WHOI Theses

Permanent URI for this collection

WHOI's educational role, at the graduate level, was formalized in 1968 with a change in its charter and the signing of an agreement with the Massachusetts Institute of Technology for a Joint Program leading to doctoral (Ph.D. or Sc.D.) or engineer's degrees. Joint master's degrees are also offered in selected areas of the program. Woods Hole Oceanographic Institution is also authorized to grant doctoral degrees independently.

New theses are added as they are published.


Recent Submissions

Now showing 1 - 20 of 1054
  • Thesis
    The behavior of the atmospheric boundary layer in the vicinity of the Gulf Stream sea surface temperature front
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-09) Clayson, Carol A. ; Edson, James B.
    The evolution of the marine atmospheric boundary layer (MABL) in the vicinity of a sea surface temperature (SST) front is of particular research interest, as the large air-sea temperature and humidity differences at the surface fuels various physical processes inside the boundary layer, causing intense heat and momentum exchange. Such processes make the mesoscale MABL an ocean-drive-atmosphere scenario. Dominant mechanisms, although having been studied intensively, are still yet to be fully understood due to the highly turbulent nature of the MABL. Previous studies often relied on satellite-derived SST and wind fields to investigate boundary layer dynamics, yet the coarse spatial and temporal resolution of such a method limits the understanding of the MABL evolution on shorter timescales. In this thesis, a combination of in situ data and model simulations is used to investigate the MABL response to the SST front in the Gulf Stream region on a timescale of one day or less. Analysis of MABL structure is divided into three categories depending on the background wind strength and its direction relative to the front: cold to warm, parallel/weak, and warm to cold. Two mechanisms identified in previous studies, vertical mixing and thermally induced pressure gradient, and their role in MABL evolution, are studied quantitatively. A comparison between observations and model simulations allows further analysis of the contribution of moist processes that were often considered to be of secondary importance in the past even over the ocean. Results show that vertical mixing is responsible for the majority of the MABL deepening, while the pressure adjustment’s effect is more significant when the cross-frontal wind is weak. Sensitivity tests conducted in the Weather Research and Forecast (WRF) also show that moisture processes, including surface latent heat, boundary layer transport of moist, and cloud formation, further enhance the mixing that drives MABL changes.
  • Thesis
    Connecting consumer plastic formulations to marine fates and impacts
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-09) Walsh, Anna N. ; Ward, Collin P. ; Reddy, Christopher M.
    Solutions to plastic pollution have been impeded by knowledge gaps surrounding plastic’s environmental persistence and implications. To fill some of these gaps, this thesis aims to connect consumer plastic formulations (the specific mixture of polymers and additives) to marine fates and impacts. First, I explored relationships between consumer polyethylene (PE) bag formulations, degradation by sunlight, and dissolved organic carbon (DOC) release to seawater. I found that the bags contained 15-36% inorganic additives, mainly calcium carbonate and titanium dioxide (TiO2). Bags and pure PE produced 3- to 80-fold more DOC during sunlight exposure than darkleaching, with more DOC generated by the bags than the pure PE. High resolution mass spectrometry revealed that photo-produced DOC comprised tens of thousands of unstudied chemicals. Additives strongly influenced degradation rates and DOC compositions. Second, I examined the interplay between sunlight and marine microbes on degradation of pure and TiO2-containing cellulose diacetate (CDA) fabrics. I found that sunlight reduced CDA’s average molecular weight (MW) and, ultimately, converted it to CO2. TiO2 accelerated MW reduction 2-fold and conversion to CO2 24-fold. Prior degradation by sunlight expedited microbial degradation in both fabrics. Finally, I assessed inorganic additive compositions in consumer plastics, their potential for liberation by sunlight, and potential impacts on local and global biogeochemistry. Consumer plastics contained ~8% inorganic additives comprising nearly 50 elements. Additive zinc (Zn) isotopic signatures appeared unique relative to other marine sources, which may be evident in the marine Zn isotopic balance. Light exposure accelerated release of elements into water relative to dark-leaching. Based on the most-cited estimate of plastic leakage to the ocean, plastic-derived antimony and Zn may be 3% and 1%, respectively, of natural riverine fluxes and quadruple by 2060. Proportions in heavily polluted rivers appear even greater. However, plastic leakage estimates span orders of magnitude, translating to high uncertainty in element fluxes. Collectively, this thesis demonstrates that additives and sunlight are overlooked drivers of marine plastic fates and impacts; integrating them into studies and models may transform our understanding of plastic pollution. Furthermore, leveraging the connection between formulation and fate may enable us to reduce environmental impacts using existing materials.
