Ellyn M. Murphy

Processes in microbial transport in the natural subsurface

This is a review of physical, chemical, and biological processes governing microbial transport in the saturated subsurface. We begin with the conceptual models of the biophase that underlie mathematical descriptions of these processes and the physical processes that provide the framework for recent focus on less understood processes. Novel conceptual models of the interactions between cell surface structures and other surfaces are introduced, that are more realistic than the oft-relied upon DLVO theory of colloid stability. Biological processes reviewed include active adhesion/detachment (cell partitioning between aqueous and solid phase initiated by cell metabolism) and chemotaxis (motility in response to chemical gradients). We also discuss mathematical issues involved in upscaling results from the cell scale to the Darcy and field scales. Finally, recent studies at the Oyster, Virginia field site are discussed in terms of relating laboratory results to field scale problems of bioremediation and pathogen transport in the natural subsurface.

Interaction of Hydrophobic Organic Compounds with Mineral-Bound Humic Substances

The sorption of hydrophobic organic compounds (HOC) on mineral-associated peat humic acid (PHA) was evaluated under different pH and electrolyte regimes. Relative size distribution measurements indicated that PHA was [open quotes]coiled[close quotes] in solution at high ionic strength (I) and elongated at low I. The sorption of PHA to hematite and kaolinite varied with I and electrolyte cation, suggesting that the configuration of the humic acid in solution influenced its structure on the mineral surface. The sorption maxima for PHA on kaolinite indicated that PHA occupies twice the mineral surface area at low I (0.005) as that observed at high I (0.1). HOC sorption to mineral-bound PHA in Na[sup +] electrolyte was greater at lower I, indicating that humate structure was a plausible determinant of HOC sorption. Freundlich isotherms of dibenzothiophene on the PHA-coated kaolinite did not display unit slope, regardless of pH, I, or cation. Carbazole and anthracene displayed competitive behavior for sorption onto PHA-coated kaolinite. Collectively, the experimental observations indicate that hydrophobic adsorption rather than phase partitioning was the dominant mode of HOC binding. 70 refs., 8 figs., 1 tab.

The influence of physical heterogeneity on microbial degradation and distribution in porous media

Intermediate-scale experiments (meter-long, two-dimensional flow cell) were performed with aerobic biodegradation of benzoate substrate in physically heterogeneous (bimodal inclusive) media. Clastic heterogeneities were represented in a quasi-two-dimensional field, with low-conductivity inclusions embedded in a high-conductivity sandy matrix. The two media had similar pore-scale dispersivities but the conductivity ratio (∼1∶50) incurred macrodispersive spreading in the longitudinal direction. The high-conductivity sand was uniformly inoculated with Pseudomonas cepacia sp., and a pulse input of substrate and chloride ion tracer were evaluated. Degradation and growth were oxygen-limited under nonlinear dual-Monod kinetics and controlled by spatial and temporal variations in nutrient flux. The low-conductivity inclusions created regions of slow transport that prolonged the dual availability of both oxygen and substrate, which in turn enhanced microbial growth in these regions. Bacterial detachment was significant, and the fivefold increase in biomass due to growth was entirely accounted for in the aqueous effluent which displayed a complicated nonlinear breakthrough curve. High-resolution deterministic modeling was applied to simulate the intermediate-scale experiment, with parameters of the relevant constitutive relations calibrated independently through batch and small-scale column experiments. Parameter fitting to match flow cell data was avoided. This approach was taken in order both to test the predictive modeling capability as it would necessarily be used in a field application and to avoid the a priori assumption that all relevant processes were adequately represented in the respective constitutive theories. Analyses of the fit between the independently calibrated model and the flow cell data were then used to isolate processes for further experimental study. This iterative experimental/modeling approach identified processes that contributed (surprisingly) to biodegradation in heterogeneous media and yet are not currently incorporated in most mathematical models: (1) buoyancy effects associated with very small solution density variations, amplified in heterogeneous media, and (2) dynamic biological processes associated with growth, namely, endogenous respiration, cell division partitioning to the aqueous phase, and active adhesion/detachment that are strongly coupled to the transport of dissolved nutrients or microorganisms.

