Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 151-163). / Population connectivity is a fundamental process that governs the spatial and temporal dynamics of marine ecosystems. For many marine species, population connectivity is driven by dispersal during a planktonic larval phase. The ability to obtain accurate, affordable, and meaningful estimates of larval dispersal patterns is therefore a key aspect of understanding marine ecosystems. Although field observations provide insight into dispersal processes, they do not provide a comprehensive assessment. Individual-based models (IBMs) that couple ocean circulation and particle-tracking models provide a unique ability to examine larval dispersal patterns with high spatial and temporal resolution. Obtaining accurate results with IBMs requires simulating a sufficient number of particles, and the sequential Bayesian procedure presented in chapter 2 identifies when the number of particles is adequate to address predefined research objectives. In addition, this method optimizes the particle release locations to minimize the requisite number of particles. Even after applying this method, the computational expense of IBM studies is still large. The model in chapter 3 seeks to increase the affordability of IBM studies by transferring some of the calculations to graphics processing units. Chapter 4 describes three algorithms that assist in interpreting IBM output by identifying coherent geographic clusters from population connectivity data. The first two algorithms have existed for nearly a decade and recently been applied separately to marine ecology, and we provide a direct comparison of the results from each. Additionally, we develop and present a new algorithm that simultaneously considers multiple species. Finally, in chapter 5, we apply these tools and a trait-based modeling framework to assess which species traits are most likely to impact dispersal success and patterns in the Gulf of Maine. We conclude that the traits influencing spawning distributions and habitat requirements for settlement are most likely to influence dispersal. / by Benjamin Thomas Jones. / Ph. D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Quorum sensing (QS) via acylated homoserine lactones (AHLs) was discovered in the ocean, yet little is known about its role in the ocean beyond its involvement in certain symbiotic interactions. The objectives of this thesis were to constrain the chemical stability of AHLs in seawater, explore the production of AHLs in marine particulate environments, and probe selected behaviors which might be controlled by AHL-QS. I established that AHLs are more stable in seawater than previously expected and are likely to accumulate within biofilms. Based on this result, I chose to study AHLQS in the bacterial communities inhabiting biofilms attached to Trichodesmium spp. and detrital (photosynthetically-derived sinking particulate organic carbon, POC) particles. These hot spots of microbial activity are primary sites of interaction between marine primary producers and heterotrophs and crucial components of the biological pump. Biofilm communities associated with Trichodesmium thiebautii colonies in the Sargasso Sea differed considerably from seawater microbial communities. In addition, there was no overlap between the communities associated with tuft and puff colonies. These results suggest that bacterial communities associated with Trichodesmium are not random; rather, Trichodesmium selects for specific microbial flora. Novel 16S rRNA gene sequences are present both in clone libraries constructed from DNA extracted from colonies of Trichodesmium spp. and in culture collections derived from wild and laboratory cultivated Trichodesmium spp., supporting the idea that the phycosphere of Trichodesmium is a unique microenvironment. Using high performance liquid chromatography-mass spectrometry, I demonstrated that bacteria isolated from Trichodesmium synthesize AHLs. In addition, I detected AHLs in sinking particles collected from a site off of Vancouver Island, Canada. AHLs were subsequently added to laboratory cultures of non-axenic Trichodesmium colonies and sinking POC samples. This is the first time AHLs have been detected in POC and indicates that AHL-QS was occurring in POC. Further, I showed that AHLs enhanced certain organic-matter degrading hydrolytic enzyme activities. My results suggest that AHL-QS is a factor regulating biogeochemically relevant enzyme activities on sinking POC and within the biofilms attached to Trichodesmium colonies and thereby may impact the timing and magnitude of biogeochemical fluxes in the ocean. / by Laura Robin Hmelo. / Ph.D.