The focus of my research program is the analysis and modeling of environmental transport processes. This work integrates fluid mechanics, aquatic chemistry, and environmental microbiology to predict the transport of reactive substances under complex hydrodynamic conditions. My approach to this problem is to initially conduct a fundamental analysis of solute or particle motion. Nonconservative processes that influence mobility must then be integrated into a transport model for each substance of interest. We are utilizing complementary laboratory and field experiments to study these interdisciplinary problems. This approach is useful for investigating the transport of an extraordinarily diverse range of substances-conservative tracers, dissolved contaminants (e.g., metals), natural suspended sediments, particulate contaminants (e.g., mine tailings), dissolved nutrients, particulate organic carbon, and pathogenic microorganisms. Information on each of these areas can be found by following the links below.

Environmental Fluid Dynamics and Solute Transport

Exchange between streams and the surrounding subsurface plays a major role in the transport and fate of contaminants in watersheds. This process is generally referred to as hyporheic exchange, and is now known to play a very important role in the migration of contaminants, nutrients, and pathogens in streams. We are developing fundamental understanding of the basic hydrodynamic processes that control fluxes between free-surface flows and pore water flows, and then using this information to interpret the transport of various reactive solutes and particles in streams.

Flow over a loose sediment bed produces a range of characteristic morphological features, such as dunes, bars, and meanders. The interaction of the stream flow with these features produces hyporheic exchange. In order to study hyporheic exchange processes under controlled conditions, we conduct experiments in laboratory flumes to directly observe the exchange of solutes and particles between the water column and the underlying sediment bed. We are also developing theory to explain these observations and predict exchange under the wide variety of conditions that are found in river systems, and then testing this theory by conducting field experiments in small natural streams. Recently, we and others have determined that the exchange processes interact over the entire spectrum of river topography, producing fractal scaling in the surface-groundwater exchange process. This places considerable emphasis on understanding not only how exchange is induced by a very wide range of morphological features, but also how the flows induced at various scales interact to control the behavior at any location of interest.

  • Hyporheic exchange flowpaths in a heterogeneous streambed constructed in one of our laboratory flumes.

  • Fluorescent dye is used in a classroom demonstration to visualize complex surface-subsurface mixing patterns.

  • Flow-boundary interactions in a meandering stream studied at the Saint Anthony Falls Hydraulics Lab.

  • Dye mixing in a dead zone observed in the Morsa Catchment, Norway.

  • Simulated interfacial flux on a simple meandering stream with and without bedforms.

  • Bedforms at Clear Run (Wilmington, North Carolina).

  • Colloid deposits within a bed of glass beads imaged by synchrotron X-ray difference microtomography.

  • Clay clogging the surface of a sand bed.

  • Time-lapse photography captures sediment transport behavior of burrowing organisms.

  • Confocal micrograph of the accumulation of micron-size fluorescent microspheres (green) in a benthic biofilm.

  • Flow Cytometer Plot using FlowJo to demonstrate separation of 5μm diameter Day Glo Paint Particles from background noise in a flume study at Stroud Water Research Center.

  • Simulated distribution of heterogeneous fine particle accumulation under a dune based on information obtained from X-ray difference microtomography measurements of sediment cores.

Fine Sediment and Colloid Transport in Rivers and Porous Media

Much of the research in my group involves interactions with sediments. One focus has been to understand the processes that control the migration of very small particles, and how these particles influence the behavior of other substances of interest, such as nutrients and contaminants. Particles smaller than 50 microns are ubiquitous in surface water environments, and often carry a disproportionate fraction of the contaminant load due to their high surface area and reactivity. Fine sediments can sometimes represent an ecological hazard in their own right because they reduce light levels and degrade habitat. In fact, sediment contamination is one of the most frequent causes of functional impairment of streams and rivers in the U.S.

