate pore structure (5.7%). Simulation results from a pore-scale reactive transport model indicate mass transfer limitations within aggregates along the center mixing line decreased overall reaction; hence, slower biomass growth rates relative to the homogeneous micromodel are expected. Results from this study contribute to a better understanding of the coupling between mass transfer, reaction rates, and biomass growth in complex porous media and suggest successful implementation and analysis of bioremediation systems requires knowledge of subsurface heterogeneity.

A review of non-invasive imaging methods and applications in contaminant hydrogeology research

Contaminant hydrogeological processes occurring in porous media are typically not amenable to direct observation. As a result, indirect measurements (e.g., contaminant breakthrough at a fixed location) are often used to infer processes occurring at different scales, locations, or times. To overcome this limitation, non-invasive imaging methods are increasingly being used in contaminant hydrogeology research. Four of the most common methods, and the subjects of this review, are optical imaging using UV or visible light, dual-energy gamma radiation, X-ray microtomography, and magnetic resonance imaging (MRI). Non-invasive imaging techniques have provided valuable insights into a variety of complex systems and processes, including porous media characterization, multiphase fluid distribution, fluid flow, solute transport and mixing, colloidal transport and deposition, and reactions. In this paper we review the theory underlying these methods, applications of these methods to contaminant hydrogeology research, and methods' advantages and disadvantages. As expected, there is no perfect method or tool for non-invasive imaging. However, optical methods generally present the least expensive and easiest options for imaging fluid distribution, solute and fluid flow, colloid transport, and reactions in artificial two-dimensional (2D) porous media. Gamma radiation methods present the best opportunity for characterization of fluid distributions in 2D at the Darcy scale. X-ray methods present the highest resolution and flexibility for three-dimensional (3D) natural porous media characterization, and 3D characterization of fluid distributions in natural porous media. And MRI presents the best option for 3D characterization of fluid distribution, fluid flow, colloid transport, and reaction in artificial porous media. Obvious deficiencies ripe for method development are the ability to image transient processes such as fluid flow and colloid transport in natural porous media in three dimensions, the ability to image many reactions of environmental interest in artificial and natural porous media, and the ability to image selected processes over a range of scales in artificial and natural porous media.

Linear exchange model for the description of mass transfer limited bioavailability at the pore scale

Reactive transport simulations are a common approach for the quantitative assessment of contaminant biodegradation in the subsurface. To use knowledge on microbial kinetics for the simulation of in situ biodegradation, the mass transfer processes controlling the bioavailability of the contaminants need to be described appropriately. A common approach to account for this problem is using a linear exchange model controlling the link between bulk and bioavailable concentration. Assuming that the subsequent degradation is controlled by the bioavailable concentration, only, these two steps can be combined to an analytical expression for the overall reaction rate know as the Best-Equation. In our work, we evaluate this approach for its ability to describe biodegradation kinetics limited by pore-scale mass transfer. Results from explicit numerical and analytical simulations of mass transport and reactive consumption at the pore scale are used to test the accuracy of results obtained using the Best-Equation. Our analysis shows that strictly spoken the Best-Equation is not valid. However, a good approximation can be achieved with errors of less than 6% in cases of moderate bioavailability and much lower errors in cases of either low or high bioavailability. These results support the description of mass transfer processes used in many reactive transport models. Furthermore, we present a method to obtain an accurate estimate of the unknown rate parameter controlling the diffusive mass transfer processes at the pore scale.

