Dissertations
Permanent URI for this collectionhttps://hdl.handle.net/1969.6/1139
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Browsing Dissertations by Department "Life Sciences"
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Item Carbon Budgets in Coastal Estuaries of the Northwestern Gulf of Mexico Under Hydrologic Control(2019-08) Yao, Hongming; Hu, Xinping; Montagna, Paul; Shinoda, Toshiaki; Jin, LeiGlobally, estuaries are considered as important CO2 sources to the atmosphere. However, previous studies on estuarine carbon fluxes have mostly focused on temperate and high latitude regions, leaving a significant knowledge gap in subtropical and tropical estuaries. In addition, the drivers that cause large spatiotemporal variability in estuarine inorganic and organic carbon fluxes remain insufficiently explored. In this dissertation, carbon budgets in four northwestern Gulf of Mexico (nwGOM) estuaries along a climatic gradient, Lavaca-Colorado Estuary (LCE), Guadalupe Estuary (GE), Mission-Aransas Estuary (MAE), and Nueces Estuary (NE), were -2 -1 evaluated. All these estuaries, with annual CO2 emission ranging 2.7—35.9 mol·C·m ·y , are moderate to strong CO2 sources. However, there was large spatiotemporal variability that corresponded to changes in hydrologic conditions. The two northern estuaries (LCE and GE), due to larger riverine discharges, had an order of magnitude higher CO2 emissions than the southern estuaries (MAE and NE). In addition, episodic flooding made the entire regional CO2 fluxes differ significantly under dry (-0.7—20.9 mmol·C·m-2·d-1) and wet (11.6—170.0 mmol·C·m-2·d-1) conditions. A mass balance model for carbon budget predicted lateral transport of total organic matter (TOC) and dissolved inorganic carbon (DIC) from tidal wetlands, which accounted for ~95% and 70% of total TOC and DIC inputs to the open estuarine water, respectively. However, the loss of coastal saltmarsh-mangrove habitats due to sea level rise could result in ~1% per year decline in estuarine CO2 fluxes at the expense of decreasing lateral carbon transport. Finally, this dissertation suggested that the average estuarine CO2 flux from nwGOM was about 8 times higher than previously estimated North America estuarine CO2 flux. Additionally, flooding condition was estimated to elevate CO2 emission and lateral fluxes by 10 times in this region.Item Characterization of an induced morphological defense in the Eastern Oyster Crassostrea virginica(2017-05) Scherer, Avery E.; Smee, Delbert Lee; Pollack, Jennifer Beseres; Hogan, J. Derek; Bird, Christopher E.; Piker, AndrewTo reduce their risk of consumption, many prey species use plastic defenses that are employed in situations where predators pose high risk of injury or death. By modifying prey traits, predators often exert strong influence on community structure and function. These nonconsumptive effects can be stronger than effects from prey consumption, but have only become the focus of study in recent decades. Further, they are often more complicated than consumptive effects because they can be influenced by characteristics of the predator, the prey, the response type, and the environment. In order to fully understand the effects of predator species on prey organisms, prey responses must be fully characterized and understood in an ecological context. Eastern oysters Crassostrea virginica were selected as a model organism to investigate the costs, benefits, and mechanisms of predator-induced changes in prey traits. Oysters are an ecologically and economically valuable species, known to increase their shell weight and strength in response to crab predators. In this study, oyster responses were investigated by 1) fully characterizing the mechanism and cost of oyster responses to predation risk, and determining the effect of 2) risk cue type (predator versus prey), 3) an ecological prey characteristic (size), 4) an ecological predator characteristic (diet), and 5) an environmental characteristic (food availability) on defense induction. In response to risk, oysters increased calcium carbonate production to rapidly reach a size refuge from predators. This led to an inverse relationship between shell thickness and shell density. Although not significant, there was a trend for reduced gonad investment in oysters which had thick, low density shells. As this study provides a conservative estimate of defense costs, this suggests oysters may experience reductions in reproduction under conditions of high predation risk which may be exacerbated under conditions of ocean acidification. Oysters responded to all tested cues indicative of risk, but responses were less intense when oysters were exposed to cues from injured prey organisms or to predators which were food deprived or fed aged oyster tissue. In addition, oyster responses were inversely related to oyster size. Oysters responded to predators regardless of resource availability, despite reduced shell metrics in response to limited food under control conditions. There is a diverse array of factors which influence oyster defenses and which may be altered by anthropogenic disturbance. If oyster defenses reduce investment in reproduction, this could have important long-term consequences for oyster populations and oyster reef communities. Therefore, understanding factors which influence prey responses allows us to understand conditions which promote or attenuate nonconsumptive predator effects. And understanding the costs of these effects for organisms allows us to predict the effect of disturbances on community structure and function.Item Characterization of the mechanisms underlying food deprivation-induced memory deficits in the marine mollusk Aplysia(2021-08) Deng, Xin; Mozzachiodi, Riccardo; Cammarata, Kirk V.; Scarpa, John; Turner, Jeffrey W.Malnutrition can cause many severe consequences to brain functions, including memory deficits. The invertebrate Aplysia was chosen as a model system to study prolonged food deprivation-induced memory impairments for its ability to sustain up to 14 days of food deprivation (14DFD) without health deterioration, nervous system damage or behavioral alterations. Here, a well-known learning paradigm in Aplysia was utilized. When presented with aversive stimuli (i.e., electrical shocks to the body wall that mimic attacks of a predator), Aplysia concurrently enhance their defensive responses (an elementary form of learned fear known as sensitization), including the tail-induced siphon withdrawal reflex (TSWR), and suppress feeding. The duration of these behavioral changes depends on the amount of aversive training. Precisely, short-term sensitization (STS) and short-term feeding suppression (STFS) are induced by a single trial of training and last for at least 15 min, while long-term sensitization (LTS) and long-term feeding suppression (LTFS) are induced by 4 consecutive trials and last for at least 24 h. Cellular correlates of sensitization and feeding suppression include increased excitability of the tail sensory neurons (TSNs) controlling TSWR, and decreased excitability of feeding decision-making neuron B51, respectively. A reduced in vitro preparation containing the neural circuits of TSWR, and feeding can express the above cellular correlates of sensitization and feeding suppression following the delivery of an aversive training protocol in vitro. Serotonin (5- HT) is known to mediate sensitization, but not feeding suppression. Recently, 14DFD was reported to cause memory deficits in Aplysia, exhibited as completely blocked sensitization, and attenuated feeding suppression. However, neuronal expressions of TSNs and B51, or the role of 5-HT in 14DFD-induced memory deficits, remain uninvestigated. The goal of this project was to characterize the mechanisms underlying memory deficits caused by prolonged food deprivation in Aplysia. Two feeding regimens were utilized: 2 days of food deprivation (2DFD), which is the standard feeding protocol and control for prolonged food deprived regimens, and 14DFD, which is the maximum period that Aplysia can sustain without health deterioration. Three specific aims were developed. In Aim 1, the expression of the learned neuronal modifications associated with STS and STFS under 14DFD was investigated. The aversive training was delivered in vitro in the reduced preparation described above and membrane properties of TSNs and B51were recorded before and after the in vitro training. In Aim 2, the effects of 14DFD on 5-HT levels were examined. 