Freshwater inflows are essential to the health of estuaries and minimum discharge levels must be maintained in order to sustain a healthy ecosystem. Due to the predicted 50% increase in urban population growth along the Texas coastline by the year 2050, water regulators and managers are faced with the challenge of meeting human needs, while maintaining essential freshwater inflows into estuarine ecosystems. Galveston Bay is of particular concern because 10 million people currently living within its watershed. Freshwater inflows into Galveston Bay during 2006 were determined by using daily discharge data from a United States Geological Survey (USGS) sampling gauge in the Trinity River. Changes in water quality parameters, primary productivity, and phytoplankton community structure in response to freshwater inflows, were monitored monthly to determine how the phytoplankton community responded to inflow events. Freshwater inflow into Galveston Bay during 2006 was indicative of a low-inflow year, with seven large (>7,000 ft.3 sec-1) inflow events occurring throughout the year. There were significant differences in phytoplankton biomass (Fm), photosynthetic efficiency (alpha), and photosynthetic potential (yield) of the phytoplankton community, between wet (January-April and October-December) and dry (May-September) months. Significant differences in the biomass of phytoplankton groups also occurred with cyanobacteria being present in higher concentrations during the dry months and diatoms & dinoflagellates during the wet months. Low flow periods favored cyanobacteria, which lead to decreased secondary productivity, while pulsed inflow events resulted in enhanced secondary productivity by favoring diatoms and dinoflagellates. Resource Limitation Assays (RLAs) indicated that nitrogen was a potential limiting nutrient in Galveston Bay during spring/summer, with light limitation of phytoplankton communities possibly occurring near the mouth of the Trinity River. This study demonstrates the role of freshwater inflows in determining the primary productivity and community composition of the phytoplankton in Galveston Bay over an annual cycle. Inter-annual studies are needed to elucidate the impact of freshwater inflows in years with higher inflows to Galveston Bay and determine which of these impacts need to be incorporated into water management decisions to maintain a healthy ecosystem.

Corpus Christi Bay (TX, USA) is a shallow wind-driven bay which is designated as a National Estuary due to its impact on the economy. But this bay experiences periodic hypoxia (dissolved oxygen <2 mg/l) which threatens aerobic aquatic organisms. Development of the Coastal Margin Observation and Assessment System (CMOAS) through integration of real-time observations with numerical modeling helps to understand the processes causing hypoxia in this energetic bay. CMOAS also serves as a template for the implementation of observational systems in other dynamic ecosystems for characterizing and predicting other episodic events such as harmful algal blooms, accidental oil spills, sediment resuspension events, etc. State-of-the-art sensor technologies are involved in real-time monitoring of hydrodynamic, meteorological and water quality parameters in the bay. Three different platform types used for the installation of sensor systems are: 1) Fixed Robotic, 2) Mobile, and 3) Remote. An automated profiler system, installed on the fixed robotic platform, vertically moves a suite of in-situ sensors within the water column for continuous measurements. An Integrated Data Acquisition, Communication and Control system has been configured on our mobile platform (research vessel) for the synchronized measurements and real-time visualization of hydrodynamic and water quality parameters at greater spatial resolution. In addition, a high frequency (HF) radar system has been installed on remote platforms to generate surface current maps for Corpus Christi (CC) Bay and its offshore area. This data is made available to stakeholders in real-time through the development of cyberinfrastructure which includes establishment of communication network, software development, web services, database development, etc. Real-time availability of measured datasets assists in implementing an integrated sampling scheme for our monitoring systems installed at different platforms. With our integrated system, we were able to capture evidence of an hypoxic event in Summer 2007. Data collected from our monitoring systems are used to drive and validate numerical models developed in this study. The analysis of observational datasets and developed 2-D hydrodynamic model output suggests that a depth-integrated model is not able to capture the water current structure of CC Bay. Also, the development of a threedimensional mechanistic dissolved oxygen model and a particle aggregation transport model (PAT) helps to clarify the critical processes causing hypoxia in the bay. The various numerical models and monitoring systems developed in this study can serve as valuable tools for the understanding and prediction of various episodic events dominant in other dynamic ecosystems.

