Dissertations
Permanent URI for this collectionhttps://hdl.handle.net/1969.6/1139
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Browsing Dissertations by Department "Physical and Environmental Sciences"
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Item Assessing the occurrence, social vulnerability, and legal implications of sargassum influxes in Puerto Rico using a social-ecological systems approach(2023-5) Leon-Perez, Mariana C.; Gibeaut, James; Porter, Kateryna Wowk; McLaughlin, Richard; van Tussenbroek, BrigittaSargassum spp. influxes are causing significant alterations to both natural and human systems in the Wider Caribbean Region. To understand and respond to this situation, a holistic approach is needed that considers the distribution and dynamics of pelagic sargassum and the impacts and feedback between the natural and human systems. This research aimed to provide information for the decision-making processes regarding sargassum accumulations on the coasts of Puerto Rico. Remote sensing techniques implemented in Google Earth Engine were used to detect and spatiotemporally assess sargassum accumulations along the shoreline. The model developed was able to identify both fresh and decomposing sargassum, as well as Sargassum-brown-tide generated from decomposing sargassum. A combination of a participatory exercise and surveys were used to assess the social vulnerability of an impacted coastal community and to identify factors to reduce their social sensitivity and improve their adaptive capacity, such as establishing mitigation actions to reduce the exposure of residents to toxic gases and improving access to sargassum information. Lastly, legal barriers to implementing effective mitigation strategies and agencies jurisdictions in the permitting process were clarified using a co-production approach with local and federal agencies. Recommendations provided include the development of a territory-wide and priority areas response plans and the continuation of meetings with agencies to clarify legal aspects of sargassum mitigation actions including its disposal on land. This dissertation provides much needed information for household, community, and national decision-making. Methods and findings of this dissertation can also be applied to inform decisions in other coastal areas in the region affected by these recurrent events.Item Assessment of the planetary boundary layer over the Northesatern Pacific Ocean: Impact of ducting and horizontal inhomogeneity on GNSS radio occultation measurements(2023-12) Winning Jr., Thomas E.; Xie, Feiqin; Liu, Chuntao; Shinoda, Toshiaki; Starek, Michael; Spaniol, FrankIn the northeastern Pacific Ocean, strong free tropospheric subsidence and cooler sea surface temperatures due to upwelling result in a distinctive planetary boundary layer (PBL), marked by a sharp temperature inversion and moisture gradient. This distinct subtropical eastern ocean region showcases a unique transition from a shallow stratocumulus-topped PBL near the southern California coast to a deeper trade cumulus PBL regime closer to Hawaii. The shallow PBL coupled with frequent cloudiness poses significant challenges for conventional space-based observations and simulations in weather and climate models. The Global Navigation Satellite System (GNSS) radio occultation (RO) technique excels in sensing the PBL due to its superior vertical resolution, global coverage, and all-weather observation capability. This dissertation is comprised of three major tasks aimed at assessing the potential and limitation of GNSS RO for PBL sensing over the northeastern Pacific Ocean. First, the RO refractivity data from the first Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC-I) for the years 2007 to 2012 were used to derive the PBL height (PBLH) climatology over the Northeastern Pacific Ocean. The PBL in this region is characterized by pronounced temperature inversions and moisture gradients across the PBLH, leading to dominant ducting conditions that introduce significant negative biases in RO refractivity retrievals. Consequently, the second task examines the characteristics of the elevated ducting layer along the transect between Los Angeles, California and Honolulu, Hawaii with high-resolution radiosondes from the MAGIC field campaign and ERA5 global reanalysis data. A systematic negative refractivity bias (N-bias) below the ducting layer is observed throughout the transect, peaking approximately 70 meters below the PBL height (−5.42%), and gradually decreasing towards the surface (−0.5%). Third, the noticeable horizontal inhomogeneity, especially near the PBLH along the transect, may introduce additional RO retrieval errors, warranting further investigation. Using MAGIC radiosonde observations, a 2-dimensional (2D) model of atmospheric refractivity is created which integrates key PBL parameters. An asymmetry index is introduced to measure the extent of horizontal inhomogeneity. Then multiple phase screen (MPS) simulations were carried out to assess the impact of ducting and horizontal inhomogeneity on GNSS RO soundings. Preliminary findings highlight ducting as the primary cause of negative N-bias in RO retrieval, while horizontal inhomogeneity within the PBL contributes an additional −1% near the PBL top. This research enhances understanding of RO data quality within the PBL, paving the way for improved RO data assimilation and advancing weather and climate prediction capabilities.Item Associations between chlorophyll and wind forcing in the Gulf of Mexico derived from satellite observations(2015-08) Trnka, Maureen C.; Zimba, Paul; Shirley, Thomas C.; Thomas, AndrewThe Gulf of Mexico supports many industries that rely on its natural resources. Primary production is required to sustain fish populations and contributes to ocean carbon exchange. Ocean color satellites make it possible to observe large geographic areas; however, an individual sensor has limited coverage. The GlobColour project merges observations from multiple satellites into a single product. The purpose of this study is to use GlobColour and QuikSCAT to investigate the seasonal and non-seasonal associations between chlorophyll and wind from 2000-2008 in the Gulf of Mexico. An overview of the Gulf of Mexico’s physical setting, circulation, and main features is presented. The Gulf is divided into: Interior Basin, West Florida Shelf, Louisiana-Texas Shelf, Tamaulipas-Veracruz Shelf, Bay of Campeche, and Campeche Bank. Phytoplankton biomass is discussed in the context of nutrient-transport mechanisms including coastal upwelling, Ekman pumping, horizontal advection, and vertical turbulent mixing. Seasonal associations are evaluated between chlorophyll and wind using Empirical Orthogonal Functions and Singular Value Decomposition. Chlorophyll has strong seasonal variability over the shelves. The interior variability of chlorophyll and wind speed is in-phase with annual periodicity, increasing in winter and decreasing in summer. Strong winter winds increase the upward turbulent transport of nutrients into the mixed layer. The northern chlorophyll variability has a dipole with increased anomalies over the Western Shelf and decreased anomalies around the Mississippi mouth; associated with intensified easterly winds. Non-seasonal anomalies of chlorophyll and wind are similarly investigated. Increases in wind speed are associated with chlorophyll increases over the Campeche Bank, Bay of Campeche, and West Florida Shelf; the mechanism is upward entrainment of nutrients by turbulent mixing. Northerly winds are associated with coastal upwelling in the Bay of Campeche, offshore advection in the west, and a chlorophyll dipole across the Mississippi mouth. The non-seasonal coupled patterns are predominantly intraseasonal and spatially coherent with interannual modulations. This study is the first to apply a merged ocean color product to research in the Gulf of Mexico. Overall, this project provides baseline information on the seasonal and non-seasonal variability of chlorophyll and winds, identifies statistical associations, and proposes dynamical mechanisms.Item Dazed and confused: pesticides alter physiology, behavior, and predator-prey interactions of juvenile and adult blue crabs (Callinectes sapidus)(2017-05) Schroeder-Spain, Kaitlyn J; Smee, Delbert Lee; Shirley, Thomas; Wetz, Michael S.; Zimba, Paul V.; Deis, DonaldToxicants (i.e., pesticides) and predators may have large and interacting effects on natural communities by removing species (lethal effect) or by altering organismal physiology or behavior (sublethal effect). Studies evaluating the effects of sublethal concentrations of pesticide mixtures are limited, especially in coastal systems [1]. The purpose of this dissertation research was to investigate both lethal and sublethal effects of realistic pesticide exposure scenarios on two life-stages (juvenile and adult) of