Oyster reefs provide valuable ecosystemservices that contribute to coastal resilience. Unfortunately, many reefs have been degraded or removed completely, and there are increased efforts to restore oysters in many coastal areas. In particular, much attention has recently been given to the restoration of shellfish reefs along eroding shorelines to reduce erosion. Such fringing reef approaches, however, often lack empirical data to identify locations where reefs are most effective in reducing marsh erosion, or fully take into account habitat suitability. Using monitoring data from 5 separate fringing reef projects across coastal Louisiana, we quantify shoreline exposure (fetch + wind direction + wind speed) and reef impacts on shoreline retreat. Our results indicate that fringing oyster reefs have a higher impact on shoreline retreat at higher exposure shorelines. At higher exposures, fringing reefs reduced marsh edge erosion an average of 1.0 m y-1. Using these data, we identify ranges of shoreline exposure values where oyster reefs are most effective at reducing marsh edge erosion and apply this knowledge to a case study within one Louisiana estuary. In Breton Sound estuary, we calculate shoreline exposure at 500 random points and then overlay a habitat suitability index for oysters. This method and the resulting visualization show areas most likely to support sustainable oyster populations as well as significantly reduce shoreline erosion. Our results demonstrate how site selection criteria, which include shoreline exposure and habitat suitability, are critical to ensuring greater positive impacts and longevity of oyster reef restoration projects.

Fishes within the family Scombridae (i.e. tunas, mackerels and bonitos) are of high ecological and economic value, as they are heavily targeted by commercial and recreational fisheries. In coastal and open-ocean environments, adults are high-level predators, while larvae and juveniles serve as prey for numerous species. Much is known about the distribution and abundance of adult tunas, but high taxonomic uncertainty and limited knowledge regarding the distributional patterns of larval and juvenile tunas have led to an “operational taxonomic unit” gap in our understanding of tuna ecology. Scombrids were collected across the Gulf of Mexico (GoM, hereafter) during seven research cruises from 2010-2011, as part of the NOAA-supported Offshore Nekton Sampling and Analysis Program, and during five research cruises from 2015-2017, as a part of the GOMRI-supported Deep Pelagic Nekton Dynamics of the Gulf of Mexico Consortium. In this thesis, species composition, distribution, and abundance of tunas collected from the surface to 1500 m depth are characterized in relation to depth, time of year, and physical oceanographic features. A synthesis of the morphological characteristics used to identify the taxonomically challenging larval and juvenile stages of tunas is presented, along with length-weight regressions to fill the data gap on the growth patterns of these early life stages. A total of 945 scombrid specimens were collected, representing 11 of the 16 species that occur in the GoM. The dominant species included: Euthynnus alletteratus (Little Tunny), Thunnus atlanticus (Blackfin Tuna), Auxis thazard (Frigate Mackerel), and Katsuwonus pelamis (Skipjack Tuna). Evidence of sampling gear selectivity was observed, with a MOCNESS (rectangular, research-sized trawl) collecting larvae predominantly, and a large, high-speed rope trawl catching only juveniles. Scombrids were collected primarily in the upper 200 m of the water column. Species-specific environmental preferences and seasonality were identified as the main drivers of tuna spatial distributions across the epipelagic GoM. Integrating aspects of scombrid ecology in neritic and oceanic environments improves management and conservation efforts for this highly important taxon.

