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.     

Development of a screening relationship to describe migration of contaminant vapors into buildings

The relationship between subsurface contaminant concentrations and indoor air concentrations, arising from the migration of contaminant vapors into buildings, is affected by a number of complex processes and parameters, many of which are subject to uncertainty. A study was undertaken to develop a simplified relationship between subsurface contaminant concentrations and indoor air concentrations. This relationship is intended for use as a screening tool to determine the relative significance of vapor transport and inhalation as an exposure scenario in the establishment of soil quality guidelines. The relationship was developed using a proprietary model to analyze the infiltration of subsurface vapors into buildings. A probabilistic analysis of the relationship, using a form of Monte Carlo simulation, was undertaken to estimate the dilution of contaminant concentrations between the source (soil gas) and point of exposure (indoor air). Using standardized values for certain parameters and generic distributions for key variables, probability distributions were generated for the dilution factor as a function of contaminant depth and soil type.     

Health Risk Assessment and Vapor Intrusion: A Review and Australian Perspective

Soil contamination by volatile hydrocarbons is of public health importance due to vapor intrusion and indoor inhalation exposures. These are assessed using measurement or predictive modeling and need to consider the key areas of subsurface partitioning and transport, dwelling ventilation, and receptor inhalation dosimetry. While subsurface partitioning and transport have been subject to intensive international investigation, limited consideration has been given to the latter. Building ventilation research has developed multi-zone airflow and contaminant dispersal models including AccuRate, an Australian model that examines natural ventilation modeling, roof and sub-floor ventilation, and identifies the importance of geometry and thermal factors on ventilation (the most sensitive variable) and indoor pollutant concentrations. Inhalation dosimetry has received recent attention due to concerns over child inhalation susceptibility and dose metrics. Research using coupled computational fluid dynamics (CFD) and physiologically based pharmaco-kinetic (PBPK) models has reported variance from previous animal models’ extrapolation while CFD modeling of transient lung vapor absorption suggests the significance of transient versus steady-state evaluation of volatiles absorption into tissue and blood. The transient nature of sub-surface fate and transport, ventilation, and inhalation uptake thus warrants integrated exploration and application in order to realize improvements in vapor intrusion assessments. These perspectives and Australian modeling initiatives are presented in this article.     

A Simulation-Assessment Modeling Approach for Analyzing Environmental Risks of Groundwater Contamination at Waste Landfill Sites

An integrated simulation-assessment modeling approach for analyzing environmental risks of groundwater contamination is proposed in this paper. It incorporates an analytical groundwater solute transport model, an exposure dose model, and a fuzzy risk assessment model within a general framework. The transport model is used for predicting contaminant concentrations in subsurface, and the exposure dose model is used for calculating contaminant ingestion during the exposure period under given exposure pathways. Both models are solved through the Monte Carlo simulation technique to reflect the associated uncertainties. Based on consideration of fuzzy relationships between exposure doses and cancer risks, risk levels of different exposure doses for each contaminant can be calculated to form a fuzzy relation matrix. The overall risks can then be quantified through further fuzzy synthesizing operations. Thus, probabilistic quantification of different risk levels (possibilities) can be realized. Results of the case study indicate that environmental risks at the waste landfill site can be effectively analyzed through the developed methodology. They are useful for supporting the related risk-management and remediation decisions.     

Analytical Integration Procedures for the Derivation of Risk-Based Generic Assessment Criteria for Soil

