Thesis (M. Sc.)--College of William and Mary. / Typescript (photocopy). Vita. Includes bibliographical references (leaves 96-100).

Thesis (Ph.D.), Memorial University of Newfoundland, 2000. / Restricted until June 2001. Bibliography: leaves 183-193. Also available online.

Thesis (Ph. D.)--Rutgers University, 2008. / "Graduate Program in Environmental Sciences." Includes bibliographical references.

Thesis (Ph. D.)--Hong Kong University of Science and Technology, 2003. / Includes bibliographical references (leaves 174-185). Also available in electronic version. Access restricted to campus users.

The presence of agrochemical residues in both urban and agricultural water bodies has become ubiquitous, often producing deleterious effects in the impacted watershed including reductions in biodiversity, alterations in species interactions, and toxicity to non-target organisms. While these effects have been studied on metazoan consumers, the consequences of agrochemical contamination on microorganisms, such as bacteria, protozoa, and viruses, are poorly understood. Agrochemicals could act directly on microorganisms, including pathogens, by either facilitating their survival or decreasing their abundance. Further, a multitude of indirect effects of agrochemicals on microorganisms are possible, whereby agrochemicals alter predation, competition, or parasitism on or available nutrient to microbes. The primary method by which agrochemicals enter water bodies is through stormwater and agricultural runoff, which can also introduce agriculturally-associated zoonotic pathogens. Presently, regulatory standards utilize fecal indicator bacteria (FIB) to predict the presence of pathogens in contaminated watersheds. However, if agrochemicals have different effects on FIB and bacterial pathogens, then these regulatory standards might be confounded by the presence of pesticide residues in impacted water bodies. Additionally, if agrochemicals promote the survival of zoonotic pathogens, then the presence of pesticide residues could potentially increase risks to human health. The studies in this dissertation investigated both the direct and indirect effects of agrochemicals on the growth and survival of FIBs ( Escherichia coli and Enterococcus faecalis), zoonotic bacterial pathogens (E. coli O157:H7, and Salmonella enterica), and two virus groups (human polyomaviruses and adenoviruses). The agrochemicals utilized in these experiments are among the most prominently used in their respective pesticide classes and included the herbicide atrazine, the insecticide malathion, the fungicide chlorothalonil and inorganic fertilizer containing phosphate and fixed nitrogen. Initially, complex mesocosms containing zooplankton, phytoplankton, leaf litter, and vertebrate and invertebrate species were used to examine net (direct and indirect) effects of agrochemicals on FIB in sediments. Subsequent studies utilized experiments in simplified microcosms to detect direct or indirect effects (i.e., predation, competition or effects on nutrient resources) on FIBs and pathogens. In complex mesocosms, atrazine and fertilizer significantly increased FIB densities in the sediment; however, because of the complexity of the mesocosms, it was not possible to determine whether these results were the product of direct or indirect agrochemical effects. Simplified microcosms, limited to predominantly direct effects, as well as in vitro growth curves, revealed no direct effects of any agrochemical treatment on either growth or survival of FIB or bacterial pathogens. When algal communities were allowed to establish, however, atrazine significantly reduced both phytoplankton and E. coli densities in the water column, but increased E. coli densities within the sediments. These effects on E. coli were indirect because they required the presence of algal species. To investigate indirect effects of predation on FIBs and E. coli O157:H7, we manipulated the presence and absence of an obligate heterotroph, Tetrahymena pyriformis, a facultative heterotroph, Ochromonas danica, and natural protozoan populations. In both laboratory and greenhouse microcosm experiments, the fungicide chlorothalonil significantly reduced all protozoan populations, which resulted in increased densities of FIBs and E. coli O157:H7 because of reduced predation. Atrazine was not found to have any significant direct effect on the densities of T. pyriformis or natural protozoans; however, atrazine did significantly reduce O. danica densities in greenhouse experiments. In laboratory experiments with O. danica, atrazine treatments resulted in decreased densities of E. coli O157:H7. Presumably, atrazine prevented or reduced photosynthesis forcing O. danica to increase its predation on E. coli thus shifting its trophic level. These studies reveal that agrochemicals can have a significant effect on microbial communities, but that these effects are often indirect and mediated through alterations of nutrient resources and predation. Atrazine application reduced FIB and pathogen densities in the water column via reduction of phytoplankton and increased predation by O. danica. These data suggest that the net effects of atrazine is deleterious to FIB survival in the water column and that application of this herbicide could result in an ecosystem service, reducing the abundance of zoonotic pathogens and lessening the risk to human health. However, elevation of FIB densities was observed in the sediments when atrazine was applied. The potential resuspension of increased sediment bacteria may negate or out-weigh the deleterious effects of atrazine on bacteria in the water column. Chlorothalonil application decreased protozoan densities, lessening the stress of predation on the bacterial targets and increasing FIB and E. coli O157:H7 densities. The use of chlorothalonil may therefore have negative implications for human health risks, as the reduction in predation seems to facilitate the survival of zoonotic waterborne pathogens. Understanding the net effects of agrochemicals is important for public health, as pesticide applications can act to either maintain or diminish potential bacterial and protozoan pathogens of humans. These studies show that indirect effects of agrochemicals on non-target microbes tend to be more prominent than direct effects and can significantly impact the fate of bacterial pathogens in aquatic environments.

