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), 2003. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 299-310). / Inertial terms dominate the single-gyre ocean model and prevent western-intensification when the viscosity is small. This occurs long before the oceanically-appropriate parameter range. It is demonstrated here that the circulation is controlled if a mechanism for ultimate removal of vorticity exists, even if it is active only in a narrow region near the boundary. Vorticity removal is modeled here as a viscosity enhanced very near the solid boundaries to roughly parameterize missing boundary physics like topographic interaction and three dimensional turbulence over the shelf. This boundary-enhanced viscosity allows western-intensified mean flows even when the inertial boundary width is much wider than the frictional region because eddies flux vorticity from within the interior streamlines to the frictional region for removal. Using boundary-enhanced viscosity, western-intensified calculations are possible with lower interior viscosity than in previous studies. Interesting behaviors result: a boundary-layer balance novel to the model, calculations with promise for eddy param- eterization, eddy-driven gyres rotating opposite the wind, and temporal complexity including basin resonances. / (cont.) I also demonstrate that multiple-gyre calculations have weaker mean circulation than single-gyres with the same viscosity and subtropical forcing. Despite traditional understanding, almost no inter-gyre flux occurs if no-slip boundary conditions are used. The inter-gyre eddy flux is in control only with exactly symmetric gyres and free slip boundaries. Even without the inter-gyre flux, the multiple-gyre circulation is weak because of sinuous instabilities on the jet which are not present in the single-gyre model. These modes efficiently flux vorticity to the boundary and reduce the circulation without an inter-gyre flux, postponing inertial domination to much smaller viscosities. / by Baylor Fix-Kemper. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2013. / Pages 181 and 182 blank. Cataloged from PDF version of thesis. / Includes bibliographical references. / Steroidal estrogens are potent endocrine disrupting chemicals that are naturally excreted by vertebrates (e.g., humans and fish) and can enter natural waters through the discharge of treated and raw sewage. Because estrogens are detrimental to aquatic organisms at picomolar concentrations, many studies have measured so-called "free" estrogen concentrations in wastewater effluents, rivers, and lakes. Yet, to our knowledge, no studies have characterized the broader range of estrogens that includes free, conjugated, and halogenated forms. Conjugated estrogens are important because they can be easily converted to potent free forms by bacteria in wastewater treatment plants and receiving waters. And halogenated estrogens, produced during wastewater disinfection, are only slightly less potent than free estrogens but much more likely to bioaccumulate. We have developed a tandem mass spectrometry method that is capable of simultaneously quantifying free, conjugated, and halogenated estrogens at picomolar levels in wastewater effluent and coastal seawater. The method was validated using treated effluent from the greater Boston metropolitan area, where we found that halogenated estrogens represented over 50 % of the total estrogen discharge flux. A kinetic model of estrogen halogenation was used to predict the distribution of free and halogenated forms in wastewater effluent and suggested that chlorinated estrogens may be formed en route to the wastewater treatment plant. In the receiving waters of Massachusetts Bay, we detected a range of conjugated, free, and halogenated forms at concentrations that were well-predicted by dilution near the sewage outfall. Farther downstream, we found significantly higher estrone concentrations which points to large inputs of estrogens from sources other than sewage. Finally, we have used compound-specific measurements of 13C and 14C in commercial and pharmaceutical estrogen preparations to evaluate the potential for using carbon isotopes to distinguish between synthetic and endogenous steroids in wastewater and other environmental matrices. Our results show that synthetic estrogens and progestogens exhibit significantly depleted [delta]13 C values (~30 0/00) compared to endogenous steroids (-16 0/00 to -26 0/00). This isotopic difference should make it possible to apportion synthetic and endogenous hormone sources in complex environments. / by David R. Griffith. / 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. / Organic carbon (OC) preserved in marine sediments acts as a reduced carbon sink that balances the global carbon cycle. Understanding the biogeochemical mechanisms underpinning the balance between OC preservation and degradation is thus critical both to quantifying this carbon reservoir and to estimating the extent of life in the deep subsurface biosphere. This work utilizes bulk and spatially-resolved X-ray absorption spectroscopy to characterize the OC content and composition of various environmental systems in order to identify the role of minerals and surrounding geochemistry in organic carbon preservation in sediments. Biogenic manganese (Mn) oxides formed either in pure cultures of Mn-oxidizing microorganisms, in incubations of brackish estuarine waters, or as ferromanganese deposits in karstic cave systems rapidly associate with OC following precipitation. This association is stable despite Mn oxide structural ripening, suggesting