Oyster reefs in the western Mississippi Sound (WMS) are dependent on the salinity moderation by freshwater input. However, freshwater brings in high amount of pollutants, which affect the oysters negatively. Oyster diebacks happened as a result of hypoxia caused by excessive organic matter input to WMS in summer 2017. Colored dissolved organic matter (CDOM) is widely used as a proxy for determining organic matter distribution. In this study, hyperspectral and multispectral remote sensing data collected using unmanned aerial systems and in situ CDOM data were used to develop algorithms in order to retrieve CDOM remotely. Collected physical and biogeochemical parameters were used to understand the carbon fluxes regulating the quality and quantity of CDOM. Developed algorithms showed high accuracy after accounting for seasonal variations of CDOM. Further, seasonal induced photodegradation, photosynthesis, calcification, and exchange of CO2 were identified as possible factors that affect the carbon dynamics in the study area.

No description available.

<p>St. Joseph peninsula is situated on the panhandle of Florida west coast in the northeastern Gulf of Mexico at N29°50‘ and W85°20‘ and is located at the west edge of the westernmost portion of the Apalachicola Barrier Island Complex (ABIC) on the Gulf of Mexico shoreline. Three vibra-cores were collected on Saint Joseph Bay side of Cape San Blas which is part of St. Joseph peninsula to determine its evolution in context of previous work by Rink and Lopez (2010). The study uses detailed textural analysis (PSD - Particle Size Distribution plots), multivariate statistics on the PSDs (Q-mode cluster analysis) and organic matter geochemistry (C/N and δ13C). In addition, Ground Penetrating Radar (GPR) profiles are used to provide broader stratigraphic context.</p> <p>The stratigraphic analysis found that CSB has an older nucleus of strandplain deposits dating to >12 Ka that were subsequently flooded and modified through Holocene sea-level rise at ≈ 2.2 Ka. Actual barrier formation began sometime between 2.2. Ka and 0.6 Ka which is the oldest beach ridge measured by Rink and Lopez (2010). Progradation of the barrier on the St Joseph Bay side began at least by 0.3 Ka and likely earlier. There is no evidence to indicate a higher than present sea-level in our core data and our data follows that of other sea-level studies using submerged offshore samples</p> / Master of Science (MSc)

Ocean acidification is the reduction in seawater pH due to the absorption of anthropogenic carbon dioxide by the oceans. Reductions in seawater pH can inhibit the precipitation of aragonite, a calcium carbonate mineral used by marine calcifiers such as corals. Lophelia pertusa is a cold-water coral that forms large reef structures which enhance local biodiversity on the seafloor, and is found commonly from 300-600 meters on hard substrata in the Gulf of Mexico. The present study sought to investigate the potential impacts of ocean acidification on L. pertusa in the Gulf of Mexico through combined field and laboratory analyses. A field component characterized the carbonate chemistry of L. pertusa habitats in the Gulf of Mexico, an important step in establishing a baseline from which future changes in seawater pH can be measured, in addition to collecting in situ data for the design and execution of perturbation experiments in the laboratory. A series of recirculating aquaria were designed and constructed for the present study, and support the maintenance and experimentation of live L. pertusa in the laboratory. Finally, experiments testing L. pertusa's mortality and growth responses to ocean acidification were conducted in the laboratory, which identified thresholds for calcification and a range of sensitivities to ocean acidification by individual genotype. The results of this study permit the monitoring of ongoing ocean acidification in the deep Gulf of Mexico, and show that ocean acidfication's impacts may not be consistent across individuals within populations of L. pertusa. / Biology

