The balance between river and marine influences is important in governing landscape sustainability in river deltas. River- and atmospherically driven sea level variability, sediment loading, and estuary-ocean exchange in the Mississippi River delta are examined in this study. Subtidal estuarine sea level variability in the Breton Sound estuary was driven by a combination of remote atmospheric forcing outside the estuary over the continental shelf and controlled river inputs through a gated diversion structure at the estuary head. The highly-frictional deltaic landscape acted as a low-pass filter to coastal fluctuations near the estuary mouth. When substantial quantities river water were discharged into the estuary, upper estuary sea levels responded to a combination of river and atmospheric forcing, while sea levels in the lower estuary responded only to coastal forcing. Annual sediment loading into Breton Sound through a Mississippi River diversion was approximately 1 × 105 metric tons yr-1. Four pulsed, high-discharge diversions were conducted during the study, and sediment loading across each pulse was highly variable and was greatest during rising limbs of Mississippi River floods. Overland flow was induced when diversion discharge exceeded 100 m3 s-1. These results indicate timing and magnitude of diversion events are both important factors governing marsh sediment deposition in river diversion receiving basins. Sediment inputs measured during this study were negligible compared to historical loading through crevasses in the region. An investigation of estuary-shelf exchanges through Barataria Pass revealed that tidal exchange accounted for approximately 80% of the observed flow variability. Two dominant vertical subtidal exchange modes were identified. A barotropic mode, which accounted for most of the flow variance, was most coherent with cross-shelf wind stress. A second mode resembling baroclinic estuarine circulation recurred over fortnightly timescales, apparently in response to variations in tidal stirring. The baroclinic mode also appeared to be modulated by variability in freshwater inputs to the estuary. These findings provide a greater understanding of the physical dynamics that govern landscape sustainability in microtidal river deltas

A number of environmental stressors have been shown to interfere with reproductive and behavioral processes of fish by interfering with endocrine function. Most biomarkers of endocrine disturbance tend to be static measurements from dynamic systems making them difficult to evaluate within the context of an individual, or subtle effects that do not relate well to endpoints of ecological significance. I present an approach that uses a series of models, based on Atlantic croaker, to extrapolate laboratory results to indicators of individual and population health. First, I created a physiologically based model that simulates vitellogenesis in a female fish. The model simulates the major biochemical reactions from the secretion of gonadotropin to the production of vitellogenin. I simulated the effects of three environmental stressors that affect vitellogenin production differently. Model simulations demonstrated that it is possible to relate contaminant-induced changes in biomarkers to vitellogenin production and fecundity. A field application of the vitellogenesis model showed potential utility in interpreting field-measured biomarkers and to infer potential population hazards. Uncertainty analyses identified parameters that contributed most to variability of predictions. Second, I used a statistical model linked to an individual-based model to convert changes in behavior of ocean larvae exposed to two different contaminants to population relevant endpoints. Each contaminant imposed different effects and the effects were largely driven by impaired foraging abilities. Finally, I developed a matrix population model that realistically simulated two distinct populations of Atlantic croaker: Gulf of Mexico and Mid-Atlantic Bight. Simulations incorporated contaminant induced changes that were predicted by the other models, and compared population dynamics for 100 years under baseline conditions and under two separate contaminant scenarios. Predictions generated from the matrix model suggested that contaminant exposures at higher levels than observed in field measurements have the potential to impact populations, and that contaminant residency time within fish and the number of individuals exposed, interact with site-specific factors and life history traits, to determine population effects. The bottom-up approach employed here suggests that it is possible to scale laboratory effects to the population and provides a framework from which to base future model development and testing.

Mapping coastal marshes is an important component in the management of coastal environments. Classification of marshes using remote sensing data has traditionally been performed by employing either parametric supervised classification algorithms or unsupervised classification algorithms. The implementation of these conversional classification methods is based on the underlying distributions concerning the probability density functions (PDF). Neural networks provide a practical approach to this classification because they are essentially non-parametric data transformations that are not restricted by any underlying assumptions. The major objective of this study was to evaluate the ability of neural networks using Moderate Resolution Imaging Spectro-radiometer (MODIS) data to classify coastal marshes based on the phenelogical stages of plants. The first stage of the study was to develop a neural network model. The analysis has shown that six day images with eight input variables each are required to perform the classification. The variables are: MODIS bands - the near infrared and the near infrared composite bands, biophysical variables the leaf area index (LAI) and the fraction of photosynthetically active radiation (fPAR). Other variables are vegetation indices the normalized difference vegetation index (NDVI), the enhanced vegetation index (EVI), and the wetness index (WI), and, the day time land surface temperature. The near infrared and the wetness index were found to be the strongest predictor variables in the classification. Six hidden neurons and one output neuron were required in the neural network model for the output of six classes. The second stage of the dissertation was the model application. Images from four years: 2001, 2002, 2003, and 2004 were classified using the model. Accuracy assessment of the classification indicated that neural network techniques using MODIS data could achieve an accuracy of over 80% (at 0.95 confidence level). Using the classified images change detection was performed to determine the loss and gain of four marsh types; saline marsh, brackish marsh, intermediate marsh, and, fresh water marsh found in the south eastern coastal areas of Louisiana. The greatest gain was in the intermediate marsh, 3.0% of the study area, and the greatest loss was in the saline marsh, 3.8% of the study area.

