WHOI Theses

Thesis

Decadal to centennial climate in the Indo-Pacific

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2025-02) Wang, Shouyi ; Ummenhofer, Caroline C. ; Oppo, Delia W.

An improved understanding of decadal to centennial-scale climate variability is critical for properly attributing recently observed low-frequency changes to internal climate oscillations and/or anthropogenic forcings as well as improving predictability of decadal variability. This thesis investigates ocean and atmospheric circulation changes and associated impacts within the tropical Indo-Pacific, where low-frequency changes in heat and freshwater impact the livelihoods of billions of people. Because the instrumental record is too short to investigate centennial variability, this thesis leverages numerical simulations and records from paleoclimate archives to provide insights into low-frequency tropical dynamics. In Chapter 2, we explore the dynamics that drive Indonesian Throughflow surface transport variability using a series of forced global high-resolution ocean simulations. We show that surface wind changes associated with Pacific decadal variability drive changes in the western boundary currents that modulate the Indonesian throughflow, consistent with mechanisms identified on interannual timescales. This work identifies a relationship between atmospheric circulation and transport through a key lowlatitude passageway. Motivated by paleoclimate evidence of multi-year droughts in Southeast Asia, we investigate their potential drivers in Chapter 3 using an ensemble of coupled climate model simulations. These simulations illustrate that Indo-Pacific internal variability dominated Southeast Asian rainfall extremes during the last millennium, although the influence of volcanic eruptions was detectable. We found that multi-year pluvials were contributed by both Pacific and Indian Ocean modes, while droughts were largely only driven by Pacific Ocean impacts. Our analysis not only quantifies the role of internal and external drivers to Southeast Asia rainfall but also presents a probabilistic analysis framework that may be useful for water resources prediction. Lastly, in Chapter 4 we reconstruct the Indian and Pacific Walker circulations and the Indian Ocean Basin Mode by synthesizing tropical records (corals, tree-rings, and speleothems) of past ocean and atmospheric conditions to investigate basin interactions over the past four centuries. Our results demonstrate that Indo-Pacific climate was generally coupled on decadal-centennial timescales throughout the past four centuries but was notably decoupled in the early 19th century. Using climate models, we attribute this decoupling to a series of strong volcanic eruptions. Dynamically, we link this inter-basin decoupling to volcanically induced changes in hemispheric temperature gradients, which modulate the teleconnections across the Indo-Pacific. These past disruptions in basin interactions provide context for ongoing and simulated future decoupling under a high emission scenario, as global warming also alters interhemispheric temperature gradients. This thesis sheds light on the complex dynamics that drive ocean-atmosphere variability across the Indo-Pacific on decadal to centennial timescales.

Thesis

Tracking carbon fluxes across ocean interfaces using dissolved gas observations

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2025-02) Traylor, Shawnee N. ; Nicholson, David P.

The cycling and exchange of carbon between Earth’s systems play a pivotal role in regulating climate, yet two major carbon fluxes remain poorly constrained: the biological carbon pump (BCP) and carbon release from Arctic permafrost. This thesis focuses on dissolved gases as tracers and drivers of these processes through both autonomous and field-based observations. It encompasses (i) improvements to sensor-based measurements of O2, (ii) the use of these measurements to assess the strength of the BCP in two distinct export regimes, and (iii) isotopic approaches to carbon dioxide (CO2) and methane (CH4) dynamics at a coastal permafrost site. The first part of the thesisis centered around the NASA EXPORTS campaign and studies the BCP at two contrasting field sites. Using autonomous platforms, carbon export was evaluated at both sites and demonstrated that at the lower productivity site, a greater proportion of fixed carbon was routed to sinking particulate organic carbon (POC), while the higher productivity site resulted in near equal proportions of dissolved organic carbon production and sinking POC. These findings underscore the value of autonomous sensors in capturing spatial and temporal variability in oceanic carbon cycling. The second part of this thesis shifts focus to the Arctic, where rapid warming threatens to mobilize vast (~1,500 Pg) amounts of carbon currently stored in permafrost. This study presents observations from the spring thaw at a coastal Arctic site and demonstrated that even sites with high CH4 and CO2 concentrations drew less than 10% of their carbon source from ancient permafrost sources. The variability in CH4 and CO2 emissions reflects the complex interplay between hydrological changes, primary productivity, and microbial processes. The research highlights the need for regular monitoring of Arctic rivers, which integrate changes in the terrestrial system, as a potential early warning system for abrupt permafrost thaw. This thesis leverages the fundamentals of dissolved gas geochemistry to examine key climate-relevant biogeochemical cycles across diverse environments that are sensitive to global change. These insights contribute to refining Earth system models and emphasize the need for expanded monitoring to predict future shifts in global carbon cycling and climate dynamics.