Ocean models are increasingly able to synthesize a large temporal domain with fine spatial resolution. With this increase in functionality and availability, ocean models are in high demand by researchers, establishing a critical need for validating a model’s ability to represent interior ocean dynamics. Satellite measurements are typically used for validation, however these measurements are limited to the upper layers of the ocean and therefore satellite measurements of sea surface height and sea surface temperature are the most validated output parameters of three-dimensional ocean models. Unfortunately there is a paucity of model validation studies for the interior ocean. This study fills a knowledge gap by contrasting model data from the Hybrid Coordinate Ocean Model (HYCOM) for the interior ocean in the Tongue of the Ocean (TOTO), Bahamas and the Gulf of Mexico (GoM) against observational (i.e., in situ) data collected in both locations. Conductivity temperature and depth (CTD) data in the GoM were collected during five research cruises by the DEEPEND Consortium between May of 2015 and May 2017. These data were collected as part of the investigation into the impact of oil spills on faunal communities in deep water of the GoM. CTD and expendable CTD (XCTD) data in the TOTO were collected by the Naval Undersea Warfare Center (NUWC) detachment Atlantic Undersea Test and Evaluation Center (AUTEC) in support of U.S. Navy acoustic testing between 1997 and 2017 to characterize the sound velocity profile of the water column. The global 1/12° HYCOM configuration (GLBu0.08) was found to be a better fit in the upper 400 and 250 meters of the TOTO for temperature and salinity, respectively, than the GoM 1/25° HYCOM configuration (GOMI0.04 1/25°) fit the GoM in situ data for the same depths. The GoM 1/25° HYCOM configuration (GOMI0.04 1/25°) provided a better fit in the GoM for depths of 500 and 300 meters and deeper for temperature and salinity, respectively, than the global 1/12° HYCOM configuration (GLBu0.08) fit the TOTO in situ data at the same depths. A comprehensive comparison of the vertical profile between the model and observational data for each of the regions of interest provides insight into using HYCOM forecast data for future applications.

Human population growth and global industrial development are driving potentially irreversible anthropogenic impacts on the natural world, including altering global climate and ocean conditions and exposing oceanic environments to a wide range of pollutants. While there are numerous studies highlighting the variable effects of climate change and pollution on marine organisms independently, there are very few studies focusing on the potential interactive effects of these stressors. The deep-sea is under increasing threat from these anthropogenic stressors, especially cold-water coral (CWC) communities which contribute to nutrient and carbon cycling, as well as providing biogenic habitats, feeding grounds, and nurseries for many fishes and invertebrates. The primary goals of this dissertation are to assess the vulnerability of CWCs to independent and interacting anthropogenic stressors in their environment; including natural hydrocarbon seepage, hydrocarbon and dispersant concentrations released during an accidental oil spill (i.e. Deepwater Horizon), and the interacting effects of climate change-related factors and hydrocarbon/dispersant exposure. To address these goals, multiple stressor experiments were implemented to assess the effects of current and future conditions [(a) temp: 8C and pH: 7.9; (b) temp: 8C and pH: 7.6; (c) temp: 12C and pH: 7.9; (d) temp: 12C and pH: 7.6] and oil spill exposure (oil, dispersant, oil + dispersant combined) on coral health using the CWC Lophelia pertusa. Phenotypic response was assessed through observations of diagnostic characteristics that were combined into an average health rating at four points during exposure and recovery. Regardless of environmental condition, average health significantly declined during 24-hour exposure to dispersant alone and increased temperature resulted in a delay in recovery (72 hours) from dispersant exposure. The overall gene expression patterns varied by coral colony, but the dispersant exposure elicited the strongest response. Gene ontology (GO) enrichment analysis revealed that L. pertusa likely experienced varying stages of the cellular stress response (CSR) during exposure to oil, dispersant, and a decrease in pH. The most severe responses were associated with the dispersant exposure including GO terms related to apoptosis, the immune system, wound healing, and stress-related responses. However, the oil exposure induced an upregulation of metabolic pathways and energy transfer but a downregulation of cell growth and development, indicating that the coral nubbins could have been reallocating resources and reducing growth to maintain cellular homeostasis. The decrease in seawater pH elicited a similar response to oil through the enrichment of terms associated with a reduction in the cell cycle and development. Interestingly, the increase in temperature did not elicit a CSR that was detectable in the gene expression data. To further investigate the influence of hydrocarbon exposure on CWCs, comparisons of gene expression profiles were conducted using Callogorgia delta colonies that live in close proximity to active hydrocarbon seepage (“seep”) areas with no current active seepage (“non-seep”) at two different sites in the Gulf of Mexico. There were fewer differentially expressed genes in the “seep” versus “non-seep” comparison (n=21) than the site comparison (n=118) but both analyses revealed GO terms indicating slight alterations in natural biological housekeeping processes, as opposed to a CSR. Our results indicate that distinct stages of the CSR are induced depending on the intensity of stress. This bolsters the idea that there is a stress response shared by all corals in response to a variety of stressors. These data provide evidence that CWCs can be more negatively impacted, both on the phenotypic and molecular levels, by exposure to chemical dispersants than to hydrocarbons alone. Gaining an understanding of how these communities respond, not only to independent stressors, but the combination of these stressors, provides vital information about how CWC communities will fair in current and future conditions. / Biology

