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 1074
  • Thesis
    Distribution and behavior of trace metals in the subterranean estuary of an Arctic coastal lagoon
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-02) Schaal, Isabel V. ; Charette, Matthew A.
    Subterranean estuaries (STEs) can be an important location for biogeochemical reactions that may alter concentrations of chemical constituents of groundwater. With warming in the Arctic and the subsequent permafrost thaw, the relative importance of submarine groundwater discharge (SGD) to ocean chemical budgets will grow. In this study, we examined the distribution of select trace metals (Fe, Mn, V, U, Mo and Ba) in the STE, lagoon surface waters, and coastal sediments of Simpson Lagoon along the Beaufort Shelf of Alaska. This location is unique among studies as the STE consists of organic-rich sediments. Samples were collected over two years and throughout seasonal water conditions, including the melting, open-water, and freeze-up periods. Fe, Mn, V, and Ba mainly exhibited non-conservative additions within the estuary, with Fe concentrations being some of the highest among groundwater studies. U exhibited both non-conservative removal and addition in the estuary, and Mo exhibited mainly removal. In the lagoon, non-conservative addition of U allowed for the calculation of an SGD flux. This flux, along with a Ra-derived flux, was used to estimate metal fluxes into the lagoon. Fluxes for all metals were similar to or greater than river flux estimates in all months except for June, when SGD was likely nonexistent. These fluxes can be used to assess SGD impact on the coastal Arctic; however, for reactive metals, processes in the lagoon may continue to alter metal concentrations before mixing with the greater Arctic Ocean. This study provides some of the first estimates of trace metal concentrations and fluxes within Arctic subterranean estuaries and exhibits the importance of considering SGD when assessing metal input to the coastal Arctic.
  • Thesis
    Tracking Sargassum in the Caribbean: the design, deployment, and validation of a low-cost surface drifter
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-09) Pixa, Chase R. ; Michel, Anna P. M.
    This thesis presents the development of a low-cost surface drifter designed to track and monitor the abundant Sargassum seaweed in the Caribbean. The phenomenon of the Great Atlantic Sargassum Belt (GASB), inundating coastlines in the northern equatorial Atlantic and Gulf of Mexico, has raised concerns due to its negative impacts on marine ecosystems, coastal communities, and tourism. The introduction section provides background information on the arrival of Sargassum in the Caribbean and its ecological significance. One of the key motivations behind the drifter’s development is the potential use of Sargassum as a feedstock for biofuel production. A comprehensive literature review assesses the feasibility of utilizing Sargassum for biofuels, taking into account infrastructure, economics, and scientific challenges. Although Sargassum holds promise as a renewable biomass source, several hurdles must be addressed, including consistent biomass production, processing techniques, and lack of industrial-scale biofuel plants using macroalgae. The core of the thesis is dedicated to the surface drifter development and field trials. Iterative trials are conducted to design a drifter that entangles with Sargassum, providing in situ movement data to complement remote sensing and modeling efforts. The drifter’s design is optimized to mimic Sargassum rafts, and successful deployments off the coast of Puerto Rico demonstrate the potential for effective tracking. The drifter’s association with Sargassum rafts is validated through satellite imagery and wind and current data. In parallel, a low-cost chemical sensing drifter is introduced in the thesis. This advanced drifter iteration incorporates self-validation mechanisms for Sargassum entanglement and enables the measurement of dissolved gases. The chemical sensing capabilities enhance the understanding of Sargassum rafts’ dynamics and their environmental impact. The thesis concludes by summarizing the key findings and implications of the research. The low-cost surface drifters have shown promising potential for tracking Sargassum and studying its movement patterns within the GASB. The drifter’s effectiveness in entangling with Sargassum provides valuable insights into the seaweed’s behavior and could help improve existing remote sensing and modeling techniques.
  • Thesis
    Acoustic minimization of Ocean Twilight Zone Vehicle, Mesobot
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-09) Davis, Cameron J. ; Yoerger, Dana R.
    The OTZ is defined as the region of the water column between 200 and 1,000 meters in depth. It plays a vital role in the global carbon cycle, pushing carbon from the surface layer into the deep ocean. It has a very diverse population of fauna, known and unknown, that migrate up and down the water column to feed and reproduce. The migration pattern occurs based on the amount of radiated sunlight into the water column. The mid-water column vehicle, Mesobot, was designed to mimic the migration patterns of mesopelagic organisms. Unmanned Underwater Vehicles (UUVs) have become a staple of ocean exploration for years, going where man is not able to. Although much quieter than noise from shipping traffic, the noise radiated from Mesobot could present potential for error in observation, tracking, and sampling. In this thesis, I have analyzed the effect of commutation methods and propeller design on the acoustic noise radiated from a single BlueRobotics T200 thruster. The propeller design choices are a standard three-blade propeller and a three-blade toroidal propeller. The commutation methods analyzed are trapezoidal control and field-oriented control. After analyzing four different alternatives, quantitative evidence was found to recommend using field-oriented control as the commutation scheme to minimize the radiated noise from the thrusters on Mesobot. The radiated noise from the thurster was dominated by motor noise, and no conclusive evidence was found to recommend the three-blade propeller over the toroidal propeller.