The transport of very fine particles tends to be difficult to analyze because they are influenced by both physical and chemical processes, and sometimes by microbiological processes as well. We are studying a wide range of fine sediment transport processes both in order to examine the evolution of sedimentary environments and to understand the effects of fine sediments on contaminant transport and stream ecology. We are investigating mechanisms of fine sediment deposition in streambeds, interaction with biofilms, and the evolution of depositional structures at both micro- and macro-scales. In collaboration with Jean-François Gaillard, we are now applying advanced x-ray based methods for analysis of the evolution of sediment structure (3D x-ray microtomographic analyses performed at the Advanced Photon Source, Argonne National Lab). Examples of projects that examine the influence of fine sediment transport on other important environmental processes include studies of fine particle deposition to and resuspension from biofilms, colloidal-phase contaminant transport in streams, and the reduction in hyporheic exchange fluxes due to siltation (clogging) of streambeds.

Contaminant Transport

Stream-subsurface exchange has significant implications for contaminant transport in streams because many substances are transformed or immobilized by subsurface (bio)chemical processes. Hydrodynamic transport processes carry stream-borne contaminants across the stream-subsurface interface and enhance reactions within the streambed sediments (in the subsurface hyporheic mixing zone). These processes can be substantially mediated by colloidal particles. In addition, hydrodynamic flow coupling and particle transport also control fluxes out of contaminated sediments.

We are investigating these contaminant transport processes using both theoretical and experimental approaches. We have carefully conducted controlled experiments in laboratory flumes to investigate the exchange of reactive substances with the subsurface and contaminant interactions with both suspended sediments and bed sediments. We have also developed physical/chemical models for contaminant and colloid transport, particularly for multi-phase (colloid-mediated) contaminant exchange with streambeds. Our models reliably simulated the transport of metals and phosphorous in the presence of colloidal silica, kaolinite clay, and iron oxides. The combination of experimentation and modeling also indicated the importance of feedback processes that are not normally considered in studies of colloid and contaminant transport. For example, we found that contaminant sorption could substantially alter colloid transport behavior by modifying the particle surface charge. Recently, we have utilized this information to help develop regulatory standards for metals contamination of sediments in Europe. We are also beginning a new project for the U.S. Department of Defense on improved assessment of ecological risk associated with contaminated sediments at military installations. This work will feature an integrated physical/chemical/biological approach to assess feedbacks between pore fluid flow, redox conditions, and contaminant behavior (speciation, efflux, and bioavailability).

This work has been supported by a CAREER award from the NSF.

We currently have funding for two Ph.D. students (or one student and one post-doc) on a related project at Northwestern.

For more information click Here.

  • Multi-phase transport of metals and phosphate in the presence of iron oxide colloids studied in a laboratory flume.

  • Stream-subsurface exchange of zinc in the presence of silica colloids. The pH substantially alters the extent of contaminant-particle interactions and thus the contaminant mobility.

  • Alteration of iron oxide particle deposition patterns by contaminant-colloid interactions. Solute sorption alters the particle surface charge, which influences the mobility of the particles and the extent to which they penetrate into the streambed.

  • Direct observations of oxygen microprofiles in the benthic biofilm and underlying hyporheic sediments show that high oxygen concentrations from either photosynthesis or hydrodynamic delivery of oxygen from the water column can both strongly suppress denitrification (Arnon et al., L&O, 2007).

  • Biofilm growth and fine sediment deposition affects the streambed ecosystem.

  • Confocal Laser-Scanning Microscope image of periphyton structure.
    Green: Bacterial cells (SYTO 9)
    Red, blue, purple: Algae (auto-fluorescence)
    White: Mixed bacteria and algae

  • Stream-side flumes at the Stroud Water Research Center.

Stream Ecology and Biogeochemistry

It is well known that physical and chemical conditions define the environment within which organisms grow. Recent research has emphasized that local environmental conditions are critical in establishing microhabitats, or ecological niches. We are exploring in several ways the role of environmental transport processes in controlling the development of diverse microhabitats and the resulting effects on overall ecosystem processes.

