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The first section of this dissertation describes the ichthyofaunal community of a mesohaline Chesapeake Bay April--November. Fish assemblages were sampled using two seine gears, a small seine that sampled 352 m 2 and a 914m haul-seine that sampled 144,473 m2. The small seine collected 32 finfish species. The larger gear captured 31 finfish species, including 17 that were not sampled by small gear. Sampled diversity was greater but density estimates were similar to those determined previously by other investigators using flume-net, drop-ring, and otter trawl techniques. Nocturnal abundance of larger fishes far exceeded daylight. Fish abundance and size distribution varied seasonally in both gears. The second section describes the littoral diet composition of striped bass (Morone saxatilis ), bluefish (Pomatomus saltatrix), and weakfish (Cynoscion regalis). These species were the most abundant piscivores sampled in the littoral zone. as in previous Chesapeake Bay diet studies the importance of pelagic prey increased with predator size, however, littoral diets evidenced greater dietary diversity and dependence on crustacean prey items. The third section consists of bioenergetic models that predict piscivore growth based on estimated nocturnal consumption and test energetic consequences of diel thermal refugia. Bluefish and weakfish were predicted to achieve better growth rates than those evidenced by field samples of aged fishes collected from across random Chesapeake habitats. Models predict that striped bass experience declining condition during warm water periods due to physiological stresses and poor prey acquisition. Theoretical diel relocation models illustrated how important species and age specific metabolic restrictions due to physical parameters are to fish health. Findings suggest that habitat specific physical dynamics may be as important as prey provision in determination of and spatial assessments of essential fish habitats.

One of the main threats to water quality in the Chesapeake Bay is contamination by bacterial loading from point and non-point sources. While only very high levels of fecal bacteria (greater than 200 MPN/100ml) indicate the potential of a health threat to humans from contact with water, lower concentrations (14 MPN/100 ml) make the shellfish from contaminated waters unfit for human consumption. Many nearshore areas that are vulnerable to bacterial contamination also are suitable for the propagation of shellfish, including the hard clam (Mercenaria mercenaria). This is especially true on Virginia’s Eastern Shore, where shallow, sheltered waters with optimal salinity and little pollution support a hard clam aquaculture industry that had an economic impact upwards of $48 million in 2004 (Murray and Kirkley, 2005). Over the past decade, however, development pressures on the Eastern Shore have increased, and land has been converted from forests and fields to subdivisions and strip malls at a faster rate than in the past. Even in the absence of a point source of bacteria such as a wastewater treatment plant, bacterial loads from non-point sources associated with increased land development have the potential to degrade water quality to the detriment of marine life and marine resource users. One area where the conflict between aquaculture and other water qualitydependent uses, and development pressure is building is the Old Plantation Creek watershed on the Eastern Shore of the Chesapeake Bay. Using a GIS-based watershed model to simulate land use and associated fecal bacteria loads, linked to a Tidal Prism Water Quality Model to estimate the disbursement of bacteria throughout the water body, this study predicts that if development continues to the maximum buildout allowed under current regulations it would lead to the condemnation of a large portion of the shellfish growing waters in Old Plantation Creek. By coupling this linked watershed-water quality model with an economic Input/Output (I/O) model, it was possible to determine the economic impact of those condemnations to the aquaculture industry and the economy of Virginia.

Blue marlin diversity was assessed at mtDNA, scnDNA, microsatellite DNA, and allozyme molecular markers. Hierarchical analysis of molecular variance (AMOVA) revealed that most genetic variation was maintained within populations, with a non-significant fraction attributable to variation among temporal replicates and between locations within oceans. In contrast, inter-ocean divergence was highly significant for a majority of loci within each marker class. Previous studies of mitochondrial DNA (mtDNA; n = 104) genetic variation within the blue marlin revealed two distinct clades of haplotypes, one of which was present only in the Atlantic (the 'Atlantic clade'), at a frequency of 40% &(F\sb{lcub}st{rcub}& = 0.39). ScnDNA and allozyme markers exhibited lower levels of diversity and inter-ocean divergence than mtDNA (average &F\sb{lcub}st{rcub}& = 0.08). Enhanced genetic drift among populations, due to the four-fold lower effective population size of mtDNA, was emphasized as causing the greater mtDNA inter-ocean divergence. The low mutation rate of nuclear markers, and greater male dispersal may have contributed to the difference detected. Microsatellite loci were hypervariable, and displayed a wide range of divergence estimates (average &F\sb{lcub}st{rcub}& = 0.14). A nuclear 'Atlantic clade' of alleles was detected at one locus, indicating that the historical forces that generated the mitochondrial Atlantic clade (Pleistocene allopatry) also strongly influenced the nuclear genome. Although some microsatellite loci were much more sensitive than scnDNA markers, on average, these differences were not significant, due to the wide range of microsatellite patterns detected. The mean and variance of inter-ocean divergence &(F)& estimates were not significantly different among marker classes, suggesting a minor influence of selection. Correlations between diversity and divergence within and among marker classes were non-significant, indicating that difference in mutation rate can not explain the lower nuclear divergence. The patterns of diversity obtained within and among marker classes is consistent with expected values under migration-drift equilibrium.

