This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / 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), 2019 / Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references. / Harmful algal blooms (HABs) can produce potent neurotoxins that accumulate in seafood and affect human health. One HAB toxin of concern is domoic acid (DomA), a glutamate analog produced by the marine diatom Pseudo-nitzschia spp. Current regulatory limits are designed to prevent acute neurotoxicity in adult humans. However, research shows that low-level exposure during early life can lead to long-term changes in behavior, neural connectivity, and brain morphology. To determine the underlying mechanisms of developmental toxicity, this dissertation used zebrafish as a tool to: i) Establish the developmental window of susceptibility for DomA toxicity, ii) Characterize the behavioral consequences of exposures, and iii) Identify the cellular targets and processes perturbed by DomA. I found that DomA exposure particularly at 2 days post fertilization (dpf) led to altered startle response behavior, myelination defects, and the downregulation of axonal and myelin structural genes. / Using vital dyes and immunolabeling, I assessed DomA-induced alterations in cells required for the startle response. I found no differences in the number of sensory neuromasts or in the sensory cranial ganglia structures that detect the acoustic stimuli. However, the majority of DomA-treated larvae lacked one or both Mauthner cells - hindbrain neurons critical for fast startle responses. DomA-treated larvae also had oligodendrocytes with fewer and shorter myelin sheaths, and appeared to aberrantly myelinate neuronal cell bodies. The loss of the Mauthner neurons and their axons may lead to a cellular environment where oligodendrocytes myelinate neuronal cell bodies in the absence of adequate axonal targets. Indeed, pharmacological treatment that reduced the oligodendrocyte number also led to the reduction in the number of these aberrant, myelinated cell bodies. / These results indicate that exposure to DomA at a particular period in neural development targets specific cell types, disrupts myelination in the spinal cord, and leads to prolonged behavioral deficits. These mechanistic insights support hazard assessments of DomA exposures in humans during critical periods in early development. / "Funding for my research came from the Ocean Ventures Fund, Hill family foundation, Woods Hole Sea grant NA14OAR4170074, and the Woods Hole Center for Oceans and Human Health (COHH), which is jointly funded by the National Institutes of Health (P01ES02192, P01ES028938), and the National Science Foundation (OCE-1314642, OCE-1840381). My funding came from the National Institutes of Health (NIH) P01ES021923-04S1, the Ocean Ridge Initiative Fellowship, the Von Damm Fellowship, and the MIT/WHOI Joint Program Academic Programs Office"--Page 5 / by Jennifer Martinez Panlilio. / Ph. D. / Ph.D. Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution)

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), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 193-220). / Southern Ocean net community productivity plays an out sized role in regulating global biogeochemical cycling and climate dynamics. The structure of spatial-temporal variability in phytoplankton ecosystem dynamics is largely governed by physical processes but a variety of competing pathways complicate our understanding of how exactly they drive net population growth. Here, I leverage two coupled, 3-dimensional, global, numerical simulations in conjunction with remote sensing data and past observations, to improve our mechanistic understanding of how physical processes drive biology in the Southern Ocean. In Chapter 2, I show how different mechanistic pathways can control population dynamics from the bottom-up (via light, nutrients), as well as the top-down (via grazing pressure). In Chapters 3 and 4, I employ a higher resolution, eddy resolving, integration to explicitly track and examine closed eddy structures and address how they modify biomass at the mesoscale. / Chapter 3 considers how simulated eddies drive bottom-up controls on phytoplankton growth and finds that division rates are, on average, amplified in anticyclones and suppressed in cyclones. Anomalous division rates are predominately fueled by an anomalous vertical iron flux driven by eddy-induced Ekman Pumping. Chapter 4 goes on to describe how anomalous division rates combine with anomalous loss rates to drive anomalous net population growth. Biological rate-based mechanisms are then compared to the potential for anomalies to evolve strictly via physical transport (i.e. dilution, stirring, advection). All together, I identify and describe dramatic regional and seasonal variability in when, where, and how different mechanisms drive phytoplankton growth throughout the Southern Ocean. Better understanding this variability has broad implications to our understanding of how oceanic biogeochemisty will respond to, and likely feedback into, a changing climate. / Specifically, the uncertainty associated with this variability should temper recent proposals to artificially stimulate net primary production and the biological pump via iron fertilization. In Chapter 5 I argue that Southern Ocean Iron Fertilization fails to meet the basic tenets required for adoption into any regulatory market based framework. / by Tyler W. Rohr. / Ph. D. / 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)