This dissertation presents an investigation of the effects of a stochastic component of sediment transport in sandy rivers in an attempt to gain information about the transport system and its implications for the evolution of Earth's surface topography. First, a method for characterizing the geometries of bed forms is introduced and compared to previously proposed methods. This new method is then implemented on a field dataset as well as laboratory dataset and the results are compared to those obtained by traditional methods. Second, a method for characterizing the dynamic evolution of the bed geometries is demonstrated. It produces a velocity scale, the mean migration rate of the bed topography, and a deformation scale, the evolutionary departures of the bed topography from pure migration. These scales are calculated for the field and laboratory data and are compared. The flux of bed sediment is then shown to depend on the stochastic component of bed evolution. The fluxes for each dataset are calculated, they are related to the environmental conditions causing the transport of sediment, and suggestions are made for the design of field campaigns that attempt to measure sediment transport by repeated surveys of bed topography. Finally, the implications of stochasticity for sediment transport are investigated. A null hypothesis is formulated for topographic change by a stochastic process. Then the effects of measurement and field collection methods on the null hypothesis are evaluated. The most important prediction is non-trivial behaviors in measurable rates of surface change at short timescales. This prediction is then evaluated with field data from a growing sandy channel network whose behaviors can be determined at timescales of decades to centuries (dendrochronology), tens of thousands of years (cosmogenic radiochemistry), and hundreds of thousands to millions of years (age of channel system and sediments through which it cuts). These three investigations create a coherent account of the expressions and implications of variability in the transport of sediment, and therefore the evolution of topography, in sandy river systems that can then be generalized to changes across Earth's surface. / text

We investigate evolution of mountain channel morphology and riverbed surface roughness by conducting laboratory experiments. The experimental flume is 4m long by 0.1m wide with a working length of 2.5m. We control initial sediment size distribution, flume slope, water discharge, and sediment feed rate. Measurements include topographic profiles, flow depth, surficial grain-size distribution, sediment transport rate, and sediment size distribution. Experiments begin with a gravel bed of a broad sediment size distribution, at two initial flume slopes: 8.2% and 12.4%. Discharge is held constant until transport rates and topographic changes indicate the system is at near steady state. Coarse sand is then fed into the channel at 1,000 g/min as a means to perturb the system. Sediment feed is held constant until the perturbed bed reach steady-state conditions. The feed is subsequently ceased and measurements continue until sediment transport rates and topography stabilize. These laboratory experiments provide first-hand observations of channel systems evolving after perturbations. Transport rates decay exponentially following perturbations and remain very low when the channel bed is stabilized. The introduction of coarse sand acts to smooth the channel bed by filling in topographic lows in the 8.2% sloped channel. At a 12.4% slope, increased mobility of sand allows steady state conditions to be met with little smoothing of the bed. The sand also increases the mobility of coarser sediment that was previously stable, likely due to local surface smoothing at grain scale. The increased fraction of surface sand cover maintains increased scouring and mobilization of coarser grains. These post-perturbation mechanisms are interpreted to be responsible for topographic adjustments as the system readjusts towards new steady-state conditions. Surface sorting and transporting distributions reflect high sand fractions well after perturbations have ceased. This suggests that brief pulses of fine sediment can increase coarse sediment mobility for prolonged periods. / text

