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.

Using gravity, magnetic, bathymetric and seismic refraction data, I have constructed a geophysical cross-section of the central part of the northern Gulf of California. The section exhibits a crustal thickness of 18 km and features an anomalous block of high density lower basement (3.15 g/cm³) which probably resulted from rifting processes during the opening of the Gulf. The magnetization of the upper basement ranges from 0.0005 to 0.0030 emu/cm³. Three different layers of sediments are modeled, ranging from unconsolidated (1.85 g/cm³) to compacted (2.50 g/cm³). I present a deconvolution method for automated interpretation of magnetic profiles based on Werner's (1953) simplified thin-dike assumption, leading to the linearization of complex nonlinear magnetic problems. The method is expanded by the fact that the horizontal gradient of the total field caused by the edge of a thick interface body is equivalent to the total field of a thin dike. Statistical decision making and a seven point operator are used to insure good approximations of susceptibility, dip, depth, and horizontal location of the source. After using synthetic models to test the inversion method, I applied it to the Northern Gulf of California using data collected in 1984 by the Continental Margins Study Group at Oregon State University. Fault traces, computed by the deconvolution, are plotted on a map. The faulting pattern obtained is in good agreement with that proposed by other workers using other methods. The depths to the top of the faults range from 4 to 5 km in the eastern part of the Gulf, where they may be interpreted as the top of the structural basement. Deeper estimates are obtained for the western part of the Gulf. / Graduation date: 1990

The deep ocean (> 200-m depth) covers more than 65 percent of earth's surface and is known as the largest active carbon sink of the planet. Photosynthesis fixes inorganic carbon into organic rich-compounds to fuel the biological production in the upper ocean. A small portion of the photosynthetic carbon eventually sinks to the seafloor to support diverse deep-sea life. In this dissertation, the phytoplankton production and export flux of particulate organic carbon (POC) to the seafloor were linked to standing stocks and compositional changes of the deep-sea soft bottom assemblages. The pattern and processes of energy transfer from the surface ocean to the deep sea was examined by modeling the global benthic bacteria, meiofauna, macrofauna, and megafauna biomass from remotely sensed ocean color images and the seafloor relief. The analysis was then scaled down to the macrofauna of the Gulf of Mexico (GoM) to examine the global pattern on regional oceanic features with contrasting productivity regimes. These results suggested a universal decline of benthic standing stocks down the continental margins that is caused by an exponential decrease of export POC flux with depth. A revisit of historical epibenthic invertebrate sampling in the North Atlantic showed that both individual species and multi-species assemblages occurred in narrow depth bands that hugged the topography from the upper continental slope out to the Hatteras Abyssal Plain. The continuum compositional change suggested that the continuous decline of benthic food supply with depth was the potential driving force for the pattern of bathymetric faunal zonation. A broad, systematic survey across multiple depth transects in the northern GoM suggested that macrofauna zonation is not only taking place across isobaths, but also form the northeast to the northwest GoM due to a horizontal productivity gradient created by the nutrient-laden Mississippi River. Analyses of long-term demersal fish data from 1964 to 2002 in the northern GoM showed no evidence of large-scale faunal change across different sampling times. Base on the pooled data, a shift in rate of fish species replacement may be caused by complex biological interactions or changes in environmental heterogeneity along depth or productivity gradients.

I investigated how land use and human activities affect the sources and cycling of carbon (C) in subtropical rivers. Annually rivers receive a large amount of terrestrial C, process a portion of this C and return it to the atmosphere as CO 2 . The rest is transported to the ocean. Land use and human activities can affect the sources and fate of terrestrial C in rivers. However, studies on these effects are limited, especially in the humid subtropics. I combined measurements of the partial pressure of dissolved CO 2 (pCO 2 ), C isotopes ( 13 C and 14 C) and solid-state 13 C nuclear magnetic resonance (NMR) to study C cycling in three subtropical rivers in Texas, two small rivers (Buffalo Bayou and Spring Creek) and a midsized river (the Brazos). My pCO 2 data show that small humid subtropical rivers are likely a large source of atmospheric CO 2 in the global C cycle. My measurements on pCO 2 , C isotopic and chemical composition of dissolved inorganic C (DIC) and particulate organic C (POC) revealed four types of effects of land use and human activities on river C cycling. First, oyster shells and crushed carbonate minerals used in road construction are being dissolved and slowly drained into Buffalo Bayou and the lower Brazos and may be a source of river CO 2 released to the atmosphere. Second, river damming and nutrient input from urban treated wastewater stimulate algal growth and reduce CO 2 evasion of the middle Brazos. Third, urban treated wastewater discharge is adding old POC to the middle Brazos and decomposition of the old POC adds to the old riverine DIC pool. Fourth, agricultural activities coupled with high precipitation enhance loss of old organic C (OC) from deep soils to the lower Brazos, and decomposition of the old soil OC contributes to the old CO 2 evaded. I document for the first time the river C cycling effects of the use of carbonate minerals in construction and the riverine discharge of urban wastewater. Results presented here indicate the need to study disturbed river systems to better constrain the global C budget.