an important invertebrate estuarine predator, prey, and fishery species, the blue crab (Callinectes sapidus). Importantly, blue crab populations are declining throughout the U.S., but the potential role of pesticides in declines remains largely unexplored. In a series of laboratory experiments, I investigated: (1) lethal and sublethal effects of a single exposure to carbaryl (carbamate), malathion (organophosphate) and resmethrin (pyrethroid) + PBO (synergist), individually and in mixtures, on juvenile and adult blue crab survival and neuromuscular functioning by measuring changes in mortality, righting time (RT), and eyestalk reflexes. These responses serve as a proxy for the direct effects of exposure on survival and indirect effects on coordinated behaviors critical to blue crab survival (e.g., predator escape or foraging). Pesticides were selected because they are three of the mostly commonly used throughout the U.S. and have different modes of action. Effects observed at the organismal level were subsequently evaluated and linked with changes in (2) predator-prey interactions (mesocosms), and (3) physiological responses (enzyme assays). Lastly, (4) differences in susceptibility between juvenile (post-planktonic) and adult life-stages were also evaluated in behavioral and predator-prey experiments. Sublethal, legally allowable concentrations of individual pesticides and pesticide mixtures negatively affected juvenile and adult blue crabs by (1) reducing survivorship and locomotor functioning, (2) altering predator-prey interactions via changes on foraging rates and increased vulnerability to predators, and (3) increasing metabolic costs (e.g., AChE synthesis). These findings underscore the importance of studying pesticide effects in an ecological context, as juvenile life-stages were not always the most vulnerable, some effects varied non-linearly with concentration, and interactions between individual pesticides in mixtures were not necessarily predicable based on individual exposures. Notably, blue crabs were most sensitive to exposures including pyrethroid (resmethrin) + PBO, which are representative of common co-components of vector control products. Pyrethroid use for mosquito abatement and disease control is expected to increase, and the application of such products near aquatic systems should be carefully evaluated. In blue crabs, behavioral changes (e.g., RT) provided a reliable and sensitive endpoint, indicating altered physiological (i.e., increased AChE activity) and predator-prey interactions (i.e., reduced foraging, increased vulnerability to predators) in the pesticide exposures studied. Results also highlight the importance of studying individual responses with increasing levels of biological organization, e.g., changes in species interactions, as increases in RT unexpectedly corresponded with increased consumption rates in juvenile crabs (e.g., hyperactivity, Chapter 2). In the context of fisheries management and environmental regulations, RT may be a useful endpoint when measured in combination with other responses to indicate chances of survival or altered trophic relationships [2, 3].Item Defining essential fish habitat in an ecosystem context: practical identification and relevance to management(2019-08) Olsen, Zachary; Stunz, Gregory W.; Tolan, James; Montagna, Paul; Pollack, Jennifer Beseres; Rios, JoWhile traditional fisheries management has been that of a single species approach, ecosystem-based management would allow for greater confidence and efficiency in fisheries management decision making. However, there is no consensus regarding what ecosystem-based management would look like in practice. The goal of this dissertation was to create a conceptual framework that will guide the incorporation of habitat data into existing fisheries management paradigms. This framework consists of three focus areas: (1) functional examination of fisheries-habitat relationships, (2) identification of linkages from habitat to population level impacts, and (3) identification of relevant application to specific management scenarios. The Black Drum (Pogonias cromis) population in the Upper Laguna Madre (ULM) was used as a case study to exemplify the quantification of functional habitat relationships (focus area 1) and to further link stage-specific habitat relationships (e.g., nursery habitat) to the population dynamics of the full population (focus area 2). These analyses were conducted using data from fisheries independent bag seine surveys collected by Texas Parks and Wildlife Department. Relationships between habitat variables (salinity, water temperature, and dissolved oxygen) and juvenile vital rates (mortality and growth) were modeled and then employed in a stage-specific population model. The salinity – juvenile mortality relationship was found to substantially influence the finite rate of increase for the full population. Two specific application of habitat data in fisheries management decision making were then demonstrated (focus area 3). The first application used habitat suitability models for three estuarine species to examine changes in the extent and distribution of suitable habitat within three classes of estuary (positive, neutral, and negative) across three salinity regimes (low, moderate, and high). The second application was a formal decision support tool that usedItem Determining source apportionment of Din and Don in a Gulf of Mexico watershed and airshed(2023-5) Qiu, Yixi; Felix, Joseph; Murgulet, Dorina; Abdulla, Hussain; Wetz, MichaelDissolved organic nitrogen (DON) profiles and contributing sources are poorly characterized in estuarine systems despite studies showing it constitutes a significant portion of the total nitrogen pool and inputs. The characterization of dissolved inorganic nitrogen (DIN) and DON processing along the pathways of surface/subsurface flow and wet deposition is also not well constrained. This dissertation work used stable isotope techniques to complete a comprehensive investigation of DIN and DON profiles, transformations, and sources across the hydrosphere (ground, surface, pore and rainwater) of a semi-arid estuary system (Baffin Bay, TX). Rainwater directly deposited 5.2 kg N/(ha*yr) to the watershed and had relatively low concentrations and varied nitrogen isotopic compositions of NH4+ (~27 µM; -10-7‰), NO3- (~17 µM; -7-10‰), and DON (~11 µM; -7-18‰). Isotope mixing model results implied agriculture and vehicle emissions as the two primary competing sources to ambient NH3 in the atmosphere. Vehicles were the dominant contributors to NOx emissions, however intermittent sources (e.g., lightning and biomass burning) rivaled vehicle emission during different seasons. Vehicle, fertilizer, and marine emissions were primary contributors to atmospheric DON and higher secondary DON formation contributions were observed when agriculture and/or biomass burning emissions were more prevalent. Tributaries in the watershed had varied NH4+ (0-300 µM), NO3- (0-272 µM), and DON (1-302 µM) concentrations that can reach the bay through riverine discharge. Several DIN hotspots were found at downstream WWTP outfalls, indicating wastewater contamination, which was consistent with the DON and NO3- dual isotope mixing model results. Groundwater had high NO3- (~1064 µM) and DON (~65 µM) concentrations, which could reach the bay through subsurface discharge. The varied ?15N-NO3- (7-56‰) and ?18O-NO3- (4-25‰) values in groundwater evidenced varying processes (i.e., anaerobic denitrification, aerobic denitrification and nitrification) affecting the NO3- isotopic composition. Isotope mixing model results suggested septic effluent and agriculture as the main NO3- and DON sources in the groundwater. As a result of source loadings and subsequent processing along the surface and subsurface runoff transport pathways, Baffin Bay surface water had high DON concentrations but low NO3- (~0.3 µM) and NH4+ (~2.3 µM) concentrations. The high NO3- and/or NH4+ concentrations in the groundwater and tributaries might be further processed by dissimilatory NO3- reduction to NH4+, denitrification, nitrification, and assimilation along the pathways and/or in the bay. Surface water had ?15N-DON values of 8‰ and significant negative ?15N-DON: ln[DON] correlations were intermittently observed, suggesting DON consumption. Isotope mixing model results suggested wastewater and manure as the primary allochthonous sources and the autochthonous source can contribute 20-40% of DON to Baffin Bay. High NH4+ concentrations (~325 µM) and varied ?15N-NH4+ values (-9-20‰) were found in porewater. Porewaters displayed a negative NH4+: DON and a positive temperature: ln[NH4+] correlation and decreased ?15N-NH4+ values in the summer. This presumably indicated a temperature- or/and solar irradiance-dependent process (e.g., remineralization and photo-ammonification) producing NH4+ from DON/PON in