The Mississippi Alluvial Valley (MAV) was dominated by extensive lowland forests, but during the 20th century most of the MAV was converted to agricultural, aquaculture, and other human uses. These land-use changes created stopover migration and wintering habitats for waterfowl, shorebirds and other waterbird species. Before landscape modification of the MAV, shorebirds likely migrated past the MAV to wetlands along the northern Gulf of Mexico (NGoM). In 2010, the Deepwater Horizon oil spill impacted coastal marshes of the NGoM. The USDA Natural Resources Conservation Service implemented the Migratory Bird Habitat Initiative (MBHI) to provide waterbirds with wetlands inland of oil-impacted areas. My objectives were to 1) statistically model the waterbird community on wetlands in the MAV and NGoM, 2) estimate relative abundance of shorebird and other waterbirds in idled aquaculture ponds enrolled in MBHI and associated wetlands in the MAV and NGoM, and 3) collect shorebird feathers and blood for stable isotope analysis (13C/12C, 15N/14N) to assess foraging niches and potential migratory connectivity between MAV and NGoM habitats during 2012 – 2013. Consequently, autumns of these years were under a drought, extensively wet from Hurricane Isaac, and exhibited average precipitation in the post-hurricane recovery period which may have had an effect on waterbird assemblages differing by year, month, twice-monthly survey period, latitude, region, state, site, and water depth index. Latitude shifted north and water depth was narrowest when abundant wet habitat existed on the landscape in 2012. Bird abundances were greatest in 2011 and never recovered to these levels in 2012 or 2013, which may have reflected effects of drought concentrating birds on remaining wetlands in 2011 and subsequent to the hurricane. Stable isotope analysis of blood indicated spatial segregation of shorebird species. Neither blood nor feather carbon and nitrogen values revealed definitive linkage of sites between the MAV and NGoM. Shallow water habitat inland may be a limiting resource during migration for waterbirds, especially in drought years when other wetlands may have been limited. Thus, provision of wetlands (mudflat – 15 cm) by MBHI and other conservation strategies across the landscape may allow waterbirds access to needed resources during migration.

The objective of this study is to estimate the willingness to pay of U.S. Gulf Coast residents to support oyster reef restoration. The Gulf Coast is the leading commercial oyster- producing region in the United States, accounting for approximately 46% of the total commercial oyster harvest in 2021. My benefit estimates were based on data obtained from a contingent valuation survey of 6,475 Gulf Coast respondents. I estimated the willingness to pay (WTP) for oyster reef restoration using interval regression and Turnbull lower-bound methods. The estimated mean WTP value is in the range of $142 and $436 per household. The results show respondents who eat oysters and those that hold saltwater fishing licenses have significantly higher WTP.

No description available.