  • Thesis
    Joule heating and pore pressure evolution, magmatic intrusions at continental rifts, and microseisms in Yellowstone Lake
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-09) Smalls, Paris T. ; Einstein, Herbert
    The goal of this thesis is to investigate research topics related to geothermal resources. Chapter 1 introduces the thesis and motivates the need to study research topics in relevant geothermal environments, and develop new technologies to economically extract heat from these resources. In Chapter 2, microseism events in Yellowstone National Park are studied. Yellowstone is located in one of the most seismically active volcanic calderas in the world and is a widely studied area for investigating physical (e.g., faulting) and chemical (e.g., hydrothermal venting) relationships in geothermal systems. Chapter 3 describes dike intrusion modeling research I conducted early in my graduate studies including the feedback mechanisms between magma injection at plate spreading centers and topographic development. Chapter 4 represents a shift in my research interests from science to engineering problems relevant for geothermal heat extraction. In this chapter, I describe the design process for developing a novel experimental approach to study the effects of applying a high-voltage to saturated rock specimens under in-situ states of stress. This novel “Electric Rock Fracturing” experimental set-up is used in Chapter 5, the final chapter of this thesis, to study the effects of high-voltage application on the temperature, electrical conductivity, and permeability of brine saturated Berea Sandstone rock specimens.
  • Thesis
    Picophytoplankton of the Northeast U.S. Shelf: community composition and dynamics
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-09) Stevens, Bethany L. F. ; Neubert, Michael G. ; Sosik, Heidi M.
    Marine picophytoplankton are the most abundant primary producers in the ocean and are expected to be favored by the ongoing effects of climate change. Predicting the response of marine ecosystems to these changes requires mechanistic knowledge of picophytoplankton ecology. This thesis uses a combination of long-term monitoring, cruise data, population models, and high-throughput sequencing to investigate the dynamics of picophytoplankton across scales of space and time that are relevant both to the physiology of the individual cells and to the structure of the Northeast U.S. Shelf (NES), a productive and economically important coastal ecosystem. To identify the drivers of seasonal changes in picophytoplankton abundance, I first estimate daily division and loss rates for a nearshore community of picoeukaryotes over a 16-year period. I compare their cell concentrations, vital rates, and responses to environmental variables to those of the cyanobacteria, Synechococcus. Next, to reveal how these dynamics relate to changes in community composition, I analyze 9-years of monthly metabarcoding data and characterize taxonomic variability within the picoeukaryote assemblage. In the second half of this thesis, I explore spatial environmental variability and test the extent to which data from the nearshore observatory are representative of the picophytoplankton communities across the NES. I analyze flow-cytometry data collected from 22 regional research cruises, estimate daily Synechococcus and picoeukaryote division rates from underway data, and describe the distinct depth distributions of the two groups from subsurface samples. The major findings of this thesis are that, across the NES, the picoeukaryotes divide at much higher rates than the more abundant Synechococcus and are subject to greater top-down control from grazing or viral lysis. Both groups are light limited in the fall, temperature limited in the spring, and undergo earlier spring blooms in warmer offshore waters. For Synechococcus, the relationships between cell concentration, division rate and environmental parameters are consistent across the continental shelf, while the picoeukaryote community appears to be nutrient-limited farther from shore. Together, this work creates a detailed picture of the various controls on picophytoplankton abundance within a dynamic coastal ecosystem and advances our understanding of how picophytoplankton communities respond to environmental change.
  • Thesis
    Causes and consequences of pair-bond disruption in socially monogamous species
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-09) Sun, Ruijiao ; Jenouvrier, Stephanie
    Many animals, from crustaceans to humans, form socially monogamous pair-bonds which are maintained during one or more consecutive breeding seasons. However, the ecological consequences of the disruption of monogamous pair-bond have rarely been addressed because it is difficult to estimate the rates and demographic impacts of pairbond disruption (divorce or widowhood). This dissertation investigates the effect of global changes and individual heterogeneity on pair-bond disruption (divorce or widowhood) and their consequences for vital rates and life-history outcomes for socially monogamous species. In Chapter 2 and Chapter 4, analyses of long-term demographicdatasets reveal different patterns of pair-bond dynamics between the population of wandering albatross (Diomedea exulans) breeding in sub-Antarctica and the snow petrel (Pagodroma nivea) breeding in Antarctica. In wandering albatross, divorceis nonadaptive with no improvement in breeding success, while divorce triggered by breeding failure is adaptive in Snow Petrels, resulting in a higher subsequent breeding success. Widowhood rates are male-biased due to lower survival rates of females in wandering albatrosses. In both wandering albatross and snow petrel, remaining single after a pair-bond disruption results in a reduction in individual lifetime reproductive success due to missed breeding seasons. Chapter 3 presents a link between individual personality and divorce in wandering albatrosses demonstrating the important implications of behavior types for the dynamics of social relationships. Personality was measured on a shy-bold continuum, linked to individual risk-taking tendencies, with bolder individuals more likely to take risks and shyer individuals. In wandering albatrosses, shyer males exhibit higher divorce rates than bolder males but no such relationship was found in females. Chapter 4 shows that environmental fluctuations can affect the prevalence of pair-bond disruption in snow petrels, with higher rates of pair-bond disruption under unfavorable environmental conditions. Moreover, the findings suggest a potential increase in the prevalence of pair-bond disruption towards the end of the current century. As a whole, this thesis advances our understanding of the effects of pair-bond disruption on demography which should not be ignored when providing guidelines for the conservation and management of endangered species.