that mineral-associated OC could persist during early diagenetic reactions. OC associated with bacteriogenic Mn oxides is primarily proteinaceous, including intact proteins involved in Mn oxidation and likely oxide nucleation and aggregation. Pelagic sediments from 16 sites underlying the South Pacific and North Atlantic gyres and spanning a gradient of sediment age and redox state were analyzed in order to contrast the roles of oxygen exposure, OC recalcitrance, and mineral-based protection of OC as preservation mechanisms. OC and nitrogen concentrations measured at these sites are among the lowest globally (<0.1%) and, to a first order, scale with sediment oxygenation. In the deep subsurface, however, molecular recalcitrance becomes more important than oxygen exposure time in protecting OC against remineralization. Deep OC consists of primarily amide and carboxylic carbon in a scaffolding of aliphatic and O-alkyl moieties, corroborating the extremely low C/N values observed. These findings suggest that microbes in oxic pelagic sediments are carbon-limited and may preferentially remove carbon relative to nitrogen from the organic matter pool. As a whole, this work documents how interactions with mineral surfaces and exposure to oxygen generate a reservoir of OC stabilized in sediments on at least 25-million year time scales. / by Emily Racz Estes. / 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), 2009. / Includes bibliographical references. / Tropical cyclone activity over the last 5000 years is investigated using overwash sediments from coastal lagoons on the islands of Vieques, Puerto Rico and Koshikijima, Japan. A simple sediment transport model can reproduce the landward fining deposits observed at Vieques, and reveals that although the record exhibits centennial-tomillennial changes in hurricane overwash frequency, the magnitude of these flooding events has remained relatively constant. Stochastic simulations of hurricane overwash show that breaks in activity at Vieques are extremely long and unlikely to occur under the current hurricane climatology and the present barrier morphology. Periods of less frequent hurricane deposition at Vieques are contemporaneous with intervals of increased El Nifio occurrences and reduced precipitation in West Africa, suggesting a dominant influence by these two climatic phenomena. Hiatuses in overwash activity between 3600-to-2500 and 1000-500 years ago are longer than what is generated by overwash simulations under a constant El Niflo-like state, indicating that mechanisms in addition to variability in the El Nifio/Southern Oscillation are required to completely produce the overwash variability at Vieques. Periods of low overwash activity at Vieques are concurrent with increased overwash activity at Kamikoshiki and may indicate a correspondence between tropical cyclone activity in the western Northern Atlantic and the western North Pacific. / by Jonathan D. Woodruff. / Ph.D.

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), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Hydrothermal vents and coral ecosystems are conspicuous biological hot spots in the deep-sea. These ecosystems face increasing threats from human activities. Having thorough taxonomic inventories as well as understanding species' relatedness, genetic diversity, connectivity patterns, and adaptive potential is fundamental for the implementation of conservation strategies that help mitigate these threats. This thesis provides fundamental high-priority knowledge in taxonomic, evolutionary, and ecological aspects of deep-sea coral and vent species, by harnessing the power of genomic tools and overcoming long-standing methodological barriers. First, I develop bioinformatic tools that help guide the design of studies aiming to characterize eukaryotic genome diversity using restriction-site associated DNA sequencing. Using these tools I find that the predictability of restriction site frequencies in eukaryotic genomes is chiefly determined by the phylogenetic position of the target species and the recognition sequence of the selected restriction enzyme. These tools are then applied to test global-scale historical biogeographic hypotheses of vent fauna using barnacles as model. Phylogeographic inferences suggest that the western Pacific was the place of origin of the major vent barnacle lineage, followed by circumglobal colonization eastward along the southern hemisphere during the Neogene. I suggest that the geological processes and dispersal mechanisms discussed here can explain distribution patterns of many other marine taxa in addition to barnacles. Regional-scale analyses indicate that vent barnacle populations are well connected within basins and ridge systems, and that their diversity patterns do not conform to the predictions from the hypothesis that seamounts are centers of endemism. I then move on to resolve long-standing questions regarding species definitions in recalcitrant deep-sea coral taxa, by unambiguously resolving evolutionary relationships and objectively inferring species boundaries. Finally, I explore the adaptive potential of deep-sea coral species to environmental changes by examining a case of adaptation to shallow water from the deep sea. Candidate positive-selection markers shared between pairs of shallow and deep populations are identified as likely makers for genomic regions involved in adaptation. Overall, the results from this thesis constitute critical baseline data with which to assess potential effects of anthropogenic disturbances on deep-sea ecosystems. / by Santiago Herrera Monroy. / Ph. D.