Thesis

Investigating the atmospheric and oceanic drivers of Atlantic Multidecadal Variability and predictability

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2025-02) Liu, Glenn Y. ; Kwon, Young-Oh

Despite its numerous impacts across the Earth system, the relative importance of ocean and atmospheric dynamics in generating Atlantic Multidecadal Variability (AMV) remains an open question. This thesis presents three pathways to understanding how oceanic and atmospheric processes generate key spatio-temporal signatures of AMV through a combination of processed-based and data-driven approaches. Part 1 (Chapter 2) takes a "bottom up" approach, building a hierarchy of stochastic models to identify the contributions of vertical entrainment and seasonality in local upper-ocean processes to sea surface temperature (SST) variability. Through this hierarchy, I highlight unrealistic features present in slab ocean models widely used to isolate atmospheric contributions to AMV. On the opposite end of the spectrum, Part 2 (Chapter 3) utilizes a "top-down" data-driven approach where deep neural networks are trained to predict the North Atlantic SST Index in both the Community Earth System Model 1 Large Ensemble (CESM1) and observation-based datasets using atmospheric and oceanic predictors. I apply explainable artificial intelligence techniques to highlight a significant source of multidecadal predictability over the Transition Zone in oceanic predictors such as sea surface salinity (SSS) and sea surface height in the presence of external forcings. Part 3 (Chapter 4) returns to the process-based hierarchy, but applies this to understanding SSS variability. The stochastic salinity model is used to investigate the role of mixed-layer re-emergence, subsurface ocean damping and SST-evaporation feedback in shaping the pattern and amplitude of AMV.

Thesis

A Lagrangian perspective of mesoscale biophysical interactions in the subtropical ocean

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2025-02) Jones-Kellett, Alexandra E. ; Follows, Michael J.

The most kinetic energy in the ocean is at the mesoscale, which includes highly dynamic physical perturbations that persist for months, a biologically relevant timescale for phytoplankton growth and bloom development. Importantly, mesoscale currents and the associated biological responses (i.e., biophysical interactions) are not spatiotemporally static, so they are difficult to characterize. In this thesis, we interpret phytoplankton observations in an objective Lagrangian manner, or with a frame of reference that follows the motion of water parcels experienced by drifting organisms. We build a Lagrangian coherent eddy tracking algorithm that identifies the boundaries of water masses trapped for a month or longer. Using this tool, we assess the variability of the lateral advective properties of eddies across the North Pacific Subtropical Gyre, finding that only half of the remotely sensed eddies identified from the traditional, Eulerian sea level anomaly method trap waters for these timescales. We then statistically compare satellite-observed chlorophyll-a anomalies associated with eddies that trap versus mix across their boundaries. Lagrangian coherent vortices have more anomalous biological signatures in the gyre, so we argue that the role of leaky eddies in altering biogeochemistry may be underestimated due to lateral dilution. We also highlight substantial regional and seasonal variability in the dominant biophysical interactions within the oligotrophic regime, helping to explain inconsistencies of in situ eddy observations across this region. Lastly, we show how the Lagrangian water mass histories of in situ samples shape the phytoplankton community in the open ocean, quantified with amplicon sequencing and internal genomic standards. In non-eddy waters, we found that cyanobacteria are advantaged over eukaryotic phytoplankton when lateral mixing is minimized for several months. In or near mesoscale eddies, where vertical perturbations are a source of new nutrients, eukaryotic phytoplankton gene abundance has no dependence on the lateral mixing histories. The results suggest dispersal and niche generation drive phytoplankton variability but in different ways in and outside eddies. This thesis emphasizes how Lagrangian tools reveal mesoscale structures (otherwise invisible with Eulerian reference frames) that trap, transport, and transform ecosystems, generating phytoplankton patchiness and variability in the surface ocean.