  • Thesis
    Enabling robotic manipulation in remote environments with shared autonomy
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-06) Phung, Amy ; Camilli, Richard ; Williams, Brian
    The evolution of robotics technology continues to facilitate exploration and scientific study in remote environments, enabling research in areas that were previously impossible to reach. Robots operating in space and marine environments encounter similar operational challenges, as both face high operational costs, bandwidth-limited conditions, and natural, unstructured environments where dynamic obstacles might be present. Within the oceanographic domain, conventional deep-sea sampling operations involve remotely operated vehicles (ROVs) equipped with robotic manipulator arms to complete dexterous tasks at depth. While effective, deep-sea ROV operations require specialized instrumentation, highly trained shipboard personnel, and large oceanographic vessels, which make deep-sea samples inaccessible to most. This thesis presents the SHared Autonomy for Remote Collaboration (SHARC) framework, and evaluates its utility within an oceanographic context. By leveraging shared autonomy, SHARC enables shore-side operators to collaboratively carry out underwater sampling and manipulation tasks, regardless of their prior manipulator operations experience. With SHARC, operators can conduct manipulation tasks using natural language and hand gestures through a virtual reality (VR) interface. The interface provides remote operators with a contextual 3D scene understanding that is updated according to bandwidth availability. Evaluation of the SHARC framework through controlled lab experiments indicates that SHARC’s VR interface enables novice operators to complete manipulation tasks in framerate-limited conditions (i.e., <0.5 frames per second) faster than expert pilots using the conventional topside controller. For both novice and expert users, the VR interface also increased the task completion rate and improved sampling precision. During sea trials, SHARC enabled collection of an underwater in-situ X-ray fluorescence (XRF) measurement at more than 1000 meters water depth in the Eastern Pacific with centimeter-level precision by remote scientists with no prior piloting experience. This demonstration provides compelling evidence of SHARC’s utility for conducting delicate operations in unstructured environments across bandwidthlimited communications, which holds relevance for improving operations in other sensitive domains where dexterity is required. SHARC’s ability to relax infrastructure requirements and engage novice shore-side users provides a promising avenue for democratizing access to deep-sea research.
  • Thesis
    Siderophore cycling in the North Pacific Subtropical Gyre
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-06) Li, Jingxuan ; Repeta, Daniel J.
    Across large regions of the surface ocean, the essential micronutrient iron (Fe) limits the growth of microbes, including phytoplankton and heterotrophic bacteria. In order to adapt to chronic low Fe conditions, some heterotrophic bacteria are able to produce siderophores, which are small organic ligands with extraordinarily high stability constant for Fe(III), to facilitate Fe uptake. The recently developed mass spectrometry based techniques allow for the characterization and quantification of siderophores in seawater for the first time, and the use of siderophores as biomarker of Fe limitation on heterotrophic bacteria. However, there has been no depth resolved transect data on siderophores distribution, and the prevalence, turnover, and of controlling factor of siderophores in the ocean remain unknown. In this thesis, I report the distribution of siderophores in the upper 1000 m of the US GEOTRACES GP15 Pacific Meridional Transect. Siderophore concentration ranges from 0-70 pM, and there is no correlation between the concentration of siderophores and dissolved Fe (dFe, <0.2 μm). In contrast, most siderophore hotspots, defined by concentration that is higher than 20 pM, are associated with a dFe:NO3- ratio that is lower than 50 μmol/mol, suggesting that the distribution of siderophores which are N rich molecules might be controlled by dFe:NO3- ratio. In the North Pacific Subtropical Gyre, hotspots of siderophores are found at 200-400 m. In the upwelling regions where nitracline is lifted to shallower depths, the hotspots are also lifted, to up to 20 m. The transect is dominated by marinobactins, a suite of non polar siderophores with a peptidic head group for Fe binding and a fatty acid chain. In addition, we found that the same siderophore could bind either Fe or Al, which is the first time Al-siderophores are reported in seawater samples. The hotspots of siderophore could be explained by either a dynamic turnover, or slow turnover and accumulation. To investigate the turnover of siderophores, I report the measurement of 57Fe uptake from siderophores by heterotrophic bacteria at Station ALOHA, which is representative for the North Pacific Subtropical Gyre - using enclosed bottle incubations. Between 200 and 400 m, we found almost complete consumption of 57Fe-siderophores for all of the siderophores over a period of 5 days. At the end of the incubation, approximately 60% of the added siderophores were present as nonmetallated apo siderophores. The presence of apo siderophores demonstrates that the drawdown of 57Fe-siderophore was largely due to Fe uptake from siderophores. Therefore, heterotrophic bacteria are Fe limited at 200-400 m, which is in accordance with the high concentration of siderophores in the North Pacific Subtropical Gyre. Our results reveal that the zone of potential Fe limitation in the ocean extends well below the euphotic zone and includes oligotrophic gyres that are not classically Fe limited.