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), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Marine populations are increasingly subjected to changing conditions whether through harvest or through broad-scale habitat change. Historically, few models have accounted for such trends over time, and even fewer have been used to study how trends affect optimal harvests. I developed and analyzed several models that explore, first, endogenous change caused by harvest and, second, exogenous change from factors (such as rising ocean temperatures) outside harvesters' control. In these models, I characterized the profit-or yield-maximizing strategy when harvesting damages habitat in a multispecies fishery, when harvest creates a selective pressure on dispersal, and when rising temperatures cause changes in vital rates. I explore this last case in both deterministic and stochastic environments, and also allow the harvester to learn about unknown parameters of the stock recruitment model while harvesting. I also develop an unambiguous definition of and describe a statistical test for a shift in a species' spatial distribution. My results demonstrate that optimal harvesting strategies in a changing environment differ in important ways from optimal strategies in a constant environment. / by Emily Alison Moberg. / Ph. D.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution); and, (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005. / Includes bibliographical references (p. 149-151). / Despite the great achievements obtained with fast-field and parabolic equation models, normal mode programs still remain a very efficient, simple and practical tool for describing ocean acoustics in range-independent environments. Numerical implementations of wave-theory solutions for range-dependent acoustic problems can be classified as: normal-mode techniques (adiabatic or coupled modes); parabolic-approximation techniques (narrow- or wide-angle parabolic equations solved by split-step or finite-difference techniques); and finite-element/finite- difference solutions of the full wave equation. The mode techniques provide approximate field solutions if implemented in the adiabatic approximation, while complete wave theory solutions can be obtained by including full mode coupling. Parabolic approximations to the elliptic wave equation have been extensively studied over the past 10 years([15], [23]). The advantage of using a parabolic wave equation is that it can be efficiently solved by noniterative forward marching techniques. However, any form of the parabolic equation is an approximate wave equation derived under the assumptions of: (1) forward propagation only, and (2) that energy is propagating within a limited angular spectrum around the main propagation direction. The last category of models based on finite-difference and finite-element solutions of the full wave equation([22]) is well suited for providing solutions for propagation in general range-dependent environments. / (cont.) The existing codes, however, are extremely computer intensive. My thesis focuses on a two-dimensional two-way coupled modes model, and then expend it to a three-dimensional coupled modes model for two-dimensional, range- dependent waveguides. Numerical examples of two-dimensional and three-dimensional problems are presented, and comparisons with the results from analytical solution, as well as from COUPLE are also considered. / by Wenyu Luo. / S.M.

Thesis: Ph. D. in Mechanical and Oceanographic Engineering, Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 117-135). / A fundamental problem in autonomous underwater robotics is the high latency between the capture of image data and the time at which operators are able to gain a visual understanding of the survey environment. Typical missions can generate imagery at rates hundreds of times greater than highly compressed images can be transmitted acoustically, delaying that understanding until after the vehicle has been recovered and the data analyzed. While automated classification algorithms can lessen the burden on human annotators after a mission, most are too computationally expensive or lack the robustness to run in situ on a vehicle. Fast algorithms designed for mission-time performance could lessen the latency of understanding by producing low-bandwidth semantic maps of the survey area that can then be telemetered back to operators during a mission. This thesis presents a lightweight framework for processing imagery in real time aboard a robotic vehicle. We begin with a review of pre-processing techniques for correcting illumination and attenuation artifacts in underwater images, presenting our own approach based on multi-sensor fusion and a strong physical model. Next, we construct a novel image pyramid structure that can reduce the complexity necessary to compute features across multiple scales by an order of magnitude and recommend features which are fast to compute and invariant to underwater artifacts. Finally, we implement our framework on real underwater datasets and demonstrate how it can be used to select summary images for the purpose of creating low-bandwidth semantic maps capable of being transmitted acoustically. / by Jeffrey W. Kaeli. / Ph. D. in Mechanical and Oceanographic Engineering

