Aquaculture of the hard clam, Mercenaria mercenaria, has steadily increased in the United States over the past 25 years. In some areas, including along Virginia’s coast, this industry has grown to such a scale that aquaculture systems now exist as agroecosystems within coastal waters. Several features of these aquaculture systems, such as high clam densities and protective mesh netting, may modify the availability of habitat, food, and nutrients and may be expected to affect benthic and nektonic community structure. Few studies, however, have evaluated these effects. We conducted seasonal (May – September) sampling in a tidal tributary of Chesapeake Bay in three shallowwater habitat types – clam aquaculture, seagrass beds, and unvegetated bottom. Multiple trophic levels were sampled, including attached macroalgae, resident epibenthos, and mobile demersal and nektonic fishes and crustaceans. We compared biomass and abundance of trophic assemblages across the three habitat types. Trophic linkages were quantified through diet analyses of top predators. Results indicate that less-mobile communities showed more differentiation across the three site types. Assemblages supported by clam aquaculture and seagrass sites tend to be more similar to each other than they are to the assemblages at the unvegetated sites. Prey assemblages demonstrate a distinct shift, however, from May/July to September; during May/July the seagrass site supports the highest biomass and abundance of prey, but in September the clam aquaculture site supports the highest biomass and abundance of prey. This shift seems to correlate with the presence of structure (natural and man-made) within each site. Highly mobile top-predators show little preference among clam aquaculture, seagrass, and unvegetated sites. Diets of top predators do not exhibit a consistent pattern based on the site in which the individual was caught, but the diets of some species do correlate to the prey communities at a specific site. The added structure and organic matter deposition associated with clam aquaculture sites appear to create functional redundancy and temporal variability within Cherrystone Creek, potentially enhancing the stability of the creek system.

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Two groups of juvenile summer flounder maintained at 5�C were experimentally infected with the hemoflagellate Trypanoplasma bullocki. Another group maintained at 5�C was not infected. The water temperature of one infected group was raised stepwise to 12�C, 18�C, and 24�C for 2 to 3 weeks at each level. The other infected group was maintained at 5�C for 12 weeks, the duration of the experiment. In addition, juvenile flounder were collected over a temperature range of 6�C to 22�C from February to June, 1982 to monitor natural infections. Live T. bullocki were incubated in plasma from fish at each temperature to monitor the host's humoral response. Trypanoplasmacidal lysis occurred in experimental infections maintained at 24�C and in natural infections over a range of 10�C to 22�C. Complete elimination of trypanoplasms occurred in experimental infections at 24�C and in natural infections at 22�C. Differences in temperature where lytic activity occurred was mainly attributable to the short time exposure of experimental infections to increasing temperatures in contrast to that occurring in nature. Trypanoplasmacidal lysis with increasing water temperatures in flounder indicates that the fish's humoral immunity is responsible for the annual spring decline in prevalence and eventual elimination of T. bullocki infections. Elevated levels of macroglobulins were detected in the sera of juvenile flounder recovering from T. bullocki infections, and this may be associated with antibody production in response to the parasite.

A one dimensional finite element model for the prediction of transient water quality in an estuary is developed. Ten water quality constituents, salinity, coliform bacteria, organic nitrogen, ammonia nitrogen, nitrite-nitrate nitrogen, organic phosphorous, inorganic phosphorous, phytoplankton as measured by chlorophyll 'a', DO and CBOD are included in the model. The effects of temperature, solar radiation and zooplankton predation are incorporated into the model as external forcing functions. The concentration distributions are obtained by solving the conservation of mass equations successively. A compatible hydrodynamic model is also developed to provide the driving transport processes to the water quality model. The finite element method is chosen in the numerical formulation because of its flexibility in grid layout. Linear interpolation functions are used for the spatial discretization. The time scale of the model is tidal time. The downstream boundary condition is related to the direction of tide. On flood tide the concentration of the inflowing water is prescribed. On ebb tide the dispersive flux is determined by the concentration distribution within the estuary. Two time integration methods, trapezoidal and explicit method with split time scheme, are developed. The trapezoidal scheme is found to be very stable and the accuracy is adequate for most applications. The explicit version of the computer program is shorter and the execution time is faster, but the size of the integration time step is more restricted. Both versions are validated against known analytical solutions for a rectangular channel with constant upstream boundary concentrations and uniform velocities. The implicit model was used to simulate the water quality in the James River estuary from March to October 1971. The model has also been applied to the Potomac River in Virginia, and is being applied to the Chester River in Maryland. A network version of the water quality model is also developed. The model is capable of simulating water quality in estuaries that have interconnecting channels or estuarine networks such as the lower portion of the Appomatox River. This model was used to simulate average water quality conditions in the Appomatox River.

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