Kinetics of trichloroethylene and toluene toxicity to Pseudomonas putida F1

The goal of the present study was to elucidate the distribution of viable bacteria in chemical gradients and to evaluate the toxic effect of high concentrations of contaminants on contaminant-degrading bacteria under prolonged exposure. Accumulations of viable Pseudomonas putida F1 (P. putida F1) cells were observed surrounding trichloroethylene (TCE)-containing plugs. Results from this work indicate that P. putida F1 immediately adjacent to a TCE source become nonviable, whereas cells accumulating farther away use chemotaxis to migrate toward regions with optimal chemical concentrations in the form of concentrated bacterial bands. A method was developed to test the toxicity of model contaminant stressors, TCE and toluene, to P. putida F1; data obtained from toxicity experiments were fit to linear and exponential bacterial viability-decay models. Toxicity of TCE to P. putida F1 was best described with an exponential viability-decay model, with a viability-decay constant k(TCE) = 0.025 h(-4.95) (r(2) = 0.965). Toluene toxicity showed a marginally better fit to the linear viability-decay model (r(2) = 0.976), with a viability-decay constant k(toluene) = 0.208 h(-1). Best-fit model parameters obtained for both TCE and toluene were used to predict bacterial viability in toxicity experiments with higher contaminant concentrations and matched well with experimental data. Results from the present study can be used to predict bacterial accumulation and viability near nonaqueous-phase liquid (NAPL) sources in groundwater and may be helpful in designing bioremediation strategies for sites contaminated with residual NAPLs.

Biofilm formation by exopolysaccharide mutants of Leuconostoc mesenteroides strain NRRL B-1355

Leuconostoc mesenteroides strain NRRL B-1355 produces the soluble exopolysaccharides alternan and dextran in planktonic cultures. Mutants of this strain are available that are deficient in the production of alternan, dextran, or both. Another mutant of NRRL B-1355, strain R1510, produces an insoluble glucan in place of alternan and dextran. To test the effect of exopolysaccharide production on biofilm formation, these strains were cultured in a biofilm reactor. All strains grew well as biofilms, with comparable cell densities, including strain NRRL B-21414, which produces neither alternan nor dextran in planktonic cultures. However, the exopolysaccharide phenotype clearly affected the appearance of the biofilms and the sloughed-off biofilm material produced by these biofilms. For all strains, soluble glucansucrases and soluble polysaccharides produced by biofilm cultures appeared to be similar to those produced by planktonic cultures. Biofilms from all strains also contained insoluble polysaccharides. Strain R1510 biofilms contained an insoluble polysaccharide similar to that produced by planktonic cultures. For most other strains, the insoluble biofilm polysaccharides resembled a mixture of alternan and dextran.

Application of stereolithographic custom models for studying the impact of biofilms and mineral precipitation on fluid flow

Here we introduce the use of transparent experimental models fabricated by stereolithography for studying the impacts of biomass accumulation, minerals precipitation, and physical configuration of flow paths on liquid flow in fracture apertures. The internal configuration of the models ranged in complexity from simple geometric shapes to those that incorporate replicated surfaces of natural fractures and computationally derived fracture surfaces. High-resolution digital time-lapse imaging was employed to qualitatively observe the migration of colloidal and soluble dyes through the flow models. In this study, a Sphingomonas sp. and Sporosarcina (Bacillus) pasteurii influenced the fluid dynamics by physically altering flow paths. Microbial colonization and calcite deposition enhanced the stagnant regions adjacent to solid boundaries. Microbial growth and calcite precipitation occurred to a greater extent in areas behind the fabricated obstacles and less in high-velocity orifices.

Impact of microbial activity on the hydraulic properties of fractured chalk

The impact of microbial activity on fractured chalk transmissivity was investigated on a laboratory scale. Long-term experiments were conducted on six fractured chalk cores (20 cm diameter, 23-44 cm long) containing a single natural fracture embedded in a porous matrix. Biodegradation experiments were conducted under various conditions, including several substrate and oxygen concentrations and flow rates. 2,4,6-Tribromophenol (TBP) was used as a model contaminant (substrate). TBP biodegradation efficiency depended mainly on the amount of oxygen. However, under constant oxygen concentration at the core inlet, elevating the flow rates increased the removal rate of TBP. Transmissivity reduction was clearly related to TBP removal rate, following an initial slow decline and a further sharp decrease with time. The fracture's transmissivity was reduced by as much as 97% relative to the initial value, with no leveling off of the clogging process. For the most extreme cases, reductions of 262 and 157 microm in the equivalent hydraulic apertures were recorded for fractures with initial apertures of 495 and 207 microm, respectively. The reductions in fracture transmissivity occurred primarily because of clogging by bacterial cells and extracellular polymeric substances (EPS) produced by the bacteria. Most of the biodegradation activity was concentrated near the fracture inlet, where the most suitable biodegradation conditions (nutrients and oxygen) prevailed, suggesting that the clogging had occurred in that vicinity. The clogging must have changed the structure of the fracture void, thereby reducing the active volume participating in flow and transport processes. This phenomenon caused accelerated transport of non-reactive tracers and doubled the fracture's dispersivity under constant flow rates.