Sandstone modal compositions and detrital zircon U-Pb analysis of the Paleocene-Eocene Wilcox Group of the southern Gulf Coast of Texas indicate long-distance sediment transport primarily from volcanic and basement sources to the west, northwest and southwest. The Wilcox Group of south Texas represents the earliest series of major post-Cretaceous pulses of sand deposition along the western margin of the Gulf of Mexico (GoM). Laramide basement uplifts have long been held to be the provenance of the Wilcox Group, implying that initiation of basement uplifts was the driving factor for this transition from carbonate sedimentation to clastic deposition. To determine the provenance of the Wilcox Group and test this conventional hypothesis, 40 thin sections were point-counted using the Gazzi-Dickinson method to determine sandstone composition and 10 detrital zircon samples were analyzed by LA-ICP-MS to determine U-Pb age spectra for each of the sampled areas. Modal data for sand grain populations suggest mixed sources including basement rocks, magmatic arc rocks and subordinate sedimentary rocks for the Wilcox Group. Zircon age spectra for these sandstones reveal a complex grain assemblage derived from older sediments and crystalline rocks ranging in age from Archean to Cenozoic. Sediment was primarily derived from Laramide uplifted crystalline blocks of the central and southern Rocky Mountains, the Cordilleran arc of western North America, and arc related extrusive and intrusive igneous rock of northern Mexico. Comparisons of Upper and Lower Wilcox zircon age spectra show that more arc related material was deposited in the Lower Wilcox, whereas more basement material was deposited in the Upper Wilcox. / text

The initiation, persistence, and termination of harmful algal blooms (HABs) can all be influenced by nutrient availability. Recent studies have highlighted the role of both organic and inorganic nitrogen sources in HAB dynamics. The pelagophyte Aureoumbra lagunensis causes ecosystem disruptive algal blooms and is responsible for the longest recorded harmful algal bloom (1989-1997). Because of Aureoumbra's small size and its inability to use nitrate, it has been hypothesized that its ability to use ammonium and organic nitrogen, especially at low concentrations, contributed to the unusual persistence of this bloom. This project aimed to assess the response of Aureoumbra to inorganic and organic nitrogen sources by examining the expression of genes responsible for nitrogen assimilation, with an eventual intent of developing expression assays that are indicative of nitrogen source use and/or sufficiency in Aureoumbra. Large volume batch cultures of Aureoumbra were grown with either ammonium or urea as a nitrogen source. Physiological characteristics (C:N, chlorophyll [alpha] cell⁻¹, and Fv/Fm) were monitored throughout the growth period, and the expression of the AMT-1, AMT-2 and UREC genes was assayed at early-, mid- and late-exponential phases. The results show that Aureoumbra can use both ammonium and urea, and that it is well adapted to low-nutrient environments. Only one gene, AMT-1, appeared to be transcriptionally regulated in response to changing nitrogen concentration, and only to ammonium. The results of this study contribute to our understanding of how algae in general cope with low nutrient availability and should ultimately help to define the dynamics of these HAB events. / text

By examining halokinetics and channel evolution in a deep-water system, we investigate how submarine channel morphology is affected by changing seascape linked to diapirism. The study area is located in Mississippi Canyon, Gulf of Mexico (GOM), situated directly off the continental slope in a prominent salt dome region. Interactions of salt domes with submarine channels in the GOM are poorly documented. Utilizing 3D seismic data and seismic geomorphology techniques, a long-lived Plio-Pleistocene submarine channel system has been investigated to develop a relationship between variable phases of salt movement and plan-form morphology of preserved channels. We suggest that halokinetics acts as a driver for topographic-channel evolution in the study area. We show how submarine channel morphology can be directly controlled by halokinetics, where salt movement can act as a structural control on both location and morphology of meandering channel complexes. Channels are able to move towards an equilibrium state only when holokinetics decreases.