  • Thesis
    Remote sensing of ice dynamics in the Beaufort Sea
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-09) Flores, Matthew A. ; Maksym, Ted
    Arctic summer sea ice extent has undergone dramatic declines over the past several decades, particularly in the Beaufort Sea. The comprehension of the sea ice decline requires an understanding of the annual sea ice retreat during the summer melt season. While there are observations of the seasonal sea ice retreat, there is no accurate data on the evolution of sea ice thickness during the melt season. This thesis presents an analysis of sea ice in the Beaufort Sea using available sea ice freeboard data taken from NASA’s Ice, Cloud, and Elevation Satellite-2 (ICESat-2) mission. Through tracking bi-weekly changes in freeboard for Lagrangian tracked parcels of sea ice, the patterns of sea ice retreat are examined from 01 June – 30 September for 2020-2022. This method provides realistic patterns of sea ice thinning through mid-summer, with the most pronounced thinning occurring in the eastern Beaufort Sea. By September, freeboard changes are difficult to detect, with some subregions showing an increase in freeboard (thickening). The increase in freeboard likely reflects uncertainty due to changes in the distribution of ice types, particularly preferential disappearance of thinner ice but an also reduced rate of thinning. Although these results are preliminary, suggest that ICESat-2 can be used to track seasonal changes during the melt season to help identify trends and drivers of sea ice retreat. Further work is necessary to improve these results, especially in understanding how different ice types evolve. Other remote sensing data or in-situ observations are needed to reduce the uncertainty in the subregional estimates of ice melt.
  • Thesis
    Inferences on the influences of age & porosity on oxidative weathering of seafloor massive sulfide deposits at the endeavour segment of the Juan de Fuca Ridge
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-02) Herrera, Erica L. ; Hansel, Colleen M.
    Hydrothermal activity at mid-ocean ridge spreading centers occurs during the formation of new oceanic crust and is responsible for the accumulation of mineral deposits comprised mainly of inorganic metal sulfides that precipitate from mixtures of seawater and high-temperature, sulfide-rich, oxygen-poor vent fluid. These mineral aggregates are known as seafloor massive sulfide deposits and occupy unique biogeochemical niches that remain largely unexplored. Upon the cessation of hydrothermal activity, massive sulfide deposits undergo alteration via both biotically- and abiotically-mediated geochemical reactions. These processes are collectively described as oxidative weathering. While the observed textures of these deposits suggest significant variation in weathering rates, neither the causes of this variation nor the drivers that govern biogeochemical oxidation of massive sulfides are well-characterized. To begin to describe the mechanisms that dictate these processes, massive sulfide samples were collected from deposits along the Endeavour Segment of the Juan de Fuca Ridge. Coupled synchrotron-based X-ray Absorption Near Edge Spectroscopy (XANES) and X-Ray Fluorescence (XRF) microscopy were utilized to create comprehensive redox maps that allow for characterization of the localized redox environment and identification of weathering products. These techniques are a powerful and so far underutilized tool with which to examine the geochemical landscapes of seafloor massive sulfide deposits. Mineral identifications and spatial distributions were corroborated with optical microscopy and X-Ray Diffraction (XRD). The Juan de Fuca Ridge massive sulfide samples are composed of iron-sulfide phases, primarily pyrite (FeS2), with minor amounts of other metal-bearing sulfides, such as sphalerite ((Zn,Fe)S2) , wurtzite ((Zn,Fe)S2), and cubanite (CuFe2S3). The samples contain rinds comprised of oxides and (primarily iron-bearing) clays that occur along massive sulfide exteriors and within pore channels. Greater amounts of secondary oxides and clays are observed concurrent with increased porosity and internal pore distribution and are inferred to be products of weathering. This study contributes to current understanding of the mineralogy and composition of seafloor massive sulfide deposits and provides new insight into relationships between age, porosity, and oxidative weathering.
  • Thesis
    Energetics and similarity theory in the wave-affected atmospheric boundary layer
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-02) Keefe, Oaklin R. ; Zippel, Seth F. ; Scully, Malcolm E.