  • Thesis
    Examining coral reef ecosystem dynamics using microorganisms and metabolites
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-06) Becker, Cynthia C. ; Apprill, Amy
    Microorganisms and metabolites are foundational to the success and productivity of biodiverse and economically important coral reef ecosystems and are also tightly connected. Metabolites are small organic compounds produced by reef organisms and are the chemical currencies exchanged by unicellular microorganisms (bacteria and archaea) within the seawater. Although central to reef biogeochemical cycling, we still lack fundamental information on the dynamics of these components of reefs. In this dissertation, I analyzed microorganisms in Caribbean coral reef habitats over temporal, spatial and reef health gradients as well as metabolites in a spatial reef study. In Chapter 2, I applied a rapid sequencing methodology to corals afflicted with the lethal stony coral tissue loss disease and identified specific microorganisms which were biological indicators of the disease. In Chapter 3, I investigated the dynamics of microorganisms over short temporal tidal and diurnal cycles, as well as spatially across US Virgin Island (USVI) coastal habitats. In these habitats, I found tidal cycles were driving changes in microbial communities within mangroves, but diurnal patterns were more important in reef habitats. In Chapter 4, I examined reefs over a longer temporal scale by contributing to the building of a 7-year time-series of USVI reef ecology and found that reef water microorganisms were predictive of hurricane and stony coral tissue loss disease impacts. Finally, in Chapter 5, I combined analyses of untargeted and targeted metabolomics, microbial taxa, and functional genes from metagenomics across 300 km of reefs in Florida, in addition to microorganisms in healthy and diseased corals. With this unprecedented combination of ‘omics datasets, I found that biogeographic zones, environmental features, and underlying habitat characteristics were related to microbial and metabolite features in the reef ecosystem. Further, I identified microorganisms and metabolites which were characteristic of specific reef biogeographic zones. Collectively, my work advances our understanding into the dynamics of microorganisms and metabolites in biodiverse coral reef habitats across natural temporal and spatial gradients and in the face of unprecedented stress and disturbance.
  • Thesis
    Impacts of channel curvature on drag, mixing, and stratification in estuaries
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-06) Bo, Tong ; Ralston, David K.
    Estuaries often have sinuous planforms, and channel curvature can lead to distinct flow processes in bends, e.g., secondary circulation and flow separation. An integrated approach combining field observations, idealized modeling, and realistic modeling is used to understand how curvature-induced flow processes affect hydrodynamic drag, salinity mixing, and stratification in estuaries. In the North River (MA, USA), a sinuous, tidally-dominated estuary, drag is observed to be much greater than typically found in straight channel estuaries, and data analysis points to links between the high drag and curvature-induced processes. Idealized models and a realistic North River model are developed to investigate the mechanisms of drag increase in sinuous estuaries. Two key processes are found to dominate. First, flow separation leads to low-pressure eddies on the lee side of bends and thus creates bend-scale form drag. Second, curvature-induced secondary circulation transports higher momentum fluid from the surface toward the bed. Consequently, the near-bed shear and bottom stress are enhanced compared with a logarithmic velocity profile. The form drag due to flow separation and enhanced bed stress due to secondary circulation combine to increase the drag in the North River by a factor of 2-5 compared to the expected values. In addition to increasing the drag, channel curvature also affects the salinity distribution, mixing, and stratification. During ebb tides, secondary circulation in bends interacts with the salinity field to create bottom salinity fronts upstream of bend apexes. Intense mixing occurs at these curvature-induced fronts and leads to overall decreased stratification in sinuous estuaries compared to straight channels. In addition, flow separation in bends and at channel constrictions can create sharp lateral salinity gradients through differential advection during flood tides, and the resulting baroclinic forcing influences secondary circulation. Surface convergence fronts are generated at bends and constrictions as secondary circulation interacts with the laterally sheared flow, resulting in intensified mixing near the fronts. This thesis advances our understanding of how flow curvature affects the hydrodynamics, salinity, and mixing in estuaries with complex topographic features found in natural systems.
  • Thesis
    Modeling ocean transport and its biogeochemical impacts at global, regional, and sub-meso scales
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-06) He, Jing ; Mahadevan, Amala
    Improving understanding of how carbon is cycled through the ocean is crucial for predicting, mitigating, and adapting to climate change. This thesis explores how horizontal and vertical currents at different scales impact biogeochemical cycling through the redistribution of tracers such as alkalinity, nutrients, and carbon. Starting at the large scale in Chapter 2, we use a mesoscale-permitting global ocean model to investigate ocean alkalinity enhancement as a negative emissions technology. We find that local ocean dynamics are crucial for determining optimal alkalinity addition locations that maximize carbon removal, while minimizing adverse ecological impacts. Among the best locations identified are coastal upwelling systems, which are also regions of high primary productivity due to the large influx of nutrients to the surface. We take a closer look at coastal upwelling systems in Chapter 3 to identify the dynamics that impact source waters of steady-state upwelling at a regional scale, and we propose a scaling relation in which wind stress and stratification sets the upwelling source depth. Looking more closely at an upwelling front in a high-resolution submesoscale-permitting model, we see enhanced vertical velocities that reach 𝒪(100 m d−1). These submesoscale vertical velocities can enhance vertical transport, but they are very difficult to measure. In Chapter 4, we demonstrate the possibility of diagnosing the 3D submesoscale vertical velocity field from remotely-observable surface ocean observations with machine learning, which motivates future satellite missions for high-resolution remote-sensing of the surface ocean. Finally in Chapter 5, we evaluate the importance of resolving smaller scale submesoscale dynamics on the vertical transport of nutrient and phytoplankton carbon biomass in upwelling systems.
