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.

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. / This thesis presents the results of four discrete investigations into processes governing the organic and inorganic chemical composition of seafloor hydrothermal fluids in a variety of geologic settings. Though Chapters 2 through 5 of this thesis are disparate in focus, each represents a novel investigation aimed at furthering our understanding of subsurface geochemical processes affecting hydrothermal fluid compositions. Chapters 2 and 3 concern the abiotic (nonbiological) formation of organic compounds in high temperature vent fluids, a process which has direct implications for the emergence of life in early Earth settings and sustainment of present day microbial populations in hydrothermal environments. Chapter 2 represents an experimental investigation of methane (CH4) formation under hydrothermal conditions. The overall reduction of carbon dioxide (C02) to CH4, previously assumed to be kinetically inhibited in the absence of mineral catalysts, is shown to proceed on timescales pertinent to crustal residence times of hydrothermal fluids. In Chapter 3, the abundance of methanethiol (CH3SH), considered to be a crucial precursor for the emergence of primitive chemoautotrophic life, is characterized in vent fluids from ultramafic-, basalt- and sediment-hosted hydrothermal systems. Previous assumptions that CH3SH forms by reduction of CO2 are not supported by the observed distribution in natural systems. Chapter 4 investigates factors regulating the hydrogen isotope composition of hydrocarbons under hydrothermal conditions. Isotopic exchange between low molecular weight n-alkanes and water is shown to be facilitated by metastable equilibrium reactions between alkanes and their corresponding alkenes, which are feasible in natural systems. In Chapter 5, the controls on vent fluid composition in a backare hydrothermal system are investigated. A comprehensive survey of the inorganic geochemistry of fluids from sites of hydrothermal activity in the eastern Manus Basin indicates that fluids there are influenced by input of acidic magmatic solutions at depth, and subsequently modified by variable extents of seawater entrainment and mixing-related secondary acidity production. / by Eoghan Reeves. / 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), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Key players in the marine carbon cycle are the ocean-dwelling microbes that fix, remineralize, and transform organic matter. Many of the small organic molecules in the marine carbon pool have not been well characterized and their roles in microbial physiology, ecological interactions, and carbon cycling remain largely unknown. In this dissertation metabolomics techniques were developed and used to profile and quantify a suite of metabolites in the field and in laboratory experiments. Experiments were run to study the way a specific metabolite can influence microbial metabolite output and potentially processing of organic matter. Specifically, the metabolic response of the heterotrophic marine bacterium, Ruegeria pomeroyi, to the algal metabolite dimethylsulfoniopropionate (DMSP) was analyzed using targeted and untargeted metabolomics. The manner in which DMSP causes R. pomeroyi to modify its biochemical pathways suggests anticipation by R. pomeroyi of phytoplankton-derived nutrients and higher microbial density. Targeted metabolomics was used to characterize the latitudinal and vertical distributions of particulate and dissolved metabolites in samples gathered along a transect in the Western Atlantic Ocean. The assembled dataset indicates that, while many metabolite distributions co-vary with biomass abundance, other metabolites show distributions that suggest abiotic, species specific, or metabolic controls on their variability. On sinking particles in the South Atlantic portion of the transect, metabolites possibly derived from degradation of organic matter increase and phytoplankton-derived metabolites decrease. This work highlights the role DMSP plays in the metabolic response of a bacterium to the environment and reveals unexpected ways metabolite abundances vary between ocean regions and are transformed on sinking particles. Further metabolomics studies of the global distributions and interactions of marine biomolecules promise to provide new insights into microbial processes and metabolite cycling. / by Winifred M. Johnson. / 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. / Nutrients and trace metals are vital for supporting life in the ocean, but the boundary processes that control the distributions of these elements are poorly constrained. Radium isotopes are well suited to studying inputs of elements from ocean margins because they are produced in sediments and soluble in seawater. The half-lives of the four isotopes (223Ra, 224Ra, 228Ra, 226Ra) range from days to thousands of years, thus these isotopes can be used to study oceanographic processes occurring over a range of time scales. In this thesis I have applied the quartet of radium isotopes to investigate boundary inputs, including seafloor hydrothermal vents, continental shelves, and rivers. First, radium isotope ratios were used to constrain the age of hydrothermal plumes emanating from vents along the Mid-Atlantic Ridge and East Pacific Rise. These radium-derived ages were applied to determine the iron residence time in the Pacific plume that emanates from near 15°S, providing an important constraint on the hydrothermal delivery of iron to the deep ocean. Next, 228Ra was used to show that shelf inputs to the Arctic Ocean have increased over the last decade, implying that the fluxes of other shelf-derived materials are also increasing and could impact primary production in this basin. The ratio of 228Ra and 226Ra was also applied to determine the ventilation time of Arctic intermediate waters with respect to shelf inputs, and the first measurements of 226Ra in the deep Canada Basin were used to estimate the residence time of deep waters with respect to benthic sediment inputs. Finally, a study of the Mackenzie River Estuary illustrated the importance of deltaic and estuarine processing on the ultimate delivery of nutrients, trace metals, dissolved organic matter, and radium to the Arctic Ocean. By applying radium isotopes as tracers of boundary inputs in these diverse environments, the work presented in this thesis improves our understanding of nutrient and trace metal inputs to the coastal and open ocean. / by Lauren Elizabeth Kipp. / 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), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references. / This thesis investigates three processes that control the evolution of oceanic margins. Chapter 2 presents seismic images of a ~2-km-thick evaporite body in Guaymas Basin, central Gulf of California. In rifts, evaporites form under conditions unique to the latest stages of continental rupture, and the presence, age, thickness, and shape place new constraints on the history of early rifting there. Chapter 3 presents numerical experiments that show that diapirs can form in sediments on the down-going plate in subduction zones and rise into the mantle wedge, delivering the sedimentary component widely observed in arc magmas. Chapter 4 presents measurements of seismic anisotropy from wide-angle, active-source data from the Middle America Trench that address the hypothesis that the upper mantle is hydrated by seawater flowing along outer-rise normal faults. These measurements indicate that the upper mantle is ~1.57 to 6.89% anisotropic, and this anisotropy can be attributed to bending-related faulting and an inherited mantle fabric. Accounting for anisotropy reduces previous estimates for the amount of water stored in the upper mantle of the down-going plate from ~2.5 to 1.5 wt%, a significant change in subduction zone water budgets. / by Nathaniel Clark Miller. / Ph.D.