the porewater. This study provides a comprehensive DIN and DON assessment within a coastal watershed and its associated nutrient delivery pathways. It provided insights to future nutrient control management and watershed restoration plans in the region. This isotopic approach and assessment to investigate N sources and processing can be applied to similar systems worldwide and our findings add to the body of work needed to enhance global understanding of N biogeochemical cycles.Item Developing comparative indices, valuation of nitrogen bioextraction ecosystem services, and scenario modeling to support decision-making in the Texas oyster mariculture industry(2023-12) Lima, Anthony Rocha; Pollack, Jennifer; Fox, Joe; Bricker, Suzanne; Yoskowitz, David; Elwood, SusanThis dissertation aims to develop information that supports decision-making surrounding oyster aquaculture in Texas. Each chapter presents a different product, valuation, or modeling approach that addresses concerns or management of oyster aquaculture. The first research chapter developed a four-part index composed of production, policy, and economic attributes related to oyster aquaculture in the U.S. Data used in this index was derived from two studies comparing GIS tools and policy attributes of American aquaculture, and two more sections using both qualitative and quantitative data were developed as part of this study. The results of this index found that the U.S. Mid-Atlantic and New England regions have the greatest number of resource and policy attributes to facilitate and support oyster aquaculture. Among policy attributes, Texas differed from other U.S. states as lease transferability and applicant guides are not found in the state. Additionally, publicly available GIS map viewers, which are currently in development, can assist in decision-making. The second research chapter in this dissertation focused on nitrogen bioextraction as an ecosystem service provided by cultivated oysters. First, eutrophication screening was performed using the Assessment of Estuarine Trophic Status (ASSETS) model, with results indicating that Copano Bay is a candidate for eutrophication treatment based upon high levels of expression of influencing factors. Nitrogen estimates were found using Farm Aquaculture Resource Modeling (FARM), with a representative 7-acre farm capable of removing around 4,400 -6,500 lbs. of nitrogen from the water through assimilation into tissue and shell, based upon different environmental extremes in Copano Bay. A valuation model using five wastewater treatment plant (WWTPs) with two cost estimates were used to derive a monetary range of nitrogen bioextraction. The potential monetary range in value from $37,532 to $212,887 (based on various levels of WWTP efficiencies), depending on environmental growing conditions. This represents $11.49-$32.69 per pound of removed nitrogen, a valuable ecosystem service that will expand with subsequent leases as oyster aquaculture expands in Texas. The final research chapter utilized the FARM model to simulate oyster farming under different environmental and cultivation scenarios. Historically, some risks, such as hurricanes, low salinity events, or Vibrio outbreaks, have occurred more often in summer, which may be mitigated by planning seeding and harvest dates to avoid warmer months. Model results indicate that persistent low salinity, such as that found in Copano Bay in 2010, can delay harvests due to poor growth that extends past the simulated 270-day grow-out cycle. Seeding of oysters during periods of moderate temperatures in April resulted in faster growth rates than in January or October. Increasing initial oyster stocking densities from 200 to 250 oysters m-2 resulted in ≤ 1% decrease in oyster length. Triploid oysters grew slightly slower (4-5%) than diploids, based upon 270-day crop cycles. Chlorophyll a did not appear to be a limiting factor for oyster growth, even using a high oyster stocking density scenario of up to 1,000 oysters m-2. Salinity was the most apparent factor influencing oyster growth in scenario modeling; understanding freshwater inflow is among the most critical factors for long-term aquaculture siting. Together, the results from this dissertation can be used to inform policy, understand ecosystem service value, and demonstrate the utility of scenario modeling to evaluate cultivation strategies that mitigate risk with predictable harvests.Item DISTRIBUTION AND DIVERSITY OF OCTOCORALS IN THE GULF OF MEXICO(11/11/2014) Etnoyer, Peter; T. C. ShirleyOctocorals are broadly distributed throughout the world’s oceans, from the shallow intertidal zone to deeper than 5800 meters. Fishermen refer to large colonies as ‘trees’. This is appropriate because colonies provide complex structural habitat for associated species, they are broadly distributed, and they are threatened by industrial practices, such as bottom trawling. Below the warm water layer (50 – 70 m deep), octocorals are presumed to be cosmopolitan in the West Atlantic, with a broadly homogenous distribution. This creates a problem for conservation and management because it is difficult to justify conservation of one place, if all others are the same. This dissertation tested the null hypothesis of no difference in octocoral assemblages at the three spatial scales (referred to as basin, region, and site scale) through meta-analysis of two large, original datasets. The first was 1881 records of octocoral occurrences in the Gulf of Mexico from cruise reports and museums. The second was 8495 seafloor images from six outer continental shelf banks, and one site between banks, in the northwestern Gulf region. Univariate, multivariate, and spatial analysis techniques were used to compare genera, depth zones, regions, and banks within a Geographic Information System framework.Octocoral assemblages in the Gulf of Mexico differed significantly between depth zones and regions, but there was no difference in diversity between depth zones less than 800 m, due to species replacement. Composition of octocoral assemblages varied significantly between sites, and hotspots for richness and abundance were evident within sites. Null hypotheses of no difference between banks, depth zones, and regions were rejected with confidence. The findings support the broad distribution of octocorals in the Gulf of Mexico, but not homogeneity of octocoral assemblages. Based on these results, place-based conservation of deep octocoral habitat is justified, because some sites have higher diversity and abundance of octocorals than others.Item Drivers of carbon and oxygen dynamics in disparate marine ecosystems(2018-05) Wang, Hongjie; Hu, Xinping; Wetz, Michael S.; Montagna, Paul; Rabalais, Nancy N.Determining the change of sea surface CO2 fugacity (fCO2) is important as the fCO2 gradient between the atmosphere and the ocean dictates the direction of CO2 flux and the fate of this greenhouse gas. While substantial efforts have been dedicated to the study of fCO2 trends in the open ocean, little is known regarding how fCO2 levels change in ocean margins. Meanwhile, hypoxia (i.e., dissolved oxygen concentration, or DO, less than 2 mg L-1) is becoming an increasing global threat in coastal areas. Elucidating the carbon sources that consume DO is important because it helps to make proper mitigation plans. In Chapter II, I used a newly available, community-based global CO2 database (Surface Ocean CO2 Atlas version 3) to develop a new statistical approach based on Generalized Additive Mixed Modeling (GAMM) to interpret oceanic fCO2 changes in ocean margins. This method utilized Julian day of year, sea surface salinity, sea surface temperature, and sampling date as predictors. Using the GAMM method, I was able to derive multi-decadal fCO2 trends with both improved precision and greater robustness to data gaps compared to the existing method. In Chapter III, I used the GAMM method on global ocean margins (within 400 km from the shore and 30°S-70°N) and found that fCO2 trends closely followed the atmospheric fCO2 increase rate. Further analysis suggested that fCO2 trends in Western Boundary Current- and Eastern Boundary Current-influenced areas differed in response to thermal (temperature) and nonthermal (chemical and biological) effects. These differences were due to heterogonous physical, chemical, and biological responses under climate change forcing, leading to divergent trends in CO2 sinks and sources among different ocean margins. To address the hypoxia formation mechanism question, I adopted the stable carbon isotope (δ13C) of dissolved inorganic carbon (or DIC, the end product of organic carbon degradation) as a proxy to trace back the δ13C of remineralized organic carbon that was responsible for DO consumption in the northern Gulf of Mexico (Chapter IV) and two semi-arid coastal bays in south Texas (Baffin Bay and Oso Bay) (Chapter V), the two