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), 2019 / Cataloged from PDF version of thesis. "The pagination in this thesis reflects how it was delivered to the Institute Archives and Special Collections. TOC pagination for Bibliography section is off by one page"--Disclaimer Notice page. / Includes bibliographical references (pages 115-123). / Submesoscale currents, with horizontal length scales of 1-20 km, are an important element of upper ocean dynamics. These currents play a crucial role in the horizontal and vertical redistribution of tracers, the cascade of tracer variance to smaller scales, and in linking the mesoscale circulation with the dissipative scales. This thesis investigates submesoscale flows and their properties using Lagrangian trajectories of observed and modeled drifters. We analyze statistics of observed drifter pairs to characterize turbulent dispersion at submeso-scales. Contrary to theoretical expectations, we find that nonlocal velocity gradients associated with mesoscale eddies dominate the separation of drifters even at the kilometer scale. At submeso-scales, we observe energetic motions, such as near-inertial oscillations, that contribute to the energy spectrum but are inefficient at dispersion. / Using trajectories in a model of submesoscale turbulence, we find that, if drifters have a vertical separation, vertical shear dominates the dispersion and conceals horizontal dispersion regimes from drifter observations. Particularly in submesoscale flows, vertical shear is orders of magnitude larger than horizontal gradients in velocity. Since conventional drifters in the ocean are not affected by vertical shear, it is likely that drifter-derived diffusivity underestimates the diffusivity that a tracer would experience. Lastly, we test and apply cluster-based methods, using three or more drifters, to estimate the velocity gradient tensor. Since velocity gradients become large at submesoscales, the divergence, strain, and vorticity control the evolution and deformation of clusters of drifters. Observing the velocity gradients using drifters, enables us to further constrain the governing dynamics and decipher submesoscale motions from inertia-gravity waves. / These insights provide a Lagrangian perspective on submesoscale flows that illuminates scales that are challenging to observe from other platforms. We reveal observational and theoretical challenges that need to be overcome in future investigations. / "Funded by the National Science Foundation (OCE-I434788) and the Office of Naval Research (N00014-13-1-0451, Grant N00014-16-1-2470)"--Page 5 / by Sebastian Essink. / Ph. D. / 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)

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), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 113-121). / Submesoscale ocean dynamics and instabilities, with characteristic scales 0.1-10 kin, can play a critical role in setting the ocean's surface boundary layer thickness and associated density stratification. Submesoscale instabilities contribute to lateral stirring and tracer dispersal. These dynamics are investigated in the Bay of Bengal, motivated by the upper ocean's potentially coupled interactions with Monsoon winds and convection. The region's excess precipitation and runoff generates strong salinity gradients that typically set density fronts and stratification in the upper 50 m. Since we cannot synoptically measure currents containing fast-evolving and oscillating components across the submesoscale range, we instead analyze passive tracer distributions (spice = density-compensated temperature (T) and salinity (S) anomalies), identifying signatures of flows and testing dynamical theories. / The analysis is based on over 9000 vertical profiles of T and S measured along ~4800 km of ship tracks in the Bay of Bengal during ASIRI and MISO-BOB expeditions in 2013, 2015, and 2018. Observations in the surface mixed layer reveal ~1 km scale-selective correlation of surface T and S, with compensation reducing cross-front density gradients by ~50%. Using a process study ocean model, we show this is caused by submesoscale instabilities slumping fronts, plus surface cooling over the resultant enhanced salinity stratification, potentially thwarting the forward cascade of energy. In the stratified interior, we present a spectral analysis of horizontal spice variance statistics from wavenumber k ~0.01 cpkm to ~1 cpkm. At scales <10 km, stratified layers that are closer to the surface exhibit redder passive tracer spectra (power spectra k⁻³, gradient spectra k⁻¹) than predicted by quasi-geostrophic or frontogenetic theories. / Complimentary observations reveal spice patterns with multiple, parallel, ~10 m thin layers, crossing isopycnals with O(10⁻⁴) slopes, coherent over at least 30-80 kin, with coincident layers of stratification anomalies. Comparison with shear measurements, and a numerical process study, suggest that both submesoscale sheared eddies, and thin near-inertial waves, form such layers. Fast formation timescales and large aspect ratios suggest they enhance horizontal mixing by shear dispersion, reducing variance at ~1-10 km scales. / by Gualtiero Victor Rudi Spiro Jaeger. / Ph. D. / 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)