Risk assessment models commonly used in contaminated sites employ a simple integration procedure by only partially combining exposure pathways from surface soil with vapor pathways from subsurface soil being excluded in the combination. The simplified approach can approximate the integrated generic assessment criteria only when there is a dominant exposure pathway. But these models are often based on a simple partitioning of a chemical in soil between the sorbed, dissolved, and vapor phases without consideration of the presence of non-aqueous phase liquid, and critically fail to consider non-soil background exposure for non-carcinogenic compounds. As a result, the generic assessment criteria derived may not be considered protective of human health. This article describes analytical integration procedures for the derivation of the generic assessment criteria that consider non-soil background exposure while limiting the average daily exposure for vapor pathways calculated from soil saturation limits. Significance of consideration of soil saturation limits for the derivation of the generic assessment criteria using an integrated approach is illustrated for organic compounds having varied levels of background exposure and soil saturations. The analytical integration procedures for the derivation of the soil generic assessment criteria under the linear chemical partition approach are also reviewed aiming to provide a single source of complete integration procedures for the derivation of the integrated generic assessment criteria.     

A Whole Cell Bioreporter Approach to Assess Transport and Bioavailability of Organic Contaminants in Water Unsaturated Systems

Bioavailability of contaminants is a prerequisite for their effective biodegradation in soil. The average bulk concentration of a contaminant, however, is not an appropriate measure for its availability; bioavailability rather depends on the dynamic interplay of potential mass transfer (flux) of a compound to a microbial cell and the capacity of the latter to degrade the compound. In water-unsaturated parts of the soil, mycelia have been shown to overcome bioavailability limitations by actively transporting and mobilizing organic compounds over the range of centimeters. Whereas the extent of mycelia-based transport can be quantified easily by chemical means, verification of the contaminant-bioavailability to bacterial cells requires a biological method. Addressing this constraint, we chose the PAH fluorene (FLU) as a model compound and developed a water unsaturated model microcosm linking a spatially separated FLU point source and the FLU degrading bioreporter bacterium Burkholderia sartisoli RP037-mChe by a mycelial network of Pythium ultimum. Since the bioreporter expresses eGFP in response of the PAH flux to the cell, bacterial FLU exposure and degradation could be monitored directly in the microcosms via confocal laser scanning microscopy (CLSM). CLSM and image analyses revealed a significant increase of the eGFP expression in the presence of P. ultimum compared to controls without mycelia or FLU thus indicating FLU bioavailability to bacteria after mycelia-mediated transport. CLSM results were supported by chemical analyses in identical microcosms. The developed microcosm proved suitable to investigate contaminant bioavailability and to concomitantly visualize the involved bacteria-mycelial interactions.     

History and perspectives of bioanalytical methods for chemical warfare agent detection

This paper provides a short historical overview of the development of bioanalytical methods for chemical warfare (CW) agents and their biological markers of exposure, with a more detailed overview of methods for organophosphorus nerve agents. Bioanalytical methods for unchanged CW agents are used primarily for toxicokinetic/toxicodynamic studies. An important aspect of nerve agent toxicokinetics is the different biological activity and detoxification pathways for enantiomers. CW agents have a relatively short lifetime in the human body, and are hydrolysed, metabolised, or adducted to nucleophilic sites on macromolecules such as proteins and DNA. These provide biological markers of exposure. In the past two decades, metabolites, protein adducts of nerve agents, vesicants and phosgene, and DNA adducts of sulfur and nitrogen mustards, have been identified and characterized. Sensitive analytical methods have been developed for their detection, based mainly on mass spectrometry combined with gas or liquid chromatography. Biological markers for sarin, VX and sulfur mustard have been validated in cases of accidental and deliberate human exposures. The concern for terrorist use of CW agents has stimulated the development of higher throughput analytical methods in support of homeland security.     

Effect of Starvation on Induction of Quinoline Degradation for a Subsurface Bacterium in a Continuous-Flow Column