The Moresby and Pandora Troughs of the northern Coral Sea are components of the deep-sea depositional system that is the ultimate sink for the Source to Sink Papua New Guinea (PNG) Focus Area. Cores collected from the R/V Melville during March-April 2004 reveal marine volcaniclastic and terrigenous turbidites deposited in these troughs during the Quaternary. Constraining the spatial, temporal, and provenance characteristics for these terrigenous sands through mineralogical, chemical, and textural analysis is the primary focus of this study. All cores contain thinly-bedded sandy turbidite packages interlayered with hemipelagic marls and typical centimeter-to-meter-thick turbidite sequences. The Moresby Trough core JPC22 appears to be generally finer-grained then the Pandora trough core JPC 66. Typical QFL percentages from JPC22 are 13:65:23, respectively, and plagioclase/ total feldspar ratios are near 0.90. These basal turbidite sands contain well-preserved rhyolitic pumice fragments and glass shards, with phenocrysts of amphibole, plagioclase, biotite, pyroxene and oxides. Typical QFL percentages from Pandora Trough core JPC66 are 69:14:17, and plagioclase / total feldspar ratios are near 0.47. These basal turbidite sands are predominantly quartzofeldspathic with a significant amount of heavy minerals (zircon, amphibole and oxides). The contrast in submarine sand mineralogy and mineral chemistry between 66JPC and 22JPC reflects distinct sedimentary sources composed of both fluvial and volcaniclastic material. The Moresby Trough has received secondary monomagmatic volcaniclastic turbidite sands derived mostly from volcanic/collision margin highlands of SE PNG, and the Pandora Trough has received quartzo-feldspathic sands from the Fly/Strickland system, more akin to a trailing-edge margin. Mineral textures and chemistry suggests minimal associations between sand bodies, and may represent isolated basins controlled by complex sea-floor bathymetry and episodic turbidity flows from diverse sources. The signature of the adjacent submarine fan deposits may aid the interpretation of continental margin growth as a function of sediment flux, sediment source, and dispersal pathways. These deposits may also give insight into the evolution of volcanic island arcs on longer time scales. This investigation concludes that the Pandora and Moresby trough turbidite sand bodies record varying sediment sources and somewhat isolated volcanic events contributing to the evolution of the southern PNG continental margin.

Two ophiuroid species, Hemipholis elongata and Ophiophragmus spp. were studied in laboratory microcosms to elucidate patterns of sediment mixing for key bioturbators in the Mississippi Sound, Mississippi. The effects of bioturbation on artificially stratified sediments in microcosms were traced via time-series digital x-radiography. Preliminary results indicate that for three population densities of the brittle stars (comparable to field densities), a steady state volumetric bioturbation rate of 1-2 cm3/d is reached within two months of introduction to a fresh system. The preservation quotient, q, a fractional measure of preserved primary fabric, reached a minimum of 0.5 during the 16-week experiment. Maximum depth of bioturbation appears to be inversely proportional to population density in these species, with individuals in sparser populations also being less mobile. Thus, greater dispersive mixing occurs to shallower depths in sediments hosting greater population densities. In addition, bioturbation rates appear to decrease exponentially with depth, with volumetric reworking at the base of the mixed layer being approximately 1x10-3 those at the surface. Field measurements after event layer deposition showed that re-colonization by the original key bioturbators was not immediate and a lag time of at least 8 months may valid for future modeling attempts in similar settings.

