Tsunamis and storms are the most devastating coastal hazards that can cause great loss of life and infrastructure damage. To assess tsunami and storm hazard, the magnitude and frequency of each type of event are needed. However, major tsunamis and storms are very infrequent, especially tsunamis, and the only reliable record is the deposits they leave behind. Tsunami and storm deposits can be used to calculate the magnitudes of the respective event, and to contribute to the hazard frequency where there is no historical records. Therefore, for locations where both events could occur, it is crucial to differentiate between the two types of events. Existing studies on the similarities and differences between the two types of deposits all suffer from paucity of the number of events and field data, and a wide range of initial conditions, and thus an unequivocal set of distinguishing deposit characteristics has not been identified yet. In this study, we aim to tackle the problem with the MEso-SCAle Particle Transport model (MESCAPT) that combines the advantages of concentration-based Eulerian methods and particle-based method. The advantage of the former is efficiency and the latter is detailed sediment transport and deposit information. Instead of modeling individual particles, we assume that a group of sediment grains travel and deposit together, which is called a meso-scale particle. This allows simulation domains that are large enough for tsunami and storm wave propagation and inundation. The sediment transport model is coupled with a hydrodynamic model based on the shallow water equations. Simulation results of a case study show good agreements with field measurements of deposits left behind by the 2004 Indian Ocean Tsunami. Idealized tsunami and storm case studies demonstrate the model's capabilities of reproducing morphological changes, as well as microscopic grain-size trends. / Ph. D.

This study focuses on the interaction of wash load particles with gravel bed rivers. The effects of excess fine sediment loading to streams on general water quality, contaminant transport, and benthic organism mortality has been well examined. A fundamental assumption in fluvial geomorphology and river engineering is that wash load particles ($d<63mu m$) do not deposit to stream beds, but are instead transported downstream until they deposit in reservoirs or estuaries. The goal of this study is to determine if wash load sized particles can deposit to gravel beds, where within the bed substrate deposition occurs, under what hydraulic conditions it occurs, and how the composition of the bed affects the spatial and temporal deposition pattern. Further, this study attempts to quantify the mass flux of wash load to the bed based on a simple mass conservation model using the aforementioned conditions as model parameters. This was accomplished through a series of experiments in which a mixture of pure kaolinite clay was allowed to deposit at constant shear over an acrylic, gravel, or sand-gravel mixture. Discharge was then increased to determine the effects of increased bed shear stress on deposited material and further wash load interaction with the bed. Results indicate that wash load will deposit to acrylic, gravel, and sand-gravel beds during conditions where no bedload movement is occurring. Bed composition is the primary factor controlling the mass flux of wash load from the water column to the bed. Deposition on acrylic beds forms clay ripples which translate downstream, while deposition in porous beds occurs primarily within the bed substrate. Shear stress also affects mass flux and the magnitude of its effects are related to the bed composition. Discharge increases below the threshold of bedload movement only cause large scale entrainment of deposited particles over non-porous beds. Periods of higher discharge over porous beds result in continued deposition within the bed substrates. This research enhances not only our knowledge of sediment processes within fluvial systems, but also allows for the quantification of the wash load portion of those processes given minimal initial condition information. The model developed here may be used within larger hydrologic models when examining contaminant spills or mass loading of stream networks with wash load to estimate the mass deposition to the bed. Instances where wash load is contaminated the mass of contaminated sediment retained by the bed is of great importance to local communities given a reliance of residents on that water source for water, livelihood, and recreation. / Master of Science

Best management practices (BMPs) are used in the nursery and greenhouse industry to increase production efficiency, and also serve to help meet clean water limitations on contaminants entering waters such as the Chesapeake Bay Watershed. Research is lacking on which BMPs are most widely used or most efficacious for Virginia nursery and greenhouse growers. Objectives of this work were to determine BMP use, barriers to adoption, and scientific efficacy. We conducted a survey of Virginia growers to find the 1) most widely used BMPs, 2) reasons behind BMP use, and 3) any barriers to BMP adoption. Sixty growers (17%) responded to the survey. The most widely used BMPs included irrigation scheduling, integrated pest management, optimized irrigation efficiency, plant need based watering, grouping plants by water needs, on-site water capture and collection, and use of controlled-release fertilizers (CRFs). Cost was a barrier to BMP adoption, and environmental concern was a commonly reported reason for BMP use. We documented the science supporting selected water-related BMPs (grass buffer strips, CRFs, and irrigation optimization BMPs). Providing the science supporting BMP use gives growers confidence in implementing BMPs to limit water contamination, and prevent waste. / Master of Science