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 40-41). / The purpose of this study is to understand the interactions of tropical cyclones with ocean eddies. In particular we examine the influence of a cold-core eddy on the cold wake formed during the passage of Typhoon Fanapi (2010). The three-dimensional version of the numerical Price-Weller-Pinkel (PWP) vertical mixing model has previously been used to simulate and study the cold wakes of Atlantic hurricanes. The model has not been used in comparison with observations of typhoons in the Western Pacific Ocean. In 2010 several typhoons were studied during the Impact of Typhoons on the Ocean in the Pacific (ITOP) field campaign and Fanapi was particularly well observed. We use these observations and the 3DPWP to understand the ocean cold wake generated by Fanapi. The cold wake of Fanapi was advected by a cyclonic eddy that was south of the typhoon track. The 3DPWP model outputs with and without an eddy are compared with observations made during the field campaign. These observations are compared to model outputs with eddies in a series of positions right and left of the storm track in order to study effects of mesoscale eddies on ocean vertical mixing in the cold wake of typhoons. / by Alexander Reid Miltenberger. / S.M.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), June 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 55-56). / Throughout this thesis we will discuss the theoretical background and empirical observation of a swell band shore normal flux divergence reversal. Specifically, we will demonstrate the existence and persistence of the energy flux divergence reversal in the nearshore region of Atchafalaya Bay, Gulf of Mexico, across storms during the March through April 2010 deployment. We will show that the swell band offshore component of energy flux is rather insignificant during the periods of interest, and as such we will neglect it during the ensuing analysis. The data presented will verify that the greatest flux divergence reversal is seen with winds from the East to Southeast, which is consistent with theories which suggest shoreward energy flux as well as estuarine sediment transport and resuspension prior to passage of a cold front. Employing the results of theoretical calculations and numerical modeling we will confirm that a plausible explanation for this phenomena can be found in situations where temporally varying wind input may locally balance or overpower bottom induced dissipation, which may also contravene the hypothesis that dissipation need increase shoreward due to nonlinear wave-wave interactions and maturation of the spectrum. Lastly, we will verify that the data presented is consistent with other measures collected during the same deployment in the Atchafalaya Bay during March - April 2010. / by Shmuel G. Link. / S.M.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2011. / "June 2011." Cataloged from PDF version of thesis. / Includes bibliographical references (p. 253-293). / Sampling the vast volumes of the ocean requires tools capable of observing from a distance while retaining detail necessary for biology and ecology, ideal for optical methods. Algorithms that work with existing SeaBED AUV imagery are developed, including habitat classification with bag-of-words models and multi-stage boosting for rock sh detection. Methods for extracting images of sh from videos of long-line operations are demonstrated. A prototype digital holographic imaging device is designed and tested for quantitative in situ microscale imaging. Theory to support the device is developed, including particle noise and the effects of motion. A Wigner-domain model provides optimal settings and optical limits for spherical and planar holographic references. Algorithms to extract the information from real-world digital holograms are created. Focus metrics are discussed, including a novel focus detector using local Zernike moments. Two methods for estimating lateral positions of objects in holograms without reconstruction are presented by extending a summation kernel to spherical references and using a local frequency signature from a Riesz transform. A new metric for quickly estimating object depths without reconstruction is proposed and tested. An example application, quantifying oil droplet size distributions in an underwater plume, demonstrates the efficacy of the prototype and algorithms. / by Nicholas C. Loomis. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 321-351). / Many chemical constituents are removed from the ocean by attachment to settling particles, a process referred to as "scavenging." Radioisotopes of thorium, a highly particle-reactive element, have been used extensively to study scavenging in the ocean. However, this process is complicated by the highly variable chemical composition and concentration of particles in oceanic waters. This thesis focuses on understanding the cycling of thorium as affected by particle concentration and particle composition in the North Atlantic. This objective is addressed using (i) the distributions 228,230,234 Th, their radioactive parents, particle composition, and bulk particle concentration, as measured or estimated along the GEOTRACES North Atlantic Transect (GA03) and (ii) a model for the reversible exchange of thorium with particles. Model parameters are either estimated by inversion (chapter 2-4), or prescribed in order to simulate 230Th in a circulation model (chapter 5). The major findings of this thesis follow. In chapters 2 and 3, I find that the rate parameters of the reversible exchange model show systematic variations along GA03. In particular, k1 , the apparent