The sorption of humic acids to mineral surfaces and their role in contaminant binding

Abstract Humic substances dissolved in groundwater may adsorb to certain mineral surfaces, rendering hydrophilic surfaces hydrophobic and making them sorbents for hydrophobic organic compounds (HOC). The sorption of humic and fulvic acids (International Humic Substances Society, IHSS, reference samples) on hematite and kaolinite was investigated to determine how natural organic coatings influence HOC sorption. The sorption behavior of the humic substances was consistent with a ligand-exchange mechanism, and the amount of sorption depended on the concentration of hydroxylated surface sites on the mineral and the properties of the humic substance. The sorption of the humic substances to two solids was proportional to their aromatic carbon content and inversely proportional to the O/C ratio. Increasing quantities of sorbed humic substances ( f oc , 0.01–0.5%) increased the sorption of carbazole, dibenzothiophene and anthracene. Peat humic acid, the most aromatic coating, showed the greatest sorption enhancement of HOC when sorbed to hematite. In addition, HOC sorption was greater on organic coatings formed at low ionic strength ( I = 0.005) as compared to higher ionic strength ( I = 0.1). We suggest that both the mineral surface and the ionic strength of the electrolyte affect the interfacial configuration of the sorbed humic substance, altering the size or accessibility of hydrophobic domains on the humic molecule to HOC.

The influence of microbial activity and sedimentary organic carbon on the isotope geochemistry of the Middendorf Aquifer

Microorganisms present in deep Atlantic coastal plain sediments affect the geochemical evolution of groundwater and its chemical and isotopic composition, yet the factors controlling their origin, distribution, and diversity are poorly understood. The evolution of the groundwater chemistry, the fractionation of stable carbon isotopes, and the groundwater age are all indicators of the inorganic and microbial reactions occurring along a given flow path from groundwater recharge to groundwater discharge. In this study, tritium, 14C, and groundwater chemistry along three flow paths of the Middendorf aquifer in South Carolina were analyzed. The 14C ranged from 89 percent modern carbon (pmC) in the recharge zone to 9.9 pmC in the distal borehole; the δ13C remained relatively constant at ∼−22‰, suggesting microbial oxidation of organic carbon. Carbon isotope analyses of particulate organic carbon from core sediments and groundwater chemistry were used to model the carbon chemistry; the groundwater ages obtained from 14C ranged from modern to 11,500 years B.P. The highest frequencies of occurrence, numbers, and diversity of aerobic and anaerobic bacteria were found in boreholes near the recharge zone where the calculated ages were <1000 years B.P. The transport of microorganisms from the recharge zone may be responsible for this distribution as well as the electron acceptors necessary to support this diverse community of bacteria. The presence of both aerobic heterotrophs and anaerobic sulfate- and iron-reducing bacteria in the core sediments suggested the occurrence of anaerobic microsites throughout this otherwise aerobic aquifer. The highest in situ microbial respiration rate, as determined by modeling, was found along a flow path near the recharge area. It is likely that the electron acceptors necessary for supporting a diverse microbial community are depleted by the time the groundwater residence time in the Middendorf aquifer exceeds several hundred years.

Geochemical Estimates of Paleorecharge in the Pasco Basin: Evaluation of the Chloride Mass Balance Technique

The Pasco Basin in southeastern Washington State provides a unique hydrogeologic setting for evaluating the chloride mass balance technique for estimating recharge. This basin was affected by late Pleistocene catastrophic floods when glacial dams in western Montana and northern Idaho were breached. It is estimated that multiple Missoula floods occurred between ∼13,000 and 15,000 years B.P. and reached a high water elevation of ∼350 m. These floods removed accumulated chloride from the sediment profile, effectively resetting the chloride mass balance clock at the beginning of the Holocene. The rate of chloride accumulation qCl in the sediments was determined by two methods and compared. The first method measured qCl by dividing the calculated natural fallout of 36Cl by a measured ratio of 36Cl/Cl in the pore water, while the second method used the total mass of chloride in the profile divided by the length of time that atmospheric chloride had accumulated since the last flood. Although the two methods are based on different approaches, they showed close agreement. In laboratory studies the sediment to water ratio for chloride extraction was sensitive to the grain size of the sediments; low extraction ratios in silt loam sediments led to significant underestimation of pore water chloride concentration. Br/Cl ratios were useful for distinguishing nonatmospheric (e.g., rock) sources of chloride. Field studies showed little spatial variability in estimated recharge at a given site within the basin but showed significant topographic control on recharge rates in this semiarid environment. An extension of the conventional chloride mass balance model was used to evaluate chloride profiles under transient, time-varying annual precipitation conditions. This model was inverted to determine the paleorecharge history for a given soil chloride profile, and the parameters of the root extraction model required to estimate paleoprecipitation