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), 2019 / Cataloged from PDF of thesis. / Includes bibliographical references (pages 151-174). / This thesis explicates aspects of the basic structure of oceanic lithosphere that are shaped by the processes that form the lithosphere. The strength of lithospheric plates relative to the underlying mantle enables the surface plate motions and plate boundary processes that characterize plate tectonics on Earth. Surprisingly, we have a relatively poor understanding of the physical mechanisms that make the lithosphere strong relative to the asthenosphere, and we lack a reference model for ordinary lithospheric structure that can serve as a baseline for comparing geophysical observations across locations. Chapters 2 and 3 of this thesis investigate the seismic structure of a portion of the Pacific plate where the simple tectonic history of the plate suggests that its structure can be used as a reference model for oceanic lithosphere. We present measurements of shallow azimuthal seismic anisotropy, and of a seismic discontinuity in the upper mantle, that reflect the effects of shear deformation and melting processes involved in the formation of the lithosphere at mid-ocean ridges. Chapter 4 uses numerical models to explore factors controlling fault slip behavior on normal faults that accommodate tectonic extension during plate formation. / by Hannah F. Mark. / Ph. D. / 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)

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), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references. / Antibiotics are naturally occurring chemicals in bacteria that were recently discovered and utilized by humans. Despite a relatively short time of use, anthropogenic use of antibiotics has increased natural levels of antibiotic resistance, which has caused a looming antibiotic resistance crisis, where antibiotics may not work. Understanding resistance patterns is critical to allow for continued therapeutic use of antibiotics. While resistance is often thought of in hospitals, antibiotics and antibiotic resistance genes from human activity are disposed of into nature where they are able to interact with naturally occurring antibiotics and resistance. In this dissertation, I examine the ocean as an understudied region of the environment for antibiotic resistance. The ocean represents an area of human activity with recreation and food consumption and it is an enormous region of the planet that is affected by both land and sea activities. / In Chapter 2, I explore the policies that have contributed to the antibiotic resistance crisis. I offer explanations of market and political failures that contributed to the situation, areas for growth in terms of assessing scientific knowledge, and finally, recommendations for mitigating antibiotic resistance. In Chapters 3 and 4, I collected individual bacterial cultures from Cape Cod, MA beaches to assess the phenotypic response to antibiotic resistance. I show that 73% of Vibrio-like bacteria and 95% of heterotrophic bacteria (both groups operationally defined) are resistant to at least one antibiotic. These results indicate that antibiotic resistance is prevalent and persistent on beaches over both spatial and temporal scales. In Chapter 5, I used metagenomics to assess the abundance and types of resistance genes at coastal impacted Massachusetts sites. I found that, even in sites that seem distinct in terms of anthropogenic impact, prevalence of resistance remained the same. / Finally, in Appendix A, I examined part of the TARA Ocean dataset for prevalence of antibiotic resistance genes across the world's ocean. Here, I found that there are distinctions between different ocean biomes based upon antibiotic, metal, and mobile genetic elements. This dissertation has increased the understanding of temporal and spatial dynamics of antibiotic resistance in the coastal and open ocean. / "This work has be funded by the National Science Foundation Graduate Research Fellowship under Grant No. 1122374 and a Martin Fellows for Sustainability Fellowship (both to MKM). Grants from Woods Hole Oceanographic Institution from the Coastal Ocean Institute, Grassle Family Foundation, Hill Family Foundation, and Biology Department also supported this work"--Page 6 / by Megan Katherine May. / Ph. D. / Ph.D. Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution)