As the impacts of human activities increase sediment transport by aquatic systems the need to accurately quantify this transport becomes paramount. Turbidity is recognized as an effective tool for monitoring suspended sediments in aquatic systems, and with recent technological advances turbidity can be measured in-situ remotely, continuously, and at much finer temporal scales than was previously possible. Although turbidity provides an improved method for estimation of suspended-sediment concentration (SSC), compared to traditional discharge-based methods, there is still significant variability in turbidity-based SSC estimates and in sediment loadings calculated from those estimates. The purpose of this study was to improve the turbidity-based estimation of SSC. Working at two monitoring sites on the Roanoke River in southwestern Virginia, stage, turbidity, and other water-quality parameters and were monitored with in-situ instrumentation, suspended sediments were sampled manually during elevated turbidity events; those samples were analyzed for SSC and for physical properties; rainfall was quantified by geologic source area. The study identified physical properties of the suspended-sediment samples that contribute to SSC-estimation variance and hydrologic variables that contribute to variance in those physical properties. Results indicated that the inclusion of any of the measured physical properties, which included grain-size distributions, specific surface-area, and organic carbon, in turbidity-based SSC estimation models reduces unexplained variance. Further, the use of hydrologic variables, which were measured remotely and on the same temporal scale as turbidity, to represent these physical properties, resulted in a model which was equally as capable of predicting SSC. A square-root transformed turbidity-based SSC estimation model developed for the Roanoke River at Route 117 monitoring station, which included a water level variable, provided 63% less unexplained variance in SSC estimations and 50% narrower 95% prediction intervals for an annual loading estimate, when compared to a simple linear regression using a logarithmic transformation of the response and regressor (turbidity). Unexplained variance and prediction interval width were also reduced using this approach at a second monitoring site, Roanoke River at Thirteenth Street Bridge; the log-based transformation of SSC and regressors was found to be most appropriate at this monitoring station. Furthermore, this study demonstrated the potential for a single model, generated from a pooled set of data from the two monitoring sites, to estimate SSC with less variance than a model generated only from data collected at this single site. When applied at suitable locations, the use of this pooled model approach could provide many benefits to monitoring programs, such as developing SSC-estimation models for multiple sites which individually do not have enough data to generate a robust model or extending the model to monitoring sites between those for which the model was developed and significantly reducing sampling costs for intensive monitoring programs. / Master of Science

A scarcity of comparable research on the transport of bacteria has forced hydrologic models to assume that bacteria travel as dissolved chemicals. In reality, most bacteria preferentially attach to soil aggregates, and behave very differently from planktonic bacteria. The goal of this research project was to identify and evaluate a laboratory method for partitioning between attached and planktonic bacteria that could be used to improve hydrologic modeling. Attachment was measured indirectly as the difference between total and planktonic bacterial concentration. Planktonic concentration was defined as the concentration of bacteria that could pass through an 8 μm screen. Total concentration was determined by disaggregating attached bacteria through a dispersion treatment. A randomized complete block design was structured to test for the effects of filtering, two dispersion treatment options, and the presence of soil on concentration. Tween-85 surfactant was selected as the best dispersant for use in further studies. About 78% of bovine <I>E. coli</I> in the laboratory samples were adsorbed/associated with sterile soil particles. Twenty samples of different bacteria-soil ratios were analyzed using this method to develop an isotherm equation describing <I>E. coli</I> partitioning. The <I>E. coli</I> used to inoculate these samples was cultured using a chemostat reactor to control cell growth stage and control variability. A linear isotherm (R²=0.88) was selected to describe this experimental data; however, future studies characterizing the partitioning behavior of <I>E. coli</I> under different environmental conditions are recommended in order to better understand attachment prior to modeling attached and planktonic <I>E. coli</I> separately. / Master of Science