areas that both experience seasonal bottom water hypoxia. My findings suggested that terrestrial carbon contributed to oxygen consumption in limited extent and mostly focused in areas where river water influence was significant in the northern Gulf of Mexico, while for the vast shelf areas marine-produced organic carbon was the dominant contributor to hypoxia formation. In Baffin Bay and Oso Bay, however, phytoplankton, seagrass/marsh organic carbon, and refractory terrestrial organic carbon all contributed to the DO loss under different hydrological conditions. This study provided a comprehensive data-driven analysis on ocean margin fCO2 changes on a multi-decadal timescale and revealed different behaviors of the two types of boundary current-dominated systems. Regarding the hypoxia formation mechanism in the different coastal and estuarine environments, my study suggested that eutrophication remained the top stressor that could lead to hypoxia formation. Therefore, sustained efforts that focus on reducing nutrient pollution should still be carried out to mitigate the hypoxia stress for the both ecologically and economically important coastal and estuarine systems.Item Eastern oysters offer no pearl, but they might be in peril: understanding how lethal and non lethal predator effects influence oyster distribution and reef community(7/23/2014) Johnson, Keith; Smee, Delbert LeeThe purpose of this dissertation research was to investigate how predation affects oyster distribution and reef community structure by examining: 1) non lethal predation effects on bivalves by size of prey; 2) the lethal and non lethal effects that influence survival and resource allocation in oysters; 3) predation affects distribution patterns of oysters; 4) top-down forces and seasonal effects on oyster reef community structure. Although Eastern oysters, Crassostrea virginica, are ecologically and economically important, oyster populations are declining in many areas and have decreased 85% worldwide. Like many communities, predation or top-down forces can have significant effects on the structure and function of oyster reef communities. The purpose of this study was to ascertain how oyster recruitment, survival, growth and distribution as well as oyster reef community structure were influenced by lethal and non lethal effects of predators. Results from a series of manipulative field experiments indicate that predators have significant effects on oyster reef community structure and oyster recruitment, but, these effects are significantly more important in the fall than spring. Oyster recruitment and spat survival is strongly affected by the abundance of intermediate consumers, most notably the Atlantic mud crab (Panopeus herbstii). In the absence of higher order predators including blue crabs (Callinectes sapidus) and red drum (Scianops ocellatus), mud crabs increased in number and preyed more heavily on newly settled oysters. Mud crabs also caused oysters to change their resource allocation to more shell and less tissue at a cost of lowering fecundity. Finally, oysters are limited to intertidal habitats in Corpus Christi Bay, and these results indicate that oysters are restricted to intertidal habitats by predators. This study elucidates how predators have significant lethal and non lethal effects on oysters and their associated fauna and that top-down forces should be considered when developing oyster reef conservation, management, and restoration efforts.Item Ecological structure and function of restored habitats across a range of coastal environments(2017-12) Rezek, Ryan Joseph; Pollack, Jennifer Beseres; Lebreton, Benoit; Sterba-Boatwright, Blair; Stunz, Gregory W.; Bridges, DavidCoastal habitat loss represents a major threat to biodiversity and ecosystem services worldwide. Habitat restoration plays a key role in efforts to mitigate this loss by supporting the recovery of ecological communities (i.e., structure) and important ecosystem processes (i.e., functions). The objective of this dissertation was to evaluate the ability of constructed habitat restorations to support equivalent ecological communities and functions to reference habitats across a range of coastal environments. This was accomplished through an analytical framework combining community structure analysis with stable isotope based food web analysis. In Chapter I, the scale and implications of coastal degradation, the use of constructed habitats for coastal restoration, and the use of stable isotope analysis to study food webs and function are outlined. In Chapter II, the development of a constructed subtidal oyster reef in the Mission-Aransas estuary was surveyed alongside a natural oyster reef over a 5- to 29-month post-restoration timeframe to evaluate recovery. The results demonstrated structural and functional recovery occurring between 12-15 months post-restoration, as oysters and predatory consumers increasingly colonized the developing reef. In Chapter III, a constructed salt marsh was monitored alongside a natural reference marsh in Nueces Bay over a 4- to 6-year post-restoration timeframe. The results of this study demonstrated the ability of the restored marsh to support communities with similar composition as the natural marsh, however, stable isotope mixing models demonstrated that dominant macrofauna in the restored marsh consumed less organic matter originating from macrophyte production than their natural counterparts. This functional variation was attributed to the relatively low amounts of organic matter and detritus contained in the recently constructed salt marsh sediments. In Chapter IV, I examined the epibenthic community and food web structure of subsurface “Rigs-to-Reefs” artificial reefs in comparison to standing operational platforms in the Texas offshore Gulf of Mexico shelf region. Reefed platforms were found to support similar communities as standing platform habitats at similar depths (30-m), however shallow standing platform sites (5-m) were found to support communities that were distinct from deeper standing platform and clearance-limited reefed platform sites. Reefed platform and standing platforms at 5- and 30-m depths were found to support similar food web structure, indicating that reefed platforms replicate the fundamental ecological functions associated with standing platforms. Although, the loss of shallow water substrate, associated with platform reefing, could be expected to reduce the biodiversity associated with these structures. In Chapter V, I conclude with a summary of the findings in this dissertation and outline general patterns of functional recovery between different coastal habitat types that can be inferred from these results and established theory. This study provides strong evidence for the ability of constructed habitats to support similar communities as natural/pre-existing habitats across a range of coastal environments. The results suggest that constructed habitats in systems driven by microalgal producers are likely to functionally recover as community structure develops. However, functional recovery in systems driven by vascular plant production are limited by the recovery of detrital food web intermediaries. The insights obtained from this study have broad implications for coastal restoration practitioners and resource managers.Item Effects of contamination from Antarctic research stations on marine benthic fauna(2021-08) Palmer, Terence Aaron; Pollack, Jennifer Beseres; Montagna, Paul A.; Klein, Andrew G.; Withers, KimAntarctica is our most pristine continent, home to many unique and scientifically interesting ecosystems. But the presence of researchers and supporting infrastructure are unintentionally causing localized pollution at research stations, which is adding to the stress of climate change in Antarctica. Therefore, it is important to determine the extent of this contamination so that careful environmental management can be ensured. This dissertation identified long-term decreases in mercury, copper, organochlorine, and polycyclic aromatic hydrocarbon (PAH) contamination at McMurdo Station, the largest, and possibly most polluted, research station in Antarctica. However, these long-term (13 year) decreases in contaminants were not great enough to allow the recovery of affected macrobenthic communities. Instead, changes in macrobenthic communities at both polluted and references areas coincided with climate cycles and changes in sea ice characteristics, indicating effects of global climate change. Bioaccumulation of trace metals, pesticides, and/or organochlorines from McMurdo Station occurred in ten of twelve epibenthic species sampled, although polychlorinated biphenyls (PCBs) in benthic fish (Trematomus spp.) were of most concern. Bioaccumulation of PAHs, copper, lead, and zinc in a limpet (Nacella concinna) occurred at Palmer Station, a medium sized Antarctic research