I sought to assess the enhancement potential of mimic artificial oyster reefs (MAORs) on trophic dynamics of juvenile estuarine fishes in marsh ponds. Tropic dynamics were investigated by determining the impacts of MAOR addition on meiofauna and macrofauna and then comparing these results to the gut contents and condition of four abundant estuarine fishes: Atlantic croaker (Micropogonias undulatus), bay whiff (Citharichthys spilopterus), sand seatrout (Cynoscion arenarius), and pinfish (Lagodon rhomboides). Samples were collected every other month for two years (March 2009 11) employing a Before-After-Control-Impact (BACI) design. Halfway through the experiment (March 2010), two mud sites in two marsh ponds were converted to MAORs and samples were collected for the remaining period of study. Meiofuanal communities were numerically dominated by infaunal nematodes and harpacticoid copepods, which showed order of magnitude declines in response to MAOR addition. Shannon-Weaver diversity indices (H´) increased significantly at MAOR sites from six to 13 taxa with SIMPER analyses indicating that nematodes, copepods, tanaids, gastropods, and ostracods contributed to ≥ 95% of the cumulative dissimilarity between periods and habitats. Macrofauna communities were numerically dominated by grass shrimp (Palaemonetes pugio), blue crabs (Callinectes sapidus), and white shrimp (Litopenaeus setiferus), all of which decreased in density in response to MAOR addition. Shannon-Weaver diversity indices for macrofauna decreased at MAOR sites declining from 21 to eight species. Of the eight species present at MAOR sites only blue crabs, estuarine mud crabs (Rithropanopeus harrisii), naked gobies (Gobiosoma bosc), pinfish (Lagodon rhomboides), gulf toadfish (Opsanus beta), and sheepshead (Archosargus probatocephalus) showed increased mean densities, lengths or weights at MAOR sites. Based upon percent IRI, fish diets were dominated by insect larvae, calanoid copepods, amphipods, mysids, and polychaetes, but the relative proportions of each prey item differed among species. Statistical analyses of gut contents from each of the four fishes showed no significant effects associated with MAOR addition, but energy density analyses showed a significant effect of MAOR addition for pinfish. Energy densities were similar or higher at MAOR sites after addition and when compared between habitats. These data suggest little community level enhancement attributable to MAORs in marsh ponds. However, some specially adapted, reef-associated fishes may be able to effectively utilize MAOR-associated resources to enhance feeding or condition.

Numerical phase-averaged wave models are the best option to obtain the spatial and temporal distribution of the wave energy over a large domain, such as the Gulf of Mexico. Parallel implementation of unstructured SWAN and WAVEWATCH-III were engaged in this research to evaluate the performance of third generation wave models for different conditions. Met-ocean data from a network of NDBC buoys and WAVCIS stations were used to assess the predictive skills of the wave models. Deep water wave energy dissipation formulations were carefully analyzed and modified to improve the accuracy of the bulk wave parameters. Moreover, the importance of the assumptions for choosing the high frequency cut-off and the slope of the power law for the frequency tail were highlighted by several simulations using SWAN and WAVEWATCH-III. The results show that previous underestimation of wave period reported from the WAM-3 formulation of SWAN was partially attributed to the different assumptions used on the high frequency end of the spectrum. When waves propagate to shallow water, several other processes affect the wave spectrum such as dissipation of wave energy by bed friction in non-cohesive environments. The wave model with an optimized set of coefficients for the Gulf of Mexico was used to skill assess two widely used bed friction formulations. Simulation results showed that the incorporation of sediment information in an eddy viscosity formulation led to more accurate wave hindcast than the JONSWAP formulation. The computation cost required to use the proposed formulation increased by less than 4%. The turbid plume exiting the Atchafalaya Bay system significantly influences the wave spectrum of western Louisiana coast. Using extended deployments during low and high discharge periods of the Atchafalaya River, meteorological, hydrodynamic and bottom boundary layer parameters were monitored from Tiger and Trinity Shoals. These datasets were used to evaluate the mud-wave interaction in SWAN. The numerical algorithm to solve the complex dispersion equation of SWAN was optimized. Moreover, the model was extended to incorporate the damping term in non-stationary simulations. The results show that without including the mud-effects, the high frequency waves were overestimated close to Tiger Shoal during northerly winds.