Feeding selectivity by the rainbow mussel (Villosa iris) was examined for three age groups; 2-3 days old, 50-53 days old, and 3-6 years old. The mussels were fed an algal diet consisting of Scenedesmus quadricauda (22.3 - 44.5 μm), Nannochloropsis oculata (2.8 – 8.1 μm), and Selenastrum capricornutum (3.6 – 8.5 μm) in equal cell densities. The change in relative abundance of each algal species within feeding chambers over a 5 hr feeding trial was used to discern selectivity. At the conclusion of the feeding trials, the gut contents of mussels were analyzed for preferential ingestion. The mussels selected for N. oculata and S. capricornutum over S. quadricauda (p < 0.05). This may be an indication of particle size-dependent selection. Feeding trials also suggest that selectivity by the rainbow mussel does not change with age. Gut content analyses showed a preferential ingestion of algae, in the sequence N. oculata, S. capricornutum, then S. quadricauda. The suitability of two algal diets, S. quadricauda and N. oculata, for rearing captive juveniles of V. iris in 145-L recirculating culture systems was compared. Juveniles were fed their assigned diet at a density rate of approximately 30,000 cells/ml for 42 days, and sampled weekly for percent survival and shell length. Regardless of diet, juvenile survival decreased rapidly after 21 days, and growth did not exceed approximately 450 μm. High mortality rates and slow growth of juveniles was likely due to inadequate diets. Juveniles that were fed S. quadricauda lacked chlorophyll coloration in their guts, indicating that the juveniles did not ingest this species of algae. Colonies of S. quadricauda were likely too large for the juveniles to ingest. The gut content of juveniles fed N. oculata showed chlorophyll coloration, indicating that the juveniles ingested this species, but N. oculata may have been difficult for the juveniles to assimilate. Under the culture conditions provided, survival and growth did not compare favorably to those of other studies with V. iris. Newly metamorphosed juveniles of V. iris were reared in 145-L recirculating culture systems containing sediment (< 600 μm) of two depths, 5 mm and 15 mm. Mussels were fed a bi-algal diet of Nannochloropsis oculata and Neochloris oleoabundans. Survival differed significantly between treatments (p=0.04), and was higher for juveniles reared in 5 mm of sediment over a 40-day period. Growth was not significantly different between treatments. After 40 days, juveniles achieved a mean length of approximately 578 μm in both treatments. Survival and growth of juveniles compared favorably to those of other culture studies using juveniles of V. iris. A shallow layer of sediment is recommended for the culture of juvenile mussels. / Master of Science

ANSWERS-2000, a continuous simulation, distributed parameter nonpoint source model for simulating runoff, sediment, and nutrients from disturbed watersheds was updated to include a critical-shear rill detachment subroutine, an improved interrill detachment subroutine, and a channel scour subroutine. The existing version of ANSWERS-2000 did not simulate channel scour. The original detachment equations used in the model were developed through regression analysis of data from a northeast Indiana watershed, and were not directly applicable to other watersheds. The new detachment equations are based on process-oriented equations developed for the WEPP model and they can be applied to ungaged watersheds with a wide variety of soils and land use conditions. The new model (ANSWERS-2000) was evaluated on three watersheds and its predictions were compared with the previous version of ANSWERS. On the largest watershed (2070 hectares), both models appeared to predict sediment loss adequately. On the second watershed (1053 hectares), ANSWERS-2000 improved sediment yield predictions compared to the original model. Neither model adequately described sediment loss from the smallest watershed (1.2 ha) used for validation. The sediment prediction errors were caused by errors in runoff prediction, despite an attempt to increase runoff prediction accuracy by calibration. The channel scour subroutine was evaluated by comparison with observed channel erosion data from the largest watershed. The new model appeared to consistently over predict scoured depth. However, more research is required to determine if the channel scour component is flawed or if the uncertainty in the observed channel scour data was large as suspected. Ultimately, the erosion prediction accuracy of the ANSWERS-2000 model was improved in two of the three upland evaluation data sets. The channel scour data set was not successfully validated. Model input parameter requirements increased significantly as a result of the new erosion and channel scour submodels. / Master of Science