Purpose: When the Deepwater Horizon oilrig in the Gulf of Mexico faced disaster in late April 2010, news coverage immediately began of the disaster that would unfold. BP took the blame and its financial resources were strained as it struggled with stopping the oil leak, cleanup work as well as its PR image. While the US took many blows of the consequences to ecosystem and tourism, financial consequences swept across the world, mainly Britain, where BP had its headquarters.The event gives an excellent chance at comparing the media coverage from both the US and Britain. By studying The Daily Telegraph and The New York Times, we want to see both similarities and differences in the themes they focused on as well as seeing trends in the themes over time. Theories: The theory chapter is heavily based around the Agenda-setting theory in the media communication field. Methodology: A quantitative content analysis (QCA) of some 500 news articles in The Daily Telegraph and The New York Times from April 22 to July 15. The QCA was made to find the main theme of articles to give us data on how many articles of each theme, as well as their distribution over time. The collected data was ultimately made into diagrams. Conclusion: The two newspapers have a clear difference in that the New York Times have a more than twice the articles published compared to The Daily Telegraph. They do however both share some trends in the themes with some exceptions. Looking at the distribution of these themes within each newspaper, it’s clear that the British newspaper focused more heavily on BP while the American was focusing more heavily on consequences.

Artificial reefs are becoming a popular biological and management component in shallow water environments characterized by soft seabed, representing both important marine habitats and tools to manage coastal fisheries and resources. An artificial reef in the marine environment acts as an open system with exchange of material and energy, altering the physical and biological characteristics of the surrounding area. Reef stability will depend on the balance of scour, settlement, and burial resulting from ocean conditions over time. Because of the unstable nature of sediments, they require a detailed and systematic investigation. Acoustic systems like high-frequency multibeam sonar are efficient tools in monitoring the environmental evolution around artificial reefs, whereas water turbidity can limit visual dive and ROV inspections. A high-frequency multibeam echo sounder offers the potential of detecting fine-scale distribution of reef units, providing an unprecedented level of resolution, coverage, and spatial definition. How do artificial reefs change over time in relation to the coastal processes? How accurately does multibeam technology map different typologies of artificial modules of known size and shape? How do artificial reefs affect fish school behavior? What are the limitations of multibeam technology for investigating fish school distribution as well as spatial and temporal changes? This study addresses the above questions and presents results of a new approach for artificial reef seafloor mapping over time, based upon an integrated analysis of multibeam swath bathymetry data and geoscientific information (backscatter data analysis, SCUBA observations, physical oceanographic data, and previous findings on the geology and sedimentation processes, integrated with unpublished data) from Senigallia artificial reef, northwestern Adriatic Sea (Italy) and St. Petersburg Beach Reef, west-central Florida continental shelf. A new approach for observation of fish aggregations associated with Senigallia reef based on the analysis of multibeam backscatter data in the water column is also explored. The settlement of the reefs and any terrain change are investigated over time providing a useful description of the local hydrodynamics and geological processes. All the artificial structures (made up by water-based concrete for Senigallia reef and mainly steel for St. Petersburg Beach reef) are identified and those showing substantial horizontal and/or vertical movements are analyzed in detail. Most artificial modules of Senigallia reef are not intact and scour signatures are well depicted around them, indicating reversals of the local current. This is due to both the wind pattern and to the quite close arrangement of the reef units that tend to deflect the bottom flow. As regards to the St. Petersburg Beach reef, all the man-made steel units are still in their upright position. Only a large barge shows a gradual collapse of its south side, and presents well-developed scouring at its east-northeast side, indicating dominant bottom flow from west-southwest to east-northeast. While an overall seafloor depth shallowing of about 0.30 m from down-current deposits was observed for Senigallia reef, an overall deepening of about 0.08 m due to scour was observed at the St. Petersburg Beach reef. Based on the backscatter data interpretation, surficial sediments are coarser in the vicinities of both artificial reefs than corresponding surrounding sediments. Scouring reveals this coarser layer underneath the prevalent mud sediment at Senigallia reef, and the predominant silt sediment at St. Petersburg Beach reef. In the ten years of Senigalia reef study, large-scale variations between clay and silt appear to be directly linked to large flood events that have occurred just prior to the change. As regards the water column investigation, acoustic backscatter from fish aggregations gives detailed information on their morphology and spatial distribution. In addition, relative fish biomass estimates can be extrapolated. Results suggest that most of the fish aggregations are generally associated with the artificial modules showing a tendency for mid- and bottom-water depth distribution than for the surface waters. This study contributes to understanding the changes in artificial reefs over time in relation to coastal processes. Moreover, the preliminary results concerning the water column backscatter data represents progress in fisheries acoustics research as a result of three-dimensional acoustics. They demonstrate the benefits of multibeam sonar as a tool to investigate and quantify size distribution and geometry of fish aggregations associated with shallow marine habitats.