  • Thesis
    Physical and biological processes at the Middle Atlantic Bight shelf-break front
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-02) Hirzel, Andrew ; McGillicuddy, Dennis J.
    The Middle Atlantic Bight (MAB) is a highly productive ecosystem, supporting several economically important commercial fisheries. Chlorophyll enhancement at the MAB shelf-break front has been observed only intermittently, despite numerous studies that suggest persistent upwelling at the front. High resolution cross-frontal transect crossings were collected from three two-week cruises in April 2018, May 2019, and July 2019. Chapter 2 focused on applying a novel method of classifying planktonic images taken by a Video Plankton Recorder to enable processing of the large volumes of data collected with the instrument. Chapter 3 investigated cross-frontal trends by temporally averaging in both Eulerian and frontally-aligned coordinates. For April 2018, transient chlorophyll enhancement was seen at the front in individual transects and within the frontally-aligned mean transect, but not within the Eulerian mean transect. The Eulerian mean for May 2019 showed chlorophyll enhancement as a result of frontal eddies, which were further explored in chapter 4. No frontal enhancement was observed in July 2019. The frontal eddies observed in May 2019 were simulated using an idealized model, which showed that upwelling occurred within both of the frontal eddies, despite having opposite rotational directions. This result was consistent with nutrient enhancement observed within the centers of both eddies. Biological enhancement within each eddy was observed, which may have been a result of advection from source waters and/or a local response to upwelled nutrients. The influence of frontal variability and frontal eddies on nutrients and plankton at the front argues for the necessity for 3-D models to fully explain frontal behavior and its effects on biological responses.
  • Thesis
    Lifelong, learning-augmented robot navigation
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-02) Doherty, Kevin J. ; Leonard, John J.
    Simultaneous localization and mapping (SLAM) is the process by which a robot constructs a global model of an environment from local observations of it; this is a fundamental perceptual capability supporting planning, navigation, and control. We are interested in improving the expressiveness and operational longevity of SLAM systems. In particular, we are interested in leveraging state-of-the-art machine learning methods for object detection to augment the maps robots can build with object-level semantic information. To do so, a robot must combine continuous geometric information about its trajectory and object locations with discrete semantic information about object classes. This problem is complicated by the fact that object detection techniques are often unreliable in novel environments, introducing outliers and making it difficult to determine the correspondence between detected objects and mapped landmarks. For robust long-term navigation, a robot must contend with these discrete sources of ambiguity. Finally, even when measurements are not corrupted by outliers, long-term SLAM remains a challenging computational problem: typical solution methods rely on local optimization techniques that require a good “initial guess,” and whose computational expense grows as measurements accumulate. The first contribution of this thesis addresses the problem of inference for hybrid probabilistic models, i.e., models containing both discrete and continuous states we would like to estimate. These problems frequently arise when modeling e.g., outlier contamination (where binary variables indicate whether a measurement is corrupted), or when performing object-level mapping (where discrete variables may represent measurement-landmark correspondence or object categories). The former application is crucial for designing more robust perception systems. The latter application is especially important for enabling robots to construct semantic maps; that is, maps containing objects whose states are a mixture of continuous (geometric) information and (discrete) categorical information (such as class labels). The second contribution of this thesis is, a novel spectral initialization method which is efficient to compute, easy to implement, and admits the first formal performance guarantees for a SLAM initialization method. The final contribution of this thesis aims to curtail the growing computational expense of long-term SLAM. In particular, we propose an efficient algorithm for graph sparsification capable of reducing the computational burden of SLAM methods without significantly degrading SLAM solution quality. Taken together, these contributions improve the robustness and efficiency of robot perception approaches in the lifelong setting.