Capping is typically used to control contaminant release from the underlying sediments. However, the presence of conventional caps often eliminates or slows natural degradation that might otherwise occur at the surface sediment. This is primarily due to the development of reducing conditions within the sediment that discourage hydrocarbon degradation. The objective of this study was to develop a novel active capping method, an electrode enhanced cap, to manipulate the redox potential to produce conditions more favorable for hydrocarbon degradation and evaluate the approach for the remediation of PAH contaminated sediment. A preliminary study of electrode enhanced biodegradation of PAH in sediment slurries showed that naphthalene and phenanthrene concentration decreased significantly within 4 days, and PAH degrading genes increased by almost 2 orders of magnitude. In a sediment microcosm more representative of expected field conditions, graphite cloth was used to form an anode at the sediment-cap interface and a similar cathode was placed a few centimeters above within a thin sand layer. With the application of 2V voltage, ORP increased and pH dropped around the anode reflecting water electrolysis. Various cap amendments (buffers) were employed to moderate pH changes. Bicarbonate was found to be the most effective in laboratory experiments but a slower dissolving buffer, e.g. siderite, may be more effective under field conditions. Phenanthrene concentration was found to decrease slowly with time in the vicinity of the anode. In the sediment at 0-1 cm below the anode, phenanthrene concentrations decreased to ~70% of initial concentration with no bicarbonate, and to ~50% with bicarbonate over ~70 days, whereas those in the control remained relatively constant. PAH degrading gene increased compared with control, providing microbial evidence of PAH biodegradation. A voltage-current relationship, which incorporated separation distance and the area of the electrodes, was established to predict current. A coupled reactive transport model was developed to simulate pH profiles and model results showed that pH is neutralized at the anode with upflowing groundwater seepage. This study demonstrated that electrode enhanced capping can be used to control redox potential in a sediment cap, provide microbial electron acceptors, and stimulate PAH degradation. / text

Analysis of scattered, or diffraction energy (the seismic response of small-scale objects) in the seismic data from Canterbury Basin, New Zealand reveals additional geological information about depositional patterns in sedimentary deposits. Diffrac- tion images from the seismic response for Canterbury Basin provide complementary interpretation tools to the conventional specular reflection images. To image diffrac- tions for a dataset from Canterbury Basin, I take the following steps: First, I attenuate multiples using a surface multiple prediction algorithm to predict multiples and apply regularized nonstationary regression to adaptively subtract the predicted multiples. Next, I separate diffractions using the plane-wave destruction method. The plane- wave destruction method removes conventional reflected energy in order to enhance the diffracted energy. I then apply a velocity continuation method on diffraction data to estimate migration velocities and then migrate the data using Kirchhoff migration in the dip-angle-gather domain. The resultant conventional and diffraction images are improved images suitable for geological interpretation of prograding sediment drifts. / text

Mercury -contaminated sediments often act as a sink of mercury and produce methyl-mercury, an acute neurotoxin which readily bio accumulates, due to the presence of bacterial communities hosted by the sediment. One common remediation approach to manage methyl-mercury is to amend the sediment by capping or directly mixing with a sorbent. This thesis aims to assess the capabilities of some calcium-based sorbent to act in that capacity. Laboratory experiments were implemented to simulate mercury fate and behavior in geochemical conditions that capping would likely create. Well-mixed slurries showed that gypsum materials were disparate and their behavior was similar from sand to organocaly. Mercury sorption capacities of these gypsums were poor with a sorption coefficient approximately equal to 300 L/kg. Reduction of methylmercury was minimal and even increased in two of the three materials. Therefore, the three gypsums, which tend to be more cohesive when wetted, doesn’t constitute a viable material for sediment capping. / text