    Here we examine the magnitude of the production and consumption terms of the turbulence kinetic energy (TKE) budget equation using observational data. This data is from two periods, each containing two months of continuous observations collected at the Woods Hole Oceanographic Institution’s (WHOI) Buzzards Bay Air-Sea Interaction Tower (BB-ASIT). BB-ASIT held a vertical co-located array of over 30 sensors spanning the ocean and the atmosphere, and twelve of those sensors are used in this analysis to examine atmospheric fluxes occurring within the wave-affected boundary layer (WBL). Using Monin-Obukhov (MO) Similarity Theory, we analyzed the fluxes and energy balance under different atmospheric stability conditions. Through a comparison of non-dimensional data with the universal functions given in Edson and Fairall (1998), we determined that the Edson and Fairall (1998)’s functions likely overestimate the shear and dissipation occurring within 5 m of the sea surface. Additionally, after quantifying the TKE production (shear production and buoyancy) and the TKE consumption (dissipation rate) we found that the production of TKE often exceeds the consumption of TKE in the WBL during high wind conditions, resulting in a dissipation deficit. We proposed wave-coherent pressure-work as another TKE consumption term that could offset this deficit, as theorized by Janssen (1999), and found that the wavecoherent pressure-work consumes a significant amount of TKE, but not enough to fully close the TKE budget equation. Future works should continue to examine how wave-coherent processes may contribute to fully closing the TKE budget equation within the WBL.
  • Thesis
    Automatic baleen whale detection and 2D localization using a network of unsynchonized passive acoustic sensors
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-02) Goldwater, Mark H. ; Bonnel, Julien ; Zitterbart, Daniel
    Underwater acoustics is a powerful tool for learning about the ocean’s soniferous marine life. However, most modern acoustic sensing systems consist of expensive arrays of timesynchronized recorders which require a crewed research vessel and significant expertise to deploy, operate, and recover. Recently, there has been a growing corpus of research related to algorithms for low-cost and accessible acoustic hardware. Deep learning methods have shown great promise when applied to underwater acoustics inverse problems. While many signal processing or physics-based algorithms exhibit long run times and require manual labor to extract signals of interest, tune parameters, as well as visually verify the results, an appropriately trained neural network can quickly process data with no human supervision. Both low-cost passive acoustic monitoring (PAM) sensing platforms and algorithms that can analyze massive amounts of raw data are critical to accessible and scalable approaches in ocean acoustic monitoring. This thesis presents a method for detection and 2D (latitude-longitude) localization of underwater acoustic sources without requiring synchronized sensors. The signals of interest here are the dispersive low-frequency impulsive gunshot vocalizations of North Pacific and North Atlantic right whales (NPRWs, NARWs). In shallow-water channels, the timefrequency representation of the received signal is strongly dependent on source-receiver range, making these impulses ideal candidates for range-based localization. The first step in the localization pipeline uses a temporal convolutional network (TCN) to simultaneously detect gunshot vocalizations and predict their ranges. Trained on spectrograms of synthetic data simulated in a variety of environments, the TCN is applied to PAM data from moorings in the Bering Sea. Gunshots are detected with high precision, and the range estimates are comparable to those estimated using traditional physics-based processing. Both methods use a minimal set of a priori environmental information including water column depth, sound speed, and density. Depending on the sensor layout, the TCN may need to scan large windows of data, so the number of unique acoustic sources is unknown. To automatically associate and localize range measurements, the proposed method seeks subsets of measurements across unique sensors which are internally consistent. For every considered measurement subset, locations are estimated with single constituent measurements left out and checked to be sufficiently close to the excluded measurement’s set of potential locations. If a measurement subset is entirely consistent in this manner, the measurements are added as neighboring nodes in a graph-based representation, and strongly connected components are used to determine data associations and calculate the final source location estimates. Informed by the methods developed in this thesis, an array of low-cost TOSSIT moorings was deployed in Cape Cod Bay and used to collect experimental PAM data. The localization results are comparable to another similar physics-based inversion approach. Overall, this thesis aims to fill a gap in acoustic data processing methods where data from a low-cost network of unsynchronized acoustic sensors are fused to localize acoustic sources. The presented methods and data processing pipeline demonstrate the great potential of low-cost acoustic sensing systems.