Scour around important foundation elements for bridges and other coastal infrastructure is the leading cause of failure and instability of those structures. Traditional scour mitigation methods, such as the placement of riprap, the use of collars or slots, embedding foundations deeper, or a combination thereof can be costly, require long-term maintenance, and can potentially have detrimental environmental effects downstream. These difficulties with traditional methods are potentially alleviated with the implementation of self-sustaining bivalve (e.g., mussel, oyster, scallop) farms that could act as mats of interconnected living barriers, protecting the seabed from scour. The mats would help to attract larval settlement by making the substrate a more suitable habitat, contributing to the sustainability of the bivalve farms. Colonies of bivalves are already being used as living shorelines for retreatment mitigation, embankment stabilization, and supporting habitat for other marine life. These applications are accomplished, in part, by bivalves' strong attachment capabilities from the bioadhesives they secrete that act as a strong underwater glue, adhering their shells to granular substrate. Some species of mussels have been shown to withstand water flow velocities greater than 6 m/s without detaching. For reference, riprap with a median grain size of about 655 mm has been shown to require a flow velocity of at least 1.7 m/s for incipient motion of the boulder-sized riprap. In addition to the contiguous living bivalve mat offering scour protection, the whole or fragmented shells (i.e., shell hash) that are left behind from dead bivalves are hypothesized to reduce erosion potential. Shell hash-laden sediments should be able to better withstand shearing, thereby increasing the critical shear stress required to erode material, compared to sediment without shell hash. Habitat suitability for bivalve colonies is also an important consideration to evaluate what surface enhancements may be needed for a site to be selected for implementation of bivalve scour mats. Bed surfaces that consist of unconsolidated fine-grained sediment are unlikely to be able to support bivalve species as the organisms could sink into the sediment, not allowing solid anchoring points. In contrast, harder substrates typically found in granular sediments offer much more suitable habitats. Along with testing the influence of shell hash and bioadhesive on sediment behavior, this thesis aims to establish a methodology to evaluate whether a section of seafloor can support bivalves or enhancement materials (e.g., shell, shale, or slag fragments) without them sinking, thereby depriving them of oxygen. Together, the examining of geotechnical aspects of bivalve habitat enhancement through seabed soil alteration and the influence of shell hash and bioadhesives on sediment shear behavior are part of a novel multidisciplinary approach toward this proposed bioengineered scour solution. Consequently, the research objectives explored in this thesis are as follows: (1) characterize morphology of existing bivalve colonies through acoustic and direct field measurements; (2) evaluate the spatial variation of the sediment shear strength in terms of proximity to bivalve colonies; (3) expand the domain of confining pressures and shell hash weight fractions used in sediment strength testing; (4) quantify the changes in shear strength and erodibility from laboratory tests on sampled material with and without the presence of bioadhesives, as well as shell fragments mixed in with the sediment; and, (5) develop a methodology ranking system for the suitability of a surficial sediments to support seeding material to improve benthic life habitat substrates. Three exploratory field surveys were conducted where colonies of oysters and other benthic life were present: in the Piankatank River in Virginia, in the Northwest Arm of the Sydney Harbour in Nova Scotia, Canada, and at the Rachel Carson Reserve in North Carolina. Field sampling techniques included Ponar grab samples, hand-dug samples, X-ray rectangular prism cores, and cylindrical push cores, which were all pivotal to understanding sediment composition, size and shape of particle distributions, as well as in-situ depth profiles of shells. Remote sensing and intrusive instrumentation included a rotary scanning sonar, acoustic Doppler current profilers, CTD (Conductivity, Temperature, Depth) probes, underwater cameras, a portable free-fall penetrometer, and in-situ jet erosion testing which helped to characterize the morphology of the bivalve colonies and the spatial variability of sediment strength. Subsequent laboratory experiments included grain size distribution analyses, vacuum triaxial tests to measure changes in shear strength with and without shell hash, and miniature vane and pocket erodometer tests on bioadhesive-treated sediments. The results showed: (1) a significant increase in the standard deviation of the backscatter intensity where the oyster reef was located; (2) the in-situ sediment shear strength increased slightly closer to the oyster reef at the Piankatank River site; (3) samples with a higher oyster density exhibited less uniform particle size distributions; (4) the presence of less than approximately 4% (by weight) of shell fragments increased the secant friction angle by approximately 6° relative to samples with no shell fragments; and, (5) the harbor bed of the Northwest Arm of the Sydney Harbour is a suitable stiffness for enhancement with shell hash over about 23% of its area. Preliminary testing showed a subtle increase in the torsional shear resistance and a decrease in erodibility for bioadhesive-treated samples; however, further testing is needed for confidence to be achieved in the results due to bioadhesive supply issues. / Master of Science / Oysters and mussels are aquatic mollusks (i.e., bivalves) that are known to be able to withstand strong storm flows without detaching from rocks and other hard surfaces. Knowing this and the increasing need for environmental- and ecological-friendly solutions in engineering and construction further accelerated by climate change and sea level rise are the motivations for studying whether bivalves can be used in this capacity. Traditional methods to protect against bridge failures caused from individual piers that become unstable from sediment eroding away from their bases can be costly, require long-term maintenance efforts, and can potentially have detrimental environmental impacts. As an alternative to or supplement to traditional methods, bivalves could be laid down in mats near the base of piers to act as a protective interconnected layer, diverting strong water flows away from the otherwise exposed sediments susceptible to erosion while strengthening the seabed. Much is known and has been investigated on the biology of bivalves but understanding how these organisms influence the sediments near them has not been studied extensively from a geotechnical engineering perspective. Specifically, within geotechnical engineering, this study is focused primarily on the influence of oyster shell fractures, naturally found in the vicinity of bivalve colonies, and the organic glue that bivalves use to attach themselves to rocks on the engineering behavior of nearby sediments. Secondary to that main objective is to establish a methodology to evaluate whether a section of seafloor can support bivalves without them sinking, thereby suffocating them. In summary, this thesis investigates methods to evaluate whether the seafloor is suitable for supporting bivalves and if their presence changes the way sediments behave after various forces are applied. To accomplish these research goals, three exploratory field surveys were conducted for this thesis: in the Piankatank River in Virginia, in the Northwest Arm of the Sydney Harbour in Nova Scotia, Canada, and at the Rachel Carson Reserve in North Carolina where bivalves were present. Through field sediment sampling, underwater sonar imagery, penetrating probes, and subsequent geotechnical laboratory testing, shell-sediment interactions were characterized. The results showed: (1) an oyster reef in the Piankatank River could be observed in great detail with sonar imagery; (2) sediment strength increased slightly the closer to the oyster reef; samples with more oyster shells in them exhibited (3) a wider range of particle sizes and (4) an increase in sediment strength; and (5) less than a quarter of the harbor bed of the Northwest Arm of the Sydney Harbour is suitable for armoring the seafloor with pieces of shell, shale, and slag to support bivalve growth. Initial tests with the organic underwater glue from bivalves showed promising results with respect to improvements in sediment strength and decreased erodibility, however, further testing is needed as supply of the organic glue was limited.