Hurricane induced storm surges can be destructive and can pose great threats to coastal communities. There are many factors affecting storm surges, including the hurricanes intensity and movement, the bathymetry and coastline of affected area, rainfall, tide, and river stage. This thesis focuses on the effects of hurricane approach angle (θ) and forward speed (U), which together describe the hurricanes motion. The problem is approached through several numerical experiments with increasing complexity. First are some process studies of long wave propagations near the coast, followed by examination of the generation of long waves by a traveling wind field. The central part consists of a systematic experiment looking into the two hurricane parameters θ and U, with additional tests on bottom friction and hurricane size. In the end is an experiment with more realistic bathymetry and inundation treatment. Storm surge is a surface wave caused by atmospheric forcing. In the open ocean it has small amplitude and propagates at the speed of a shallow water gravity wave once it is away from the area of generation. After reaching the coast, it increases to a more dangerous level and extends up and down-coast. It is found in this study that θ and U have significant effects on storm surge. The mechanism is related to Kelvin waves characteristics of propagation. Because of the boundary-confinement and the unidirectional propagation of the Kelvin wave, certain hurricane movements defined by a combination of θ and U may either be favorable or non-favorable for storm surge development. It was also found that hurricane size can have important effects on storm surge amplitude. When more realistic bathymetry is used, experiments suggest that the conclusions made with simplified experiments are still valid and should not be overlooked.

The ecological and economic value of sandy shoals off the Louisiana coast is not well understood. During three years of comprehensive benthic sampling and environmental measurements I studied the Ship, Trinity, Tiger Shoal Complex (STTSC), which comprises changing and discrete benthic habitats including high relief sandy shoals, and muddier, mostly deeper off-shoal areas, prone to hypoxia. Benthic macrofaunal assemblages of shoals included endemic species, and shoal communities were significantly different from each other and the muddier offshoal habitat, contributing to northern Gulf of Mexico (GoM) regional biodiversity. Sand percentage was the most influential environmental parameter shaping macrofaunal community composition across the region. My study revealed several more potential shoal-based functions such as providing a conduit for GoM sandy-habitat metapopulations, serving as an oxygenated benthic refuge from seasonal bottom water hypoxia, and functioning as offshore blue crab (Callinectes sapidus) spawning grounds. I discovered unexpectedly high concentrations of spawning female blue crabs, greatly expanding what was previously understood about blue crab reproductive migrations. Blue crab abundances were significantly higher on Ship and Trinity Shoals than the surrounding muddier and deeper seafloor. STTSC blue crabs compared favorably with those from nationally recognized spawning grounds in terms of condition factor (an index of health), abundance, and fecundity. This work is the first to use an ecological field study to predict the number of days (~21) between successive spawns for blue crabs, suggesting STTSC blue crabs produce at least seven broods per spawning season (~April October). My morphometric predictors of crab weight were 12 to 16% better than the traditionally used method. In addition, I used natural abundance isotopes (δ13C, δ15N) to link blue crabs from the STTSC to the inshore blue crab fishery. I analyzed isotopic variations in crab muscle and ovary tissue and found relationships with salinity and proximity to the Atchafalaya River, indicating that crabs predominately migrate directly offshore from their home estuary, including from low salinity environments. Isotopic analysis also suggests that crabs utilize offshore prey resources and do not re-enter inshore estuaries during the spawning season but rather remain offshore for the season, continually spawning and hatching their eggs.

Thesis (M.S.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 124-128). Also available on the World Wide Web.