station, although concentrations have decreased since the 1990s. The effects of local contamination on macrobenthic fauna communities adjacent to Palmer Station could not be differentiated from the effects of natural variables, which indicates that smaller stations may have a smaller influence (intensity and/or spatial extent) on the local environment. Legacy contamination in the marine environment persists adjacent to Antarctic research stations. However, continued careful environmental management and varying amounts of time (years to decades) may allow contamination to further decrease and ecosystems to recover.Item Estimated increase in inundation probability with confidence intervals for the Gulf of Mexico(2013-04-15) Warner, Natalya N.The main objective of this research is to study the impact of sea level rise on the relative increase in frequency of inundation for the low-lying coastal zones of the Gulf of Mexico caused by storms of different sizes. The research is based on locations around the Gulf of Mexico that benefit from existing long term sea level records and are located near population centers: Galveston Pier 21, Galveston Pleasure Pier, Port Isabel, Rockport, Texas, Grand Isle, La, and Pensacola, Key West, and St Petersburg, Florida stations. The stations' long-term water level records are divided into a long term sea level trend, a tidal component and a stationary surge component. Several extreme value distributions, such as three and four parameters Burr, Dagum, log-logistic, and generalized extreme value distribution (GEV), are compared using multiple statistical measures for the modeling of maximum annual storm surges. While differences are small the GEV and log logistic distributions are selected for this work based on performance, sensitivity to the series outliers and ease of implementation. Increases in inundation frequencies are computed by combining the stations' respective annual maximum surge models with two possible sea level rise scenarios, a conservative linear continuation of the past century trend and a scenario based on the upper limit of the sea level range in the IPCC (Intergovernmental Panel on Climate Change) AR4 report (Assessment Report 4), i.e. the A1FI scenario. Differences in oceanographic setting are discussed and affect vulnerability to sea level rise. To compare vulnerability to sea level rise, the ratios of future and present exceedance probabilities are computed for a range of water levels. The locations' respective vulnerabilities to sea level rise are assessed by comparing the maximum ratios of future to present water level exceedance probabilities and the corresponding water levels. Water levels at maximum ratios have a strong correlation with most common moment- and quantile - based statistics of surges, except the maximum annual surges. This indicates that the results of this study are not overly sensitive to the most extreme values or largest surge on the record provided that the record includes at least one large surge. Statistical bootstrap methods are used to estimate 90% and 95% confidence intervals for increases in inundation probability. For most cases the confidence intervals show a substantial decrease in interval width for stations with lengths of datasets of 50 years or longer indicating a preferred data length provided that a large surge event is included. For all locations the lower bounds of the confidence intervals imply significant increase in exceedance probabilities for both sea level rise scenarios. While expected increases in inundation frequencies are substantial for all stations, the results show considerable variation depending on the sizes of the surges, the station locations and the sea level rise scenarios. Annual maximum water levels resulting from small storms/surges will have higher frequencies, typically by a factor of 3 or more, than the historical frequency of water levels resulting from large hurricanes. As a result more frequent, smaller storm surges may have a larger impact on coastal communities than the effects of the less frequent, larger storm surges. Ratios of the exceedance probabilities depend mostly on sea level trends and the shape of the curves of the exceedance probabilities. The relative importance of these parameters depends on the sea level rise scenario. For a continued linear sea level rise maximum ratios are strongly correlated to the sea level trends or vertical land motion. For the conservative sea level rise scenario the study's highest increase in water level exceedance probability of 17 times is computed for a water level of 1.23m above present mean sea level for Grande Isle, Louisiana. For higher rates of global sea level rise local subsidence becomes less important and the dominant factor becomes the range of the locations' surges. For the study's A1FI based sea level rise scenario, the highest increase in water level exceedance probability is over 100 times for a water level of 0.83m above present mean sea level for Key West, Florida. The results of this research provide coastal decision makers quantitative estimates of future inundation risks for two sea level rise scenarios and a calibrated method to compute such risks for more sea level rise scenarios. This research is relevant for engineers, planners, insurance executives, and others to take into account the increasing impacts of storm surges of various sizes as sea level rises. The results will help develop better insurance rates, plan structures, land-use zoning, and others as the century progresses. The models, methodology and estimates developed as part of this research may be used to estimate the time before specific locations may become economically uninhabitable due to surge inflicted damages as sea level rises. Particularly, it is expected that this work will allow better to quantify coastal vulnerability to sea level rise along the Gulf of Mexico.Item Evaluating success of oyster reef restoration(2015-12) Blomberg, Brittany Nicole; Montagna, Paul A; Pollack, Jennifer B; Yoskowitz, David; Stunz, Greg; Foret, JohnOyster reefs are the most degraded marine habitat type, with estimated global losses of 85% from historic abundances. Restoration efforts have increased to restore important ecosystem functions and services associated with oyster reefs. The objective of this study was to evaluate the success of oyster reef restoration projects from a variety of perspectives. The importance of oyster reefs, causes of degradation, and methods of restoration were reviewed (Chapter I). Oyster reef restoration projects across the United States were analyzed to examine temporal trends and influences of national policies (Chapter II). Oyster reef habitat was restored in Copano Bay, Texas and monitored for two years to examine habitat value (Chapter III), oyster diet composition (Chapter IV), and nutrient regulation functions (Chapter V). Finally, the results and implications of each chapter are summarized (Chapter VI). In Chapter II, data were compiled from the National Estuaries Restoration Inventory to analyze oyster reef restoration projects. Over $45 million has been invested for the restoration of more than 150 ha of oyster reef habitat. Trends over time indicate projects are being implemented at larger scales with improved cost efficiency. However, this analysis revealed a lack of available monitoring data or project assessments. In Chapter III, an oyster reef complex was constructed in Copano Bay, Texas. The restored reef and natural reference habitats were monitored for two years to examine oyster and nekton communities. The restored reef had substantial oyster recruitment and growth, with oyster abundance and size comparable to reference conditions within the first year. Fishes and crustaceans recruited to the restored reef within six months post-construction, and abundance and diversity were comparable to reference habitats. High densities of oysters and nekton relative to other studies indicate this restored reef complex was successful in providing important ecological functions associated with habitat provision and oyster production. In Chapter IV, a dual stable isotope (δ13C and δ15N) approach was employed to assess oyster diet composition. Oysters and potential composite food sources — water column and sediment surface organic matter — were sampled from restored and reference habitats. Oyster diet composition was similar among habitats, but changed over time with increasing contributions of sediment organic matter. Results demonstrate that benthic food resources are important components of oyster diets, and that oysters may enhance the development of benthic algal food resources. In Chapter V, nitrogen removal attributed to the burial and mineralization of oyster deposits was quantified at the restored and natural oyster reefs through emergy analysis. Emergy evaluations can represent environmental and economic values of a