  • Thesis
    An assessment of the biodistribution, persistence, and health impacts of microplastics and nanoplastics in fish
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024) Pitt, Jordan A. ; Hahn, Mark ; Aluru, Neelakanteswar
    Microplastics have been found in a diverse range of organisms across trophic levels. Although organisms are continuously exposed to microplastics (1 μm - 5 mm) and nanoplastics (< 1 μm), the risk of these exposures are not understood. A risk assessment for microplastics and nanoplastics is urgently needed, but first more information is required on the biodistribution, persistence, and subsequent health impacts of microplastics and nanoplastics in organisms. My thesis addresses these key knowledge gaps through a combination of environmental measurements and laboratory experiments. I first reviewed the microplastics literature to determine the state of knowledge regarding the trophic transfer, bioaccumulation, and biomagnification of microplastics and nanoplastics. I found that in most of the literature there was clear evidence of trophic transfer, equivocal evidence for bioaccumulation, and no evidence for biomagnification. I drew upon these noted knowledge gaps to guide my measurements of microplastic abundance in Atlantic killifish (Fundulus heteroclitus) captured near Falmouth, MA. I found that microplastics were both more abundant and diverse in the GI tract, compared to those in the muscle. Small microplastics, which are often not analyzed, were the most abundant, and I found evidence that these small microplastics may bioaccumulate. Following this, I compared the impact of the route of exposure on the biodistribution and persistence of polystyrene nanoplastic particles (50 nm and 500 nm) in zebrafish (Danio rerio). I found that exposure routes other than an oral exposure (i.e. dermal, respiratory) contribute to nanoplastic biodistribution, and that the nanoplastics were not persistent in tissues 2 days after exposure. I then examined the impact of a 50 nm polystyrene nanoplastic exposure on cardiovascular development and function in larval zebrafish. Larvae exposed to high concentrations of nanoplastics had significant defects in cardiovascular function. Altogether, my research indicates that nanoplastics and small microplastics might be slightly bioaccumulative in tissues, but that 50 nm polystyrene nanoparticles are not hazardous except in high concentrations; however, nanoplastics and microplastics are diverse. Future work should focus on expanding our knowledge of the toxicity of different types of plastic. This work lays the foundation for future risk assessments for microplastics and nanoplastics.
  • Thesis
    Broadband acoustical scattering in coastal environments: application to gelatinous organisms
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-02) Kahn, Rachel E. ; Lavery, Andone C.
    Broadband acoustical technology revolutionized our ability to explore, monitor, and operate in the ocean. While strides have been made in numerous physical and biological applications, there remain many standing scientific questions well suited to broadband approaches. Physics-based sound scattering models allow us to interpret and draw quantitative observations from measurements. Such models have been developed and used to assess the biomass of many types of marine organisms of ecological significance, but we lack rigorous scattering models for gelatinous organisms despite their possibly accounting for a significant proportion of global marine biomass. Additionally, acoustical techniques for characterizing microbubble populations have been established for decades, yet little is known about the spectral characteristics of dense microbubble clouds associated with estuarine tidal fronts. These bubbles facilitate air-sea gas exchange and could interfere with acoustical operations in coastal environments; however, the density and size distribution of the bubbles must be known to assess their impacts. This dissertation addresses these deficiencies in our application of broadband techniques. In Chapter 2, a sound scattering model for gelatinous organisms is developed based on the Distorted Wave Born Approximation. The 3-D model is applied to a species of scyphomedusa and verified withlaboratory measurements of broadband backscattering from live individuals. The model predicts backscattering levels and broad spectral behavior within <2 dB. In Chapter 3, a towable instrument is developed for measuring broadband excess attenuation from bubbles from which the size distribution is inferred. The instrument is tested under breaking waves in a laboratory wave tank and then used to characterize the bubble size distribution in the Connecticut River tidal ebb plume front. In Chapter 4, broadband backscattering measurements from the Connecticut River front are used to infer the associated bubble size distribution. Spatial trends in the bubble size distribution are examined within the context of frontal kinematics. An observed disparity between the bubble size distribution measured with excess attenuation and volume backscattering is hypothesized to arise from a sampling bias caused by bubbles concentrated in the upper water column.
  • Thesis
    Interactions between rivers and coastal margins in the Alaskan Arctic
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-02) Catipovic, Luka ; Laney, Samuel R.
    Arctic coastal margins serve as the interface between Arctic terrestrial and oceanic carbon reservoirs. Characterized by extreme seasonality and annual variability, Alaskan Arctic coastal margins only receive riverine input of terrestrial organic material from late spring through late summer. This work examines the delivery, transformation, and distribution of organic material within Stefansson Sound, an Alaskan river-fed estuary, at the beginning and end of this period. We found that during the spring freshet, the landfast icescape over Stefansson Sound is composed of five ice and water features that are optically unique in terms of their surface reflectance spectra. One of these features is representative of freshwater flooding on ice which was found to persist in Stefansson Sound until late July. This floodwater is characterized by decreased reflectance in the blue portion of the visible light spectrum which indicates strong absorption by organic material contained within the freshet waters. Alaskan Arctic rivers drain watersheds composed of mixed proportions of tundra and mountains. During the freshet, organic material leached from the thawed soil surface horizons in the tundra is more available for microbial consumption over short periods than organic material originating in the mountains. This labile material is estimated to be higher molecular weight and more aromatic according to absorbance and fluorescence optical proxies. Fluorescence analysis revealed that tundra water contained more humic material and less amino acids when compared to water originating in the Brooks Range. This result challenges traditional assumptions that high molecular weight material in Arctic fluvial networks is refractory. In late summer, distributions of organic material in the surface waters of Stefansson Sound are driven by meteorological conditions such as precipitation over the watersheds and wind direction and speed in the estuary. Increased riverine discharge results in higher concentrations of organic material in the surface waters while faster wind speeds create deeper, well-mixed riverine plumes. Strong linear relationships between salinity and organic material indicate conservative mixing of freshwater in Stefansson sound, while new relationships between optical properties of water and organic material provide avenues forward for monitoring future climate driven changes regarding the biogeochemistry of this delicate ecosystem.