Growth of Leuconostoc mesenteroides NRRL-B523 in an alkaline medium: suboptimal pH growth inhibition of a lactic acid bacterium

Bacterial profile modification (BPM), a form of tertiary oil recovery, diverts water from the water-flooded high-permeability zone into the oil-bearing low-permeability zone. During field use, exopolymer-producing bacteria plug the high-permeability zone only in the immediate vicinity of the injection point (the near-well bore region). For effective BPM the plug must penetrate far into the formation. Slowing the specific growth rate, lengthening the lag phase, and slowing the polymerization rate are techniques that can prolong the onset of biopolymer gelation and extend the depth of the biological plug. In batch experiments, the growth of Leuconostoc mesenteroides NRRL-B523 was inhibited by the synergistic effects of high substrate loading and an alkaline pH. Exponential growth was delayed up to 190 h. It was observed that cell division was significantly retarded until the medium pH, reduced by the acid byproducts of fermentation, reached a critical value of 6.79 +/- 0.06. A mathematical model was developed to describe the relationship between specific growth rate, lag time, and medium pH.

Modeling of a microbial growth experiment with bioclogging in a two-dimensional saturated porous media flow field

A model was developed simulating reactive transport in groundwater including bioclogging. Results from a bioclogging experiment in a flow cell with a two-dimensional flow field were used as a data base to verify the simulation results of the model. Simulations were performed using three different hydraulic conductivity vs. porosity relations published in literature; two relations derived from pore network simulations assuming the biomass to grow in discrete colonies and as a biofilm, respectively, and a third relation, which did not include pore connectivity in more than one dimension. Best agreement with the experimental data was achieved using a hydraulic conductivity vs. porosity relation derived from pore network simulation assuming the biomass to grow in colonies. The relation derived from pore network simulations assuming biomass to grow as a biofilm was unable to reproduce the experimental data when realistic parameter values were employed. With the third relation the clogging ability of the biomass was strongly underestimated. These findings indicate that the porous medium needs to be treated as a multi-dimensional medium already on the pore scale, and that biomass growth different than in a biofilm must be considered to get an appropriate description of bioclogging.

Recent advances in petroleum microbiology

Recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. The physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. New molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystems. By establishing conditions which maximize rates and extents of microbial growth, hydrocarbon access, and transformation, highly accelerated and bioreactor-based petroleum waste degradation processes have been implemented. Biofilters capable of removing and biodegrading volatile petroleum contaminants in air streams with short substrate-microbe contact times (<60 s) are being used effectively. Microbes are being injected into partially spent petroleum reservoirs to enhance oil recovery. However, these microbial processes have not exhibited consistent and effective performance, primarily because of our inability to control conditions in the subsurface environment. Microbes may be exploited to break stable oilfield emulsions to produce pipeline quality oil. There is interest in replacing physical oil desulfurization processes with biodesulfurization methods through promotion of selective sulfur removal without degradation of associated carbon moieties. However, since microbes require an environment containing some water, a two-phase oil-water system must be established to optimize contact between the microbes and the hydrocarbon, and such an emulsion is not easily created with viscous crude oil. This challenge may be circumvented by application of the technology to more refined gasoline and diesel substrates, where aqueous-hydrocarbon emulsions are more easily generated. Molecular approaches are being used to broaden the substrate specificity and increase the rates and extents of desulfurization. Bacterial processes are being commercialized for removal of H(2)S and sulfoxides from petrochemical waste streams. Microbes also have potential for use in removal of nitrogen from crude oil leading to reduced nitric oxide emissions provided that technical problems similar to those experienced in biodesulfurization can be solved. Enzymes are being exploited to produce added-value products from petroleum substrates, and bacterial biosensors are being used to analyze petroleum-contaminated environments.