system in equivalent units based on solar energy, and thus present an ecological approach to quantify ecosystem services. Results demonstrate that the restored reef was providing a greater function per unit area compared to the natural reef within the second year post-restoration. This study provides insight into the effects of national policies on restoration trends, and stresses the importance of project assessments and data sharing to ensure future restoration projects make meaningful scientific contributions. The restored reef in Copano Bay was successful in supporting high densities of oysters, fishes and crustaceans. Much of this success could be attributed to the design of the reef complex, and thus will support the planning of future restoration efforts. Benthic organic matter was determined to be an important food resource for oysters, which will improve the development of food web and population dynamic models. This work also demonstrates the application of emergy analysis to quantify ecosystem functions and services, which can complement traditional economic valuation methods. Overall, the work presented here makes novel contributions to the broader knowledge of oyster reef restoration practice and theory.Item Future water quality challenges to aquaculture and influences on product safety(2020-08) Siddiqui, Samreen; Siddiqui, Samreen; Conkle, Jeremy L.; Conkle, Jeremy; Sadovski, Alexey; Scarpa, John; Brooks, Bryan; Sadovski, Alexey L.; Scarpa, John; Brooks, Bryan; Scarpa, John; Brooks, BryanConcerns about water quantity and quality are increasing due to climate change and population growth. Climate change is driving changes in evapotranspiration and precipitation patterns. This is exacerbated as population growth, particularly in arid and semi-arid regions, increases water extraction and consumption. After human consumption, water is treated and discharged to the environment, but generally at lower quality than what was originally extracted. This could cause trouble for consumers of surface waters. One such consumer is the aquaculture industry, which is growing to support human protein consumption demands, while depending on surface water.Aquaculture is growing both globally and within the U.S. (worldwide 9.2% yr-11990-2000 & 6.2% yr-12000-2012). Freshwater aquaculture in the U.S. is largely dependent on surface water (80.78%) compared to ground water sources (19.32%). Surface water sources are increasingly dominated or dependent on treated wastewater effluent, potentially influencing downstream uses. Wastewater effluent generally contains trace levels of anthropogenic compounds, typically referred to as contaminants of emerging concern (CEC), for which our knowledge of their impacts is still evolving. Therefore, the introduction of CEC in aquaculture from surface waters influenced by wastewater effluent is a potential concern for cultured fish health as well as for humans when consuming farmed fish. Studies were conducted to improve our understanding of future water resource quality and quantity in relation to the aquaculture industry and safety of farmed fish. Initially, wastewater effluent data was collected (e.g., USGS), consolidated, and analyzed (e.g., GIS) to understand its influence on surface water quantity and quality, which was utilized to project potential future water quality and quantity scenarios in the USA and its potential effect on aquaculture. This was followed by laboratory-based studies to quantify the bioaccumulation and depuration in tilapia of diltiazem, an ionizable calcium channel blocker, and GenX, a perfluorinated compound, at environmentally relevant concentrations. To broadly examine the extent of U.S. surface waters to dilute wastewater treatment plant (WWTP) effluent, data from wastewater discharge and surface flow from 2007-2017 was used to calculate a WWTP wastewater dilution factor (WWDF) within United Sates Geological Society (USGS) hydrologic unit code (HUC). A WWDF less than 10 indicates poor quality water when classified on <1 to >100 DF scale. The 4 HUCs with the lowest WWDF (i.e., <2) were located in the West or Southwest U.S. and were among the 10 HUCs with the highest proportional population growth from 2010-2016, with similar projections for the future. To identify the end water user impact, U.S. aquaculture farm area with WWDF < 2 was mapped. It was quantified at ~ 2.71% of total freshwater area, out of which 69% and 44% of the area was occupied by aquaculture farms with 100-and 1000-acre areas, respectively. Water availability for the contiguous U.S. was estimated for each HUC during 2015 using a model developed from the earlier analysis of water quantity and quality in the U.S. The Mississippi River generally served as a dividing line for surface water availability, with five of the six HUC regions with very low water availability (<24,000 L/D/Km2) residing in the west. These same areas also experience more drought as well as more severe droughts than regions in the east. In regions with lower surface water flows, water quality is more susceptible to the influence of wastewater effluent discharge, especially near large and growing population centers like San Antonio, Texas. A prediction model was established for this city, which found that from 2009-2017 wastewater effluent increased by 1.8%. Diltiazem(DTZ)bioconcentrationanddepurationintilapiawasexaminedusingacontrolledtimesequence(maxtime=96hr)exposure(1μgL-1)andnon-exposure(maxtime=96hr)infreshwater.Fishcarcass,bloodplasma,liver,andmusclewereanalyzedinbothexposureanddepurationphases.Diltiazembioconcentrationwasgreatestinliver>plasma>carcass>muscle.Depurationratesweregreatestforliver>carcass>plasma>muscle.Thebiologicalhalf-life(t1/2)indicatesthatDTZtookthelongesttodepuratefrommuscleandleastfromtheliver,whichissimilarforthestablebioconcentrationfactor(BCFa)valueorder.Thet1/2ofDTZintilapiamusclewas18.8hrs,indicatingthecompoundisprocessedrelativelyquickly.Basedonthe96hrDTZuptakebytilapiafingerlingsinthisstudy,humanexposuretothehighestDTZmuscleconcentrationwouldbe~6ordersofmagnitudebelowthelowestdailyhumantherapeutic(120ppb)dose,resultinginverylowhumanexposure. GenX (ammonium 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy))bioconcentrationanddepurationintilapiawasexaminedusingacontrolledtimesequence(maxtime=96hr)exposure(1μgL-1)andnon-exposure(maxtime=96hr)infreshwaterandbrackishwater(16ppt).GenXbioconcentration (BCFa) was greatest in plasma > liver > carcass > muscle, with higher distribution in liver compared to carcass and muscle. Bioconcentration in all tissues examined increased with increasing salinity, raising concern for euryhaline organisms. Muscle was found to have the highest t1/2followed by carcass, plasma, and liver. The rate of uptake and depuration was affected bysalinity. Fish muscle (fillet) GenX concentration at 96 hrs at 0 ppt was 0.14 ppb whereas at 16 ppt it was 0.312 ppb. Therefore, a fillet serving size of ~3.5 oz (100 g) would contain 14.0 μg GenX from freshwaterfish and 31.2 μg GenX from saltwater (16 ppt) fish. This would result in a single serving exposing a person to more than the subchronic oral reference dose of 0.2 ppb as recommended by U.S. EPA. Water quality is a growing concern along with changing climate and increasing population. The projections and improved bioaccumulation models for farmed fish from this research will provide aquaculturists with knowledge to make pro-active management decisions regarding water quality in the future, while improving our general understanding of human exposure to CEC from nontraditional water use. It also helps to understand environmental exposure and ecological impacts of pharmaceuticals and other industrial chemicals for sustainable management of environmental quality, particularly in urbanizing ecosystems.Item Geoid determination in the coastal areas of the Gulf of Mexico(2013-07-01) Song, HongzhiCoastal areas of the Gulf of Mexico are important for many reasons. This part of the United States provides vital coastal habitats for many marine species; the area has seen-ever increasing human settlement along the coast, ever increasing infrastructure for marine transportation of the nation's imports and exports through Gulf ports, and ever increasing recreational users of coastal resources. These important uses associated with the Gulf coast are subject to dynamic environmental and physical changes including: coastal erosion (Gulf-wide rates of 25 square miles per year), tropical storm surges, coastal subsidence, and global sea level rise. Coastal land subsidence is a major component of relative sea level rise along the coast of the Gulf of Mexico. These dynamic coastal changes should be evident in changes to the geoid along the coast. The geoid is the equipotential gravity surface of the earth, which the best fits the global mean sea level. The geoid is not only been seen as the most natural shape of the