first-order rate "constant" of Th adsorption onto particles, generally presents maxima in the mesopelagic zone and minima below. A positive correlation between k, and bulk particle concentration is found, consistent with the notion that the specific rate at which a metal in solution attaches to particles increases with the number of surface sites available for adsorption. In chapter 4, I show that Mn (oxyhydr)oxides and biogenic particles most strongly influence k1 west of the Mauritanian upwelling, but that biogenic particles dominate ki in this region. In chapter 5, I find that dissolved 230Th data are best represented by a model that assumes enhanced values of k, near the seafloor. Collectively, my findings suggest that spatial variations in Th radioisotope activities observed in the North Atlantic reflect at least partly variations in the rate at which Th is removed from the water column. / by Paul Lerner. / Ph. D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages [191]-201). / Submesoscale flows, current systems 1-100 km in horizontal extent, are increasingly coming into focus as an important component of upper-ocean dynamics. A range of processes have been proposed to energize submesoscale flows, but which process dominates in reality must be determined observationally. We diagnose from observed flow statistics that in the thermocline the dynamics in the submesoscale range transition from geostrophic turbulence at large scales to inertia-gravity waves at small scales, with the transition scale depending dramatically on geographic location. A similar transition is shown to occur in the atmosphere, suggesting intriguing similarities between atmospheric and oceanic dynamics. We furthermore diagnose from upper-ocean observations a seasonal cycle in submesoscale turbulence: fronts and currents are more energetic in the deep wintertime mixed layer than in the summertime seasonal thermocline. This seasonal cycle hints at the importance of baroclinic mixed layer instabilities in energizing submesoscale turbulence in winter. To better understand this energization, three aspects of the dynamics of baroclinic mixed layer instabilities are investigated. First, we formulate a quasigeostrophic model that describes the linear and nonlinear evolution of these instabilities. The simple model reproduces the observed wintertime distribution of energy across scales and depth, suggesting it captures the essence of how the submesoscale range is energized in winter. Second, we investigate how baroclinic instabilities are affected by convection, which is generated by atmospheric forcing and dominates the mixed layer dynamics at small scales. It is found that baroclinic instabilities are remarkably resilient to the presence of convection and develop even when rapid overturns keep the mixed layer unstratified. Third, we discuss the restratification induced by baroclinic mixed layer instabilities. We show that the rate of restratification depends on characteristics of the baroclinic eddies themselves, a dependence not captured by a previously proposed parameterization. These insights sharpen our understanding of submesoscale dynamics and can help focus future inquiry into whether and how submesoscale flows influence the ocean's role in climate. / by Jörn Callies. / Ph. D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), June 2011. / "June 2011." Cataloged from PDF version of thesis. / Includes bibliographical references. / Atmospheric nitrous oxide N₂O concentrations have been rising steadily for the past century as a result of human activities. In particular, human perturbation of the nitrogen cycle has increased the N₂O production rates of the two major sources of this greenhouse gas, soil and the ocean. Nitrification, and particularly ammonia oxidation, is one of the major processes that produces N₂O in the ocean. In this thesis, a series of stable isotopic methods have been used to characterize the biogeochemical controls on N₂O production by marine nitrification as well as the natural abundance stable isotopic signatures of N₂O produced by marine nitrifiers. This thesis shows that in addition to chemical controls on N₂O production rates such as oxygen (O₂) and nitrite (NO₂- ) concentrations, there are also biological controls such as nitrifier cell abundances and coastal phytoplankton blooms that may influence N₂O production by ammonia oxidizers as well. Ammonia oxidizers can produce N₂O through two separate biochemical mechanisms that have unique isotopic signatures. Using culture-based measurements of these signatures, we conclude that one of these pathways, nitrifier-denitrification, may be a significant source of N₂O produced in the South Atlantic Ocean and possibly the global ocean. / by Caitlin Frame. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Global climate models project a 21st century strengthening of the Pacific Equatorial Undercurrent (EUC). The consequent increase in topographic upwelling of cool waters onto equatorial coral reef islands would mitigate warming locally and modulate the intensity of coral bleaching. However, EUC water is potentially more acidic and richer in dissolved inorganic nutrients (DIN), both widely considered detrimental to coral reef health. My analysis of the Simple Ocean Data Assimilation product indicates that the EUC has indeed strengthened over the past 130 years. This result provides an historical baseline and dynamical reference for future intensification. Additionally, I reared corals in laboratory experiments, co-manipulating food, light and CO2 (acidity) to test the role of nutrition in coral response to elevate CO2 conditions. Heterotrophy yields larger corals but CO2 sensitivity is independent of feeding. Conversely, factors that enhance zooxanthellate photosynthesis (light and DIN) reduce CO2 sensitivity. Corals under higher light also store more lipid but these reserves are not utilized to maintain calcification under elevated CO2 My results suggest that while mitigation of CO2 effects on calcification is not linked to energetic reserve, EUC fueled increases in DIN and productivity could reduce effects of elevated CO2 on coral calcification. / by Elizabeth Joan Drenkard. / Ph. D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 159-167). / Seawater is estimated to contain 4.5 billion tonnes of uranium, approximately 1000 times that available in conventional terrestrial resources. Finding a sustainable way to harvest uranium from seawater will provide a source of nuclear fuel for generations to come, while also giving all countries with ocean access a stable supply. This will also eliminate the need to store spent fuel for potential future reprocessing, thereby addressing nuclear proliferation issues as well. While extraction of uranium from seawater has been researched for decades, no economical, robust, ocean-deployable method of uranium collection has been presented to date. This thesis presents a symbiotic approach to ocean harvesting of uranium where a common structure supports a wind turbine and a device to harvest uranium from seawater. The Symbiotic Machine for Ocean uRanium Extraction (SMORE) created and tested decouples the function of absorbing uranium from the function of deploying the absorbent which enables a more efficient absorbent to be developed by chemists. The initial SMORE concept involves an adsorbent device that is cycled through the seawater beneath the turbine and through an elution plant located on a platform above the sea surface. This design allows for more frequent harvesting, reduced down-time, and a reduction in the recovery costs of the adsorbent. Specifically, the design decouples the mechanical and chemical requirements of the device through a hard, permeable outer shell containing uranium adsorbing fibers. This system is designed to be used with the 5-MW NREL OC3-Hywind floating spar wind turbine. To optimize the decoupling of the chemical and mechanical requirements using the shell enclosures for the uranium adsorbing fibers, an initial design analysis of the enclosures is presented. Moreover, a flume experiment using filtered, temperature-controlled seawater was developed to determine the effect that the shells have on the uptake of the uranium by the fibers they enclose. For this experiment, the A18 amidoxime-based adsorbent fiber developed by Oak Ridge National Laboratory was used, which is a hollow-gear-shaped, high surface area polyethylene fiber prepared by radiation-induced graft polymerization of the amidoxime ligand and a vinylphosphonic acid comonomer. The results of the flume experiment were then used to inform the design and fabrication of two 1/10th physical scale SMORE prototypes for ocean testing. The A18 adsorbent fibers were tested in two shell designs on both a stationary and a moving system during a nine-week ocean trial, with the latter allowing the effect of additional water flow on the adsorbents uranium uptake to be investigated. A novel method using the measurement of radium extracted onto MnO₂ impregnated acrylic fibers to quantify the volume of water passing through the shells of the two systems was utilized. The effect of a full-scale uranium harvesting system on the hydrodynamics of an offshore wind turbine were then investigated using a 1/150th Froude scale wave tank test. These experiments compared the measured excitation forces and responses of two versions of SMORE to those of an unmodified floating wind turbine. With insights from the experiments on what a final full-scale design might look like, a cost-analysis was performed to determine the overall uranium production cost from a SMORE device. In this analysis, the capital, operating, and decommissioning costs were calculated and summed using discounted cash flow techniques similar to those used in previous economic models of the uranium adsorbent. Major contributions of this thesis include fundamental design tools for the development and evaluation of symbiotic systems to harvest uranium or other minerals from seawater. These tools will allow others to design offshore uranium harvesting systems based on the adsorbent properties and the scale of the intended installation. These flexible tools can be tuned for a particular adsorbent, location, and installation size, thereby allowing this technology to spread broadly. / by Maha Niametullah Haji. / Ph. D.