  • Thesis
    Microbial glycerolipids in the global ocean: environmental controls and sinking flux dynamics
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-02) Holm, Henry C. ; Van Mooy, Benjamin A. S.
    The composition of glycerolipids from a range of ocean environments were analyzed to better understand the biochemical adaptations and remineralization processes of planktonic biomass. Glycerolipids compose the cell membranes and energy stores of ocean microorganisms. As a biochemical group they present a useful target for tracking a wide range of environmental stress responses. In Chapter 2 of this work, I employ high resolution mass spectrometry to assemble a global dataset of planktonic lipidomes. Using this dataset of samples mostly from the epipelagic, I find that water temperature is a major controlling factor on fatty acid saturation state and hypothesize this derives from known biophysical constraints on cell membranes. I extend this analysis further to investigate links between long-chain essential fatty acids (LCEFA) and temperature. My analysis shows that the abundance of one of these LCEFAs (eicosapentaenoic acid, 20:5 n-3) is well correlated with temperature. Using this relationship, I project temperature-based declines in its abundance due to climate change over the next century. In Chapter 3, using samples from the West Antarctic peninsula, I assess the pigments and glycerolipid compositions of microbial communities within seasonal pack ice floes to gain insights on growth in an extremophile environment. The caloric content of this glycerolipid biomass is additionally calculated to assess its value to higher trophic level consumers within the sea ice ecosystem. I find that glycerolipids’ physical distribution within sea ice core to be calorically dense but highly geographically and physically heterogenous. I additionally show evidence of a new biomarker (fatty acid hydroxy fatty acid triacylglycerols, FAHFA-TAG) which have not been detected before in an ocean system. I further evaluate the possible biochemical sources of these novel biomarkers within sea ice. Lastly, I examine the glycerolipids present in sinking material from two separate studies of carbon flux in the upper mesopelagic. These compositions revealed both sources and remineralization processes influencing lipid carbon. I find evidence that lipid biomass is mostly lost non-selectively from particles, differing from previous reports of selective degradation of lipids. However, I find compositional differences between surface-suspended and sinking material possibly pointing to selection mechanisms at sinking material conception. I use glycerolipids to create a new source metric predicting the relative amounts of sinking material derived from fecal pellets verse aggregates. The findings of this thesis extend our understanding of microbial biochemical adaptations to their environment and reveal controlling factors on glycerolipid cycling in the ocean system.
  • Thesis
    Investigating the ocean’s biological pump using thorium-235 and polonium-210
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-02) Clevenger, Samantha J. ; Buesseler, Kenneth O.
    Oceans play a critical role in the Earth’s ability to regulate atmospheric carbon dioxide, absorbing approximately one-third of all anthropogenically-emitted CO2. The biological pump is a mechanism which controls oceanic uptake of CO2 and sequestration of carbon into deeper waters. It is a complex web of processes starting with biota in the upper ocean which transform CO2 into particulate organic carbon (POC) via photosynthesis, a portion of which is ultimately sequestered from the atmosphere. Due to the massive scale of these processes, small changes in the strength of the biological pump can greatly impact atmospheric CO2 levels. Tools used to quantify the flux of biologically relevant elements such as POC and biogenic silica via the biological pump are radioisotopes – naturally-occurring clocks which allow us to look back in time to study oceanic processes. In this thesis, the two radioisotope pairs 234Th/238U and 210Po/210Pb are utilized. Chapter 2 is an update of the 234Th/238U measurement method which simplifies the protocol, and allows for expansion of use. Chapter 3 presents an unprecedentedly extensive, non-steady state study of 234Th/238U to assess POC and biogenic silica flux through NASA’s EXPORTS project. The study involved tracking an eddy for one month in the North Atlantic Ocean to quantify export over the development of a dual-phase plankton spring bloom. In Chapter 4, this study is expanded to add a non-steady state application of the 210Po/210Pb tracer to look farther back in the history of POC and biogenic silica export. Extensive comparison of the two tracer systems results in new-to-the-field conclusions about the concurrent use of tracers. This thesis culminates in Chapter 5, which compares three 234Th/238U studies with community structure data to make inferences about POC export as it relates to who is present in the ecosystem. The EXPORTS North Atlantic dataset is a “strong” export endmember, WHOI’s Ocean Twilight Zone (OTZ) project offers an “intermediate” export case in the Northwest Atlantic Slope, and the EXPORTS North Pacific study is a “weak” export endmember. Taken together, this thesis greatly expands the use of 234Th/238U and 210Po/210Pb tracers to investigate the biological pump in diverse environments.