Karenia brevis (Davis cf. Hansen & Moestrup = Gymnodinium breve) is the non-peridinin containing dinoflagellate responsible for many harmful algal blooms (red tides) in the Gulf of Mexico. These recurrent blooms can have significant negative ecological, economic, and human health impacts including fish kills, tainting of shellfish, poisoning of marine mammals, loss of tourism revenue due to beach closures, and respiratory distress and food poisoning in humans. A method for detection of Karenia brevis was developed based upon amplification of the mRNA for the plastid-encoded gene of the carbon fixing enzyme ribulose 1, 5-bisphosphate carboxylase/oxygenase (RuBisCO) large subunit (rbcL). Using sequence information from a primer set targeting a 554-bp region of the Karenia rbcL gene, a small (91 bp amplicon) primer and probe set was created for TaqMan(registered trademark) real time RT-PCR of K. brevis rbcL. The primer/probe set is sensitive to as little as 0.1 fg of target transcript and as little as 1 pg of total cellular K. brevis RNA extract, corresponding to less than 1 cell reaction-1. The primer/probe set did not amplify rbcL transcript from any of the non-target algae tested. Bloom samples analyzed by this method have shown the assay to be a reliable method, with effective enumeration and a linear relationship showing good correlation to the cell counts by microscopy (r2= 0.8344). The assay has been shown to be robust and perform well even in non-ideal conditions, with pre-extraction RNA from unialgal culture stable at room temperature for up to 3 days and up to a month at -80 degrees C in Stratagene's lysis buffer. The transcription of the rbcL gene demonstrated minor variation throughout the diel period, however the variation was not linked to the diel cycle or to carbon fixation, which showed a distinct diel signal. Due to the relatively constant expression of the rbcL gene, the real-time RT-PCR assay developed should be able to reliably enumerate K. brevis populations in the natural environment, as long as the sample is placed in Stratagene's lysis buffer and processed within one or two days or frozen at -80 degrees C and processed within a month.

This paper examines the regional longshore sediment transport pattern of the seaward coast of the United States and Gulf of Mexico from northern Maine to Tampa Bay, Florida. From previous studies it is known that along the coast there are variations in direction of sediment transport known as nodal zones as well as variations in sediment transport rate. Wave Information Study (WIS) hindcast data for the interval 1976 through 1995 (United States Army Corps of Engineers, 2003) provide a spatially continuous model of the regional longshore current directions in the study area. In chapter one, all available published field studies of longshore current direction and sediment transport directions and rates are compiled to create a description of the direction and, whenever possible, magnitude of longshore transport. A detailed compilation of regional and local published studies are provided in tables. An interpretation of sediment transport rates and directions is provided in eight regional maps of the study area. In chapter two the results of the literature compilations are compared with gross and net potential sediment transport directions and rates modeled using WIS hindcast data. The WIS deep-water wave characteristics are used to predict the directions and rate of longshore sediment transport at local outer coast positions using the method of Ashton et al. (2003a). The WIS-derived transport directions, including nodal zones, generally agree with the published field studies, although there are a few local inconsistencies particularly near inlets, shoals and irregular bathymetry. Trends in longshore transport rates, such as increases and decreases in gross transport rates are well represented by the WIS-derived potential transport rates. The discrepencies between the published field studies and WIS results are apparently primarily due to assumptions in the WIS model, such as assuming shore-parallel bathymetric contours.