This study aims to understand the role of the Tapong Bay on carbon biogeochemical cycle in the coastal zone and the influence of terrigenous inputs on ecosystem functioning in the Tapong Bay. The Tapong Bay is a semi-enclosed lagoon, occupied largely by fish farming cages and oyster culture racks. There is only one tidal inlet for exchanging water between the Tapong Bay and Taiwan Strait, which results in a low water exchange rate and oxygen deficient condition in the bottom water of the inner bay. The annual mean of water exchange time is about 10.6 days that is much longer than that in the Chiku Lagoon (5.8 days). Experimental results show that biological activity and variations of hydrochemistry primarily control the distributions of carbon and nutrients. Excess of DIP likely occurred in the Tapong Bay. Seasonal variations of primary productivity are apparently controlled by temperature, solar radiation and turbidity. The regression slope between particulate organic carbon and nitrogen approaches the Redfield ratio, indicating that organic carbon is derived primarily from biological production. The stratification of water column in the Tapong Bay was observed throughout the year. Diffusion from sediment may thus contribute significantly to nutrient distributions in bottom water. Diffusion flux estimated from porewater to bottom water is about 7.6% of annual mean input for DIN and is about 1.0% for DIP. Calcification process was observed in the Tapong Bay indicating that the oyster culture would affect the carbon budget in the bay. The annual mean production rate of organic carbon estimated from the biogeochemical model is about 5.80 mole C m-2 yr-1, implying that the Tapong Bay is an autotrophic system. The net ecosystem production (NEP) derived from diel observation is about 6.29 mmole C m-2 d-1 that is closed to 6.65 mmole C m-2 d-1 estimated from the biogeochemical modeling. The annual nitrogen fixation exceeds the annual denitrification [(nfix-denit)¡×1.30 mole m-2 yr-1] in the Tapong Bay. Carbon biogeochemical fluxes and budgets differ significantly between the Tapong Bay and the Chiku Lagoon, which may be arisen from pronounced difference in terrigenous inputs and seawater exchange rates.

A 3D numerical model ¡V COHERENS has been applied to construct a coupled hydrodynamic and ecological model for studying Tapeng Bay, which is a coastal lagoon situated in southwest of Taiwan. The simulations have been carried out to study the influences and their interacting mechanisms among the tidal currents, nutrients and micro planktons in the Lagoon. Model results have been compiled for calculating the nutrient fluxes and the primary productions in the Tapeng Bay. Tapeng Bay is a semi-enclosed coastal lagoon, which has only one tidal inlet for exchanging lagoon water with the coastal currents along the Kaoping coast on the narrow shelf in southwest of Taiwan. The study area is situated in the tropical climate zone where has sunshine through out the year except the rainy days concentrated in the summer season, which is influenced by the southwest monsoon. There are several drainage channels that collect the untreated domestic sewerage and wastewater discharged from the fish farms surround the lagoon. The discharges in these channels are usually low during the dry season. The solid contained in the water are mostly settled on the channel beds. During the raining season, high discharges due to the storm rainfalls re-suspend the sediments and carry into the lagoon. These sediments, which contain high concentrations of suspended solids and nutrients, cause the Bay water highly eutrophied. Therefore, the Bay is fully influenced by the seasonal variations. There are a lot of aquaculture, i.e. oyster farming and fish cage, in the Bay area since the water is calm and rich. But the balance between the nature and the anthropogenic disturbance is breaking. Besides the water level variation generated from the tidal inlet, the fresh water inflow from 3 major channels are included in the model to simulate their influences to the hydrodynamics and the density driven circulation due to changing salinities and temperatures from these inlets. Plankton, detritus, dissolved nutrients and dissolved oxygen is taking into account as the model variables for this marine eco-system. The plankton growth is mainly generated due to temperature, light intensity and nutrient level. Only the nitrogen cycle has been considered in the model by assuming there are enough supply of phosphate and silicate. Model runs have been carried out according to different seasonal situations of the boundary conditions. Furthermore, climates (heats, lights, winds, etc) are also included in the model to distinct seasonal characteristics. It is shown, from the model results, that the currents mainly dominate the distribution of nutrients in the Tapeng Bay. The nutrient level controls plankton growth. The nutrient sources are mainly coming from the coastal currents (through tidal inlet) in the wintertime, whereas the summer source was from the drainage channels due to the wash out by the high discharge rates. Beside these, dissolved oxygen concentrations in the Bay water are strongly influenced by the plankton growth rate, faster the photosynthesis higher the DO concentrations. The eutrophication levels of the Tapeng Bay water have been compiled using the plankton carbon level modeled at various situations. According to the Nixon standard (1995), Tapeng Bay has eutrophication through out the year. Mesotrophic condition can be observed during the wintertime, whereas the hypereutrophic level can be concluded during the raining season.

The population dynamics and the feeding of the scyphomedusa Aurelia aurita in Tapeng Bay, southwestern Taiman, were investigated from April, 1999 to April, 2000 and May, 2001 to April, 2002. A. aurita distributed mainly in the inner water of the Bay. The average abundance of A. aurita was 71¡Ó256 ind.100m¡Ð3, with higher abundance in winter and spring than in summer and autumn. The abundance of A. aurita showed no significant correlation with hydrographic features, but it seems to have one or two month¡¦s time lag with the seasonal distribution pattern of copepods. The main reproduction period of A. aurita was form autumn to next spring. The occurrence of ephyra was mainly in winter and spring, with maximum abundance of 328 ind./100m3. The average bell diameter of A. aurita was 13.9¡Ó4.2 cm. The size of bell diameter varied seasonally, generally had larger size in autumn and smaller size in spring. Seventeen zooplankton taxa were found in the stomach contents of A. aurita, copepods were the most dominant (70.3%), followed by copepods nauplius (20.1%), bivalve larva (3.0%) and fish eggs (2.3%). The average ingestion rate of A. aurita was 2165¡Ó2673 prey ind.-1 day-1 , the feeding impact of A. aurita on zooplankton was 14.69 % ~ 40.84 % %, with no significant difference among sizes.