Thesis

Algorithmic advances in range-aided navigation

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2025-02) Papalia, Alan A. ; Leonard, John J.

This thesis contributes to the advancement of range-aided simultaneous localization and mapping (RA-SLAM) through algorithmic developments and real-world demonstrations. Broadly speaking, SLAM is the process by which an agent combines sensor measurements to simultaneously create a map of the world and localize itself within this map. SLAM has been called the ‘holy grail’ of field robotics, and in many instances it is a critical enabling capability for autonomous agents to operate in the real world. RA-SLAM is the specific case of SLAM which incorporates point-to-point distance measurements (e.g., distance measurements between an autonomous underwater vehicle and an acoustic buoy) into the inference process. The ability to leverage such measurements is desirable, as they can help in resolving ambiguities (e.g., am I in hallway A or B) and the relevant sensors are often low-cost and simple to integrate (and thus pose the potential to be widely deployed). However, there are theoretical challenges that have historically limited the reliability of RASLAM approaches. At the root of these challenges is the issue that a single range measurement does not uniquely determine the relative position between two points. In state-of-the-art RASLAM formulations, this ambiguity manifests as non-convexity in the maximum a posteriori inference problem. As a result of this non-convexity, standard local-search optimizers are highly dependent on quality initializations to obtain the correct state estimate. To address this issue of reliability, this thesis presents the first certifiably correct algorithm for RA-SLAM. This algorithm, Certifiably Correct RA-SLAM (CORA), is capable of (i) obtaining globally optimal solutions for many real-world RA-SLAM problem instances and (ii) providing certificates of correctness for these solutions. CORA leverages a novel semidefinite programming (SDP) relaxation of the RA-SLAM problem, which it solves efficiently using the Riemannian Staircase methodology. This methodology allows CORA to typically obtain globally optimal solutions faster than the existing state-of-the-art local solvers. These results expand our understanding of problems suited for efficient global solvers and highlight the key problem structures that appear necessary to develop and deploy such solvers, pointing towards exciting future directions in trustworthy model-based autonomy. We demonstrated the performance of CORA on a range of real-world RA-SLAM datasets, including a set of large-scale multi-agent experiments conducted as part of this work. In these experiments CORA reliably estimates agents’ trajectories in both single- and multi-robot settings. CORA gracefully scales to large problems consisting of multiple agents and tens of thousands of robot poses. These experiments not only validate CORA’s performance, but also fill an existing gap in open-source datasets available to the research community and provide practical insights to guide future deployments of autonomous navigation systems in large, complex environments.

Thesis

Observations of surfzone vorticity using optical remote sensing

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2025-02) Dooley, Ciara J. ; Elgar, Steve ; Raubenheimer, Britt

