Human endeavors, particularly the agricultural and industrial activities of the last half century, now produce more biologically available nitrogen (N) than all other natural sources combined. The increased N availability can have consequences for the health of aquatic biota on the local, regional, and global scales. One manifestation of this problem is the formation of coastal hypoxic zones where terrestrial N loading creates eutrophic conditions in coastal waters. This dissertation examines a century of changes in land use and water quality to quantify the relationships between agricultural land use practices and riverine N yields in the Mississippi River Basin and 56 other watersheds across the continental U.S. A novel and spatially-explicit geographic information system database encompassing the continental U.S. from 1840 to present was developed to test the hypothesis that land use affects water quality. The database was compiled from semi-monthly water quality monitoring records from the U.S. Geological Survey, and from county-level Census of Agriculture data from the U.S. Bureau of the Census and Department of Agriculture. The results of this research indicate that intensive agricultural land use is statistically associated with riverine N yields at the beginning and end of the 20th Century. These findings imply that agriculture was already affecting N export at the turn of the century, but that intensive contemporary management practices have significantly increased the N export per hectare of cropland in the latter half of the century. The baseline conditions for N export from minimally impacted watersheds, however, did not change over the course of the last century indicating that rehabilitation of surface water quality is possible. Additionally, decreasing in-stream N yields are quantitatively associated with increasing landscape diversity, increasing perennial farmland cover, and decreasing commercial fertilizer applications in agricultural watersheds across the continental U.S. The results also suggest that government farm payments can be re-distributed to implement land use practices that effectively reduce in-stream N concentrations at the sub-basin scale, while potentially improving groundwater quality, soil quality, and biodiversity. These improvements will require changing land use practices on large spatial scales, however, in ecological units ranging from upland watersheds to coastal bays.

Investigations of hurricane disturbances on coastal vegetated communities are common, but relatively few are comprehensive across broad geographic regions. The 2005 hurricanes, Katrina and Rita, exposed Louisiana coastal landscapes to physical modifications and extensive and prolonged flooding, resulting in measurable physicochemical changes. This research used remote sensing and field investigations to regionally assess (1) porewater salinity and sulfide impacts to and recovery of coastal Louisiana vegetation communities, and (2) the importance of mineral sediment deposition on accretionary processes. Hurricane effects were most direct and prominent in eastern Louisiana from Katrina and western Louisiana from Rita, compared to central Louisiana exposed to indirect affects from Rita. A coastwide analysis of moderate resolution imagery found over 4,714 km2 of the prestorm coastal wetland area experienced a substantial decline in vegetation density and vigor in October 2005, with the majority of persistent damage through November 2006 in the west (1,046 km2). In the east region, 91.8% of persistent damage was accounted for by conversion of marsh to new open water; whereas in the west region, 71% was associated with other vegetation stressors. The physical landscape disruption in the east contributed to a high abundance of disturbance species in fresh and intermediate marsh from fall 2006 to fall 2007. Salinity and sulfide stress persisted throughout the west region, contributing to low vegetative cover, slow recovery of Spartina patens, and shifts towards more saline marsh classifications by fall 2007. Hydrologic barriers, including impoundments in the west, contributed to salinity and sulfide stress; however, these same structures facilitated trapping of mineral sediments delivered by Hurricane Rita, providing critical supplies of bulk sediment and nutrients. Large periodic sediment inputs partially compensate for reduced vertical accretion found in impounded marshes. However, management actions should endeavor to optimize organic matter production to support vertical accretion. Two full growing seasons after the 2005 hurricanes, marshes directly impacted in the east and west regions were still recovering. Although vegetation cover values were approaching pre-hurricane levels, species composition is still indicative of a disturbance environment.

Understanding the behavior, including movement, of red snapper (Lutjanus campechanus), around and among the many oil and gas platforms in the northern Gulf of Mexico (GOM) is crucial to the management of this important commercial and recreational species. What role oil and gas production platforms play in the attraction vs. production continuum for red snapper is unknown, but it is certain these large structures have a role at some life history stage. We used the VRAP acoustic telemetry system to track red snapper around two platforms in the GOM in 2005 and 2006. Fish detections per hour generally decreased over the course of each experiment, and detections also fluctuated with strong periodicity. Spectral analysis revealed that red snapper had a 24- hour periodicity to their movements. Probability of presence of fish likewise fluctuated within a day, perhaps indicating foraging away from the platforms. Red snapper in this study showed much lower site fidelity than in previous studies of red snapper on artificial reefs. These results appear to support the hypothesis that platforms function largely as attracting devices.