  • Thesis
    Mass transfer and chemical interactions in subduction zones
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-02) Codillo, Emmanuel A. ; Le Roux, Véronique ; Klein, Frieder
    Subduction zones are important sites of material recycling on Earth, with volatiles playing key roles in mass transfer processes and magma formation. This thesis investigates outstanding questions associated with a continuum of interrelated processes that occur as oceanic plates descend in subduction zones by integrating petrological and geochemical constraints from exhumed high-pressure rocks and erupted arc magmas, high pressure-temperature laboratory experiments, and thermodynamic calculations. Chapters 2 and 3 investigate the fluid-mediated reactions between mafic and ultramafic rocks at conditions relevant to the slab-mantle interface and show that Mg-metasomatism of mafic rocks to form chlorite-rich assemblages is favored and is likely more pervasive in subduction zones than in oceanic settings. Contrary to common belief, talc is unlikely to form in high abundance in ultramafic rocks metasomatized by Si-rich slabderived fluids. This means that talc-rich assemblages formed via Si-metasomatism along the slabmantle interface are less likely to be playing prominent roles in volatile transport, in facilitating slow-slip events, and in controlling the decoupling-coupling transition of the plate interface. Chapter 4 experimentally investigates the phase equilibria, melting, and density evolution of mélange rocks that formed by mixing and fluid-rock interactions. Results show that melting of mélanges is unlikely to occur along slab-tops at pressures ≤ 2.5 GPa. Accordingly, diapirism into the hotter mantle wedge would be required to initiate melting. The density contrast between mélanges and the overlying mantle would allow for buoyancy-driven diapirism at relatively low pressures and melting could subsequently occur in the hotter mantle wedge during ascent. However, diapir buoyancy may be limited at higher pressures due to the formation of abundant garnet especially in mélange rocks with peraluminous composition. Chapter 5 experimentally investigates the compositions of melts and mineral residues from melting of a mantle wedge hybridized with small amounts of mélange rocks to simulate an end-member scenario where solid mélange diapirs dynamically interact with the mantle wedge. Results from laboratory experiments show that melting of a mélange-hybridized mantle wedge can produce melts that display compositional characteristics similar to arc magmas. Finally, Chapter 6 presents new interpretations on the evolution of slab-to-mantle transfer mechanisms from subduction initiation to arc maturity. Analyses of published magma compositions from global arcs reveal that melting of mélange plays an increasingly important role in magma formation as slab-tops cool and arcs mature over time. This trend is attributed to the deepening of the decoupled plate interface during subduction where mélange zones can form more extensively and contribute to the melting process more significantly. Taken together, this thesis highlights (i) the dynamic connection between mechanical mixing of different lithologies and fluid-rock interactions along the slab-mantle interface, (ii) how these processes modify the petrophysical and geochemical properties of subducted materials, and (iii) how these processes collectively influence the mechanisms of slabto-mantle transfer, elemental cycles, and the formation of arc magmas worldwide.
  • Thesis
    Marine parasites in island-like disturbed habitats
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-02) Dykman, Lauren ; Mullineaux, Lauren S.
    Parasites are taxonomically and functionally diverse members of biological communities, and can play key roles in species interactions, community structure, and ecosystem functioning. For their reliance on host species, parasites are theorized to be particularly sensitive to disturbances that alter host diversity and abundance, especially in isolated habitats, which present challenges to introduction and establishment. In this thesis, I investigate habitat isolation and disturbance as drivers of parasite diversity, with an emphasis on parasite life history strategies related to colonization and persistence. I focus on an island-like, frequently disturbed habitat, deep sea hydrothermal vents at 9°50’N on the East Pacific Rise, to explore the boundaries of parasite persistence in an extreme environment. First, I analyze recovery in the vent community for 11 years after a catastrophic eruption in 2006 to test successional hypotheses in a new setting with distinct fauna and a chemosynthesis-based food web. Second, I compare parasite diversity at isolated, disturbed vents to marine ecosystems that are similarly isolated but undisturbed (atoll sandflat) and both well connected and undisturbed (kelp forest). Overall, parasite diversity within host species was not significantly lower at vents, but the vent community had many fewer parasite species because there are fewvertebrate predator species (fish). Parasites with indirect (multi-host) life cycles were relatively diverse in the disturbed environment, which contradicts expectation based on theory. To explore this further, I investigate the three-host life cycles of trematodes at vents, whichwas the most diverse and abundant parasite taxon. All life stages of the trematode life cyclewere discovered in vent fauna and several taxawere traced across multiple life stages via morphology and genetics. Finally, I use a computational model to investigate how different parasite strategies (colonization capability and impact on hosts) contribute to parasite success under a range of disturbance conditions in island habitats. Parasites that reduce host reproduction reached higher densities than parasites that cause mortality across all disturbance frequencies explored, and disturbance facilitated the evolution of more virulent parasites. These studies demonstrate that life history traits and the ability to adapt allow diverse parasite taxa to persist in isolated, ephemeral environments.
  • Thesis
    Chemical controls on the cycling and reactivity of marine dissolved organic matter
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-02) Granzow, Benjamin N. ; Repeta, Daniel J.
    Marine dissolved organic matter (DOM) is an actively cycling reservoir of carbon containing thousands of unique compounds. To describe the complex dynamics that govern the biological transformation and decomposition of compounds in this molecular black box, models of DOM reactivity use chemical characteristics, as well as environmental parameters, to describe trends in the turnover time of classes of DOM. In this thesis, I describe two projects that examine hypotheses regarding the turnover of two classes of DOM. In the 1st project, I test the assumption made by the size–reactivity continuum hypothesis that high molecular weight (> 1 kDa) DOM (HMWDOM) represents a diagenetic intermediate between large labile material and small recalcitrant compounds. Size-fractions of HMWDOM were collected using size-exclusion chromatography, and the changes in MW and chemical composition of the fractions were studied using diffusion-ordered spectroscopy. The size fraction carbon isotopic values were correlated with the proportion of humic substances in the fractions. Through linear modeling, the apparent radiocarbon ages of the two major components of HMWDOM were determined to be 1-3 yrs and 2-4 kyrs, respectively. Combined with the measurements of MW distribution this work demonstrates that HMWDOM is composed of two components that have contrasting decomposition pathways in the ocean. HMWDOM cannot be treated as a single DOM pool when incorporated into models of DOM diagenesis. The 2nd project in this dissertation examines the remineralization of phosphonates, compounds with a direct C-P bond, in the lower euphotic zone using a newly developed fluorescent assay, which measures the activity of carbon-phosphorus lyase. C-P lyase activity (CLA) profiles from the North Pacific Subtropical Gyre (NPSG) showed a sharp activity maximum near the deep-chlorophyll maximum (DCM). High-resolution nutrient measurements suggest that this subsurface CLA maximum is the result of a high nitrate flux at the top of the nitracline. The composition of particulate-P through the euphotic zone was also examined. While phosphonates were not detected in suspended particles, a significant amount of aminoethylphosphonate was measured in sinking material, suggesting eukaryotic material may be an important source of phosphonates to the ocean.