Sea level rise and changing storm frequency and intensity resulting from climate change create tremendous amounts of uncertainty for coastal species. Intertidal species may be especially affected since they are dependent on daily inundation and exposure. The eastern oyster Crassostrea virginica is an economically and biologically important sessile intertidal species ranging from Canada to the Gulf of Mexico. Declines and changes in distribution of oyster populations has forced commercial harvesting to spread from subtidal to intertidal reefs. We investigated the potential responses of intertidal C. virginica to sea level rise, and the response of larval settlement to sedimentation which is likely to increase with higher water levels and storm frequency. Inundation was used as a proxy for sea level rise. We hypothesized four possible outcomes for intertidal oyster reefs as a result of changes in inundation due to sea level rise: (a) intertidal reefs become subtidal and remain in place, (b) intertidal reefs will be lost, (c) intertidal reefs migrate shoreward upslope and remain intertidal, and (d) intertidal reefs will grow in elevation and remain intertidal. To test the plausibility of these four outcomes, oyster ladders were placed at two sites within Apalachicola Bay, Florida, USA. Ladders supported oyster recruitment mats at five heights within the range of intertidal elevations. The bottom-most mat was placed near mean low tide, and the top mat near mean high tide to investigate the effect of tidal inundation time on C. virginica. Sediment traps were attached to ladders with openings at equal elevation to the oyster mats. Ladders were deployed for one year starting in June 2012, and again in June 2013, during peak oyster recruitment season. Monthly for six months during year one, sediment was collected from traps, dried to constant weight and weighed to obtain a monthly average for total sediment at each elevation. At the end of one year, oyster mats were collected from the field and examined for the following responses: live oyster density, mean oyster shell length of live oysters, mean oyster shell angle of growth relative to the benthos, and mean number of sessile competitors. We used AICc to identify the most plausible models using elevation, site, and year as independent variables. Oyster density peaked at intermediate inundation at both sites (maximum 1740 oysters per m2), it decreased slightly at the mean low tide, and sharply at the mean high tide. This response varied between years and sites. Mean oyster shell length peaked near mean low tide (6.7 cm), and decreased with increasing elevation. It varied between years and sites. Oyster shell angle of growth relative to the benthos showed a quadratic response for elevation; site but not year affected this response. Sessile competitor density also showed a quadratic response for elevation and varied between sites and years. Barnacles were the primary spatial competitor reaching densities of up to 28,328 barnacles per m2. Total monthly sedimentation peaked at the lowest elevations, and varied by site, with an order of magnitude difference between sites. Sediment increased with decreasing elevation. Outcomes a, c, and d were found to be viable results of sea level rise, ruling out complete loss of intertidal reefs. Outcome (a) would be associated with decrease in oyster density and increase in oyster length. Outcome (c) would require the laying of oyster cultch upslope and shoreward of current intertidal reefs, as well as the removal of any hard armoring or development. Outcome (d) remained possible, but is the least likely requiring a balance between sedimentation, oyster angle of growth, and recruitment. This should be further investigated. A laboratory experiment was designed to test relative impact of varying sediment grain sizes on settlement of C. virginica larvae. Previous studies showed that suspended solids resulted in decreased larval settlement when using mixed sediment grain sizes. Predicted storm levels and hurricane levels of total suspended solids were used in flow tanks. Sediment from the field experiment was sieved into seven size classes, the most common five of which were used in the experiment since they represented 98.8% of total mass. Flow tanks were designed and built that held 12 aged oyster shells, instant ocean saltwater, and sediment. Oyster larvae were added to the flow tanks and allowed one hour to settle on shells. Each run utilized one of the five size classes of sediment at either a high or low concentration. Following the one-hour settlement period, oyster shells were removed from the flow tank and settled larvae were counted under a dissecting microscope. Settlement was standardized by settlement area using Image J. AICc model selection was performed and the selected model included only grain size, but not concentration. A Tukey's post hoc test differentiated < 63 µm from 500 – 2000 µm, with the < 63 µm grain size having a negative effect on oyster larval settlement. This indicates that the smaller grain sizes of suspended solids are more detrimental to oyster larval settlement than larger grain sizes. The oyster ladder experiment will help resource managers predict and plan for oyster reef migration by cultch laying, and or associated changes in oyster density and shell length if shoreward reef growth is not allowed to occur. The laboratory experiment will help to predict the impacts of future storms on oyster larval recruitment. Together this information can help managers conserve as much remaining oyster habitat as possible by predicting future impacts of climate change on oysters.