Ship Shoal, a shore-parallel sand body, was recently recognized as having a unique physical and biological environment and also as a potential sand resource for coastal restoration in coastal Louisiana. Little is known regarding such dynamics, in concert with fluvial sediments and winter storms, influenced in unique ecosystems, and likely in future potential sand mining. This dissertation addresses such the morphodynamics and sedimentary processes and their implications for the mining from the shoal using field measurements and numerical modeling studies. During the winter-spring season, fluvial sediment plumes shifted from the prevailing west to southeast during the post-frontal phases, resulted in accumulation of fluid mud on the eastern flank of the shoal and consequent shoal sediment heterogeneity during the spring of 2006; this fluid mud layer strongly interacted with storm waves and currents through the processes of sediment re-suspension, vertical mixing, and hindered settling and redistribution. Studies during winter 2008 represented dynamics dominated by non-cohesive bottom material and hence followed the conventional approaches. State-of-the-art numerical models for waves, currents and transport provided reasonably well estimation for the study area and showed changes in wave transformation, current variability, and sediment transport for various hypothetical post-dredging scenarios. Sediment re-suspension intensity showed spatial differences along the shoal: high on the western flank of the shoal and a decrease toward the eastern shoal due to the change in shoal bathymetry. The results indicated a favor for the fluid mud accumulation on the eastern flank of the shoal, corroborated by in-situ measurements. Data suggest that Ship Shoal appears to have recurring sandy and muddy bottoms depending on the amount of storm-induced sediment reworking and fluvially-derived sediments. The fluid mud on the shoal seems to be patchy and does not remain in place as permanently consolidated mud, given the frequency of winter storms and the dispersal shifts. Numerical simulations suggest that targeted small-scale mining would not significantly alter the hydrodynamics and sediment transport over the shoal. Dredging from the eastern flank of the shoal may give rise to lesser impacts than that from the middle and western flank of the shoal. This suggestion is consistent with that from our collaborative biological study.

Impacts of global climate change, such as sea level rise and severe drought, have altered the hydrology of coastal salt marshes resulting in submergence and subsequent degradation of ecosystem function. A potential method of rehabilitating these systems is the addition of sediment-slurries to increase the elevation of the marsh surface, thus ameliorating the effects of excessive inundation. Although this technique is growing in popularity, the successful restoration of ecological function after sediment addition has received little attention. The purpose of this research was to determine if sediment subsidized salt marshes are functionally equivalent to natural marshes and whether salt marshes restored with this technique are sustainable over time. This research addressed the following questions: 1) Does sediment-slurry addition restore important ecological functions such as primary production, organic matter decomposition and secondary production?, 2) If so, what level of sediment addition results in optimal function?, 3) What soil physico-chemical parameters associated with sediment addition influence these ecological functions? and 4) How does vegetation resilience in sediment subsidized marshes change over time? Moderate intensities of sediment-slurry addition, resulting in elevations at the mid to high intertidal zone (42-53 cm NAVD 88), successfully restored ecological function to degraded salt marshes. Additionally, salt marshes that received intermediate levels of sediment addition were more resilient than natural marshes, and maintained their resilience over time. However, all ecological functions showed a sediment addition threshold that was characterized by a decline in production and resilience and accelerated decomposition in areas of intense sediment addition, or high elevation (> 53 cm NAVD 88). The primary regulator of enhanced ecological function in the restored marshes was the alleviation of flooding stress observed in the degraded marsh. Declines in ecological function above the sediment addition threshold were principally influenced by dry conditions that resulted from insufficient and infrequent flooding at high elevations. Therefore, the addition of intermediate levels of sediment to submerging salt marshes increases marsh surface elevation, ameliorates impacts of prolonged inundation and increases production and resilience. However, too much addition of sediment results in diminished ecological function that is equivalent to the submerged or degraded system.