  • Thesis
    Quantifying pelagic primary production and respiration via an automated in-situ incubation system
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-02) Chen, Solomon ; Long, Matthew H.
    Pelagic photosynthesis and respiration serve critical roles in controlling the dissolved oxygen concentration (DO) in seawater. The consumption and production via pelagic primary production are of particular importance in surface ocean and in shallow aquatic ecosystems where photosynthetically active radiation (PAR) is abundant. However, the dynamic nature and large degree of heterogeneity in these ecosystems pose substantial challenges for providing accurate estimates of marine primary production and metabolic state. The resulting lack of data in these systems hinders efforts in scaling and including primary production in predictive models. To bridge the gap, we developed and validated a novel automated water incubator that measures in-situ rates of photosynthesis and respiration. The automated water incubation system uses commercially available optodes and microcontrollers to record continuous measurements of DO within a closed chamber at desired intervals. With fast response optodes, the incubation system produced measurements of photosynthesis and respiration with hourly resolution, resolving diel signals in the water column. The high temporal resolution of the timeseries also enabled the development of Monte-Carlo simulation as a new data analysis technique to calculate DO fluxes, with improved performance in noisy timeseries. Deployment of the incubator was conducted near Ucantena Island, Massachusetts, USA. The data captured diel fluctuations in metabolic fluxes with hourly resolution, allowed for a more accurate correlation between oxygen cycling and environmental conditions, and provided improved characterization of the pelagic metabolic state.
  • Thesis
    Distributions and perturbations of the marine dissolved cobalt cycle in a changing ocean
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-02) Chmiel, Rebecca ; Saito, Mak A.
    Cobalt is a necessary nutrient for many marine phytoplankton, but its hybrid-type nature results in small marine inventories that make it one of the scarcest bioactive trace metals in the oceans. This study examines the marine dissolved cobalt cycle in two regions: the Pacific Ocean and Antarctic coastal seas. In the North Pacific, elevated cobalt stoichiometries among phytoplankton were linked to nitrogen, iron and phosphate stress protein biomarkers at the boundaries of oceanographic provinces and upwelling zones, providing insight into the flexibility of cobalt stoichiometry. In both regions, perturbations to the marine cobalt cycle were either predicted or observed; in the equatorial Pacific, the dissolved cobalt inventory was predicted to increase by up to 28% due to the expansion of oxygen minimum zones in a warmer ocean, while in the Antarctic, melting ice shelves have the potential to shift the nutrient regime from iron limitation towards zinc and vitamin B12 limitation, resulting in higher cobalt demand and a lower dissolved cobalt inventory. When the global cobalt cycle was estimated throughout four of Earth’s systems (the lithosphere, biosphere, hydrosphere and the anthroposphere – the human environment), it was determined that the scale of the cobalt flux through the anthroposphere is only one order of magnitude lower than the inventory of the entire hydrosphere (10(9) mol Co yr-1 and 10(10) mol Co, respectively), revealing a vulnerability to anthropogenic perturbation of the marine cobalt inventory through human mining, use and disposal of cobalt if appropriate pollution abatement, disposal and recycling infrastructure is not established. In light of observed and predicted changes to cobalt biogeochemistry, this research suggests that the marine cobalt cycle is particularly vulnerable to anthropogenic perturbation from both global climate change and pollution due to its low ocean inventory and interconnection to other nutrient biogeochemical cycles.
  • Thesis
    Perceive, predict, and plan: robotic expeditionary science in oceanic spatiotemporal fields
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-02) Preston, Victoria Lynn ; Roy, Nicholas ; Michel, Anna P. M.
    An improved understanding of our ocean would allow us to characterize the largest habitable biosphere on planet Earth, quantify the geochemical processes that control Earth’s climate, and develop responsible regulations for controlling the natural resources stored in its depths. Expeditionary science is the art of collecting in situ observations of an environment to build approximate models of underlying properties that move us towards this understanding. Robotic platforms are a critical technology for collecting observations of the ocean. Depth-capable autonomous underwater vehicles (AUVs) are commonly used to build static maps of the seafloor by executing pre-programmedsurveys. However, there is growing urgency to generate rich data products of spatiotemporal distributions that characterize the physics and chemistry of the deep ocean biogeosphere. In this thesis, the problem of charting dynamic deep sea hydrothermal plumes with depth-capable AUVs is investigated. Effectively collecting samples of geochemical plumes using the operationally preferred strategy of pre-specifying surveys requires access to a dynamics model of the advective currents, bathymetric updrafts, and turbulent mixing at a hydrothermal site. In practice, however, access to this information is unavailable, imperfect, or only partially known, and so a model of plume dynamics must be inferred from observations and subsequently leveraged to improve future sampling performance. As most in situ scientific instruments yield point-measurements, considerable uncertainty is placed over the form of the dynamics in purely data-driven solutions. Challenges related to planning under uncertainty for geochemical surveys in the deep ocean are addressed in this thesis by embedding scientific knowledge as a strong inductive prior for tractable model learning and decision-making. Algorithmic contributions of this thesis show how plumes can be perceived from field data, their fate predicted far into the future (e.g., multiple days), and informative fixed trajectories planned which place an AUV in the right place at the right time. Scientific assessment of observational data collected with AUV Sentry during field trials in the Guaymas Basin, Gulf of California are interwoven with algorithmic analyses, demonstrating how intelligent perception, prediction, and planning enables novel insights about hydrothermal plumes.