5-HT concentrations in the hemolymph and ganglia were measured and compared between 14DFD and 2DFD animals. Aim 3 studied whether 5-HT alone induced sensitization and its cellular correlates under 14DFD. In this aim, the ability of 5-HT to induce sensitization (Aim 3.1) and neuronal modifications in TSNs and B51(Aim 3.2) in 14DFD Aplysia were investigated, respectively. Results indicate that 14DFD prevented training-induced increased excitability of TSNs and decreased excitability of B51. These findings suggest that prevented STS may result, at least partly, from the lack of increased excitability of TSNs, while the reduced STFS may be contributed by additional neurons in the feeding neural circuits. 5-HT concentration in the hemolymph was reduced by 14DFD, which may be one of the causes that prevented sensitization under 14DFD. In the ganglia, 5-HT level was not affected by 14DFD. 5-HT was able to induce LTS in 14DFD Aplysia at 24 h post-test, while the amount of LTS induced was significantly smaller compared to 2DFD Aplysia. This indicates that 5-HT alone cannot fully induce LTS under 14DFD. 5-HT alone was capable of inducing increased TSN excitability in 14DFD preparations. Increased TSN excitability in 14DFD preparations induced by 5-HT was comparable to that observed in 2DFD preparations. Conversely, 5-HT failed to induce decreased excitability of B51 under either 2DFD or 14DFD, which indicates that 5-HT was not involved in decreased excitability of B51. These data revealed the cellular mechanisms and role of 5-HT in 14DFD-induced memory deficits. This study lays the foundations for the future use of Aplysia as a valuable model system to investigate mechanisms underlying memory impairments caused by prolonged food deprivation.Item Characterizing the Microbial Response to Plastic and Bioplastic Debris in the Marine Environment(2019-12) Pinnell, Lee J.; Turner, Jeffrey W.; Bird, Christopher E.; Conkle, Jeremy L.; Wetz, Michael S.Plastic is the most abundant type of debris found in the marine environment, commonly representing between 60-95% of all marine debris. Plastic debris accumulation is greatest in urbanized coastal zones and closed bays or lagoons with limited flushing, and benthic environments are the final resting place for the majority of this debris, as biofouling leads to the sedimentation of floating plastics and many plastics have higher densities than seawater. However, the impact of plastic debris on benthic microbial communities is largely unknown. Similarly, the impact of bioplastics, which are promising alternatives for mitigating plastic pollution, is virtually unknown. The goal of this study was to characterize how benthic microbial communities respond to the deposition of both plastic (polyethylene terephthalate; PET) and bioplastic (polyhydroxyalkanoate; PHA) in coastal marine sediments. The microbial community colonizing ceramic served as a biofilm control while the free-living microbial community in the overlying water served as a non-biofilm control. Findings showed that biofilm communities (i.e. PET, PHA, and ceramic) were taxonomically distinct in comparison to free-living communities. Further, the PET and ceramic communities were indistinguishable. By contrast, bioplastic selected for a distinct microbial community that was enriched for depolymerases and dominated by sulfate-reducing microorganisms (SRM). Successional patterns demonstrated that the PHA- associated communities remained atypical and dominated by SRM throughout a 424-day microcosm. The isolation and whole-genome sequencing of individuals from PHA-associated biofilms led to the discovery of Bacillus strains capable of degrading PHA and reducing sulfate. The results presented here clearly demonstrate that plastic was not colonized by a unique microbial community whereas bioplastic was. Additionally, culture-independent and culture dependent experiments showed that the PHA-associated microbial community was capable of PHA degradation and sulfate reduction. Given that SRM mediate carbon mineralization in coastal sediments, bioplastic loading and the subsequent enrichment of SRM could unintendedly alter sediment biogeochemistry. Future scientific investigation and government legislation should consider the microbial response to plastic as well as bioplastic loading when developing legislation and best-management practices related to plastic pollution.Item Cross-shelf larval fish assemblage structure and trophic niche partitioning, condition, and growth of Sciaenidae larvae in the North-Western Gulf of Mexico(2022-05) McAskill, Shannan; Geist, Simon; Walther, Benjamin; Tolan, James; Portnoy, David; Shinoda, ToshiakiFluctuations in physical and biological parameters can have a profound influence on larval fish survivorship and recruitment success. The purpose of this dissertation was to investigate how differences in physical and biological parameters along cross-shelf gradients influence larval fish community assemblage structure, niche partitioning, nutritional condition and growth. It was hypothesized that sudden changes in cross-shelf temperature and salinity regimes caused by episodes of strong physical forcing, such as storms, would alter larval fish assemblage structure. To address this overarching hypothesis, Hurricane Harvey (2017) was used as a case study to investigate the effects of a large-scale flood plume on larval fish community assemblage structure in coastal north-western GOM waters. Results indicated a significant increase in sciaenids one month following the storm, with the overall assemblage composition during September more closely resembling assemblages typically found during October. This may have been related to an earlier peak in adult spawning cued by cooler than normal water temperatures following the storm. Within the sciaenids, a total of eight co-occurring species were found across September and October assemblages. To investigate factors which may support the co occurrence of multiple species with similar spatial distribution and phenology, niche partitioning among larval Cynoscion nothus, Larimus fasciatus, and Micropogonias undulatus was compared. It was hypothesized that diet composition would differ between species, development stages, and distance to shore. The study found evidence of differences in intra- and interspecific diet composition, ontogenetic dietary shifts (ODS’s), and trophic interactions differing between nearshore and mid-shelf. It was suggested that the inclusion of alternative food sources like cyclopoid crustaceans and non-copepod prey taxa alleviated potential interspecific competition allowing for larval co-occurrence. Finally, larval fish feeding success, condition, and growth, were investigated and related to changes in cross-shelf physical