Hyporheic exchange processes are particularly important for carbon and nutrient cycling in streams. In collaboration with Denis Newbold of the Stroud Water Research Center and Tom Battin of the University of Vienna, we are studying relationships between hydrodynamic transport, sedimentary conditions, and microbial processing of organic matter. We are particularly examining two phenomena: the effects of sediment structure and flow-induced heterogeneity on the activity of hyporheic biofilms, and the role of fine particle deposition in reducing hyporheic exchange and organic matter processing. This work has been conducted both in our laboratory and in stream-side flumes at the Stroud Center, and has been supported by my NSF CAREER award and a grant from the U.S. Geological Survey's Water Resources Research Institutes program. This work has been conducted both in our laboratory and in stream-side flumes located at the Stroud Center and at the Lunz Biological Station (Austria).

We have also investigated coupling between fluid flow and oxygen and nutrient dynamics in streams and wetlands. Nutrient dynamics are a pressing issue in the Midwest because high nitrogen loads in the Mississippi River system are causing chronic seasonal hypoxia in the Gulf of Mexico. We seek to understand the fundamental processes that control denitrification in Midwestern streams and wetlands in order to develop strategies to reduce nitrate export. Hydrodynamic processes play a critical role in establishing denitrifying microenvironments in the benthic microbial community (periphyton). We have integrated understanding of surface-subsurface exchange processes and biogeochemistry to show that optimal conditions for denitrification occur when there is maximal nitrate delivery to the sediments but yet still not sufficiently high transport to convert facultative organisms to primarily aerobic metabolism. Further, both overlying flow conditions and the morphology of the stream or wetland bottom can be manipulated to increase overall nitrate removal. This type of coupling generally occurs in all shallow surface water bodies. We are now exploring the general implications of these processes for evaluating nutrient dynamics at very large scales, such as throughout the entire Mississippi River basin.

Waterborne Disease Transmission

Understanding the transport of infectious microorganisms from sources to water supply systems is critical to protecting human health. The transport of microorganisms depends strongly on flow conditions, and is also mediated by background water chemistry, attachment to natural sediments, and interactions with microbial biofilms. We are evaluating the interaction of the cyst-forming protozoan pathogen Cryptosporidium parvum with suspended sediments, natural organic matter, and coarser streambed sediments. While C. parvum has no active life cycle outside of a host, the fate of bacterial pathogens is further complicated by ecological interactions with natural microbial communities. Bacteria of high current concern, such as E. coli O157:H7, Salmonella enterica, and Campylobacter jejuni are expected to have markedly different propensities for survival and growth in aquatic environments because of differences in their metabolic capabilities and interactions with natural microbial communities in soils, groundwater aquifers, and streambed sediments.

We have shown that C. parvum oocysts and other pathogens readily become incorporated into streambed sediments and biofilms. Subsequently, accumulated pathogens can be remobilization rapidly under high-flow conditions, such as floods. Further, association with other suspended particulate matter greatly influences pathogen transport. Suspended matter, including pathogens, is also incorporated into biofilms and subsequently released with sloughed biofilm material as conglomerates of cells, detritus, and organic polymers. We have recently shown that the C. parvum remains infectious after incorporation into and resuspension from biofilms. This work is being conducted in collaboration with Thomas Harter and Rob Atwill of the University of California.

  • C. parvum association with natural sediments.Left: kaolinite clay grain. Right: natural organic/inorganic aggregate

  • Retention of C. parvum oocysts (red) in a P. aeruginosa biofilm (green) resolved by confocal microscopy. This interaction strongly influences the environmental transmission of pathogens (AEM cover image, Searcy et al., 2006a).

  • Pathways for waterborne migration of zoonotic pathogens in agricultural watersheds (farms and rangeland): 1) overland runoff from fields or pastures, 2) subsurface transport to river channels via shallow groundwater, 3) larger-scale transport in groundwater, e.g., to groundwater supply wells, 4) resuspension from stream channel sediments. Image courtesy of Thomas Harter.