Differences in the induction response and the initial two reactions of quinoline degradation between short-term (2 days)- and long-term (60 to 80 days)-starved cells of a subsurface Pseudomonas cepacia strain were examined by using continuous-flow columns. The ability of bacteria that are indigenous to oligotrophic environments to respond to a contaminant was assessed by using long-term starvation to induce a cell physiology that simulates the in situ physiology of the bacteria. With quinoline concentrations of 39 and 155 μM, long-term-starved cells converted quinoline to degradation products more efficiently than did short-term-starved cells. Quinoline concentrations of 155 μM and, to a greater extent, 775 μM had an inhibitory effect on induction in long-term-starved cells. However, only the length of the induction process was affected with these quinoline concentrations; degradation of quinoline at the steady state for long-term-starved cells was equal to or better than that for short-term-starved cells. The induction time for short-term-starved cells did not increase progressively with increasing quinoline concentration. Experiments with starved cells are important for the development of accurate predictive models of contaminant transport in the subsurface because starvation, which induces a cell physiology that simulates the in situ physiology of many bacteria, may affect the induction process.     

Urine analysis of patients exposed to phenylarsenic compounds via accidental pollution

New methods involving high-performance liquid chromatography/inductively coupled plasma mass spectrometry were examined for the determination of phenylarsenic compounds derived from chemical warfare agents. Several methods were examined for the separation of diphenylarsinic acid (DPAA), phenylarsonic acid, phenylmethylarsinic acid (PMAA), phenyldimethylarsine oxide, and diphenylmethylarsine oxide. Analysis of the urine samples of the patients exposed to phenylarsenic compounds indicated that the main phenylarsenic components were DPAA and PMAA; moreover, some unknown arsenicals, which were also found in contaminated groundwater and rice samples, were also detected.     

A strategy for the production of soluble human senescence marker protein-30 in Escherichia coli

Senescence marker protein-30 (SMP30) has been reported to hydrolyze diisopropyl fluorophosphate (DFP), a surrogate compound of chemical warfare nerve agents. Thus, SMP30 has the potential to be useful as a prophylactic against chemical warfare nerve agent toxicity. Our efforts to generate human SMP30 in bacteria using a variety of expression vectors invariably resulted in insoluble and inactive preparations. In this study, properly folded and active recombinant human SMP30 (rHuSMP30) was produced in Escherichia coli by coexpressing it with molecular chaperones in a combined strategy. The coexpression of rHuSMP30 with GroES/GroEL/Tf at 15 °C, combined with the addition of a membrane fluidizer, increased osmolytes, and a two-step expression resulted in the highest enhancement of solubility and DFPase activity. Our results pave the way for exploring the use of rHuSMP30 against organophosphate and nerve agent toxicity.     

Biodegradation of neutralized sarin.

This research investigated the biotransformation of IMPA, the neutralization product of the nerve agent Sarin, by a microbial consortia. As mandated by the Chemical Weapons Convention signed by 132 countries in 1993, all chemical warfare agents are to be destroyed within ten years of ratification. Technologies must be developed to satisfy this commitment. This paper presents data from a biodegradation kinetics study and background information on the biological transformation of IMPA. Microbial transformation of organophosphate nerve agents and organophosphate pesticide intermediates can be incorporated into a treatment process for the fast and efficient destruction of these similar compounds. Sarin (isopropyl methylphosphonofluoridate), also known as GB, is one of several highly neurotoxic chemical warfare agents that have been developed over the past 50 to 60 years. Four mixed cultures were acclimated to the Sarin hydrolysis product, isopropyl methylphosphonic acid (IMPA). Two of these cultures, APG microorganisms and SX microorganisms, used IMPA as the sole phosphorus source. Extended exposure to IMPA improved the cultures' abilities to degrade IMPA to form methylphosphonic acid (MPA) and inorganic phosphate. The presence of free phosphate in the reactor suppressed the degradation of IMPA. IMPA did not inhibit either cultural consortia within the tested concentration range (0 to 1250 mg/L). The numax was 120.9 mg/L/day for the SX microorganisms and 118.3 mg/L/day for the APG microorganisms. Initial IMPA concentrations of 85 to 90 mg/L were degraded to nondetectable levels within 75 h. These results demonstrate the potential for biodegradation to serve as a complementary treatment process for the destruction of stockpiled Sarin.     