and biological parameters one and two months following a large-scale disturbance. It was hypothesized that higher plankton density, warmer water temperature, and lower salinity during September, especially nearshore, would be beneficial for larval fish feeding, condition, and growth compared to October. The results indicated temperature as the main driver supporting higher larval growth nearshore during September. Contrary to the overarching hypothesis, salinity had a negligible effect on larval fish assemblage structure. In summary the results of the different studies highlight post-storm temperature regimes as being an important factor influencing differences in assemblage composition and larval survivorship.Item Determine the effect of variability in habitat quality on dispersal(2022-05) Selwyn, Jason D.; Bird, Christopher E.; Hogan, J. Derek; Portnoy, David; Sterba-Boatwright, BlairThe dispersal of individuals between populations is a foundational process to understand at the interface of ecology and evolution. The natal habitat is theorized to strongly influence the degree of dispersal expected. However, understanding the interaction between habitat and dispersal is difficult to study empirically, particularly in a single location where other environmental factors are held constant. Understanding how habitats influence dispersal is important not only for the foundational understanding of ecological and evolutionary processes but also as they relate to the design of marine protected area networks. Here I seek to understand how heterogeneity in habitat quality influences the dispersal dynamics of the common Caribbean reef goby Coryphopterus hyalinus as a model for other species with similar life histories in different systems. To determine how variation in habitat quality influences dispersal first I had to establish what topographical features of the reef equate to greater habitat quality from the perspective of the previously presumed habitat generalist C. hyalinus. I found that as adults C. hyalinus live in mixed species shoals with their congener C. personatus and are distributed across shallow coral reef ecosystems tending to be found in greater densities in more complex, deeper reef areas at the margin of large sand patches. In Turneffe Atoll, C. hyalinus has an average dispersal distance of 3.1 ± 0.3 km with 95% of individuals dispersing less than 7.7 ± 0.65 km. However, spatially heterogeneous habitats are characterized by shorter mean dispersal distances, smaller dispersal spreads, and higher propensity for long-distance dispersal events. This observation likely has strong conservation implications for the design and futureproofing of network-based conservation designs which depend upon dispersal between individual nodes of the network for proper functioning. As anthropogenic climate change alters habitats and in the short-term leads to increasingly fragmented and heterogeneous landscapes these networks may no longer be sustainable given the shrinking of the dispersal spread of the species these networks are designed to protect.Item Development of geodetic imaging techniques and machine learning for marsh observation(2019-05) Nguyen, Chuyen; Starek, Michael J.; Tissot, Philippe; Gibeaut, James; Prouty, Daniel; Moreno, MiguelAccurate characterization of marsh elevation and landcover evolution is important for coastal management and conservation. With recent advances in the application of high-resolution geodetic remote sensing techniques, accurate and rapid acquisition of topographic and geomorphic data is possible at a fine spatial resolution over large spatial extent. These techniques include airborne-based methods, such as Airborne Laser Scanning (ALS) and Unmanned Aircraft System (UAS) photogrammetry using Structure-from-Motion (SfM), and ground-based methods, such as Terrestrial Laser Scanning (TLS). Products such as Digital Elevation Models (DEMs), above ground biomass, and fractional vegetation cover produced by these high-resolution measurement techniques are revolutionizing and accelerating our understanding of geomorphological processes and landform transformations. Hyperspatial three-dimensional (3D) point cloud data generated by TLS and UAS-SfM can provide sampling of the marsh scene at previously unforeseen spatial detail. However, these data have different characteristics and different representations of the underlying terrain and landcover. While there are differences, the challenges associated with these technologies are large data sets, often larger than 100 million points for a study area. Given their size and complexity, terrain mapping and extraction of relevant information from the complex 3D point cloud cannot be done without the use of intelligent algorithms. This research develops advanced geodetic imaging and machine learning techniques to better resolve spatial patterns in marsh elevation and landcover over larger spatial extents than is feasible using standard field surveying methods. This includes: (1) Development of a novel unsupervised learning method for robust segmentation of TLS point cloud data acquired in marshes into homogeneous features (clusters) to reduce scene complexity for measurement and monitoring of surface and vegetation evolution. (2) Assessment and evaluation of the transferability and adaptability of the unsupervised learning method to multi-perspective 3D point cloud data derived from TLS and UAS-SfM for wetland landcover segmentation. (3) Development of ensemble neural networks for modelling DEM uncertainty. These networks are able to estimate DEM error, and then apply the DEM correction to every raster cell while providing an uncertainty for every correction. Furthermore, these networks can be applied to any DEM + 3D point cloud with a flexibility in the number and selection of model inputs, any type of geomatics measurements, and applicable to any type of environments. This work combines TLS and UAS-SfM measurements of a coastal marsh with the development and application of machine learning. The novel machine learning methods are developed to segment multi-perspective 3D point clouds and to correct DEMs while quantifying the spatial variability of the tolerance interval of the predictions (DEM uncertainty). The resulting information allows for enhanced change detection analysis of short-term marsh surface evolution in varying regimes. The developed computational techniques are generalizable to a wide range of coastal problems beyond marsh observations that rely on 3D point cloud data from a variety of scanning and imaging modalities, whether derived from lidar, UAS photogrammetry, or other survey methods. The resultant methods can be applied to estimate change detection uncertainty and monitor marsh evolution with these surveying technologies. In return, this can help support regional management of marshes in terms of understanding their short-term dynamics and long-term resilience.Item Discard mortality, recruitment, and connectivity of red snapper (Lutjanus Campechanus) in the Northern Gulf of Mexico(2014-07-10) Curtis, Judson MatthewRed Snapper (Lutjanus campechanus) is the most economically important reef fish species in the Gulf of Mexico. Despite being intensively managed, stocks have been slow to recover from overharvest and the population is still rebuilding. One possible reason is that Red Snapper experience high discard mortality after catch-and-release. Additionally, there is a decoupling of the stock-recruit relationship in the fishery with high levels of recruitment despite low spawning stock biomass. This dissertation addressed these gaps in knowledge in three