Sea level rise (SLR) has the potential to affect coastal environments in a multitude of ways, including submergence, increased flooding, and increased shoreline erosion. Low-lying coastal environments such as the Northern Gulf of Mexico (NGOM) are particularly vulnerable to the effects of SLR, which may have serious consequences for coastal communities as well as ecologically and economically significant estuaries. Evaluating potential changes in tidal hydrodynamics under SLR is essential for understanding impacts to navigation, ecological habitats, infrastructure and the morphologic evolution of the coastline. The intent of this research is to evaluate the dynamic effects of SLR and coastal geomorphology on tidal hydrodynamics along the NGOM and within three National Estuarine Research Reserves (NERRs), namely Grand Bay, MS, Weeks Bay, AL, and Apalachicola, FL. An extensive literature review examined the integrated dynamic effects of SLR on low gradient coastal landscapes, primarily in the context of hydrodynamics, coastal morphology, and marsh ecology. Despite knowledge of the dynamic nature of coastal systems, many studies have neglected to consider the nonlinear effects of SLR and employed a simplistic "bathtub" approach in SLR assessments. More recent efforts have begun to consider the dynamic effects of SLR (e.g., the nonlinear response of hydrodynamics under SLR); however, little research has considered the integrated feedback mechanisms and co-evolution of multiple interdependent systems (e.g., the nonlinear responses and interactions of hydrodynamics and coastal morphology under SLR). Synergetic approaches that integrate the dynamic interactions between physical and ecological environments will allow for more comprehensive evaluations of the impacts of SLR on coastal systems. Projecting future morphology is a challenging task; various conceptual models and statistical methods have been employed to project future shoreline positions. Projected shoreline change rates from a conceptual model were compared with historic shoreline change rates from two databases along sandy shorelines of the. South Atlantic Bight and NGOM coasts. The intent was not to regard one method as superior to another, but rather to explore similarities and differences between the methods and offer suggestions for projecting shoreline changes in SLR assessments. The influence of incorporating future shoreline changes into hydrodynamic modeling assessments of SLR was evaluated for the NGOM coast. Astronomic tides and hurricane storm surge were simulated under present conditions, the projected 2050 sea level with present-day shorelines, and the projected 2050 sea level with projected 2050 shorelines. Results demonstrated that incorporating shoreline changes had variable impacts on the hydrodynamics; storm surge was more sensitive to the shoreline changes than astronomic tides. It was concluded that estimates of shoreline change should be included in hydrodynamic assessments of SLR along the NGOM. Evaluating how hydrodynamics have been altered historically under a changing landscape in conjunction with SLR can provide insight to future changes. The Grand Bay estuary has undergone significant landscape changes historically. Tidal hydrodynamics were simulated for present and historic conditions (dating back to 1848) using a hydrodynamic model modified with unique sea levels, bathymetry, topography, and shorelines representative of each time period. Changes in tidal amplitudes varied across the domain. Harmonic constituent phases sped up from historic conditions. Tidal velocities in the estuary were stronger historically, and reversed from being flood dominant in 1848 to ebb dominant in 2005. To project how tidal hydrodynamics may be altered under future scenarios along the NGOM and within the three NERRs, a hydrodynamic model was used to simulate present (circa 2005) and future (circa 2050 and 2100) astronomic tides. The model was modified with projections of future sea levels as well as shoreline positions and dune elevations obtained from a Bayesian network (BN) model. Tidal amplitudes within some of the embayments increased under the higher SLR scenarios; there was a high correlation between the change in the inlet cross-sectional area under SLR and the change in the tidal amplitude within each bay. Changes in harmonic constituent phases indicated faster tidal propagation in the future scenarios within most of the bays. Tidal velocities increased in all of the NERRs which altered flood and ebb current strengths. The work presented herein improves the understanding of the response of tidal hydrodynamics to morphology and SLR. This is beneficial not only to the scientific community, but also to the management and policy community. These findings will have synergistic effects with a variety of coastal studies including storm surge and biological assessments of SLR. In addition, findings can benefit monitoring and restoration activities in the NERRs. Ultimately, outcomes will allow coastal managers and policy makers to make more informed decisions that address specific needs and vulnerabilities of each particular estuary, the NGOM coastal system, and estuaries elsewhere with similar conditions.

The Gulf of Mexico dune system is a broad and dynamic environment that varies greatly in geomorphology and vegetative composition across the Gulf coastline. Beach mice (Peromyscus polionotus spp.) are an endangered species that rely on coastal habitat structure. I hypothesized that beach mouse occupancy would be dependent upon coastal dune land cover and landform features. I identified coastal landforms using high-resolution elevation data and landform models in GRASS GIS and identified coastal dune vegetation classes using high-resolution aerial imagery and object oriented vegetation classification. These features were used to create a dynamic occupancy model to determine occupancy patterns in three subspecies of beach mice over multiple years of sampling. Beach mice demonstrated no distinct pattern in habitat occupancy over the study period. However, dynamic occupancy models demonstrated that habitat occupancy varied between individual sites, indicating that habitat selection may be population specific.