Pelagic Sargassum is one type of marine macroalgae that is known to be abundant in the Gulf of Mexico and Sargasso Sea. It is also known to serve as a critical habitat for many marine animals. In the past few years, large amounts of Sargassum have been reported in the Tropical Atlantic and Caribbean Sea (CS), causing significant environmental and economic problems. The goal of this study is to improve the understanding of Sargassum distributions, quantity, transport pathways, and bloom mechanisms in the CS and Tropic Atlantic through combining a variety of techniques including satellite remote sensing, field and laboratory measurements, and numerical modeling. The first question is where and how much Sargassum is in the CS and Tropic Atlantic. Previous field observations revealed strong seasonal and spatial variations of Sargassum, yet these observations are all limited in their spatial and temporal coverage. Satellite observations offer an effective means to measure their distributions with synoptic coverage and high sampling frequency, yet it is technically challenging to extract and quantify the small Sargassum features in coarse-resolution satellite imagery. Chapter 2 focuses on Sargassum detection and quantification algorithm development using Moderate Resolution Imaging Spectroradiometer (MODIS) data (Appendix A). The algorithm is based on MODIS alternative floating algae index (AFAI), which examines the red-edge reflectance of floating vegetation. The algorithm includes three basic steps: 1) classification of Sargassum-containing pixels through correction of large-scale gradient, masking clouds and cloud shadows, and removal of ambiguous pixels; 2) linear unmixing of Sargassum-containing pixels; and, 3) statistical analysis of Sargassum area coverage in pre-defined grids at monthly, seasonal, and annual intervals. The algorithm is applied to MODIS observations between 2000 and 2015 over the Central West Atlantic (CWA) region (0 – 22oN, 38 – 63oW) to derive the spatial and temporal distribution patterns as well as the total areal coverage of Sargassum. Results indicate that the first widespread Sargassum distribution event occurred in 2011, consistent with previous findings from the Medium Resolution Imaging Spectrometer (MERIS). Since 2011, only 2013 showed minimal Sargassum coverage similar to the period of 2000 to 2010; all other years showed significantly more coverage. More alarmingly, the summer months of 2015 showed mean coverage of > 2000 km2, or about 4 times of the summer 2011 coverage and 20 times of the summer 2000 to 2010 coverage. Analysis of several environmental variables provided some hints on the reasons causing the inter-annual changes after 2010, yet further multi-disciplinary research (including in situ measurements) is required to understand such changes and long-term trends in Sargassum coverage. To better understand the potential ecological and environmental impacts of Sargassum, field and laboratory experiments are conducted to link the Sargassum areal coverage observations to biomass per area (density) and measure the nutrient contents and pigment concentrations (Chapter 3, Appendix B). An AFAI-biomass density model is established to derive Sargassum biomass density from the spectral reflectance, with a relative uncertainty of ~ 12%. Monthly mean integrated Sargassum biomass in the CS and CWA reached > 4.4 million tons in July 2015. The average % C, % N, and % P per dry-weight, measured from samples collected in Gulf of Mexico and Florida Straits in summer 2017, are 27.16, 1.06, and 0.10, respectively. The mean chlorophyll-a concentration is ~ 0.05% of the dry-weight. With these parameters, the amounts of nutrients and pigments can be estimated directly from remotely-sensed Sargassum biomass. During bloom seasons, Sargassum carbon can account for ~ 18% of the total particulate organic carbon in the upper water column. This chapter provides the first quantitative assessment of the overall Sargassum biomass, nutrients, and pigment abundance from remote-sensing observations, thus helping to quantify their ecological roles and facilitate management decisions. To investigate the Sargassum transport patterns and potential bloom sources, a Lagrangian particle tracking model is established to track the Sargassum transport driven by surface currents and winds (Chapter 4, Appendix C). The mean Sargassum distributions derived from MODIS observations are used to initiate and evaluate a Lagrangian particle tracking model that tracks Sargassum advection under surface currents and winds. Among the thirty-nine experiments, adding surface currents alone improves model performance (i.e., by reducing difference between modeled and observed Sargassum distributions) in 82% of the cases after tracking Sargassum for one month. Adding 1% wind forcing to the advection model also shows improved performance in 67% of the cases. Adding a time- and location-dependent Sargassum growth/mortality rate (i.e., change rate), derived from time-series of the MODIS-based Sargassum abundance and the corresponding environmental data via a Random Forest regression, leads to further improvement in