The contribution of non-point source pollution to degrading surface water quality is considerable throughout Virginia and beyond. While research on agricultural best management practices in nutrient management and nutrient and soil stabilization has made progress in reducing agricultural contributions to nutrient and sediment loading of watersheds, little is known about how land covers of different vegetation representative of urban areas (e.g., bare soil versus turfgrass lawns versus urban forest) influence the potential for non-point source pollution. Ambient rainfall volumes were manipulated to provide 50%, 100%, and 150% of natural precipitation to plots with landscape covers of bare soil, shredded wood mulch, turfgrass, and simulated urban forest (complete pin oak canopy with shredded hardwood leaf mulch). Precipitation amounts, runoff volumes, and eroded sediment masses for ten rain events between July and December 2004 were measured. Runoff was analyzed for nitrate and orthophosphate concentrations for three rain events. Turfgrass was found to be the most effective of the land covers tested at reducing components of non-point source pollution from stormwater. Turfgrass plots produced, on average, the least runoff and sediment, and lower nitrate concentrations in runoff water as compared to the other land covers tested. Results from urban forest plots apparently reflected the disturbance of tree planting, even six months later. This study contributes to a sparse body of knowledge about the influences of urban landscapes on water quality, and will inform land use policy and urban Best Management Practices. / Master of Science

The increasing demand for low carbon technology has increased the demand for some critical materials. Graphite is one of the strategic raw materials defined by the European Union as it is used in the production of for example batteries in electrical vehicles. Natural graphite is extracted through mining and the production is currently located outside the European Union. However, natural graphite deposits exist in for example Sweden. Mining activities can cause environmental issues, e.g. release of metals to the environment. By studying sediment in lakes, the historical element load can be investigated. In the Vittangi area (northern Sweden), a graphite deposit is located close to the natural lake Hosiojärvi. In the area, exploration has been conducted during the last 100 years. The latest exploration was conducted by the company Talga, who is also planning to extract the graphite. The aim of this master thesis is to determine the geochemical processes affecting the mobility of Co, Cu, Ni and Zn in Hosiojärvi, as well as their historical accumulation in the lake. Due to previous exploration in the area, the eventual impact from trace elements related to the bedrock and graphite deposit has also been studied. Based on previous elemental load to the sediment, the future impact until the mine starts have been discussed. The method used for answering the questions have been sampling of sediment, analysing metal concentrations in surface water, groundwater and sediment and dating of the sediment to determine sediment accumulation rate. The study shows that there has been an increase of Co, Ni and Zn to the lake, as the concentrations in the sediment has increased in the upper parts. By looking at those elements, the increase could be explained by the exploration during 1960 – 1970. The sediment is assumed to be in reduced conditions and the zone where redox processes can occur is assumed to be in the interface between the bottom water and the top sediment. In the sediment, framboidal pyrite is formed in the upper and lower parts of the sediment. Analysis on surface water shows that during the last four years, there is an increasing trend of  Co, Ni, Zn and SO4. The groundwater flows through the mineralisation and affects the water quality in Hosiojärvi, as the water quality of the lake has become more similar to the groundwater. The overall conclusion of the study is that the lake has been impacted by the previous exploration and is assumed to continue being affected until the planned mine is starting to operate.