Parameterizing Potential Exposure to Sulfur Mustard (HD) Using Mixed Model Regression

The possible threat posed by terrorists using chemical warfare agents (CWAs) against civilian targets is a major concern, reflecting the fact that CWAs are highly toxic to unprotected populations, with releases as vapors or aerosols likely to produce mass casualties on a highly localized basis within minutes or hours after an incident. A conceptual site model is developed and mixed model regression is used to estimate concentration values for the vesicant sulfur mustard (HD) based on the output from computational fluid dynamics (CFD) simulation following wind tunnel experimentation. The analysis provides a first-approximation of the spatial and temporal distribution of potential exposures within a set of 50 m × 50 m × 2 m grids across a 1000 m width by 300 m height by 2250 m length domain in a geographic information system (GIS) environment. The HD concentration values are calculated as log-averaged mean and the 95% confidence intervals for each grid at 1.9 d and 6.0 d after initial release. The technique offers a statistically valid means for rapidly generating unbiased first-approximations of concentration values subsequent to an initial release as an alternative to extensive monitoring or multiple runs of CFD models to parameterize potential exposure to HD spatially and temporally.     

Limitations and challenges in treatment of acute chemical warfare agent poisoning

Recent news from Syria on a possible use of chemical warfare agents made the headlines. Furthermore, the motivation of terrorists to cause maximal harm shifts these agents into the public focus. For incidents with mass casualties appropriate medical countermeasures must be available. At present, the most important threats arise from nerve agents and sulfur mustard. At first, self-protection and protection of medical units from contamination is of utmost importance. Volatile nerve agent exposure, e.g. sarin, results in fast development of cholinergic crisis. Immediate clinical diagnosis can be confirmed on-site by assessment of acetylcholinesterase activity. Treatment with autoinjectors that are filled with 2 mg atropine and an oxime (at present obidoxime, pralidoxime, TMB-4 or HI-6) are not effective against all nerve agents. A more aggressive atropinisation has to be considered and more effective oximes (if possible with a broad spectrum or a combination of different oximes) as well as alternative strategies to cope with high acetylcholine levels at synaptic sites should be developed. A further gap exists for the treatment of patients with sustained cholinergic crisis that has to be expected after exposure to persistent nerve agents, e.g. VX. The requirement for long-lasting artificial ventilation can be reduced with an oxime therapy that is optimized by using the cholinesterase status for guidance or by measures (e.g. scavengers) that are able to reduce the poison load substantially in the patients.     

The Bioutilization of Thiodiglycol (a Detoxication Product of Mustard Gas): Isolation of Degrading Strains and Investigation of Degradation Conditions

The Alcaligenes xylosoxydans subsp.denitrificans strain TD1 capable of degrading thiodiglycol (TDG), a product of mustard gas hydrolysis, was isolated from soil contaminated with breakdown products of this chemical warfare agent. The selected stable variant of TD1 (strain TD2) can grow on TDG with a lag phase of 4–8 h and a specific growth rate of 0.04–0.045 h^–1. Optimal conditions for the biodegradation of TDG (pH, the concentration of TDG in the medium, and specific substrate loading) were determined. TDG was found to be degraded with the formation of diglycolsulfoxide and thiodiglycolic acid as intermediate products. The data obtained can be used to develop approaches to the bioremediation of mustard gas–contaminated soils.     

Selection of Specific Endophytic Bacterial Genotypes by Plants in Response to Soil Contamination