principal chapters. In Chapter II, I evaluated if certain release methods reduced discard mortality of Red Snapper at different depths and temperatures. I used acoustic telemetry to determine the best-release practices for enhancing survival and to estimate the extent of delayed mortality. Venting and rapid recompression release methods were more beneficial for enhancing survival, and delayed mortality events occurred within a 72-hour time period. In Chapter III, I used novel acoustic transmitters to analyze the post-release behavior and activity patterns of Red Snapper that survived catch-and-release. Red Snapper had different acceleration and depth activity over diel time periods, and increases in acceleration were correlated with higher depth in the water column. Release treatments did not affect long-term behavior and activity. In Chapter IV, I examined the stock-recruit relationship for the Red Snapper fishery by assessing whether localized cryptic spawning stock biomass is responsible for maintaining high recruitment levels. Acoustic telemetry and catch data were used to show that large, sow Red Snapper have high site fidelity and residency patterns in the western Gulf of Mexico, suggesting high recruitment observed in the stock may be originating locally from non-targeted sites. By identifying the source of the high spawning stock biomass, protection measures and regulations can be implemented to ensure that the current high recruitment to the fishery is sustained. Determining the best-release practices to enhance survival of discarded fish will result in larger stock sizes. Ultimately, implementation of findings from this dissertation into the management process will further assist and expedite the rebuilding of Red Snapper stocks and promote the recovery towards sustainability in this historically important Gulf of Mexico fishery.Item Ecology of red snapper in the western Gulf of Mexico: comparisons among artificial and natural habitats(2016-12) Streich, Matthew Karl; Stunz, Gregory W.Artificial reef development is a popular management tool used to enhance fish stocks, mitigate degradation or loss of natural habitats, and provide additional recreational opportunities. Despite the popularity and support for artificial reef programs, our understanding of how artificial reefs affect marine fisheries is surprisingly limited. Thus, the goal of my study was to use concurrent comparisons of artificial reefs and natural habitats to provide key information to evaluate the utility of artificial reefs for reef fishes, in particular Red Snapper, in the western Gulf of Mexico (GOM). In Chapter 1, I used remotely operated vehicle surveys to show fish communities differ between artificial reefs and natural banks. While Red Snapper density was greater over artificial structures, estimates of total abundance and biomass were much greater on natural banks—approximately 7.6% of the 2012 GOM annual catch limit. In Chapter 2, I examined whether Red Snapper size structure and age and growth differ between artificial and natural habitats. Size and age distributions suggested natural banks supported more large and old individuals, and the logistic growth model suggested fish at artificial reefs reached larger sizes-at-age than those from other habitats. In Chapter 3, I assessed vertical line gear performance and demonstrated differences in gear efficiency between artificial reefs and natural banks. The use of paired video revealed a high prevalence of gear saturation, which should be accounted for if vertical lines are used in providing indices of abundance. In Chapter 4, I examined the effects of a newly created artificial reef using a before-after control-impact study. Following reef construction, juvenile Red Snapper abundance dramatically increased, and cohorts could be identified through time suggesting site fidelity. Because juvenile Red Snapper were present in high densities, appeared to be in good condition and growing quickly, and were no longer exposed to shrimp trawl mortality, the new reef likely enhanced the export of juveniles (i.e., production) to the adult population. Collectively, my findings suggest artificial reefs can be a valuable tool for enhancing the Red Snapper population. Given the large area of natural habitats in the GOM, artificial reefs may also be an effective management option for diverting fishing effort away from a large portion of the stock. Furthermore, fish at artificial habitats appear to grow as well as those on natural habitats, and artificial reefs can provide nursery habitat to juveniles. To increase the role artificial reefs play in supporting the GOM Red Snapper stock, future research should identify reef designs that maximize growth, survival, and production.Item Effects of Oil on the Deep Gulf of Mexico Benthos(2017-05) Washburn, Travis William; Montagna, Paul A.; Pollack, Jennifer Beseres; Demopoulos, Amanda W.J.; Yoskowitz, David W.The deep sea ( > 200 m) is the largest habitat on Earth. However, the deep sea ecosystem is poorly understood relative to most other habitats due to the difficultly in accessing it. As human activities increase in the deep sea, the need to understand processes occurring in the deep and impacts on these processes by human activities also increases. This study examines the importance of the deep sea to humans as well as the impacts of oil on deep-sea communities. Approximately 5 million barrels of oil were released during the Deepwater Horizon spill, much of which remained in the deep sea. Shortly after the spill ended, benthic diversity and abundance were lower near the Deepwater Horizon wellhead compared to deep-sea areas not affected by the spill. Diversity increased with increasing distance from the wellhead while abundances peaked at intermediate distances suggesting a toxicity vs. enrichment effect. There were also several benthic taxa identified as potential indicators of oil-contaminated and uncontaminated areas. Oil is released from the seafloor via natural seepage as well. Benthic abundance and diversity differed among different types of seep communities (microbial mats, tubeworms, and soft-bottom seeps), between seep and non-seep areas, and between seep and spill areas. Unlike communities impacted by the DWH spill, there did not appear to be taxa specifically associated with natural seepage. In fact, high variability in community structure appeared to be the best indicator of natural seepage, with specific seep communities not only different from background and spill communities, but also different from other seep communities. Oil that enters the oceans does not remain there indefinitely. Oil released by both natural and anthropogenic processes is removed from the marine environment naturally by burial in the seafloor, degradation by bacteria, and dilution in the water column. The removal of oil by the environment is an example of an ecosystem service termed waste regulation. Waste regulation was examined in the context of the Deepwater Horizon spill by calculating the monetary value of the natural removal of oil spilled. Estimations of fates of the DWH oil as well as cleanup costs were examined. It was estimated that 10’s of billions of dollars were saved from offshore waste regulation following the spill. This dissertation concludes that the differences among communities at natural seeps, areas impacted by the spill, and areas not impacted by oil were numerous. Benthic communities associated with deep oil spills were defined, allowing for the future assessment of damages caused by deep-sea spills. Communities associated with natural seepage were different from other habitats