A large-scale, drought-induced disturbance occurred in Louisiana during the spring and summer of 2000. Approximately 100,000 acres of Spartina dominated marshes died-back and turned brown. This die-off caused considerable concern because in the absence of recovery dieback marshes can transform to mudflats, which can subside leading to open ponds. The state of Louisiana is attempting to restore some of the dieback marshes through the addition of sediment-slurries. The sediment-slurry generated significantly different marsh elevations: high elevation (mean and 95 % confidence interval: 29, 26 to 32 cm above ambient marsh), medium elevation (21, 19 to 24 cm), low elevation (14, 11 to 16 cm), pop-up (36, 32 to 40 cm), and vegetated (20, 17 to 22 cm), which were compared to reference marshes: healthy marshes (4, -1 to 9 cm) and dieback marshes (?2, -6 to 3 cm). High and medium elevations had minimal recovery two years following the slurry addition. These areas had plant cover similar to the reference dieback marshes, which did not receive the sediment-slurry amendment. The low elevation, popup (highly organic sections of the original substrate that detached during slurry application and settled on top of the sediment-slurry), and vegetated (dieback areas that recovered by the start of the study) areas that received the sediment-slurry had rapid plant recovery. Two years following the slurry addition, vegetation structure in the low and vegetated areas was the most similar to reference healthy marshes in plant cover (~100 %) and species richness (~1.25); pop-ups had the highest species richness (2.35, 1.8 to 2.9). Marshes that did not receive the sediment-slurry amendments were more frequently flooded and had higher sulfide concentrations (~1 mM) than marshes that received the sediment-slurry. Soil salinity was similar throughout the study site and did not limit plant recruitment. Rapid recovery was governed by optimal inundation, high organic matter content concurrent with high elevation, and/or rhizome survivability following burial. If applied appropriately, sediment-slurry amendments can restore salt marshes that have subsided as a result of a drought-induced disturbance or other events that cause a lowering of marsh surface elevation.

Stock assessment methods that quantify the status of fishery resources are critical to effective fisheries management. There is a need for stock assessment methods applicable for management of tropical species based on limited, un-aged catch data. I applied four stock assessment approaches to situation with limited life-history information and with short-term, un-aged catch data. The four approaches are: life-history invariants, length-based catch analysis, individual-based modeling, and surplus production modeling. All four approaches were applied to catch data from Lingayen Gulf, Philippines. The life-history invariant, length-based catch analysis, and individual-based modeling were applied to monthly length-frequency data of commercial catch for each of the three commonly caught species (moonfish, short mackerel, and tropical anchovy); surplus production modeling was applied to total annual catch and effort (all species combined) of commercial and municipal fisheries. Catch data was analyzed to determine current fishing mortality rate (Fcurrent). The stock assessment approaches were used to compute the fundamental stock assessment benchmark of fishing mortality rate at MSY (Fmsy). Comparison of Fcurrent to Fmsy provides critical information on sustainability of current harvest rates. The application of surplus production modeling resulted in questionable parameter estimates but did suggest that Fcurrent have been increasing. The results using life-history invariant, length-based catch analysis, and individual-based modeling methods predicted that Fcurrent of moonfish and short mackerel likely were or exceeded Fmsy values. Estimated Fcurrent of tropical anchovy were lower than the other species and lower than the estimated Fmsy values, but the harvesting of many juveniles and the increasing fishing rates also make their status worth monitoring. I discuss the use of multiple approaches and year-specific analyses to bound the high uncertainty associated with the reliance of all of the species-specific methods on accurate identification of cohorts from the length-frequency catch data and other assumptions. The use of multiple methods and approaches to estimate and compare Fcurrent to Fmsy provided relatively higher degree of confidence in the results. I conclude with the implications of my results to the management of pelagic fisheries in Lingayen Gulf namely that harvesting rates of moonfish and short mackerel should be reduced from current levels.

Salt marshes are dynamic, highly productive habitats and serve as nursery grounds for many commercially and economically important species. Benthic microalgae (BMA) are considered an important food source for benthos and provide the principal source of nutrition that fuels secondary production. Estuarine sediments around the world are a repository for many contaminants from anthropogenic sources. In particular, hydrocarbons and metals are ubiquitous contaminants in coastal systems. The primary goal of this study was to study the effects of diesel fuel and copper, alone and in combination, on the BMA assemblage from a coastal salt marsh. To achieve this objective, salt marsh sediments were exposed to various combinations of diesel fuel and copper during a 20-day microcosm experiment. Response of the BMA assemblage was assessed based on the analysis of photosynthetic pigments, species composition, biomass, and production of carbohydrates. Through use of a cryopreservation technique, these variables were measured in the top 2 mm of sediment at 200-µm vertical intervals. This experiment is the first attempt to measure the influence of contaminants on BMA with such high resolution. Hydrocarbons caused significant indirect effects on the BMA assemblage, such as blooms of large diatom species (Bacillaria paxillifer), and diesel combined with copper induced responses that differed from the effects of either contaminant alone (e.g., the stimulation of diatoms was reduced). Diversity of the diatom assemblage was reduced in the presence of diesel, and copper significantly reduced species richness. Contaminants significantly influenced water-extractable but not EDTA-extractable carbohydrate concentrations. The effect of sediments contaminated with phenanthrene and Cd was evaluated in relation to its influence on the feeding activity of a harpacticoid copepod, Schizopera knabeni. My results suggest that there was no interactive effect on feeding when Cd and phenanthrene are combined. When other metals were added (Pb and Hg) to that mixture, an additive influence on feeding rate was observed. Collectively, my results indicate that the BMA assemblage is significantly affected by diesel and copper. Contaminant effects influence BMA structure and distribution within the top 2 mm of sediment, which may have important implications for the biological and physical properties of marsh sediment.