Microbial Communities in High and Low Recharge Environments: Implications for Microbial Transport in the Vadose Zone

A bstractMicrobial communities along vertical transects in the unsaturated zone were evaluated at five sites in the Pasco Basin, in southeastern Washington State. Sites with contrasting recharge rates were chosen to maximize or minimize the potential for microbial transport. Pore water ages along the vertical transects were established using natural chloride tracers, and ranged from modern to either ∼15,000 yBP (years before present) or ∼30,000 yBP at the two low-recharge sites. Unsaturated flow processes were short-circuited by preferential flow at two of the three high-recharge sites, resulting in rapid movement of water through the vertical transects. Microbial numbers and biomass, based on plate counts, and phospholipid fatty acid (PLFA) concentrations decreased with depth at all sites. The majority (55–90%) of the culturable chemoheterotrophs recovered from most samples were streptomycete bacteria. 16S rRNA gene sequence and MIDI analyses indicated that 75% of the remaining isolates were Gram-positive bacteria (most likely species of Arthrobacter and Bacillus) 25% were Gram-negative bacteria (probably members of several genera in the alpha- and gamma-Proteobacteria). Comparison of microbial communities at low-recharge sites vs. high-recharge sites, where preferential flow occurs, revealed several differences that might be attributed to vertical transport of microbial cells at the high-recharge sites. Plate counts and PLFA analyses indicated that the proportion of streptomycetes, which were abundant at the surface but present in the subsurface as spores, decreased, or remained constant, with depth at the low-recharge sites, but increased with depth at the high-recharge sites. PLFA analyses also indicated that Gram-negative bacteria displayed increased nutrient stress with depth at the high-recharge sites characterized by preferential flow, but not at the low recharge site. This may be a result of advective transport of microbes to depths where it was difficult for them to compete effectively with the established community. Moreover, PLFA community structure profiles fluctuated considerably with depth at the low-recharge sites, but not at the high-recharge sites. This might be expected if transport were distributing the microbial community along the vertical profile at the high-recharge sites. In contrast to the high-recharge sites at which preferential flow occurs, filtration likely prevented vertical transport of microorganisms at the high-recharge site that was characterized by unsaturated flow.

A transient flux model for convective infiltration: Forward and inverse solutions for chloride mass balance studies

Forward and inverse solutions are provided for analysis of inert tracer profiles resulting from one-dimensional convective transport under fluxes which vary with time and space separately. The approach is developed as an extension of conventional chloride mass balance techniques used to analyze vertical unsaturated aqueous phase transport over large timescales in arid environments. This generalized chloride mass balance (GCMB) approach allows incorporation of transient fluxes and boundary values of precipitation and chloride mass deposition and allows analysis of a tracer profile which does not remain constant with depth below the extraction zone, in terms of a purely convective water transport model. The conventional quasi–steady state chloride mass balance (CMB) can be derived from the transient GCMB model developed here. By specifying a link between precipitation and recharge, closed-form forward and inverse solutions relating soil water chloride concentrations to transient boundary fluxes are obtained. This link is necessary for quantitative analysis of variable chloride profiles arising from climatic change. The GCMB can use transient chloride mass deposition rates, transient precipitation, and transient evapotranspiration rates. If two of these quantities are known or if the time frame is constrained such that a quantity can be treated as constant, then the inverse model can be used to determine the third. When mixing processes are limited, the GCMB can provide an alternative approach for estimating paleoprecipitation for performanceassessment modeling. The GCMB model is demonstrated with the following applications: (1) determination of time-varying precipitation from a field chloride profile and (2) evaluation of transient changes in water extraction by evapotranspiration and transient recharge associated with a change in land use.