Barrier islands that overlie a compressible substrate load and consolidate the underlying subsurface. Through time, the elevation and aerial extent of these islands are reduced, making them more susceptible to inundation and overwash. Sand washed over the island and onto back-barrier marsh or into the bay or estuary begins the consolidation process on a previously non-loaded substrate, with time-dependent consolidation a function of the magnitude of the load, duration of load, and characteristics of the substrate. The result is an increase in the overwash, migration, breaching, and segmentation of these islands. This research determined the degree to which consolidation affects the evolution of barrier island systems overlying a poorly-consolidated substrate, both for natural islands and those that have been restored with an infusion of sand from an external source. A two-dimensional (cross-shore) mathematical model was developed, tested with field data, and then applied to evaluate how a compressible substrate modifies long-term barrier island evolution. The model spans time durations of years to decades and represents cross-shore evolution of a sandy barrier island due to erosion, runup, overwash, migration, and time-dependent consolidation of the underlying substrate due to loading by the island. The implications of two strategies for restoring these islands a one-time Initial large-scale infusion of sand from an external source versus traditional Incremental beach nourishment and subsequent smaller maintenance volumes were tested. Barrier islands overlying a compressible substrate are more likely to have reduced dune elevations due to consolidation, incur overall volumetric adjustment of the profile to fill in compressed regions outside the immediate footprint of the island, and experience increased overwash and migration when the dune reaches a critical elevation with respect to the prevalent storm conditions. Initial large-scale infusion of sand from an external source decreased the cross-shore migration rate, consolidation rate, and rate of dune lowering for barrier islands overlying a compressible substrate as compared to the Incremental restoration. The reduction in the migration and consolidation processes for the Initial Method resulted in more stability of the island as compared to the Incremental Method.

Barataria Bay, Louisiana is a dynamic estuary with ongoing disturbances that is in need of restoration. Development and validation of a lower Barataria Bay index of biotic integrity (IBI) for the summer season was the focus of my research. This IBI was created using 2005 data and evaluated with 2006 and 2007 data to demonstrate the feasibility of this approach in coastal Louisiana. The IBI successfully distinguished sites with differing levels of degradation using nine fish metrics. While pursuing this effort, two serendipitous events occurred when an oil spill then a hurricane impacted the study area. This gave me opportunities to examine pulse perturbations in the area. I showed immediate effects from the 2005 oil spill using a before-after-control-impact (BACI) analysis and found that fish abundances were significantly different days after the spill. I examined the recovery path of the nekton community after Hurricane Katrina and found that by the spring the year following the storm there were differences in species composition from pre-Katrina compositions. However, by two years post-Katrina species compositions and environmental variables measurements were similar to pre-storm conditions. I examined the transformation from Spartina- to black mangrove- dominated marsh edge (a long-term or press perturbation) and its effects on the nekton community. Nekton abundances were higher in the black mangrove and transition (mixed Spartina and black mangrove) vegetation dominated marsh-edge habitat type than the Spartina dominated marsh-edge. However, a fisheries species, Farfantepenaeus aztecus (brown shrimp), was more associated with Spartina than mangrove. By creating loop models of the study areas marsh-edge community, I explored three other press perturbations along with black mangrove encroachment. These other perturbations were freshwater diversions, shrimping pressure, and wetland loss. Models predicted that mangroves encroachment decreased grass shrimp, freshwater diversions increased the water column predators, shrimping decreased wading birds and algae, and wetland loss had a negative effect on algae. Variations to the model showed some differences among the community responses. This dissertation illustrates how resilient the fauna is in Barataria Bay, which along with the proper assessment techniques, makes this area a strong candidate for restoration and management efforts.