  • Thesis
    Exploring circadian rhythms, food intake, and their interactions in marine invertebrates
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-02) Berger, Cory A. ; Tarrant, Ann M.
    Circadian rhythms and energy metabolism are critical and interconnected components of animal physiology. Metabolic inputs like time of feeding modulate circadian clocks and behavioral and molecular rhythms. In turn, circadian clocks regulate metabolic processes, allowing animals to optimize energy usage on daily timescales. On longer timescales, animals require physiological responses to tolerate variation in food availability. Most of our mechanistic knowledge of these processes comes from terrestrial mammals and insects, while there are major knowledge gaps for marine invertebrates. My dissertation focuses on the interactions of circadian rhythms and metabolism in three marine invertebrate systems using a combination of behavioral, molecular, and bioinformatic approaches. In Chapter 2, to understand how sensory signals are integrated into circadian clocks, I test the effects of various light and temperature regimes on circadian rhythms in the sea anemone Nematostella vectensis. Misaligned light and temperature cycles severely disrupt behavioral rhythms and substantially alter the rhythmic transcriptome, particularly the expression of genes mediating metabolic processes. This illustrates how interactions between environmental cues shape circadian behavior and physiology. In Chapter 3, I develop a high-throughput behavioral system to study diel vertical migration (DVM) in the copepod Acartia tonsa. DVM is driven by tradeoffs related to food availability, but we do not fully understand how food availability affects this circadian process. Using high-resolution tracking software, I find that Acartia possesses group-level DVM-like circadian rhythms in the lab, and that these swimming rhythms are altered by time-restricted feeding. This illustrates that food availability can impact DVM via effects on circadian clocks. In Chapter 4, I analyze how polar copepods respond to starvation at the molecular level. I find that two species with distinct dietary strategies partially share a genetic toolkit to respond to starvation, whereas differences in their starvation responses may reflect different modes of lipid storage. I also use evolutionary analyses to show that starvation response genes are under selective constraint, underlining their importance to organismal fitness. In aggregate, this thesis provides insights into the circadian rhythms of marine organisms, explores how metabolism modulates circadian rhythms, and sheds lights on the physiological consequences of food availability in zooplankton.
  • Thesis
    From the atmosphere to the abyss: tracing organic carbon deposition, cadmium isotopes, and iron cycling using marine
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-02) Tegler, Logan ; Nielsen, Sune G. ; Horner, Tristan J.
    The marine biological pump refers to the formation and subsequent export of particulate organic carbon from the sunlit zone to the ocean’s interior. The magnitude and attenuation of this flux exert an important control over the air–sea balance of carbon dioxide. This thesis is focused on constraining this flux, the factors that control it, and developing novel tracers for it. First, I evaluate Holocene carbon depositional fluxes in margin sediment and shed light on seafloor OC deposition. I find that margins host 19.4 T mol yr-1 of marine OC and, contrary to the current paradigm, less than 4 % of the OC is buried in low-oxygen environments. However, in order to understand how the efficiency of the biological pump may have changed over time, it is necessary to use proxies. In Chapter 3, I examine cadmium isotopes as a potential paleonutrient proxy. I suggest that in addition to biological uptake, Cd isotopes may be influenced by local redox conditions, remineralization, and external Cd additions. In chapter 4, I measure Cd isotopes in the Mt. McRae shale (2.5 Ga) that was deposited across a purported ‘whiff’ of oxygen that is believed to reflect the onset of oxygenic photosynthesis. I find that the Cd isotopes are invariant and light during the ‘whiff’ interval. Rather than reflecting no changes in nutrient cycling, I suggest these compositions reflect a source–sink balance between Cd-depleted surface waters and external Cd inputs. Finally, in Chapter 5, we redirect our attention to the Fe cycle. Iron is a limiting nutrient in many ocean regions, which limits the efficiency of the biological pump. We use iron isotopes and Q-mode factor analysis to identify five sources of iron to sites in the South Pacific and Southern Oceans, including: dust, a ligand-bound background source, volcanic ash, and two hydrothermal sources. Taken together, this thesis examines elemental interactions and spans temporal scales, from ancient epochs to the modern era. While we leverage trace elements as proxies of past marine biogeochemical cycles, we also stress that careful work is needed to apply and analyze them.
  • Thesis
    The flow and fracture of Antarctic Ice Shelves
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-02) Millstein, Joanna D. ; Minchew, Brent M.