Louisiana wetlands are disappearing at a dramatic rate, providing an impetus for identifying essential fish habitat (EFH) in this region. The distribution, relative abundance, biomass, length and food web dynamics of spotted seatrout, Cynoscion nebulosus, as well as the fish assemblage structure were examined in Barataria Bay, LA, in relation to habitat type and physical/chemical properties of the water. All fish were collected from three sites located along a salinity gradient, each contained the three habitat types of interest: marsh edge, soft bottom and oyster shell, and were sampled monthly from May 2003 to May 2004 with gillnets. Habitat preference of spotted seatrout was not easily defined by habitat type alone, but rather their distribution, relative abundance, biomass and length distribution were influenced by a combination of habitat and physical/chemical properties of the water. Stable isotope analyses suggest that individual spotted seatrout may not move widely throughout Barataria Bay, but rather they may exhibit some site fidelity with preference for salinity ranges within the bay. Salinity was also an important variable structuring the fish assemblage in Barataria Bay, resulting in a distinct composition of species at the oligohaline site as compared to the mesohaline and polyhaline sites. The fish assemblage structure also differed among habitat types and could generally be divided into three categories; those species only or mostly found at the marsh edge, those species found at all three habitat types, and a few species that had a higher affinity for soft bottom and oyster shell habitats. These results suggest that habitat type and physical/chemical properties of the water work in concert with one another to provide a diverse range of available habitats important to estuarine fishes. Despite the importance of incorporating habitat in fisheries management, it may not be possible to identify which habitats are essential versus which ones are temporarily occupied. This study demonstrates that identifying EFH is a difficult task and illustrates that an ecosystem approach may be the best method when working towards identifying EFH given the influence of the physical/chemical properties of the water and the species-specific habitat associations identified in this study.

Estuaries act as sources, sinks, and biogeochemical transformation sites for natural and anthropogenically-derived nutrients. Sediment loading from watersheds provides an important source of particulate nutrients to estuaries often neglected when constructing nutrient budgets. Deposition and resuspension of these sediments are known to impact biogeochemical cycles in estuarine environments. Phosphorus (P) exists in many forms in aquatic environments, and increased P loading to coastal environments increases primary productivity potentially leading to eutrophication. Magnitude and variability of sediment deposition, resuspension, and sediment-bound P concentrations were evaluated in Upper Newport Bay (UNB), California. During 2004, seven push cores were collected from the intertidal and subtidal zones of three sites to evaluate recent sediment dynamics using ⁷Be and sediment-bound P fractions. Two sequential phosphorus extraction methods were used to determine the distribution of potentially bioavailable forms of P (labile, iron-bound, and organic), and refractory forms of P (calcium-bound and detrital) in sediment. A seasonal trend appears with greatest deposition occurring during the wet season (spring) when watershed runoff increases (0.1 to 0.4 g/cm² d), and greatest sediment resuspension occurring during the dry season (summer) when minimal input from precipitation or stream runoff occurs. The average annual short-term sediment deposition rate calculated from the ⁷Be inventories indicated that deposition is 24.7cm/yr in the upper estuary. However, the long-term sediment deposition rate of 0.15 cm/year indicates that less than 1% of the annual sediment deposited in UNB is permanently buried. Sediment P concentrations revealed enrichment of P during the spring, corresponding to increased sediment input. During time periods when net sediment resuspension dominated over net deposition (e.g. summer), total-P concentrations decreased. This decrease was attributed to increased biological uptake of water column P during summer blooms, which lead to the desorption of P from particles. Nonetheless, most of the sequentially extracted P (~66%) was contained in the refractory phase. Based on the long term deposition rate in UNB, the burial rate for the refractory P was approximately 0.97 μmol P/cm² yr. Sediment deposition and resuspension processes may act as important internal mechanisms for recycling phosphorus, particularly reactive P, and must be considered in estuarine biogeochemical cycles.