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), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 145-161). / Chemoautotrophic ecosystems at deep-sea hydrothermal vents were discovered in 1977, but not until 1995 were free-living autotrophic Epsilonproteobacteria identified as important microbial community members. Because the deep-sea is food-starved, the autotrophic metabolism of hydrothermal vent Epsilonproteobacteria may be very important for deep-sea consumers. However, quantifying their metabolic activities in situ has remained difficult, and biochemical mechanisms underlying their autotrophic physiology are poorly described. To gain insight into environmental processes, an approach was developed for incubations of microbes at in situ pressure and temperature (25 MPa, 24°C) with various combinations of electron donors/acceptors (H₂ , O₂ and NO₃- and ¹³HCO₃-) as a tracer to track carbon fixation. During short (18-24 h) incubations of low-temperature vent fluids from Crab Spa (9°N East Pacific Rise), the concentration of electron donors/acceptors and cell numbers were monitored to quantify microbial processes. Measured rates were generally higher than previous studies, and the stoichiometry of microbially-catalyzed redox reactions revealed new insights into sulfur and nitrogen cycling. Single-cell, taxonomically-resolved tracer incorporation showed Epsilonproteobacteria dominated carbon fixation, and their growth efficiency was calculated based on electron acceptor consumption. Using these data, in situ primary productivity, microbial standing stock, and average biomass residence time of the deep-sea vent subseafloor biosphere were estimated. Finally, the population structures of the most abundant genera Sulfurimonas and Thioreductor were shown to be strongly influenced by pO₂ and temperature respectively, providing a mechanism for niche differentiation in situ. To gain insights into the core biochemical reactions underlying autotrophy in Epsilonprotebacteria, a theoretical metabolic model of Sulfurimonas denitrificans was developed. Validated iteratively by comparing in silico yields with data from chemostat experiments, the model generated hypotheses explaining critical, yet so far unresolved reactions supporting chemoautotrophy in Epsilonproteo bacteria. For example, it provides insight into how energy is conserved during sulfur oxidation coupled to denitrification, how reverse electron transport produces ferredoxin for carbon fixation, and why aerobic growth yields are only slightly higher compared to denitrification. As a whole, this thesis provides important contributions towards understanding core mechanisms of chemoautrophy, as well as the in situ productivity, physiology and ecology of autotrophic Epsilonproteobacteria. / by Jesse Christopher McNichol. / Ph. D.

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), February 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 163-170). / Much of the recent research in ocean acoustics has focused on developing methods to exploit the effects that the sea surface and seafloor have on acoustic propagation. Many of those methods require detailed knowledge of the acoustic properties of the seafloor and the sound speed profile (SSP), which limits their applicability. The range-frequency waveguide invariant describes striations that often appear in plots of acoustic intensity versus range and frequency. These range-frequency striations have properties that depend strongly on the frequency of the acoustic source and on distance between the acoustic source and receiver, but that depend mildly on the SSP and seafloor properties. Because of this dependence, the waveguide invariant can be utilized for applications such as passive and active sonar, time-reversal mirrors, and array processing, even when the SSP or the seafloor properties are not well known. This thesis develops a framework for understanding and calculating the waveguide invariant, and uses that framework to develop signal processing techniques for the waveguide invariant. A method for passively estimating the range from an acoustic source to a receiver is developed, and tested on experimental data. Heuristics are developed to estimate the minimum source bandwidth and minimum horizontal aperture required for range estimation. A semi-analytic formula for the waveguide invariant is derived using WKB approximation along with a normal mode description of the acoustic field in a rangeindependent waveguide. This formula is applicable to waveguides with arbitrary SSPs, and reveals precisely how the SSP and the seafloor reflection coefficient affect the value of the waveguide invariant. Previous research has shown that the waveguide invariant range-frequency striations can be observed using a single hydrophone or a horizontal line array (HLA) of hydrophones. This thesis shows that traditional array processing techniques are sometimes inadequate for the purpose of observing range-frequency striations using a HLA. Array processing techniques designed specifically for observing range-frequency striations are developed and demonstrated. Finally, a relationship between the waveguide invariant and wavenumber integrations is derived, which may be useful for studying range-frequency striations in elastic environments such as ice-covered waveguides. / by Kevin L. Cockrell. / Ph.D.