Thesis: Ph. D. in Physical Oceanography, 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), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 121-133). / Global patterns of ocean salinity arise from the exchange of freshwater between the sea surface and the atmosphere. For a quasi-steady state system, these surface fluxes are balanced by compensating transports of salt in the ocean interior. In a warming climate, the atmosphere holds additional water vapor which acts to intensify the global water cycle. Amplified freshwater fluxes are then absorbed at the surface and propagate along ocean circulation pathways. Here, we use coupled model results from the CMIP5 experiment to identify coherent responses in the atmospheric water cycle and in ocean salinity patterns. Some aspects of the response are consistent across models, while other regions show large inter-model spread. In particular, the salinity response in the North Atlantic subpolar gyre, where the mean salinity plays a role in maintaining high surface density for deep-water formation, has low confidence in CMIP5 models. / To understand how differences in ocean circulation may affect this response, we use two techniques to diagnose the role of salt transports in the present-day climate. The first is a salt budget within the surface mixed layer, which identifies major transport processes. The second is a Lagrangian particle tracking tool, used to understand the regional connectivity of water masses. From this analysis, we find that anomalous freshwater signals become well mixed within the ocean gyres, but can be isolated on larger scales. The subpolar Atlantic salinity response generally shows freshening at the surface, but is sensitive to the transport of anomalously salty water from the subtropics, a largely eddy-driven process. As CMIP5 models use a range of eddy parameterizations, this is likely a source of uncertainty in the salinity response. / Finally, we investigate the effect of salinity changes on the deep overturning cells and other circulations, and find a complex influence that also depends on the details of advective pathways. In a warming scenario, water cycle amplification actually works to strengthen the Atlantic meridional overturning circulation due to the influence of enhanced subtropical evaporation. / by Samuel J. Levang. / Ph. D. in Physical Oceanography / Ph.D.inPhysicalOceanography 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)

Thesis: Ph. D., Joint Program in Physical Oceanography (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 137-153). / Each year, surface ocean ecosystems export sinking particles containing gigatons of carbon into the ocean's interior. This particle flux connects the entire ocean microbiome and constitutes a fundamental aspect of marine microbial ecology and biogeochemical cycles. Particle flux is also variable and intricately complex, impeding its mechanistic or quantitative description. In this thesis we pair compilations of available data with novel mathematical models to explore the relationships between particle flux and other key variables - temperature, net primary production, and depth. Particular use is made of (probability) distributional descriptions of quantities that are known to vary appreciably. First, using established thermodynamic dependencies for primary production and respiration, a simple mechanistic model is developed relating export efficiency (i.e. the fraction of primary production that is exported out of the surface ocean via particle flux) to temperature. / The model accounts for the observed variability in export efficiency due to temperature without idealizing out the remaining variability that evinces particle flux's complexity. This model is then used to estimate the metabolically-driven change in average export efficiency over the era of long-term global sea surface temperature records, and it is shown that the underlying mechanism may help explain glacial-interglacial atmospheric carbon dioxide drawdown. The relationship between particle flux and net primary production is then explored. Given that these are inextricable but highly variable and measured on different effective scales, it is hypothesized that a quantitative relationship emerges between collections of the two measurements - i.e. that they can be related not measurement-by-measurement but rather via their probability distributions. / It is shown that on large spatial or temporal scales both are consistent with lognormal distributions, as expected if each is considered as the collective result of many subprocesses. A relationship is then derived between the log-moments of their distributions and agreement is found between independent estimates of this relationship, suggesting that upper ocean particle flux is predictable from net primary production on large spatiotemporal scales. Finally, the attenuation of particle flux with depth is explored. It is shown that while several particle flux-versus-depth models capture observations equivalently, these carry very different implications mechanistically and for magnitudes of export out of the surface ocean. A model is then proposed for this relationship that accounts for measurements of both the flux profile and of the settling velocity distribution of particulate matter, and is thus more consistent with and constrained by empirical knowledge. / Possible future applications of these models are discussed, as well as how they could be tested and/or constrained observationally. / by Brendan Barry. / Ph. D. / Ph.D. Joint Program in Physical Oceanography (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution)