model performance (i.e., by increasing the matchup percentage between modeled and observed Sargassum distributions) in 64% of the cases, although the modeled change rates only explain ~ 27% of the variance of the validation dataset, possibly due to uncertainties in such-derived change rates. The Sargassum transport model, with the mean currents, winds, and change rates acting as the forcing, is applied to track the mean Sargassum distributions forward and backward. The results demonstrate the model’s capacity of simulating the Sargassum distribution patterns, with emphasis on the role of biological terms in determining the large-scale distributions. These tracking experiments also suggest that Sargassum blooms in the CS are strongly connected to the Central Atlantic regions, and blooms in the Tropical Atlantic show relatively weak connections to the Atlantic regions further north. Although it is straightforward to apply the transport model to predict Sargassum blooms, such long-term prediction could suffer from large error accumulations and unable to achieve satisfactory performance. Therefore historical Sargassum distributions derived from MODIS are used to provide an alternative way to realize the bloom prediction. Chapter 5 proposes such a prediction based on a hindcast of 2000–2016 observations from MODIS, which shows Sargassum abundance in the CS and the CWA, as well as connectivity between the two regions with time lags (Appendix D). This information is used to derive bloom and nonbloom probability matrices for each 1° square in the CS for the months of May–August, predicted from bloom conditions in a hotspot region in the CWA in February. A suite of standard statistical measures is used to gauge the prediction accuracy, among which the user’s accuracy and kappa statistics show high fidelity of the probability maps in predicting both blooms and nonblooms in the eastern CS with several months of lead time, with an overall accuracy often exceeding 80%. The bloom probability maps from this hindcast analysis will provide early warnings to better study Sargassum blooms and prepare for beaching events near the study region. This approach may also be extendable to many other regions around the world that face similar challenges and opportunities of macroalgal blooms and beaching events. Using this forecasting scheme, the summer blooms in the CS in 2017 were successfully predicted. Since February 2018, we have also generated monthly-updated 1-page Sargassum outlook bulletins to help these regions to better prepare for potential beaching events. Currently, the mean Sargassum distribution statistics used in this study are derived from MODIS, which has been operating well beyond the designed mission life, arousing concerns as to whether the Sargassum observation statistics can be continued in the future. As a follow-on sensor, the Visible Infrared Imaging Radiometer Suite (VIIRS) has the appropriate spectral bands to detect and quantify floating macroalgae. Based on previous works on MODIS, Chapter 6 presents an improved procedure to extract floating algae pixels from VIIRS AFAI imagery, with image filtering used to suppress noise and adjusted thresholds used to mask sun glint, clouds, and cloud shadows. The overall extraction accuracy is about 85%. Simultaneous daily observations from MODIS and VIIRS over the CWA show consistent spatial patterns, but VIIRS estimations of the algae coverage (in km2) are consistently lower than MODIS (around – 19% mean relative difference or MRD), possibly due to lower sensitivity of the VIIRS near-infrared (NIR) bands than the corresponding MODIS bands. Similarly, at monthly scale VIIRS also shows lower coverage than MODIS, and their difference (around – 29% MRD) is larger than the difference between MODIS-Aqua and MODIS-Terra estimates (around – 14% MRD). Despite these differences, the spatial and temporal patterns between VIIRS and MODIS observed algae distributions match very well at all spatial and temporal scales. These results suggest that VIIRS can provide continuous and consistent observations of floating algae distributions and abundance from MODIS as long as their differences are accounted for, thus assuring continuity in the future. In summary, this study has worked on four connected topics regarding Sargassum distributions, biomass and nutrients, transport pathways, and bloom predictions through combined efforts in satellite remote sensing, field and laboratory measurements, physical modelling, and statistical analyses. To my best knowledge, this is the first comprehensive and multi-disciplinary study to investigate pelagic Sargassum at synoptic scale in the Intra-Americas Sea (IAS) and Atlantic Ocean. Although several questions remain to be answered (e.g., “What cause the inter-annual variations of Sargassum blooms?” and “Where are the bloom origins?”), the outcomes of this study (remote sensing algorithms, Sargassum distribution and abundance maps, established bio-physical model, and a bloom forecast model) are expected to make significant contributions in both scientific research (including new critical baseline data) and management decision support.