    This thesis explores the deformation of glacier ice, with an aim of deriving insights into its flow and fracture through satellite remote sensing methods. Glaciers deform through the driving force of their own weight and display dramatic responses to both external forcing, such as changes in climate, and internal forcing like variations in stress. Here, we focus on Antarctic ice shelves, the fast-flowing extensions of the ice sheet that impart stabilizing resistive stresses onto the grounded area. Processes contributing to dynamic change through melting, calving, the flow and fracture ice, can be explored and quantified with expirical relationships derived from mechanical properties. To understand the stability and future projections of glaciers and ice sheets in a changing climate, it is critical that we quantify and calibrate these processes. In Chapter 2, we leverage modern satellite remote sensing products to gain new insights into the flow of glacier ice. We validate and calibrate the constitutive relation for glacier ice across Antarctic ice shelves using a simple relationship between ice thickness and surface strain rate data. We find that the constitutive relation should employ an exponent n = 4, in contrast to the commonly used n = 3. This finding implies that ice shelves are more sensitive to changes in the stress state than typically assumed. Next, in Chapter 3 we derive a spatiotemporally dense dataset of surface strain rate fields across the Brunt Ice Shelf, the site of active full-thickness fractures, known as rifts. This dataset provides a mechanical framework with which we can analyze dynamic change, allowing us to quantify surface deformation with radar remote sensing. Lastly, Chapter 4 presents a fatigue-crack growth model for active rifts. This empirical framework sets bounds on rift propagation rates over periods of weeks and months and, in doing so, presents a simple parameterization of rift growth rates that can be implemented using observational data. This work provides a promising method to resolve fracture evolution over the period of weeks to years. Ultimately, this thesis uses observational data to validate theoretical models of glacier change, advancing our grasp on the dynamics of Antarctic ice shelves.
  • Thesis
    Applying statistical analysis and machine learning to improve the Ice Sensing Algorithm
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-09) Herron, Lucas A. ; Jayne, Steven R.
    The detection of sea ice is a major problem faced by Argo floats operating in polar regions. In these areas, the presence of sea ice threatens to damage or destroy floats in the event of an impact at the surface. While methods have been proposed and implemented to combat this danger, the most successful of which is the Ice Sensing Algorithm (ISA), further work is necessary to fully mitigate the risks, particularly in the Arctic. In this analysis, past CTD profiles from the Arctic are compiled and matched with sea ice data to examine the performance of the ISA and recommend potential changes and new methods to further improve its accuracy. This is accomplished by fitting the data to statistical and machine learning models to predict the presence of ice and analyzing the results. Results show that both modifications to current methods and the inclusion of new variables may increase the predictive power of the ISA. Specifically, the analysis shows that the use of point measurements (as opposed to a metric over a pressure range) at the shallowest allowable depth provides the best performance. The additional inclusion of practical salinity and time of year as predictive variables also increases the performance of the algorithm. Results and statistics on the performance of the algorithm are provided and analyzed in various regions.
  • Thesis
    Adaptive AUV-assisted diver navigation for loosely-coupled teaming in undersea operations
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-09) O’Neill, Brendan ; Leonard, John J.
    Human divers face immense challenges in the undersea domain due to constraints on life support, sensory input, and mobility. Due to these challenges, even simple tasks are difficult, and navigation between points of interest is key among them. However, humans have progressively utilized creativity, innovation, and research to explore the Earth’s oceans at greater depths and with increased spatial and temporal detail. Autonomous underwater vehicles often lack the tools, dexterity, or flexibility to manage specific tasks or unforeseen circumstances. However, advances in inertial navigation, computation, and acoustic communication enable autonomous underwater vehicles to perform tasks outside human capability. Acoustic modem technology allows for flexible and reliable communication over an acoustic link. We propose algorithms for cooperative navigation between a diver and an autonomous underwater vehicle as a pathway toward complex undersea human-robot teams. This thesis identifies the communication, software, and algorithmic tools to enable loosely-coupled cooperative navigation between an autonomous underwater vehicle and a diver without a surface presence. Divers present new challenges for cooperative navigation based on their unique motion profile and variable pace from diver to diver. By leveraging the vehicle’s sensor suite, acoustic modem technology, and nonlinear least-squares state estimation, we enable enhanced diver localization and navigation without a surface presence. Adaptation to environmental impacts is explored through measured ocean currents as well as updates to the diver’s motion model based on state estimation analysis. These adaptations produce more efficient diver transits with fewer heading changes. In addition, maneuvering strategies for autonomous underwater vehicles are explored to assess their impact on diver localization accuracy. Experimental validation is shown through surface platforms as proxies for the autonomous underwater vehicle and diver, demonstrating the localization accuracy within a few meters for experiments under various operating conditions. These contributions provide a foundation for undersea human-robot teams to engage in complex tasks with greater efficiency through their combined strengths.
  • Thesis
    Sediment erosion and deposition within mangrove forests
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-09) Deitrick, Autumn R. ; Nepf, Heidi M. ; Ralston, David K.
