Eight species of Prionotus, collected from 5-100 m in the Gulf of Mexico along a cross-shelf transect off Freeport, Tx during October 1977-August 1981, were studied to determine life history patterns and how they partition resources. Only four species were abundant: P. tribulus, P. paralatus, P. longispinosus, and P. stearnsi. Prionotus spp. mature at 80 mm (P. stearnsi and P. rubio), 85 mm (P. tribulus and P. paralatus), 100 mm (P. ophryas), 105 mm (P. roseus), and 120 mm (P. longispinosus). Sizes at Age 1 were 99-140 mm (P. tribulus), 99-138 mm (P. longispinosus), 98-122 mm (P. paralatus), 75-125 mm (P. stearnsi), and 95-129 mm (P. ophryas). Most fish were less than 200 mm. Typical maximum sizes were 155-175 mm (P. tribulus), 145-160 mm (P. longispinosus), 160-165 mm (P. paralatus), 180-195 mm (P. rubio), 125 mm (P. stearnsi), and 155-160 mm (P. ophryas). Fish were typically 1-3 years old at these typical maximum sizes, and most were Age 1 and less. Apparent total annual mortality rates were 80-100%. The eight species fit into three categories based on their bathymetric distributions and community memberships: (1) members of the inshore white shrimp community which occurs from 5 m to about 16 m (P. tribulus); (2) members of the offshore brown shrimp community which occurs from about 36 to at least 100 m (P. paralatus, P. stearnsi, and P. roseus); and (3) members of a transition fauna which occurs between the outer edge of the white shrimp community and the inshore edge of the brown shrimp community from about 18-27 m (P. longispinosus, P. rubio, P. ophryas, and P. scitulus). Comparisons among species indicate a common pattern of population dynamics that favors r-strategy (short life spans, high mortality rates, and rapid turnover of biomass), but with temporally segregated spawning and spatially segregated distributions. Spawning grounds seem to lie toward the northcentral Gulf with current transport mechanisms carrying young toward the northwestern Gulf. Prionotus spp. from the northwestern Gulf show quite different life history attributes than their congeners from mid Atlantic and New England regions.

The disease caused by the protozoan Perkinsus marinus has been a major source of mortality in the eastern oyster, Crassostrea virginica. Variations in susceptibility to P. marinus infection among eastern oysters collected from the Chesapeake Bay and Gulf of Mexico, as well as between eastern and Pacific (Crassostrea gigas) oysters were determined. Since oyster host defense may play a role in determining susceptibility to pathogen infection, cellular and humoral defense activities of the oyster and their interactions with P. marinus were investigated. Procedures also had to be established to isolate, purify, and propagate in vitro, P. marinus. Eastern oysters from all sites were found to be highly susceptible to the pathogen. Cellular and humoral activities were significantly affected by heavy intensity of P. marinus infection. Prevalence and intensity of P. marinus infection were lower in Pacific oysters than in eastern oysters. Pacific oysters may offer a less favorable environment for the development of P. marinus compared to eastern oysters for at least two possible reasons: the elevated cellular and humoral activities may degrade the parasite more effectively, and lower plasma protein levels may limit parasite growth. Incubation of merozoites with hemocytes of eastern and Pacific oysters in vitro suggested that limited intracellular killing of P. marinus occurred but that killing was not mediated by oxygen metabolites. Perkinsus marinus was successfully propagated in vitro in a culture medium containing most of the known constituents of cell-free oyster hemolymph. Cultures of the parasite were initiated from heart fragments of infected oysters. The cultured protozoan was similar in morphology to P. marinus, enlarged in fluid thioglycollate medium, reacted with polyclonal antibodies raised against hypnospores and was infective. Continuous cultures of P. marinus could also be initiated from hypnospores. Two types of division, progressive cleavage and successive bipartition of the mother cell protoplast, were observed.

Hypoxia, low dissolved oxygen, is an important environmental stressor in estuarine systems. In this dissertation, I examine the effects of hypoxia on the macrobenthic communities of the York and Rappahannock Rivers, Chesapeake Bay, USA, and in particular its effects on the infaunal clam Macoma balthica. A survey of the macrobenthic community was performed using box-coring before and after hypoxia in 2003 and 2004 in both rivers. Hypoxia was associated with a change in the macrobenthic community towards smaller, shorter-lived, opportunistic species; and a substantial decrease in biomass. M. balthica recruited into all areas of the river but suffered local extinction in hypoxic areas, demonstrating that these areas represent sink habitats. I developed an enzyme-linked immunosorbent assay to quantify fecundity in M. balthica and used it determine the effect of hypoxia on clam fecundity. In laboratory experiments performed in 2005 and 2006, M. balthica migrated toward the sediment surface and decreased egg production in response to hypoxia. In field caging experiments, performed during the summers of 2005 and 2006, episodic hypoxia caused a three-fold increase in the rate of predation on M. balthica , suggesting that the behavioral responses of M. balthica to hypoxia make it more vulnerable to predation. These results further suggested that hypoxia may change the functional response of epibenthic predators to M. balthica from a stabilizing type III to a destabilizing type I or II. Using the results of the previous experiments, I constructed a density-independent model of the M. balthica population, which predicted that increasing the spatial extent and duration of hypoxia could cause the population to decline toward extinction. A second model, which incorporated density-dependent predation, predicted that, under mild hypoxic conditions, trophic transfer of biomass from M. balthica to predators could be enhanced, but that increasing the severity of hypoxia would decrease trophic transfer. The model further predicted that increasing hypoxia would decrease the resilience of the M. balthica population to disturbance, making functional extinction of the population more likely. This body of work underscores the negative effects of hypoxia on the levels of the individual, the population, and the ecosystem.