The diseases Dermo and MSX have devastated Chesapeake Bay populations of the eastern oyster, Crassostrea virginica. The protozoan Perkinsus marinus, which causes Dermo, is particularly problematic since it persists over a wide range of salinities and temperatures. An objective of this dissertation was to determine whether specific wild oyster stocks had developed natural resistance to Dermo and if several parameters (survival, growth, condition and energy reserves) were associated with resistance. Another objective was to characterize heat shock protein (hsp70) expression in the eastern oyster. Heat shock proteins such as hsp70 protect organisms from thermal stress and other stressors, and this function may play an important role in disease resistance in oysters. In field trials a F0 Chesapeake Bay stock from Tangier Sound (CTS) survived similarly to a disease resistant hatchery strain (XB). A Louisiana stock was also resistant to Dermo, but not MSX. Despite high mortality, a disease-susceptible stock (CRB) reached market size the fastest. Growth and condition index varied between stocks, but did not reflect Dermo resistance. Energy reserves were affected strongly by season, but not disease or stock. Results imply that Dermo resistant strains could be developed from these stocks but criteria for optimal strain selection for aquaculture and restoration may be divergent. Mortalities of F1 oysters (CRB, CTS and XB) were similar to F0 parents, demonstrating a genetic basis to Dermo resistance. Total hsp70 did not correlate with seasonal temperatures, while hsp70 isoforms (hsp69 and hsp72) varied inversely across seasons. Hsp70 did not vary significantly between strains, indicating a stronger environmental influence on hsp70 expression. In lab experiments hsp70 in oyster gills was elevated greater than two weeks after a sub-lethal heat shock. Thermal tolerance, but not hsp70, varied between CTS and Louisiana oyster stocks. Heat shock protected oysters experimentally infected with P. marinus and non-infected oysters from lethal heat stress. Infection alone induced expression of hsp70. Observed inherent and induced differences in thermal tolerance suggest that both genotype and phenotype may be manipulated to improve survival in cultured bivalves. The implications of this research for bivalve aquaculture as well as areas for future research are discussed.

Oyster production in Virginia has declined dramatically in the past ten years, causing Virginia oyster processors to rely increasingly on oyster supplies from other regions. In response to the industry problems, the Virginia Marine Resources Commission (VMRC) developed and began implementing an Oyster Fishery Management Plan (OFMP) in 1985. Primarily, the plan seeks to increase Virginia oyster production from both public and leased grounds. A large increase in production could significantly affect the oyster market. There is thus a need to understand the Virginia oyster market, which derives raw material supplies primarily from public and leased-grounds production and from other states. Although the level of competition among the three sources is uncertain, it is thought to be substantial and quite important for the success of the OFMP. This study assesses the level of competition and associated sector interaction. A simultaneous equation system is specified and estimated by Full-Information-Maximum-Likelihood procedure. Estimates and a market simulation model are used to assess the impact of the OFMP on market behavior. Analyses indicate that the market for the public ground fishery consists of an elastic demand and an inelastic supply, but the market for private oyster cultivation consists of an inelastic demand and an elastic supply. The market interaction between the eastern oyster and Pacific oyster is weak. Oysters from leased grounds compete with supplies from other regions and with Pacific oysters. Market simulations indicate that the OFMP will increase total revenue for both public and private producers, suggesting that (1) the seasonal closure on commercial oyster fishery may be extended as stock size recovers, (2) increasing private production may reduce oyster supplies from other states, and (3) from the market interaction point of view, the Pacific oyster may be an alternative for private oyster planters.