  • Thesis
    The biogeochemistry of methane isotopologues in marine and lacustrine sediments
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-02) Lalk, Ellen ; Ono, Shuhei
    Methane is a globally significant greenhouse gas, energy resource, and it is a product and reactant of microbial metabolisms. Multiple sources and sinks of methane can be challenging to distinguish from each other, thus complicating the understanding of methane budgets and the effects of microbes on mediating Earth’s carbon cycle. The relative abundances of methane isotopologues (e.g., 12CH4, 13CH4, 12CH3D, and 13CH3D) record process-based information about the formation conditions, transport, and fate of methane, and in select environments can serve as a temperature proxy. This geochemical tool is herein applied to methane from marine and lacustrine sediments to test assumptions about prevailing mechanisms of its formation and consumption in these settings. This thesis describes 1) three studies about biogeochemical insights gained by quantifying the relative abundance of clumped methane isotopologue, 13CH3D, in samples from marine and lacustrine sediments, and 2) one foray into method development to improve the quantification of methane in these environments. Chapter 2 presents a global survey of marine gas hydrates where isotope-based temperatures are used to assess whether linkages between methane sources and seepage-associated seafloor features match putative geologic models. Chapter 3 describes two kilometer-scale profiles of methane isotopologues from marine sediments, where the relationship between expected sediment temperature and isotope-based temperature is used to evaluate the temperature limit of microbial processing and abiotic re-equilibration mechanisms. Chapter 4 reports the largest set of methane isotopologue data from ebullition in a single lake basin, which is used to gauge the relative importance of aerobic and anaerobic methane oxidation in the study site and recommend a general sampling strategy to constrain methane source signatures in similar lake settings. Chapter 5 explains the development of a method to quantify the in situ concentration of methane based on ratios of dissolved gases, and its comparison to four other methane quantification methods for surface sediments from marine cold seeps. The findings from this research contribute to ongoing efforts to understand the sedimentary carbon cycle and microbial activity in remote environments.
  • Thesis
    Developing in situ instrumentation to monitor anthropogenic change
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-02) Colson, Beckett C. ; Michel, Anna P. M.
    To predict and mitigate anthropogenic impacts on the ocean, we must understand the underlying systems that govern the ocean’s response to inputs (e.g. carbon dioxide, pollutants). Analytical models can be used to generate predictions and simulate intervention strategies, but they must be grounded with empirical observations. Unfortunately, there exists a technological gap: in situ instrumentation is often lacking or nonexistent for key parameters influenced by anthropogenic inputs. While discrete bottle samples can be collected and analyzed for these parameters, their limited spatiotemporal resolution constrains scientific inquiry. To help fill the technological gap, this dissertation presents the development of instrumentation for the ocean inorganic carbon system and microplastics. The first few chapters present the development process of CSPEC, a deep-sea laser spectrometer designed to measure the ocean carbon system through alternating measurements of the partial pressure of carbon dioxide (pCO2) and dissolved inorganic carbon (DIC). CSPEC uses tunable diode laser absorption spectroscopy (TDLAS) to measure the CO2 content of dissolved gas extracted via a membrane inlet. Chapter 2 derives membrane equilibration dynamics from first principles, thus enabling informed design decisions. The analytical results showed that cross-sensitivity to other dissolved gases can be introduced by the equilibration method, regardless of the specificity of the gas-side instrumentation. A new method, hybrid equilibration, leverages the membrane equilibration dynamics to improve time response without incurring cross-sensitivity. Chapter 3 presents POCO, a surface pCO2 instrument that employs TDLAS and a depth-compatible membrane inlet. Through laboratory and field-testing, POCO demonstrated that hybrid equilibration overcame the gas flux limitation of deep-sea membrane inlets. Chapter 4 presents CSPEC, which successfully mapped the carbon system near different hydrothermal features at 2000 m in Guaymas Basin, becoming one of the first DIC instruments field-tested at depth. Chapter 5 introduces impedance spectroscopy for quantifying microplastics directly in water. Microplastics were successfully counted, sized, and differentiated from biology in the laboratory: a step toward in situ quantification. The analytical tools and measurement systems presented in this dissertation represent a significant step towards increasing the spatiotemporal resolution of carbon system and microplastic measurements, thus enabling broader scientific inquiry in the future.