Thesis (M.A.)--California State University, Chico. / Includes abstract. "Located in the Chico Digital Repository." Includes bibliographical references (p. 111-117).

Thesis (Ph. D.)--University of Rhode Island, 2003. / Typescript. Includes bibliographical references (leaves 182-191).

Thesis (M.A.)--York University, 1998. Graduate Programme in Geography. / Typescript. Includes bibliographical references (leaves 181-186). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://wwwlib.umi.com/cr/yorku/fullcit?pMQ27379.

Saltmarsh loss is occurring at high rates in Louisiana (LA), but understanding the impacts that marsh degradation has had on historical abundance of estuarine nekton in Barataria Bay, LA is lacking. I first examined the differences between fishery independent and fishery dependent data as indices of relative abundance. Previous studies used landings data to evaluate the importance of marsh habitat (e.g. distance of marsh edge and area of intertidal marsh) to fisheries production, but for most species, landings and survey data showed differing patterns of abundance through time. These findings emphasize the importance of using survey data (not landings data) to conduct habitat-related analyses in Louisiana and elsewhere. Next, I investigated the influence of a suite of environmental and fishery related predictors on fishery independent catch-per-unit-effort (CPUE) and developed descriptive models for these relationships. The descriptive models show that abundance of estuarine nekton varied only marginally with marsh habitat related predictors. Using both parametric and non-parametric statistical analyses, I then tested previous hypotheses that explained the relationship between marsh habitat and fish abundance, in addition to exploring community level effects. Results indicated that marsh and marsh edge distance do not appear to be driving nekton abundance. However, differences were found when comparing the community structure of Barataria Bay from different time periods over the last 44 years. Finally, I developed an ecosystem model to test the influence of marsh loss on nekton abundance, while accounting for changes in salinity and trophic interactions. Results indicate that marsh edge accounted for only a small portion of historical variation in nekton abundance. While this study suggests the influence of marsh loss on fisheries may be less significant than once thought, the importance of protecting coastal saltmarshes remains vital to the health and prosperity of Louisianas deltaic ecosystem.

Estuaries are biologically productive and important habitats for several fisheries. However, human intervention has separated many estuaries from their needed freshwater source and the commonly used solution is to use diversions to regulate the flow. This episodic increase in nutrients into estuaries has sometimes led to the formation of freshwater cyanobacteria HABs (CyanoHABs). The goal of this dissertation was to look at a field research study of phytoplankton bloom dynamics; management implications for cyanobacteria entering estuaries; and an outreach effort in relation to residents knowledge about cyanobacteria and algae. The first study compared the phytoplankton bloom dynamics, specifically CyanoHABs, in Lake Pontchartrain, Louisiana (LA) during a diversion opening year and a non-opening year. While variations in freshwater flow were found to be important to determine which phytoplankton group dominates the system, species diversity within a group likely was regulated by the water source. During the large flow year (21.9 km3) in 2011, chlorophytes and diatoms were the dominant groups. In 2012, with a much lower flow of 0.3 km3, again chlorophytes and diatoms were dominant in the spring, but both years cyanobacteria numbers significantly increased in the late summer. The second study was conducted in a different estuary of LA (Breton Sound) to determine the salt tolerance of toxic cyanobacteria; the ability of oysters to feed on toxic cyanobacteria; and their ability to retain those toxins in their viscera. The study found that the cyanotoxin, microcystin (MC) was present, where the native oysters inhabit (<10 g kg-1). When the oysters were exposed to toxic Anabaena sp. cells, they fed on these cells and retained MCs. This led to a concern for the public health. The last study surveyed fishermen about their knowledge of algae and HABs. This baseline data was used to create an educational brochure which was distributed to the marinas around Lake Pontchartrain and Lac Des Allemandes. There was also a follow-up survey to determine the effectiveness of the educational brochure. Many of the people surveyed had a basic understanding of algae, but 60% were not familiar with harmful algal blooms.