The bioaccumulation and metabolism of organic contaminants (PAH, PCB) by three estuarine polychaetes, Nereis succinea (Frey and Leuckart 1847), Paraprionospio pinnata (Ehlers 1901) and Polydora ligni (Webster 1879), and by the fish predator, spot (Leiostomus xanthurus Lacepede 1802), were examined in laboratory experiments. Variations in trophic transfer of these contaminants resulting from differences in prey and contaminant type were also investigated. Toxicokinetic modeling reveals that metabolism of organic contaminants by invertebrate species result in variations in uptake, metabolism and elimination rate constants. Incorporation of prey metabolism potential in kinetic models increases the latter's predictability of biota-sediment accumulation factors (BSAFs), or the net result of uptake and elimination processes. With organisms that have moderate to high metabolic capabilities and slow metabolite elimination, high rates of metabolite formation will significantly underestimate the uptake clearance rate constant and BSAFs, and the models will have low predictive capabilities. Assimilation efficiency of organic contaminants by spot varies with prey type, metabolism and size; contaminant type; and is independent of prey concentration at low contaminant concentrations. Furthermore, toxicokinetic modeling indicate that there are significant differences in uptake and metabolism formation rate constants by spot due to variations in the metabolite content of its food, and significant differences in elimination rates between spot tissues and contaminant types. In addition, aqueous soluble metabolites from prey were less available to predators, and dietary accumulation factors are reduced with contaminant metabolism. The metabolic responses by organisms to toxic organic contaminants must be considered in toxicokinetic modeling, and knowledge of benthic invertebrate prey species metabolism can be used to increase the predictability of BSAF. The metabolism potential of both the prey and contaminant is therefore important in the long term, integrated process of trophic transfer. Differences in prey contaminant forms and concentrations will strongly influence the trophic transfer of organic contaminants. Predator diet will strongly influence its contaminant exposure and possible effects through preconsumptive metabolism of organic contaminants by prey. These results have important implications for modeling organic contaminant trophic transfer and fate in estuarine and coastal systems.

In 1988 laboratory presentations, bay anchovy, and Atlantic menhaden tested positive as potential predators. Consumption of striped bass larvae by bay anchovy increased at higher prey densities to a maximum of 42 larvae/h at prey densities of 1,650/m&\sp3&. Examination of 229 stomachs of bay anchovy collected during peak spawning in 1988 and 1989 provided direct evidence of predation on striped bass eggs and larvae. The relationship between patterns of survival inferred from the back-calculation of juvenile hatchdates were compared with data sets describing predator and prey fields, egg production, food abundance, and changing environmental conditions during the 1988 and 1989 spawning seasons. The physical factors pH, rainfall, dissolved oxygen, and water temperature were measured at 30-minute intervals and observations of predator, prey, egg and larval densities were recorded weekly or semi-weekly. In 1988, a year of average recruitment, only 11% of the juveniles aged (n = 78) were born during the week of peak spawning when over 48% of the eggs were produced. In 1989, a year of high recruitment, the temporal distribution of juvenile hatchdates more closely followed the distribution of eggs with 30% of the juveniles (n = 96) born during the week of peak spawning when 40% of the eggs were spawned. Potential fish predators were collected in greater numbers during peak spawning in 1988 (61/100m&\sp3&) than during the same period of time of 1989 (12/100m&\sp3&). Water temperatures were lower during peak spawning in 1988 (16&\sp\circ&C) than during 1989 (19&\sp\circ&C). Also, prey items for first-feeding larvae decreased the week following peak spawning in 1988 from an average number of 194 to 74 individuals/l. Lower water temperatures and reduced food densities in 1988 may have produced a combined effect of prolonging developmental stages of striped bass eggs and larvae, thereby making them more susceptible to elevated predator densities. Dissolved oxygen values were inversely related to water temperature, reaching low values of about 6 mg/l after water temperature reached about 25&\sp\circ&C and spawning had ceased. Although pH values were usually around 7.0 throughout the 1988 and 1989 spawning seasons, pH depressions associated with rainfall were noted during both years.