Earth, but also it serves as the reference surface for most of the height systems. By using satellites (GRACE mission) scientists have been able to measure the large scale geoid for the Earth. A small scale geoid model is required to monitor local events such as flooding, for example, flooding created by storm surges from hurricanes such as Katrina (2005), Rita (2005), and Ike (2008). The overall purpose of this study is to evaluate the accuracy of the local coastal geoid. The more precise geoid will enable to improve coastal flooding predictions, and will enable more cost effective and accurate measurement of coastal topography using global navigation satellite systems (GNSS). The main objective of this study is to devise mathematical models and computational methods to achieve the best possible precision for evaluation of the geoid in the coastal areas of the Gulf of Mexico. More specifically, the numerical objectives of this study are 1) to obtain a continuous map of gravity anomalies and a continuous map of gravity by using spatial interpolation methods and to evaluate errors; 2) to solve the Laplace boundary value problem and evaluate errors; 3) to evaluate precision of the local geoid by using geospatial statistical tools and numerical techniques. This dissertation investigates modeling of the geoid, especially the gravimetric equipotential surface that approximates mean sea level, in the coastal areas of the Gulf of Mexico as well as errors in the geoid determination. The document begins with Chapter 1 which introduces the study of this dissertation. Different models of kriging are used to determine the precision of the geoid based on the free-air gravity anomalies data supplied by United States Naval Research Laboratory and the airborne gravity data provided by the U.S. National Geodetic Survey, which can be found in Chapters 2 and 3. Research in Chapters 2 shows that more precise evaluation of errors in gravity anomalies can be achieved by using different models of kriging. Results from Chapters 2 and 3 show that ordinary kriging with the stable semivariogram model provide better predictions. Research results from Chapter 3 provide estimation of maximum possible errors in the calculation of the geoid undulation. The dissertation also investigates behavior of gravity equipotential surfaces around coastal lines and its impact on the geoid evaluation. Chapters 4 and 5 are about evaluation of errors in the Dirichlet problem for calculation of gravity potential with uncertain boundary and boundary values has been achieved by solving the Laplace equation by means of separation of variables. Research has provided a theoretical model in Chapter 4 to estimate very small changes in gravimetric potential relative to the coast. Maximum possible error in the solution of Direchlet problem is determined in Chapter 5. Maximum possible error depends on the errors of boundary values and the precision of the boundary itself. Chapter 6 describes a novel approach to sea level rise modeling. Factor analysis is used to analyze local and global sea level rise and relationships between changing sea levels, currents, and the shape of the Earth. Results of factor analysis from Chapter 6 show that the elevation of sea level relates to the geoid and ocean circulation. Chapter 7 describes the relationship between the geoid and wetlands modeling. Research in Chapter 7 shows that the predicted continuous elevation map obtained through the ordinary stable kriging was sufficiently precise and fairly reliable. Chapter 7 is an exploratory chapter, and the ideas of this chapter will help the future research.Item Hydrological and biogeochemical controls on estuarine carbonate chemistry along a climate gradient(2022-12) Dias, Larissa Marie; Hu, Xinping; Abdulla, Hussain; Murgulet, Dorina; Felix, JosephIncreasing global atmospheric CO2 concentrations drive a net flux of CO2 into the oceans, mitigating the impacts of anthropogenic greenhouse gas emissions on the climate. This results in a reduction in pH and carbonate saturation state, a.k.a. ocean acidification, of marine waters. The acidified ocean water may advect into estuaries, leading to estuarine acidification. Many estuaries are highly sensitive to this acidification due to low buffer capacity. Because estuaries provide many important ecosystem services, alterations in their carbonate systems may have significant consequences on ecosystems and the economy. Despite the current understanding that estuaries may play a disproportionately important role in global air-sea CO2 flux, little is known about carbonate systems in subtropical estuaries. Further comprehension of estuarine carbonate systems is vital for quantification of the global carbon cycle. Specifically, subtropical estuaries in the northwestern Gulf of Mexico (nwGOM) exhibit a general long-term decrease in pH and total alkalinity (TA), with lower latitudes experiencing more extreme acidification than higher latitudes. In Chapter II, sediment cores and slurries from the semiarid Mission-Aransas Estuary of the nwGOM were incubated and surface waters were analyzed for contributions of biogeochemical processes to TA change. Changes in total TA as well as calcium and sulfate ion concentration were examined following known reaction stoichiometry. Ratio of TA: ion changes suggested that carbonate dissolution co-occurred with oxidation of reduced sulfur species, and the latter consumed TA during drought periods in Mission-Aransas Estuary. This biogeochemical (sulfide oxidation) TA consumption has been poorly studied yet may affect TA budget in other semiarid estuaries worldwide. In Chapter III, river alkalinity total load and concentration were calculated using the United States Geological Survey’s Fortran Load Estimator Program (LOADEST) and long-term trends in alkalinity and discharge of six major nwGOM rivers were determined. Stepwise multiple linear regression methods were used to generate models for predicting estuarine TA based on river alkalinity, year, and net evaporation (evaporation-precipitation). Some rivers were found to have long-term (multidecadal) declines in freshwater discharge, area-weighted alkalinity yield, of alkalinity flow-weighted concentration, with most declines occurring in the southern end of the study region. Freshwater flow-weighted alkalinity concentration (annual alkalinity load for an area divided by discharge) appeared in many of the predictive models for estuarine TA and may play a major role in regulating estuarine TA of the nwGOM. Methods for linking freshwater and estuarine carbonate dynamics are lacking in the scientific literature; this study provides a potentially useful approach for predicting estuarine carbonate chemistry based on freshwater quality and input. In Chapter IV, CO2 flux of the Trinity-San Jacinto Estuary (Galveston Bay) was calculated and compared to results from discrete samples for carbonate parameters. Inferences about spatial and temporal patterns in CO2 flux as well as ecosystem metabolism were made based on results. The Trinity-San Jacinto Estuary was found to be a net sink for atmospheric CO2, but with high seasonal and spatial variability. Specifically, large freshwater inflows in spring stimulated photosynthesis in the estuary, which increased the sink behavior. Seasons with less freshwater inflow resulted in higher heterotrophy and CO2 emission in some regions of the estuary. This research increases knowledge and research capacity in the nwGOM region on estuarine acidification and carbonate chemistry. Causes of acidification in major estuaries within the region were addressed along a latitudinal climatic gradient. This will aid with better management of fresh and estuarine water resources in the nwGOM. The results of this research will also clarify the role of semiarid, subtropical estuaries in the global carbon cycle and expand our range of knowledge on carbonate system analyses of estuaries.Item Hyperspectral analysis of seagrass in Redfish Bay, Texas(2012-11-07) Wood, John S.; James Gibeaut; John W. TunnellRemote sensing using multi- and hyperspectral imaging and analysis has been used in resource management for quite some time, and for a variety of purposes. In the studies to follow, hyperspectral imagery of Redfish Bay is used to discriminate between species of seagrasses found below the water surface. Water attenuates and reflects light and energy from the electromagnetic spectrum, and as a result, subsurface analysis can be more complex than that performed in the terrestrial world. In the following studies, an iterative process is developed, using ENVI image processing software and ArcGIS software. Band selection was based on recommendations developed empirically in conjunction with ongoing research into depth corrections, which were applied to the imagery bands (a default depth of 65 cm was used). Polygons generated, classified and aggregated