    Mangroves are highly productive ecosystems that sequester carbon in their own biomass and by trapping carbon-rich sediment imported from outside the forest and deposited in the forest. Aboveground biomass, like mangrove pneumatophores (i.e., aerial roots), creates conditions that facilitate sediment deposition by enhancing drag and slowing currents near the bed. However, pneumatophores also generate turbulence that enhances turbulent kinetic energy (TKE), which can promote sediment resuspension. Two studies were conducted to better understand the impacts of pneumatophore-generated turbulence on sediment transport. The first study investigated whether pneumatophore-generated turbulence impacted the erosion threshold and rate of natural cohesive sediment collected from a black mangrove habitat. Sediment cores with intact belowground and aboveground biomass were placed in a recirculating channel. Pneumatophores were removed from one side of each core. Each side of the core, with and without pneumatophores, was separately exposed to the same sequence of channel velocities. Although the presence of pneumatophores significantly enhanced the turbulence in the channel, the bed stress, threshold for sediment resuspension, and rate of sediment erosion were similar for the bare and vegetated sides of each core. This result differs from non-cohesive sediments, for which pneumatophore-generated turbulence has been found to increase erosion rates. The second study considered deposition. Laboratory experiments measured TKE and net deposition of non-cohesive sediment in bare and vegetated channels. For the same velocity, as pneumatophore density increased, TKE increased and net deposition decreased. The impact of TKE on deposition was described in terms of a deposition probability model. This model was used to predict deposition over a range of typical mangrove field conditions, which indicated that pneumatophore-generated turbulence can facilitate the delivery of sediment farther into the mangrove forest. Understanding how pneumatophores impact the balance of the competing processes of deposition and erosion is critical for improving the assessment and modelling of sediment retention and carbon storage in mangrove forests.
  • Thesis
    Observations of the Upper Ocean from Autonomous Platforms during the Passage of Extratropical Cyclone Epsilon (2020)
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-09) Zimmerman, Michael T. ; Jayne, Steven R.
    Hurricane Epsilon (2020) was a late-season, category-3 tropical cyclone that underwent extratropical transition and became Extratropical Cyclone Epsilon on 26 October. The upper ocean response to the passage of the storm was observed by three types of autonomous platforms: the eXpendable Spar buoy, the Air-Launched Autonomous Micro Observer profiling float, and two Seagliders. Taken together, this array enabled the rare collection of contemporaneous observations of the upper ocean, air-sea interface, and atmospheric boundary layer before, during, and after the passage of the storm. The evidence presented highlights how Extratropical Cyclone Epsilon broke down the residual North Atlantic summer stratification regime and accelerated the shift to the period of prolonged ocean cooling associated with winter. The significance of the synergistic capabilities of the array is two-fold: 1) comparing observations of the same parameters, taken from different platforms, enables a comprehensive approach to better understanding how storm-induced momentum, sensible heat, and moisture fluxes input kinetic and near-inertial energy into the ocean and thereby alter upper ocean structure; and 2) future, targeted deployments of similarly capable observational arrays will reduce the uncertainty of tropical and extratropical cyclone intensity forecasts by facilitating the assimilation of real-time subsurface ocean data into coupled numerical prediction models.
  • Thesis
    Diel vertical migration and frontal variability of acoustic backscatter in the Balearic Sea
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2023-09) Cheslack, Helena R. ; Mahadevan, Amala
    Acoustic Doppler current profilers (ADCPs) use active sonar to measure current velocities by measuring the sound returned by scatterers (most often zooplankton) in the water column. The volume of scatterers, or echo intensity, has been used to measure the abundance of zooplankton and characterize diel vertical migration (DVM). DVM is the mass vertical movement of zooplankton and fish between the surface waters where they feed at night, and the mesopelagic zone where they avoid predators during the day; it is considered the largest migration of biomass on Earth, happens in every ocean, and is important to the global carbon cycle. This thesis uses a combination of data that I helped acquire during the Office of Naval Research-funded CALYPSO 2022 field campaign in the Balearic Sea. Acoustic backscatter from a 38kHz ADCP and a 150kHz ADCP is translated into mean volume backscattering strength (MVBS) to characterize the sound scattering layers (SSLs) in the Balearic Sea. WireWalker data is used to model subsurface light. The MVBS is compared to measurements of temperature, salinity, chlorophyll concentration, and dissolved oxygen (DO) from the EcoCTD, a towed instrument that simultaneously measures hydrographic and biological parameters. The analysis reveals one permanent scattering layer at 300m – 600m and two migrating scattering layers in the top 50m and between 100m – 300m. The layers are likely made up of zooplankton like krill and pteropods and pelagic fish. The speed of vertical migration ranges from 1 – 11cms−1, and migrators are follow isolumes during migration times. DVM has the strongest effect on backscatter anomalies, but during daytime and nighttime, DO is most correlated with the backscatter anomaly. We demonstrate that ADCPS can be used to characterize SSLs and DVM. The uniquely co-located EcoCTD data from CALYPSO enables us to compare the frontal variability in scatterers to variability in biological and physical parameters. Characterizing the SSLs, DVM, and frontal variability of acoustic backscatter furthers understanding of the global carbon cycle.