Continental shelves are generally believed to play a critical role in ocean biogeochemical cycling, however this has raised the question as to the relative importance of various nitrogen flux terms such as denitrification, burial, net community production and advective fluxes. Quantifying these fluxes on an annual area-integrated basis using traditional observational means is often difficult, due to the fact that these fluxes rapidly change on relatively small spatial scales, making inadequate data resolution a significant problem. Satellite remote sensing data and numerical modeling provide alternative ways to fill the data gaps, and hence have the potential to generate quantitative estimates of these various biogeochemical fluxes. However, they both suffer from distinct shortcomings, e.g., satellite data are only limited to the surface whereas numerical modeling can be pointless without rigorous skill assessment. Thus caution is warranted when using these tools to generate quantitative estimates of biogeochemical fluxes. The two were combined in this dissertation project by assimilating the satellite-derived data into the models, selecting the optimal ecosystem model, as well as evaluating the model before using the model simulations to explore the nitrogen fluxes on the Mid-Atlantic Bight (MAE). First, multiple satellite-derived data products were assimilated into a one-dimensional assimilative model framework to determine the relative advantages of assimilating different satellite data types. The variational adjoint method, a parameter optimization method, was applied to a series of experiments assimilating synthetic and actual satellite-derived data, including total chlorophyll, size-fractionated chlorophyll and particulate organic carbon (POC). The experiments revealed the importance of assimilating data from multiple sites simultaneously as the optimal parameter sets produced by assimilating data at individual sites were often unrealistically over-tuned and deteriorated model skill at times and depths when data were not available for assimilation. The model-data misfits from the experiments also demonstrated that optimal results were obtained when satellite-derived size-differentiated chlorophyll and POC were both assimilated simultaneously. These two types of satellite data were then assimilated simultaneously to rigorously evaluate how food web model complexity affects the ability of a lower trophic level model to reproduce observed patterns in satellite-derived data. This was again implemented in the one-dimensional model framework to minimize the computational costs. Five ecosystem model variants with various levels of complexity in the phytoplankton (P) and zooplankton (Z) structures were examined by assimilating satellite-derived size-differentiated chlorophyll and POC data at four MAE continental shelf sites, and testing the optimal parameter values at five independent sites in a cross-validation experiment. Although all five models showed improvements in model skill after the assimilation, the moderately complex 2P2Z model best reproduced the surface fields throughout the MAE. Additional experiments were conducted in which random noise was added to the satellite data prior to assimilation. Whereas the most complex model was sensitive to the random noise added to the data, the simpler models successfully reproduced nearly identical optimal parameters regardless of whether or not noise was added to the assimilated data, highlighting that random noise inherent in data into these simple models. The moderately complex 2P2Z ecosystem model was thus coupled with a three-dimensional circulation model and forced by a dynamic land ecosystem/watershed model to simulate the biogeochemical cycling on the MAB shelf and to quantitatively assess key components of the annual area-integrated nitrogen budget from 2004-2007. The simulation indicated that over these four years similar amounts of nitrogen were removed by denitrification and burial (∼0.1 Tg N y-1). Net community production was larger and varied more between the four years (∼0.2 to 0.3 Tg N y-1), but overall was positive, indicating that the MAB was net autotrophic. The advective fluxes of nitrogen into and out of the MAB were dramatically different between the four years investigated (by about ∼.26 Tg N y-1), presumably as a result of changes in the positions of the Gulf Stream and Labrador Sea waters. The accumulative effects of these fluxes resulted in a near zero net rate of change in total nitrogen, indicating the MAB remained unchanged in the amount of total nitrogen in the water column over these the four years. Sensitivity tests varying the initial conditions and simplifying the modeled plankton structure showed distinct impacts on these nitrogen fluxes: the former strongly affected the advective fluxes, but had little impact on denitrification, burial or NCP, whereas the latter significantly reduced denitrification, burial, and NCP but did not significantly impact the advective fluxes. Overall the strong seasonality and interannual variability in the nitrogen fluxes highlight the importance of data coverage throughout all seasons and multiple years in order to accurately resolve the current status and future changes of the MAB nitrogen budget.

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