Thesis (Ph. D.)--Joint Program in Physical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2008. / Includes bibliographical references (p. [221]-232). / Marine ecosystems reflect the physical structure of their environment and the biological processes they carry out. This leads to spatial heterogeneity and temporal variability, some of which is imposed externally and some of which emerges from the ecological mechanisms themselves. The main focus of this thesis is on the formation of spatial patterns in the distribution of zooplankton arising from social interactions between individuals. In the Southern Ocean, krill often assemble in swarms and schools, the dynamics of which have important ecological consequences. Mathematical and numerical models are employed to study the interplay of biological and physical processes that contribute to the observed patchiness. The evolution of social behavior is simulated in a theoretical framework that includes zooplankton population dynamics, swimming behavior, and some aspects of the variability inherent to fluid environments. First, I formulate a model of resource utilization by a stage-structured predator population with density-dependent reproduction. Second, I incorporate the predator-prey dynamics into a spatially-explicit model, in which aggregations develop spontaneously as a result of linear instability of the uniform distribution. In this idealized ecosystem, benefits related to the local abundance of mates are offset by the cost of having to share resources with other group members. Third, I derive a weakly nonlinear approximation for the steady-state distributions of predator and prey biomass that captures the spatial patterns driven by social tendencies. Fourth, I simulate the schooling behavior of zooplankton in a variable environment; when turbulent flows generate patchiness in the resource field, schools can forage more efficiently than individuals. / (cont.) Taken together, these chapters demonstrate that aggregation/ schooling can indeed be the favored behavior when (i) reproduction (or other survival measures) increases with density in part of the range and (ii) mixing of prey into patches is rapid enough to offset the depletion. In the final two chapters, I consider sources of temporal variability in marine ecosystems. External perturbations amplified by nonlinear ecological interactions induce transient ex-cursions away from equilibrium; in predator-prey dynamics the amplitude and duration of these transients are controlled by biological processes such as growth and mortality. In the Southern Ocean, large-scale winds associated with ENSO and the Southern Annular Mode cause convective mixing, which in turn drives air-sea fluxes of carbon dioxide and oxygen. Whether driven by stochastic fluctuations or by climatic phenomena, variability of the biogeochemical/physical environment has implications for ecosystem dynamics. / by Ariane Verdy. / Ph.D.

Thesis (S.M.)--Joint Program in Physical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2008. / Includes bibliographical references (p. 62-63). / The work was motivated by studies of Austin and Lentz (2002) and Pedlosky (2007). The above mentioned works considered two different responses of the stratified flow to a downwelling favorable wind forcing. The first study investigated a time dependent flow with a formation of a constantly expanding relatively well mixed region near the shore and the second considered a steady flow that arises when an offshore varying wind is applied. In my thesis I use ROMS to determine which type of response will take place based on the wind amplitude near the coast. It was demonstrated that if the value of the wind is much smaller than the critical value (determined by the stratification, the rotation rate and the horizontal diffusivity) then the flow is steady (the bbl case) and similar to the one investigated by Pedlosky. If the wind is of the order, or larger than, the critical value then the response is time dependent (the pool case) and similar to the one described by Austin and Lentz. The resulting flow structure of each response was also investigated. I examined the sensitivity of the bbl response to variations in the background vertical diffusivity, the initial stratification and the bottom slope. It was shown that a higher background vertical diffusivity, a higher stratification and a shallower bottom slope correspond to thinner (vertically) and narrower (horizontally) bbl. For the pool case the time dependent structure was also examined, using a number of idealized models. It was shown that the rate of the pool region expansion is a complex function of the local wind stress amplitude and the local depth. / by Evgeny Logvinov. / S.M.