as well as other seep communities, emphasizing the unique nature of each seep location in the Gulf of Mexico. Valuation of deep-sea services will provide monetary costs for destructive practices in the deep sea. Knowledge of deep-sea services is also important to communicate to the public to ensure these services will be protected. This dissertation provides information on the effects of the first deep-sea oil release on benthic communities, differences between impacts of natural and anthropogenic oil required to assess spill damages, a unique comparison of several different seep communities throughout the Gulf of Mexico, as well as an initial, partial value of waste regulation provided by the deep-sea environment. The work performed can help guide future policies concerning deep-sea drilling and assist in the identification and protection of unique habitats in the deep sea. Communication of deep-sea benefits can provide the public with motivation to care about the fate of the deep sea, which is far beyond the reach of most people.Item Evaluation of dietary feeding stimulants for the sea urchin Lytechinus variegatus(2014-04-08) Bandolon, AdrianSea urchins shape their environment primarily through their feeding behavior. For Lytechinus variegatus this behavior is largely guided by the detection and response to chemical stimulus. The extent of which compounds and how these specific chemicals influence behavior in sea urchins has received only cursory investigation. The purpose of this study is to characterize the role of several amino acids in the feeding behavior of the sea urchin Lytechinus variegatus. Specimens of L. variegatus were collected from Cape San Blas within the Port St. Joseph Peninsula State Park, FL, USA (30 °N, 85.5 °W). Sea urchins were maintained in a semi-recirculating system and fed a standard reference diet (SRD) at ad libitum levels. This diet is used routinely in all sea urchin research at the Shrimp Mariculture Project. To standardize conditions for testing olfactory and gustatory response, a series of experiments were performed to evaluate the effects of water flow rate and hunger on the chemical response of L. variegatus. To characterize the effects of flow rate, feed consumption rate and travel speed was measured while the sea urchins were subjected to different current velocities. Lytechinus variegatus was subjected to different lengths of food deprivation to assess the effects of hunger on their feeding behavior. Finally, olfactory and gustatory response was evaluated by exposing L. variegatus to one of eight concentrations of six individual amino acids (L-alanine, L-arginine, DL-glutamate, glycine, L-leucine and L-tyrosine). Results from these studies suggest that Lytechinus variegatus is positively rheotactic and under the conditions of the study, increases feed consumption rate with increased flow rate. Also, during periods of prolonged food limitation, L. variegatus decreases physical activity but consumes larger amounts of food when it becomes available. Lytechinus variegatus also employ food-sourced amino acids to identify food sources and evaluate food palatability. These findings help expose components of scantily studied mechanisms that drive sea urchin navigation, foraging, distribution, food choice and interactions. These findings could also impact sea urchin aquaculture, affecting both feed formulation and sea urchin husbandry techniques.Item Evaluation of microalgae as a potential fishmeal replacement in the diet of oreochromis mossambicus(2019-05) Jones, Ivy Colleen; Fox, Joe M.; Gatlin III, Delbert M.; Siccardi III, Anthony J.; Zimba, Paul V.; Palaniappan, DevanayagamAlgae biomass from strains isolated from Corpus Christi, TX water were evaluated as ingredients to replace fishmeal in diets fed to Oreochromis mossambicus. Strains were selected based upon ability to be cultured on inexpensive nutrient media, biochemical composition, and ability to achieve productivity of ≥ 0.10g/L. Further selection involved evaluation of test ingredients for apparent dry matter, protein, ingredient, and amino acid digestibility when fed to juvenile (~30g) tilapia. Digestibility diets consisted of 69% reference diet, 1% Cr2O3 as an inert marker, and 30% algal test ingredient. Apparent dry matter digestibility ranged from 50.7±0.02% to 70.6±0.07% in the M. salina and Spring mix 2014 (Spmix), respectively. The Platymonas sp. and the Spmix diets exhibited the highest dry matter digestibility (69.3±5.5% and 70.6±3.9%, respectively). The dry matter in the Cylindrotheca sp. (57.9±3.5%) and the M. salina (50.7±8.5%) diets were the least digestible. Results showed that there were no significant differences in regards protein digestibility in the formulated diets (n=3). Also, there were no significant differences between the digestibilities of the ingredients (ADCI). The Platymonas sp. and the Spmix had the highest ADCI 83.1 ± 30.0% and 85.3 ± 24.6%, respectively. Methionine was 93.0% digestible in M. salina, and lysine digestibility was highest in Spmix (88.5±0.46%). In a subsequent 30-day feeding trial, ten ~0.170 mg tilapia were fed diets in which Spmix and Platymonas sp. (P) replaced various levels of fishmeal (0, 20, 40, 60, 80, 100%) in diets containing 40% crude protein. Weight gain (%), specific growth rate (SGR), final body weight, feed conversion ratio (FCR), protein efficiency ratio (PER), and percent survival were evaluated (n=5). Survival ranged from 96-100%. There were no significant differences in percent weight gain in the fish fed P20%-P80% diets. The FCR of the fish fed P20% and P40% were different from those fed the P100% diet (P=0.0145). The PER of fish fed P20%, P40%, and P80% were also significantly different from that of the fish fed the P100% (P=0.0214) diet. Fish fed the P100% diet had the lowest FCR (1.19±0.14). All performance indices were similar for tilapia fed the Spmix diets. Results showed that both test ingredients could be used to replace fishmeal at high levels of dietary inclusion, 80% for Platymonas sp. and 100% for Spmix. This indicates high potential for replacement of fishmeal in tilapia feeds with marine microalgae.Item Evolution of the genus Sicydium (Gobiidae: sicydiinae)(2015-08) Chabarria, Ryan Earl; Pezold, Frank; Conway, Kevin W; Parenti, Lynne R; Hogan, James DGobies are one of the most speciose groups of fishes on the planet. Despite their prominence little is known about their evolution and diversity. Gobies of the genus Sicydium are abundant inhabitants of tropical streams in the Atlantic and eastern Pacific basins. The amphidromous life history of Sicydium presents challenges in understanding their diversity and the evolutionary relationships among species. With this life history, the adults live and breed in freshwater streams. Newly hatched larvae are carried out to the marine environment where they live as ichthyoplankton for a period of time. Upon completion of the marine larval phase juveniles will re-enter the freshwater environment. Additionally, poor species descriptions, parochial studies, and highly variable morphological characters have resulted in taxonomic uncertainty within the genus. This dissertation presents separate phylogenetic hypotheses of the relationships between species of Sicydium based upon morphology and DNA data. In the first chapter, I present a phylogenetic hypothesis of the relationships among the species of Sicydium based upon morphological characters. This chapter shows that changes in jaw morphology are important in the evolution of Sicydium. Three clades of Sicydium were recovered, however the relationship among these clades was unresolved. Different