Plant-bacterial combinations can increase contaminant degradation in the rhizosphere, but the role played by indigenous root-associated bacteria during plant growth in contaminated soils is unclear. The purpose of this study was to determine if plants had the ability to selectively enhance the prevalence of endophytes containing pollutant catabolic genes in unrelated environments contaminated with different pollutants. At petroleum hydrocarbon contaminated sites, two genes encoding hydrocarbon degradation, alkane monooxygenase (alkB) and naphthalene dioxygenase (ndoB), were two and four times more prevalent in bacteria extracted from the root interior (endophytic) than from the bulk soil and sediment, respectively. In field sites contaminated with nitroaromatics, two genes encoding nitrotoluene degradation, 2-nitrotoluene reductase (ntdAa) and nitrotoluene monooxygenase (ntnM), were 7 to 14 times more prevalent in endophytic bacteria. The addition of petroleum to sediment doubled the prevalence of ndoB-positive endophytes in Scirpus pungens, indicating that the numbers of endophytes containing catabolic genotypes were dependent on the presence and concentration of contaminants. Similarly, the numbers of alkB- or ndoB-positive endophytes in Festuca arundinacea were correlated with the concentration of creosote in the soil but not with the numbers of alkB- or ndoB-positive bacteria in the bulk soil. Our results indicate that the enrichment of catabolic genotypes in the root interior is both plant and contaminant dependent.     

The bioutilization of thiodiglycol (a breakdown product of mustard gas): isolation of degraders and investigation of degradation conditions

The Alcaligenes xylosoxydans subsp. denitrificans strain TD1 capable of degrading thiodiglycol (TDG), a breakdown product of mustard gas, was isolated from soil contaminated with breakdown products of this chemical warfare agent. The selected stable variant of TD1 (strain TD2) can grow on TDG with a lag phase of 4-8 h and a specific growth rate of 0.04-0.045 h-1. Optimal conditions for the biodegradation of TDG (pH, the concentration of TDG in the medium, and its relative content with respect to the bacterial biomass) were determined. TDG was found to be degraded with the formation of diglycolsulfoxide and thiodiglycolic acid. The data obtained can be used to develop approaches to the bioremediation of mustard gas-contaminated soils.     

Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers

Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, “omics” approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.     

Modeling physiological resistance in bacterial biofilms

A mathematical model of the action of antimicrobial agents on bacterial biofilms is presented. The model includes the fluid dynamics in and around the biofilm, advective and diffusive transport of two chemical constituents and the mechanism of physiological resistance. Although the mathematical model applies in three dimensions, we present two-dimensional simulations for arbitrary biofilm domains and various dosing strategies. The model allows the prediction of the spatial evolution of bacterial population and chemical constituents as well as different dosing strategies based on the fluid motion. We find that the interaction between the nutrient and the antimicrobial agent can reproduce survival curves which are comparable to other model predictions as well as experimental results. The model predicts that exposing the biofilm to low concentration doses of antimicrobial agent for longer time is more effective than short time dosing with high antimicrobial agent concentration. The effects of flow reversal and the roughness of the fluid/biofilm are also investigated. We find that reversing the flow increases the effectiveness of dosing. In addition, we show that overall survival decreases with increasing surface roughness.     

Vanadium Respiration by Geobacter metallireducens: Novel Strategy for In Situ Removal of Vanadium from Groundwater

Vanadium can be an important contaminant in groundwaters impacted by mining activities. In order to determine if microorganisms of the Geobacteraceae, the predominant dissimilatory metal reducers in many subsurface environments, were capable of reducing vanadium(V), Geobacter metallireducens was inoculated into a medium in which acetate was the electron donor and vanadium(V) was the sole electron acceptor. Reduction of vanadium(V) resulted in the production of vanadium(IV), which subsequently precipitated. Reduction of vanadium(V) was associated with cell growth with a generation time of 15 h. No vanadium(V) was reduced and no precipitate was formed in heat-killed or abiotic controls. Acetate was the most effective of all the electron donors evaluated. When acetate was injected into the subsurface to enhance the growth and activity of Geobacteraceae in an aquifer contaminated with uranium and vanadium, vanadium was removed from the groundwater even more effectively than uranium. These studies demonstrate that G. metallireducens can grow via vanadium(V) respiration and that stimulating the activity of Geobacteraceae, and hence vanadium(V) reduction, can be an effective strategy for in situ immobilization of vanadium in contaminated subsurface environments.