Recharge Data Package for the Immobilized Low-Activity Waste 2001 Performance Assessment

Lockheed Martin Hanford Company (LMHC) is designing and assessing the performance of disposal facilities to receive radioactive wastes that are currently stored in single- and double-shell tanks at the Hanford Site. The preferred method of disposing of the portion that is classified as immobilized low-activity waste (ILAW) is to vitrify the waste and place the product in near-surface, shallow-land burial facilities. The LMHC project to assess the performance of these disposal facilities is known as the Hanford ILAW Performance Assessment (PA) Activity, hereafter called the ILAW PA project. The goal of this project is to provide a reasonable expectation that the disposal of the waste is protective of the general public, groundwater resources, air resources, surface-water resources, and inadvertent intruders. Achieving this goal will require predictions of contaminant migration from the facility. To make such predictions will require estimates of the fluxes of water moving through the sediments within the vadose zone around and beneath the disposal facility. These fluxes, loosely called recharge rates, are the primary mechanism for transporting contaminants to the groundwater. Pacific Northwest National Laboratory (PNNL) assists LMHC in their performance assessment activities. One of the PNNL tasks is to provide estimates of recharge rates for current conditions and long-term scenarios involving the shallow-land disposal of ILAW. Specifically, recharge estimates are needed for a fully functional surface cover, the cover sideslope, and the immediately surrounding terrain. In addition, recharge estimates are needed for degraded cover conditions. The temporal scope of the analysis is 10,000 years, but could be longer if some contaminant peaks occur after 10,000 years. The elements of this report compose the Recharge Data Package, which provides estimates of recharge rates for the scenarios being considered in the 2001 PA. Table S.1 identifies the surface features and time periods evaluated. The most important feature, the surface cover, is expected to be the modified RCRA Subtitle C design. This design uses a 1-m-thick silt loam layer above sand and gravel filter layers to create a capillary break. A 0.15-m-thick asphalt layer underlies the filter layers to function as a backup barrier and to promote lateral drainage. Cover sideslopes are expected to be constructed with 1V:10H slopes using sandy gravel. The recharge estimates for each scenario were derived from lysimeter and tracer data collected by the ILAW PA and other projects and from modeling analyses.

An Analysis Platform for Multiscale Hydrogeologic Modeling with Emphasis on Hybrid Multiscale Methods

One of the most significant challenges faced by hydrogeologic modelers is the disparity between the spatial and temporal scales at which fundamental flow, transport, and reaction processes can best be understood and quantified (e.g., microscopic to pore scales and seconds to days) and at which practical model predictions are needed (e.g., plume to aquifer scales and years to centuries). While the multiscale nature of hydrogeologic problems is widely recognized, technological limitations in computation and characterization restrict most practical modeling efforts to fairly coarse representations of heterogeneous properties and processes. For some modern problems, the necessary level of simplification is such that model parameters may lose physical meaning and model predictive ability is questionable for any conditions other than those to which the model was calibrated. Recently, there has been broad interest across a wide range of scientific and engineering disciplines in simulation approaches that more rigorously account for the multiscale nature of systems of interest. In this article, we review a number of such approaches and propose a classification scheme for defining different types of multiscale simulation methods and those classes of problems to which they are most applicable. Our classification scheme is presented in terms of a flowchart (Multiscale Analysis Platform), and defines several different motifs of multiscale simulation. Within each motif, the member methods are reviewed and example applications are discussed. We focus attention on hybrid multiscale methods, in which two or more models with different physics described at fundamentally different scales are directly coupled within a single simulation. Very recently these methods have begun to be applied to groundwater flow and transport simulations, and we discuss these applications in the context of our classification scheme. As computational and characterization capabilities continue to improve, we envision that hybrid multiscale modeling will become more common and also a viable alternative to conventional single-scale models in the near future.