oral morphology characters were important in determining the relationships between species. This includes morphology of the premaxillary teeth, which has been used as a diagnostic character for species of Sicydium. This study presents the first phylogenetic hypothesis based on morphology for the species of Sicydium. The second chapter presents a molecular assessment of species diversity and a molecular phylogenetic hypothesis of Sicydium based upon two nuclear and two mtDNA genes. Previous molecular studies that have included Sicydium were at the population or subfamily level. Here I present the first molecular hypothesis of the evolutionary relationships among the species of Sicydium. The analysis recovered two clades of a monophyletic Sicydium, one less than morphological data, with most relationships among species well resolved. The species recovered in these two clades were similar to those recovered with the morphological data. However some species were not recovered as monophyletic in the molecular analysis, most likely due to incomplete lineage sorting. In the third chapter, I present a population level study of an eastern Pacific species, Sicydium salvini, Ogilvie-Grant, 1884. This chapter explores the diversity of a species recovered by the previous chapters. This study showed that S. salvini inhabits a wide geographic range including areas previously considered to be occupied by Sicydium multipunctatum. DNA samples from across the range of this species were used to test for population structure and population expansion. A lack of structure between river populations was found which is most easily explained by the amphidromous life history. The dispersion capabilities of the marine larvae allow free exchange of genes between distant populations. I also show that tectonic activity may explain a historic population expansion for Sicydium salvini. In this dissertation I present different views on the evolution of Sicydium. In the first two chapters, I present phylogenetic hypotheses of the species of Sicydium. The third chapter shows a population level view of Sicydium salvini. These data can be used as a stepping-stone for future work involving the evolution of sicydiine gobies as well as providing new characters for a much needed taxonomic revision of Sicydium. It also clarifies population level dynamics and historical environmental influences on those dynamics.Item Fish predators maintain estuarine biodiversity and benefit ecosystem engineers(2020-05) Reustle, Joseph William Newton Leo; Smee, Delbert Lee; Walther, Benjamin D.; Turner, Jeffrey W.; Conkle, Jeremy L.; Bogucki, Darek J.Loss of top predators may lead to the proliferation of mesopredators (i.e., intermediate consumers), with significant consequences for entire food webs. Termed mesopredator release, this process is typically attributed to a decline in the abundance of top predators. We investigated the potential for moderate environmental changes, that disrupt sensing abilities, to trigger mesopredator release by diminishing the foraging ability of top predators without affecting their abundance. In estuaries, fishes occupy the upper trophic levels and many species rely on visual cues to forage. We hypothesized that increased turbidity would attenuate fish foraging ability, increase the abundance of crabs and other mesopredators, and significantly alter coastal food webs. In oyster reef communities, turbidity triggered mesopredator release in 2016 and 2017, even though freshwater inflow and ambient salinity varied significantly between years, suggesting that turbidity’s effects on estuarine food webs are robust. Following experiments in 2017, our field site was struck by Hurricane Harvey, a category 4 storm. Oyster mortality was high following Harvey due to low salinity and trophic reliance on oysters as a basal resource. Hurricane Harvey removed human fishing pressure, causing fish populations to increase dramatically, resulting in stronger top-down control on crabs that are the primary predator of newly settled oysters. We also investigated the potential for barnacles as accessible and biologically relevant flow indicators since hydrodynamics are key regulators of speciesinteractions. In summary, fish predators are important components of oyster reef ecosystems, enhancing biodiversity and, at times, benefiting oysters through a trophic cascade depending on the environmental context. Turbidity and fishing reduce top down control by fishes, leading to increases in the abundance of intermediate consumers, less diverse reef communities, and often damaging juvenile oysters.Item A hierarchical approach to incorporating habitat assessment into an existing fisheries monitoring framework(2021-08) Clarkson, Emma L.; Pollack, Jennifer Beseres; Fisher, Mark; Gibeaut, James; Walther, BenjaminThe extent and quality of estuarine habitat has a significant influence on the growth, recruitment, and survival of fish and invertebrate species. The Sustainable Fisheries Act of 1996, part of the Magnuson Stevens Fisheries Conservation and Management Act, mandated designation and monitoring of “Essential Fish Habitat” (EFH), creating the need for efficient, effective, and accurate approaches for monitoring habitat at multiple spatial scales. Because the relationships between fisheries species and their associated habitats are complex and can vary across ontogenies and regions, approaches to monitoring faunal-habitat associations are also needed to quantify the impact of EFH on fisheries stocks. However, funding limitations can prohibit monitoring fauna, habitat, and faunal-habitat associations at the multiple spatial and temporal scales necessary to accurately quantify faunal response to habitat change. The resulting information gap creates challenges to using science to inform decision making, especially in cases of reactive management decisions that are typical of state agencies. This dissertation explores the resource management potential of utilizing free, publicly available datasets to examine estuarine faunal-habitat associations at multiple spatial scales in Texas. A hierarchical approach was used to link three tiers of habitat data to faunal abundance data from Texas Parks and Wildlife Department’s (TPWD) Fisheries Independent Monitoring (FIM) program to evaluate the influence of habitat availability and quality on target species’ occurrence and abundance. Target species were selected based on their commercial and recreational importance and included Spotted Seatrout (Cynoscion nebulosus), Red Drum (Sciaenops ocellatus), Atlantic croaker (Micropogonias undulatus), Blue crab (Callinectes sapidus), Brown shrimp (Farfantepenaeus aztecus), and White shrimp (Litopenaeus setiferus). The three tiers are used to monitor fauna and associated fauna at multiple spatial and temporal scales and range from broad, large spatiotemporal scale assessments using remote sensing (Tier 1) to more detailed in-situ observations used to capture causal relationships (Tier 3). In this study, the three tiers of habitat data include: (Tier 1) a publicly available, remotely sensed habitat mapping product (2004 NOAA Benthic Atlas) that describes habitat presence and extent across large spatial scales, (Tier 2) the Texas seagrass monitoring program, in which seagrass quality (percent cover and species composition) is characterized annually at fixed sampling stations, and (Tier 3) a rapid, in-situ habitat assessment incorporated into the FIM methodology and conducted concurrently with bag seine sampling to monitor real-time faunal response to habitat change. The ability of all tiered approaches to detect known