  • The two dimensional flow cell. A) Procedure for fabrication of the planar flow cell. (B) Side-view photograph of the assembled flow cell. (C, D, E) Typical two-dimensional flow patterns: (C) a right-angle (90 degree turn) flow, (D) a 360 degree turn flow, and (E) a symmetric diffusing flow.

  • Penetration of SYTO 62 (red) into a GFP-labeled P. aeruginosa biofilm observed by time-resolved confocal microscopy. Dye penetration occurs more rapidly in porous cell towers than in the underlying dense biofilm. Radial (diffusive) penetration is visible, along with advective transport to the interior of the large cell clusters.

  • Distribution of Flavobacterium sp. (red) and P. aeruginosa (green) in biofilms.

  • Spatial killing patterns in heterogeneous biofilms after 24 hours tobramycin treatment. A) Cross-section of killing patterns in biofilms after tobramycin treatment. Live cells appear green/yellow, and dead cells appear red. B) Killing profiles along the distance from the biofilm surface for several typical clusters.

  • Global wavelet analysis of height and killing efficiency. The average spectra presented here are based on wavelet analysis along 60 streamlines in three image stacks. The thick black contours indicate the 95% confident level. The thin black lines separate zones of effective analysis from the COI shown in lighter shades, where edge effects are significant. The relative phase relationship is shown by the arrows in bottom panels with arrows to the right indicating positive relationships and arrows to the left indicating inverse relationships.

Flow-biofilm Interactions and Biofilm Heterogeneity

Most microbial biomass in freshwater systems is found in surface-attached communities, generally termed biofilms. Biofilms play a central role in aquatic ecosystems by driving many important biogeochemical cycles, influencing particle and solute transport, and changing the properties of environmental interfaces. Microbial processes in biofilms are also manipulated by engineers to achieve a variety of results, including consuming nutrients, biodegrading organic contaminants, and immobilizing metals. Conversely, biofilm growth can be disadvantageous in other contexts, such as when it produces corrosion or biofouling, and when it results in persistent infections of medical devices.

Spatial heterogeneity is a defining feature of microbial communities, but the interaction between biofilm heterogeneity and heterogeneity in surrounding environmental conditions is poorly understood. Biofilm communities exhibit large spatial gradients of growth and metabolic activity due to a range of factors, including the morphology of the underlying substratum, flow-biofilm interactions, and internal biological and biogeochemical processes. Depletion of oxygen, nutrients, and labile carbon leads to gradients of metabolic activity within biofilms. This internal variability is very important for the microbial ecology of biofilms, biogeochemistry of natural aquatic systems, manipulation of biofilms for engineering purposes, and treatment of biofilm-based infections.

We have shown that external flow conditions directly influence not only the delivery of chemicals from bulk solution to biofilm-resident cells, but also the migration of materials within biofilms. We have recently developed new experimental systems to observe biofilm growth under highly controlled physical and chemical gradients that significantly affect biofilm heterogeneity. These systems are used to evaluate the growth of different test strains and combinations of different organisms under different environmental conditions in order to understand how environmental conditions influence biofilm complexity. For example, under velocity gradients, a positive relationship was found between patterns of fluid velocity and biomass in pure biofilms, but this relationship eventually reversed because high hydrodynamic shear lead to the detachment of cells from the surface. However, organisms behaved differently in co-cultures than in pure cultures, and their interactions and spatial distributions were significantly affected by external flow conditions.

Further, we are directly observing transport of fluorescently labeled tracers to and within biofilms in order to better understand flow-biofilm interactions. Based on the flow-biofilm interactions, the efficacy of antibiotics in killing bacteria in biofilms can be evaluated, revealing that spatial patterns of killing efficiency have different relationships with biofilm morphology and flow conditions at different scales. These results provide deeper understanding of biofilm heterogeneity under flow gradients and the response of biofilms to antimicrobial treatment.