within ENVI are reclassified in ArcGIS using field site data that was randomly selected for that purpose. After the first iteration, polygons that remain classified as `Mixed' are subjected to another iteration of classification in ENVI, then brought into ArcGIS and reclassified. Finally, when that classification scheme is exhausted, a supervised classification is performed, using a `Maximum Likelihood' classification technique, which assigned the remaining polygons to the classification that was most like the training polygons, by digital number value. Producer's Accuracy by classification ranged from 23.33 % for the `MixedMono' class to 66.67% for the `Bare' class; User's Accuracy by classification ranged from 22.58% for the `MixedMono' class to 69.57% for the `Bare' classification. An overall accuracy of 37.93% was achieved. Producers and Users Accuracies for Halodule were 29% and 39%, respectively; for Thalassia, they were 46% and 40%. Cohen's Kappa Coefficient was calculated at .2988. We then returned to the field and collected spectral signatures of monotypic stands of seagrass at varying depths and at three sensor levels: above the water surface, just below the air/water interface, and at the canopy position, when it differed from the subsurface position. Analysis of plots of these spectral curves, after applying depth corrections and Multiplicative Scatter Correction, indicates that there are detectable spectral differences between Halodule and Thalassia species at all three positions. Further analysis indicated that only above-surface spectral signals could reliably be used to discriminate between species, because there was an overlap of the standard deviations in the other two positions. A recommendation for wavelengths that would produce increased accuracy in hyperspectral image analysis was made, based on areas where there is a significant amount of difference between the mean spectral signatures, and no overlap of the standard deviations in our samples. The original hyperspectral imagery was reprocessed, using the bands recommended from the research above (approximately 535, 600, 620, 638, and 656 nm). A depth raster was developed from various available sources, which was resampled and reclassified to reflect values for water absorption and water scattering, which were then applied to each band using the depth correction algorithm. Processing followed the iterative classification methods described above. Accuracy for this round of processing improved; overall accuracy increased from 38% to 57%. Improvements were noted in Producer's Accuracy, with the `Bare' vi classification increasing from 67% to 73%, Halodule increasing from 29% to 63%, Thalassia increasing slightly, from 46% to 50%, and `MixedMono' improving from 23% to 42%. User's Accuracy also improved, with the `Bare' class increasing from 69% to 70%, Halodule increasing from 39% to 67%, Thalassia increasing from 40% to 7%, and `MixedMono' increasing from 22.5% to 35%. A very recent report shows the mean percent cover of seagrasses in Redfish Bay and Corpus Christi Bay combined for all species at 68.6%, and individually by species: Halodule 39.8%, Thalassia 23.7%, Syringodium 4%, Ruppia 1% and Halophila 0.1%. Our study classifies 15% as `Bare', 23% Halodule, 18% Thalassia, and 2% Ruppia. In addition, we classify 5% as `Mixed', 22% as `MixedMono', 12% as `Bare/Halodule Mix', and 3% `Bare/Thalassia Mix'. Aggregating the `Bare' and `Bare/species' classes would equate to approximately 30%, very close to what this new study produces. Other classes are quite similar, when considering that their study includes no `Mixed' classifications. This series of research studies illustrates the application and utility of hyperspectral imagery and associated processing to mapping shallow benthic habitats. It also demonstrates that the technology is rapidly changing and adapting, which will lead to even further increases in accuracy. Future studies with hyperspectral imaging should include extensive spectral field collection, and the application of a depth correction.Item Increasing resilience of urban development on Texas barrier islands(2014-04-18) Taylor, Eleonor BarrazaThe purpose of the dissertation was to develop information, at a local scale, that can be incorporated into a spatial planning process to increase the resilience of urban development on Mustang and North Padre Islands, Texas. About 12% of U.S. barrier islands are completely urbanized, and 36% are heavily developed. This development trend is exposing more people, property, and infrastructure to coastal hazards. Therefore, coastal communities must plan for resiliency to remain functional and prosperous after a storm strikes or environmental conditions change. Each chapter presents an element of the spatial planning process, including the following: a geohazards map, an ecosystem services valuation, and a land-use policy analysis. The geohazards map describes the effect of ongoing geologic processes and future evolution of a barrier island as a geomorphic system in response to relative sea-level rise (RSLR). The assessment and monetary valuation of the storm protection provided by beaches and foredunes informs decision-making regarding beach-dune management alternatives and supports their preservation. Land-use policies are analyzed and recommendations made to preserve current and future critical environments and guide future urban growth towards safer and more stable areas. Results of the study show that RSLR could cause 50% of the study area to change by 2072. About 55% of the assessed beach-foredune areas provide overwash protection against at least a 100-year storm. Beaches and foredunes cover 6.9 sq. km; however, they save an estimated $141.4 million/year (2013 USD) in storm protection expenditures. It was found that 26% of the study area can accommodate higher density development, 23% should be left undeveloped or planned for lower density development, and 51% includes public spaces and preservation areas. Current state and federal regulations offer only limited protection to present and future locations of critical environments, with beaches and dunes receiving the most protection compared to bay-margin wetlands. A transfer of development rights program may be a sensible land-use policy for addressing the realities of a dynamic coastal environment and balancing private and public interests. While coastal vulnerability continues to increase, this dissertation provides actionable information and a process to follow for increasing the resilience of human activities on barrier islands.Item INTERACTIONS BETWEEN SUSPENDED SEDIMENTS, NUTRIENTS AND(2014-07-01) Paudel, BhanuThe objectives of the present study were to identify the effects of freshwater inflow (FWI) on sediment transport and nutrients supply to estuaries, and the effects of sediments on nutrient supply at sediment-water interface. The Nueces River and its estuary, the Guadalupe River and its estuary, and the Lavaca-Colorado Estuary were selected for field studies. Laboratory experiments were conducted to test the study hypotheses, and data was analyzed using multivariate modeling and statistical approaches. In the Guadalupe Estuary, variability of suspended solids and nutrients were correlated with FWI, whereas in the Nueces and Lavaca-Colorado Estuary they were related with seasonal differences. Suspended solids in the estuaries increased during frontal events and during windy days. In some of the field samplings, stations closer to the Gulf of Mexico had higher suspended sediments than the stations closer to the river. The increase in suspended sediments increased ammonia concentration in the Guadalupe Estuary, phosphorus and silicate concentrations in the Nueces Estuary, and silicate concentration in the Lavaca-Colorado Estuary. The presence of silicate minerals in the estuaries maintains silicate concentration as well. Organic matter and calcium carbonate shells in sediments of the estuaries can bind phosphate, thus, may have played role in decreasing phosphate concentration in the water. Guadalupe River sediments, when transported to the estuary, can release ammonia at higher concentrations the river water concentration. Salinity in the estuary, thus, has a significant role in controlling nutrient concentrations. The release of ammonia by organic matter decomposition was lower in the Guadalupe Estuary than in the Nueces Estuary. The high inflow volumes in the Guadalupe Estuary may have washed away organic matter from the sediments and may have disturbed bacterial community resulting in the lower release of ammonia from Guadalupe Estuary sediments. The research performed here demonstrates the importance of sediments, organic matter, and inflow in maintaining nutrient concentrations in estuaries. Fluctuation of these nutrients can affect water quality, and hence, may influence the ecology of the estuary.