Effect of starvation on resuscitation and the surface characteristics of bacteria

Resuscitation behavior of bacteria after starvation for carbon and nitrogen was investigated. In addition effect of carbon and nitrogen starvation conditions on the surface characteristics and adhesive properties of bacteria were studied. Two pure culture herbicide degrading bacteria were used in the study: Pseudomonas sp. strain A, and Rhodococcus corallinus strain 11. These bacteria are known to degrade cyanuric acid which is a derivative of s-triazine, a common herbicide used widely. Selected bacteria were starved for carbon (glucose) and nitrogen (cyanuric acid) in different bioreactors and their physiological responses to starvation and resuscitation were measured. Different resuscitation responses were observed under different starvation conditions such that long lag phase was, observed for Rhodococcus corallinus strain 11 subjected to cyanuric acid starvation. Slow exponential growth rates were calculated for both microorganisms subjected to cyanuric acid starvation. The surface properties of both microorganisms were investigated using MATH test with two different hydrocarbons (hexadecane and octane). Hexadecane was observed to be the best organic attachment phase for these tests. Surface hydrophobiciy for all the microorganisms stayed unchanged during carbon starvation conditions. Significant decrease in hydrophobicity was observed for both cultures starved for nitrogen. When the hydrophobicity of the cultures decreased, the attachment capabilities of the microorganisms decreased. The decrease in attachment capabilities is a result of highly hydrated extracellular polysaccharides produced in the presence of carbon in the medium. Results of this study can be used as control tools in soil remediation applications.

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.

Production of insoluble dextran using cell-bound dextransucrase of Leuconostoc mesenteroides NRRL B-523

Water-insoluble, cell-free dextran biosynthesis from Leuconostoc mesenteroides NRRL B-523 has been examined. Cell-bound dextransucrase is used to produce cell-free dextran in a sucrose-rich acetate buffer medium. A comparison between the soluble and insoluble dextrans is made for various sucrose concentrations, and 15% sucrose gave the highest amount of cell-free dextran for a given time. L. mesenteroides B-523 produces more insoluble dextran than soluble dextran. The near cell-free synthesis was validated in a batch reactor, by monitoring the cell growth which is a small (10(6)-10(7) CFU/mL) and constant value throughout the synthesis.

Glass micromodel study of bacterial dispersion in spatially periodic porous networks

Successful implementation of bioremediation clean-up strategies depends on accurate predictions of the transport of bacteria within the subsurface. In this study, etched flat-plate glass micromodels were used to examine bacterial transport in a homogenous network. These networks were created by acid-etching interconnected channels into a glass plate and then fusing it to an unetched plate forming semi-cylindrical pores. The transparent nature of the micromodel allows for both qualitative observations of the bacteria within the pores and quantitative measurements of their concentration. The micromodels are designed to allow establishment of a well-characterized step change in bacterial concentration (Escherichia coli NR50) within the network. During the experiments, bacteria are dispersed through the network by flow. Light scattering is used to detect the change in turbidity within the pores as the bacteria travel through the network. The change in turbidity is used to construct breakthrough curves and spatial concentration profiles of bacteria within the network. The breakthrough curves are fit to the one-dimensional advection/dispersion equation to determine dispersion coefficients at different interstitial fluid velocities. From the breakthrough curves, dispersion coefficients were reproducible for replicate experiments over a range of velocities in the advection-dominated regime. The dispersivity values for two network designs resembling an interconnecting capillary network and a spatially periodic network of cylinders were 0.28 and 0.33 cm respectively, which are slightly greater than the literature values found for other pore networks. Experiments were also conducted within the diffusion-dominated regime to examine the effects of bacterial motility on dispersion. The accumulation of bacteria on the pore walls became significant at the low flow rates and extended experimental times thereby rendering the use of light scattering to determine concentrations ineffective. Bacterial chemotaxis, created by a self-imposed oxygen gradient, was also observed in the micromodel under stagnant fluid conditions.

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.