In collaboration with Matt Parsek from the University of Washington, we are using genetically engineered reporter strains to extend our basic information on transport in biofilms to explain heterogeneity in biofilm metabolism and the development of internal chemical gradients. We are also working with Dave Chopp in Northwestern's Department of Engineering Sciences and Applied Mathematics to develop quantitative, predictive models for these processes. Ultimately, this work will reveal the critical role of flow gradients in the development and treatment of biofilm communities, and serves as the basis to improve the design of bioreactors and other biofilm-based technologies. It will also contribute to an improved knowledge base between microscopic and environmental system scales, which connect basic microbiology to applied and environmental microbiology.

Dynamics of metals in sediments: the effects of pore water flow and bioturbation on redox gradients, contaminant efflux, speciation, and bioavailability.

Metals in the environment are partitioned between water, sediments, surrounding fauna and flora, etc. Lack of reliable models and knowledge concerning the controls on metal partitioning in the environment hamper the management of contaminated sites, resulting in increased costs and difficulties in setting and achieving desired end points.

The objective of our project is to improve understanding of the role of interplaying physical, chemical, and biological controls in the transformation, mobility, bioavailability, and toxicity of metals in sediments. Some examples of the processes that affect contaminant speciation may include pore water fluxes due to shear stress along the sediment-water interface (SWI), bioirrigation or bioturbation, and varying sediment chemistries. Feedbacks associated with biological activity and the development of sediment structure preclude reliable linkage of contaminant distributions to organism exposure, biological uptake, and ecological effects.

In situ cores and homogenized sediment samples from several different sites (Lake DePue, IL; San Diego Bay, CA, etc.) are currently being tested within a well-defined laboratory microcosm as seen in Figure 1 and 2. These columns are advantageous because they allow us to induce a known hydrodynamic shear across the SWI under controlled conditions. Combined with a Rhizon In Situ Sampling set-up, we are able to obtain varying temporal and spatial data from the overlying water column as well as porewater. Initial results from the EPA approved sediment toxicity test (the ratio of Simultaneously Extracted Metals to Acid Volatile Sulfide SEM/AVS) suggest that metal toxicity varies greatly as a function of depth.

Further analysis from Gust chamber samples will be performed using X-Ray Absorption Spectroscopy (XAS) in order to determine bond strength, length, and speciation of different metals. Samples from bioirrigated areas as well as controls will be compared using XAS to determine the effects of biological processes on the speciation of metals. Examples of bioturbation as well as their effects on permeability (and thus porewater flux) can be seen in Figure 3 and 4. Synchrotron-based x-ray microtomography will be used to elucidate the pore structure of sediments as well as contaminant partitioning preferences. Bioturbation and bioirrigation will be further characterized using video imaging and wavelength-specific fluorophores in an oscillating grid tank.

Finally, in collaboration with Professor Allen Burton in the Institute for Limnology and Ecosystems Research at the University of Michigan, toxicity will be confirmed using a series of experiments with aquatic toxicity test organisms.

The results from this work will help pinpoint key controlling factors of the toxicity of metals in fresh water lake systems. "The distribution of contaminants in sediments is often extremely heterogeneous, resulting in large concentration gradients at short distances. A better understanding of these effects on 1) the influence of redox on metal bioavailability, 2) the complexation of metals with iron/manganese oxides and organic carbon, and 3) the vertical structure and behavior of parameters related to bioavailability, are needed. This effort is expected to lead to the development of in situ field tools and predictive models." (SERDP/ESTCP Panel 2010).

This work has been supported by a grant from Strategic Environmental Research and Development Program (SERDP), a partnership between the DOE, EPA, and DOD.

  • Figure 1: Schematic Gust-type benthic flux chamber, shown here with sediment resuspension (Thomsen and Gust, 2000).

  • Figure 2: Laboratory demonstration of full mesocosm system (Jarrett 2011).

  • Figure 3: Top-view of mound and burrow structures produced by in-dwelling benthic organisms in Lake Depue sediments.

  • Figure 4: Hypothesized dominant mechanisms of solute transport in sediments as a function of permeability and depth (Huettel and Webster, 2000)