Climate controls biotic community composition at multiple spatiotemporal scales through variability in environmental control mechanisms (assembly filters). This research investigated the role of climate variability in the community dynamics of estuarine nekton in Breton Sound estuary, Louisiana, and, specifically the effects of El Niño Southern Oscillation (ENSO), freshwater discharge, and a tropical cyclone. A teleconnection was found between ENSO and juvenile brown shrimp (<i>Farfantepenaeus aztecus</i>) abundance in Breton Sound from 1988 2007. ENSO affected winter weather conditions (air pressure, temperature and precipitation), and spring brown shrimp abundance in Breton Sound. Juvenile brown shrimp abundance lagged ENSO by three months; below-average abundance of juvenile brown shrimp was caught in springs following El Niño winters while above-average abundance of brown shrimp was caught in springs following La Niña winters. Salinity was the dominant ENSO-forced assembly filter that regulated brown shrimp abundance. Study of short-term freshwater pulses revealed higher nekton density and biomass in marshes receiving pulsed riverine flow (inflow) than in reference marshes, due to differences in water depth and flooding duration caused by the pulses. Communities consisted mainly of marsh resident species; individual-species examination revealed habitat preference related to water depth. Inflow marshes were capable of producing optimum growth of <i>Gambusia affinis</i> (0.001 g DW d^-1) and energetically valuable habitat (> 6,000 cal g^-1) for trophic transport. Riverine pulses may enhance secondary productivity in Breton Sound estuary. Breton Sound was directly hit by Hurricane Katrina in 2005, causing extreme physical habitat damage and a protracted period of elevated salinity in tidal freshwater marshes. Results included higher nekton densities and a nekton community shift from one dominated by Tidal freshwater / Resident (T/R) species toward one that included Brackish / Migrant species. Effects were short lived; by spring 2007, the nekton community had returned to T/R species, despite the lasting loss of vegetated marsh habitat. These findings provide greater understanding of large-scale climate effects on local estuarine nekton community dynamics and productivity.

Spotted seatrout, Cynoscion nebulosus, are common in estuaries and coastal waters of the south Atlantic and Gulf of Mexico and are of considerable recreational and economic importance. Still, the spatial ecology of this species is under-studied and poorly resolved, especially in Louisiana waters. To address this important knowledge gap, I examined the movements, distribution, and habitat use of adult spotted seatrout in coastal Louisiana primarily using high-resolution acoustic telemetry and secondarily, conventional tagging (mark-recapture) data. At the largest spatial scale investigated, I found that adults exhibited a high degree of estuarine fidelity and rarely undertook large-scale movements in excess of 50 km. At smaller (intra-estuarine) spatial scales, abiotic factors had a strong effect on fish distribution. Specifically, fish primarily utilized deeper channel habitats during severe weather events (cold storms and tropical fronts) and females avoided olighaline waters (0.5-5 psu). Adult spotted seatrout also showed clear habitat preferences, whereby oyster reefs and mud-bottom habitats of the estuary proper were used to a greater extent than channel and marsh regions. Seasonal and size trends in habitat use were also evident, as larger fish (> 400 mm TL) showed a high affinity for structured (reef) habitats and across size classes, artificial reefs were utilized most during spring and summer. My results have direct bearing on the assessment and management of this important species and support the current initiative of an ecosystems-approach to management by informing spatial management options. Finally, the results of my methods validation work on the effects of tagging on spotted seatrout and performance dynamics of telemetry equipment have important implications for future studies. Given the high transmitter retention and survival of telemetered spotted seatrout in my holding experiments, biotelemetry should be a feasible approach for future studies on the movement and behavior of this species. Still, in designing receiver arrays to study fish movements (of any species), it will be necessary to consider the high variability in receiver detection ranges as revealed by my extensive range testing efforts.

Harmful algal blooms are an increasing problem for coastal waters world-wide. The diatom genus, Pseudo-nitzschia, is of particular concern in Louisiana, due to the potential for several species to produce the neurotoxin domoic acid (DA). While trophic transfer of DA to consumers has repeatedly occurred along the California coast, little is known about trophic transfer of recently detected DA in the Gulf of Mexico. In this study, the presence of DA in gulf menhaden (Brevoortia patronus) and the potential for trophic transfer to higher order consumers was investigated. In addition, the effects of this transfer and other algal toxins that threaten Louisianas coastal food webs were evaluated. DA quantification in water and fish tissue samples was determined by Enzyme-Linked Immunosorbent Assay (ELISA). Food web effects of algal toxins were analyzed through the use of a qualitative modeling technique, loop analysis. The results of the toxin assay illustrated that low-levels of DA exist in both water and tissue samples, with a significant correlation between the two (n = 25, p = 0.025, significance level of 0.05). The effects of HABs on the entire food web showed the possibility of trophic cascades. This is the first documentation of a DA vector in the entire Gulf of Mexico and confirms DA contamination in food webs of coastal Louisiana. Through the use of qualitative modeling, present and future threats posed by phycotoxins to coastal food webs can be assessed, providing resource managers valuable information to aid in mitigation of their negative consequences.