Several flatfish species including southern flounder (Paralichthys lethostigma) recruit to estuaries during early life. Therefore, the evaluation of estuarine sites and habitats that serve as nurseries is critical to conservation and management efforts. I used biochemical condition and growth measurements in conjunction with catch-density data to evaluate settlement sites used by southern flounder in the Galveston Bay Estuary (GBE). In 2005, beam-trawl collections were made in three major sections of the GBE (East Bay, West Bay, Galveston Bay), and three sites were sampled in each bay. Within each sampling site, replicate collections were taken from 1) the marsh edge, 2) an intermediate zone, and 3) the open bay. The average size of southern flounder collected was between 12 and 19 mm standard length, and peak densities occurred in January and February. Catch data indicated that numeric densities of southern flounder were significantly greater in East Bay (2.75 per 100 m2) than in West Bay (0.45 per 100 m2) or in Galveston Bay (0.91 per 100 m2). Habitat-specific variation in density was not found. Otolith-based estimates of age indicated that the majority of southern flounder collected were 35-45 days old and derived from early December to early January hatch-dates. Growth rate differences were negligible across bays and habitats, with the average growth rate being 0.40 mm/day (range 0.21-0.76 mm/day). RNA:DNA ratios indicated that newly settled southern flounder in the GBE were in relatively high condition. Habitat-specific differences in RNA:DNA ratios were not observed; however, ratios were significantly lower in West Bay (average 8.0) than in East Bay (average 9.5) or in Galveston Bay (average 9.8), suggesting the condition of new recruits may vary across the GBE. Findings from this study indicate that southern flounder use a variety of habitats within the GBE during early life, and survival and recruitment success appear favorable regardless of settlement site. As a result, recruitment success of southern flounder may be less a function of the quality of nursery sites/habitats within the GBE than of other factors (e.g., larval supply to the estuary).

Knowledge of surface sediment distribution in Galveston Bay is important because it allows us to better understand how the bay works and how human activities impact the bay and its ecosystems. In this project, six areas of bay bottom were surveyed using acoustic techniques to make maps of bay bottom types and to investigate the types and extent of anthropogenic impacts. A total of 31 km2 was surveyed in six areas, one in Bolivar Roads (6.1 km2), one near Redfish Bar (3.1 km2), two in East Bay (12 km2), one southeast of the Clear Lake entrance (5.3 km2), and one in Trinity Bay (4.3 km2). Sidescan sonars (100 kHz and 600 kHz) were used to image the bay bottom, and a chirp sonar (2-12 kHz) was used to image subsurface sediment layers and bottom topography. In the side-scan records, objects as small as a few meters in extent were visible, whereas the chirp sonar records show a vertical resolution of a few tens of centimeters. The sidescan images display strong backscatter in some areas due to coarse sediments in addition to weak backscatter in areas of fine sediment. The bay bottom was classified using three levels of sonar backscatter ranging from high to low. Areas of differing sonar backscatter intensity were sampled with cores and grab-samples. High backscatter corresponded to coarse shell debris and oyster reefs, medium backscatter corresponded to a sand-silt-shell mixture, and low backscatter corresponded to silty loam. Chirp sonar records were classified as one of nine different bottom reflection types based on changes in amplitude and stratigraphy. Parallel, layered sediments are seen filling the bay valley and resting atop a sharp contact at which the acoustic signal fades out. Along the flanks of the valley fill the acoustic response revealed an absent or weakly laminated stratigraphy, whereas areas of high oyster productivity produced mounds, strong surface returns, and strong, shallow subsurface reflectors surrounding current oyster reefs. Anthropogenic features imaged with the sonar included sediment disruptions, such as the ship channels, dredge holes, gouges, and trawl marks, as well as debris, such as submerged boats, pipes, and unidentified objects.

Project (D. Min.)--Iliff School of Theology, 2006. / Includes abstract. Includes bibliographical references (leaves 162-166).

Thesis (M.S.)--Rutgers University, 2009. / "Graduate Program in Geography." Includes bibliographical references (p. 38-50).

Thesis (M.S.)--University of North Carolina at Wilmington, 2004. / Includes bibliographical references (leaves : [74]-[78]).