faunal-habitat associations demonstrates their efficacy. Structural subtidal (seagrass) and intertidal (saltmarsh and mangrove) presence and quality significantly impacted faunal occurrence and abundance. Several cases of facultative habitat use were identified, and faunal-habitat associations were typically scale-dependent and spatially explicit. The strengths and weaknesses of each tiered approach were evaluated to exemplify how complementary use of tiered data from multi-scale hierarchical monitoring can be used to fill gaps associated with any single method. The cost effective approaches utilized in this study can be translated to any management region where both Fisheries Independent Monitoring (FIM) data and existing habitat mapping and monitoring data products are available. The faunal-habitat associations characterized in this study provide a step toward quantitatively and qualitatively incorporating habitat into fisheries management decisions.Item I will survive: A guide to microbial survival in the subsurface(2021-12) Mullis, Megan; Larkin, Patrick D.; Reese, Brandi Kiel; Baker, Brett J.; Sylvan, Jason B.; Mehrubeoglu, RubyMicrobes play fundamental roles in ecosystem function through mediating biogeochemical cycles, yet we know very little about how microbes interact and what drives community diversity. They form complex communities and engage in a wide variety of biotic interactions. Fundamentally, microorganisms can utilize one or more biosynthetic pathways for survival: 1) outcompete their neighbor(s) by adapting their metabolism to the available resources; 2) work with their neighbor by forming a mutualistic cooperation; and/or 3) remove their competition through inhibition or lysis. My dissertation aims to address microorganism survival mechanisms in the subsurface in a variety of locales. My research chapters incorporate various methods including culture-dependent and -independent techniques that aim to answer what the microbial community diversity is, if any microorganisms are metabolically active, and how microorganisms are surviving within those environments. Many continental and marine subsurface environments were examined for functional genes in microbial communities, with specific focus on sediments collected from Mariana Forearc mud volcanoes and the western flank of the Mid-Atlantic Ridge. The first survival mechanism was identified in cultivated isolates from western flank sediment of the Mid-Atlantic Ridge in which microbial populations could utilize many resources including oxygen, nitrogen, sulfur, and carbon. The second survival mechanism was identified in the Mariana Forearc mud volcanoes where microbial communities were potentially coupling denitrification and anaerobic methane oxidation. The final survival mechanism was identified across many continental and marine subsurface environments using data derived from the Deep Carbon Observatory’s Census of Deep Life and across Bacteria and Archaea, including Methanobacteria, Actinobacterota, Desulfobulbia, Gammaproteobacteria, and Planctomycetes. Many of the genes identified for the third survival mechanism were similar to antimicrobial genes that are used medicinally. Microbial communities in the subsurface environments experience a wide array of environmental conditions even extreme and utilize various resources for metabolism as well as use specific mechanisms that confer a competitive advantage.Item Identifying migration flexibility and the environmental factors that influence variation in recruitment success in partially migratory Hawaiian fishes(2019-05) Heim-Ballew, Heidi; Hogan, J. Derek; Portnoy, David; Pollack, JenniferBehavior flexibility during the larval stage influences differential mortality, recruitment, and population dynamics; recruitment is poorly understood, yet important for understanding population persistence. The purpose of this dissertation was to examine fishes for migration flexibility and to identify factors at different spatiotemporal scales that are influential to differential survival within and across populations. I found that four underexplored native freshwater fishes of Hawai‘i exhibited a larval migratory strategy, but many were flexible. One species (Sicyopterus stimpsoni) showed all individuals made a migration, and the others showed 25 – 40 % did not migrate. Next, I examined if migrant (S. stimpsoni) and flexible species (Awaous stamineus) showed lunar rhythmicity at hatching and settlement. Migrants of the flexible species showed more hatching around the full moon and settlement around the new moon, and residents showed the opposite pattern. The divergence in life-history timing appears to be a balance between ecological costs and benefits. Next, I examined the influence of variation in localized conditions on the ratio of migrant to resident contingents (A. stamineus) in adult populations. Residents were least represented when stream flow and nutrients were low; however, the abundance of a common invasive predator showed a negative relationship with resident abundance. Highly urbanized systems may impose such stressful conditions that resident recruitment is diminished, which underscores the importance of stream management to conserve vulnerable native species. Lastly, I examined the frequency of contingents (A. stamineus), larval duration, and growth rates across ENSO. The proportion of migrants was highest during La Niña, and resident proportions were highest during weak La Niña and strong El Niño; once El Niño became very strong, resident proportions decreased. Migrants had faster growth than residents across all growing stages. Migrant growth rates in the early larval stage were highest during El Niño, and pre-settlement growth was highest during La Niña. Resident growth was fastest during neutral conditions. The duration of the early fast-growing period was shortest during El Niño, and the larval duration was longer. These dissertation findings show the importance of evaluating multiple influential scales to understand life-history strategies of individuals, especially those that inhabit multiple ecotypes.Item Impact of subsurface methane transport on shallow marine sediment geochemistry(2020-08) Abdullajintakam, Sajjad; Abdullajintakam, Sajjad; Coffin, Richard B.; Coffin, Richard B.; Abdulla, Hussain AN; Reese, Brandi K; Naehr, Thomas H; Lyons, Timothy W; Abdulla, Hussain; Reese, Brandi K.; Naehr, Thomas H; Lyons, Timothy WMarine sediments host a vast amount of methane, a potent greenhouse gas, in the subsurface. Transport of this subsurface methane towards the seafloor creates unique biogeochemical interactions which result in important consequences for the chemical and biological composition of the oceans at present and over the Earth’s geological history. This dissertation studied the impact of subsurface methane venting to shallow marine sediment geochemistry with a goal to quantify the role of methane induced biogeochemical processes in marine carbon cycling and to recognize geochemical proxies that will enable better reconstruction of these processes from the geological record. Key results suggest the following: (i) Globally, diffusive methane charged sediments are significantly contributing to the oceanic dissolved inorganic carbon (DIC) pool (comparable to ~20% global riverine DIC flux to oceans) and sedimentary carbonate accumulation (comparable to ~15% of carbonate accumulation on continental shelves), primarily due to microbially induced carbon-sulfur (C-S) coupling. (ii) C-S coupling induced by methane seeps and crude oil seeps can be distinguished from the sediment records using a combined stable carbon (δ13C) and sulfur (δ34S) analysis of authigenic carbonate and sulfide mineral phases formed in seep settings. (iii) Molecular fossil records of methane metabolizing archaea in the sediment column involve unique isomer patterns of Isoprenoid Glycerol dialkyl glycerol tetraether (GDGT) lipids, which can serve as an important proxy to study paleo-methane flux records. These results will substantially contribute to our existing coastal and geological carbon models as well as enhance our existing inventory of geochemical proxies to characterize the methane venting systems in the geological past.Item The importance of submarine groundwater discharge on nutrient fluxes and dissolved organic matter molecular composition in a semi-arid, highly disturbed estuary(2020-12) Douglas, Audrey; Murgulet, Dorina; Montagna, Paul; Abdulla, Hussain; Felix, Joseph D.; Peterson, RichardThis dissertation advances our understanding of the temporal and spatial variability of submarine groundwater discharge (SGD) rates, SGD-derived nutrient fluxes and its role in the nitrogen budget, and the dissolved organic matter (DOM) molecular composition of surface water and porewater in semi-arid, hydrological disturbed estuaries. Nueces Bay was selected as the study area because it is highly disturbed both anthropogenically (e.g., dredging, oil/gas development, and reduced freshwater inflows) and naturally (e.g., drought, flooding) and the nitrogen budget remains unbalanced after multiple attempts. This study collected surface water and porewater samples quarterly for 2 years and employed radon and radium mass balances and Darcy estimates to assess SGD rates, principal components analysis and a partial hierarchical two-way ANOVA to evaluate the water quality and relative importance of SGD-derived nutrient fluxes to the overall nutrient budget, and PPL-SPE and UPLC-Orbitrap Fusion Tribrid mass spectrometry to assess DOM molecular composition. This study found significant spatial and temporal variability in SGD rates that vary over 1-2 orders of magnitude depending on method (i.e., radon or radium mass balance, Darcy estimate), location, and groundwater endmember. The high SGD rates, compared to literature, are driven by steeper gradients nearshore, shortcircuiting of confining layers due to substantial oil/gas development and dredging, sediment heterogeneity, and reduced confining layer integrity favoring vertical advective flux. The observed spatiotemporal variability in SGD was related to nutrient fluxes and nitrogen budgets, suggesting that SGD brings 2-4 orders of magnitude more nitrogen and other nutrients into the system than surface runoff under all hydroclimatic conditions. Thus, the average SGD flux supplies more nitrogen to the system than previously accounted for creating an excess of vi 370.6x109 g N⸱yr-1 . Finally, a molecular characterization of the DOM indicates that surface water DOM composition is significantly different from flooding and baseflow conditions (6- and 9- months post flooding) during flood recession (3-months post flooding) with more heteroatom compounds detected. Surface water and porewater are most similar during flooding recession, indicating greater SGD-derived DOM. While other studies have suggested that semi-arid systems receive significant SGD, this dissertation further suggests that SGD in highly anthropogenically disturbed systems may be derived from both shorter (shallower) and longer (deeper) flowpaths and lag the climatic conditions by weeks (surficial aquifers) and months or longer (deeper aquifers). As anthropogenic disturbances continue to increase along with a changing climate, the groundwater-surface water interactions will be impacted and the long-term effects of these changes on nutrient and DOM composition might be significant, though potential consequences remain largely unknown.Item Improving assessments of water resources characterization and relationships to climate variabilities(2022-07-07) Gyawali, Bimal; Murgulet, Dorina; Ahmed, Mohamed; Liu, Chuntao; Tissot, PhilippeWith the increasing vulnerability of water resources due to climate change and the associated more frequent and intensive extreme events, there is a growing need to monitor the spatial and temporal variability in water resources. Coastal aquifers are a major source of freshwater for almost 40% of the world’s population living in coastal regions. Changes in groundwater level impact groundwater discharge to surface waters, which in turn affects the amount of streamflow resulting in variability in freshwater inflow to estuaries. However, lack of continuous spatial and temporal coverage of groundwater elevation data hinders direct measurements of groundwater storage (GWS). The first objective of this dissertation is to quantify the spatial and temporal variation in coastal GWS using uninterrupted monthly Gravity Recovery and Climate Experiment (GRACE) derived terrestrial water storage (TWSGRACE) utilizing the Texas Gulf Coast Aquifer as a benchmark. To accomplish this, the data gap in TWSGRACE was filled with reconstructed values from multi-linear regression (MLR) and artificial neural network (ANN) models. The reconstructed TWSGRACE was integrated with land surface model products and ground-based measurements to examine the long- and short-term trends in GWS in response to changing climate conditions. This study found a significant decline (0.35 ± 0.078 km3·yr?1, p-value: < 0.01) in GWS during the study period 2002-2019 and was able to capture extreme climate events (i.e., drought and flood). The second objective provides an innovative approach to deriving a continuous TWSGRACE record for improved evaluation of GWS at a global scale. The approach integrates three machine learning techniques (deep-learning neural networks [DNN], generalized linear model [GLM], and gradient boosting machine [GBM]) and eight climatic and hydrological input variables to fill GRACE record gaps and reconstruct the TWSGRACE data record at both global grid and basin scales. This study’s models’ performances were found to be superior to those from 61% of previous similar studies and comparable to 21%. The reconstructed TWSGRACE data captured the occurrences of extreme hydro-climatic events over the investigated basins and grid cells. In addition, the third objective evaluates the impact of individual and coupled ocean-atmospheric phenomena (El Niño Southern Oscillation [ENSO], Pacific Decadal Oscillation [PDO], and Atlantic multidecadal oscillation [AMO]) on hydrological variables (i.e., precipitation, streamflow, and freshwater inflow) across several major estuaries located along the northwestern Gulf of Mexico (nGOM), which span a significant climatic gradient. Results show that the individual and coupled climate variability phenomena have a significant impact on all three hydrological variables and the magnitude of impact varies seasonally and spatially, with the strongest modulation on cold seasons and in the wet region (of Texas). The severity of droughts increases significantly when the La Niña phase of ENSO is coupled with the PDO/AMO cold/warm. This dissertation 1) offers a reliable approach to examine the long- and short-term trends in GWS, 2) provides a robust and effective approach to fill the data gaps in TWSGRACE that can serve as a reference tool to fill the data gaps in any hydrological system across the globe, and 3) improves the understanding of the relationship between estuarine hydrology and climate variability. The results from these studies serve as valuable tools for water management strategies and benefit water resources planning and disaster management in coastal areas.