The surfzone is the dynamic interface between the land and ocean, where waves shoal and break as they reach shallow water near the shore. Currents and circulation patterns in the surfzone transport sediment, nutrients, pollutants, and other materials along and across the coast, and can create hazardous conditions for swimmers (rip currents). However, understanding of the strength and structure of eddies and vortices in the flow field primarily remains limited to numerical models and theory. Here, novel observations of surfzone vorticity at small [O(10m)] and large [O(100m)] spatial scales are presented and related to incident wave conditions and the measured underlying bathymetry. Field experiments were conducted at a sandy beach on the Atlantic Ocean, and nearshore flows were observed using optical remote sensing (coastal imaging) and in situ sensors. Remote sensing algorithms are expanded from previous applications to estimate high spatial resolution two-dimensional surface flows by tracking the motion of naturally occurring foam throughout the surfzone. Estimated currents are correlated with in situ flow measurements, and errors increase as the sea-surface viewing angle becomes more oblique and image quality decreases. Large spatial-scale vorticity estimated using remotely sensed flows increases with alongshore bathymetric inhomogeneity, and complex circulation patterns corresponding to holes and channels in the seafloor persist for days at a time. Small spatial-scale vorticity estimated from a 5-m diameter ring of 14 current meters increases with the directional spread of the incident wave field, consistent with increased vorticity injection from the crest-ends of breaking waves. Small spatial-scale vorticity estimated using remotely sensed flows is spatially variable and correlated with the amount of wave breaking observed at a given location. Enhanced vorticity at large and small spatial scales occurs in the inner surfzone, and virtual drifters released into the remotely sensed flow fields demonstrate cross-shore variability in dispersion and mixing. This thesis expands the understanding of vorticity dynamics in the surfzone through unique field observations and provides new tools for coastal research and monitoring through development of remote sensing techniques.

Thesis

Radium and mercury dynamics in the Arctic: investigating terrestrial inputs, groundwater discharge, and chemical cycling in a changing climate

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2025-02) Bullock, Emma J. ; Charette, Matthew A. ; Hansel, Colleen M.

The Arctic Ocean is distinctive due to its extreme seasonal variations in temperature and significant terrestrial inputs, including freshwater, carbon, nutrients, and toxins. Of particular concern is mercury (Hg) in its neurotoxic form, methylmercury (MeHg), which is already beginning to adversely affect Arctic human populations and wildlife. However, the region’s harsh conditions and remoteness have made conducting seasonal chemical and hydrological studies challenging. Tracers of boundary inputs, such as the radium (Ra) isotope quartet, offer potential for tracking and quantifying riverine and submarine groundwater discharge (SGD) of species like Hg into the Arctic Ocean. This thesis employs seasonal data and laboratory experiments to investigate the factors influencing terrestrial Ra inputs to the Arctic Ocean, quantifies SGD and associated Hg inputs to an Arctic coastal lagoon, and elucidates the chemical and geological factors influencing Hg cycling in Arctic groundwater. Using historical and unpublished datasets combined with new laboratory investigations, differences in inputs of riverine Ra isotopes between the North American and Eurasian land masses were identified. The findings revealed higher Ra fluxes from the North American continent, attributed to greater sediment loads and lower organic matter in rivers compared to those on the Eurasian land mass. Subsequently, Ra data from five extensive field campaigns to Simpson Lagoon, Alaska, provided insights into Ra cycling on a more localized scale. These campaigns offered the first seasonal perspective on supra-permafrost SGD along an Arctic coastline, suggesting that SGD fluxes may rival those of rivers along the Beaufort Sea coast. Concurrently collected Hg groundwater concentrations allowed for the development of the first estimates of Hg fluxes from groundwater to the Arctic Ocean. If these estimates hold true along the rest of the Pan-Arctic coastline, they could significantly alter our understanding of microbial MeHg uptake in the Arctic Ocean. Finally, sediment cores from Simpson Lagoon and two other locations along the Beaufort Sea coast were used to examine how changing groundwater conditions, such as changing salinity, temperature, and redox conditions, influence Hg cycling. These experiments, alongside findings from Simpson Lagoon groundwater, indicate that Hg cycling in recently thawed permafrost sediments involves a complex interplay between organic material, metal oxides, and sulfide species, with groundwater conditions and soil carbon content playing crucial roles in Hg mobilization.

Thesis

Mechanisms of terrestrial organic carbon export and preservation in the marine environment

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2025-02) Boehman, Brenna L. ; Galy, Valier V. ; Hansel, Colleen M.

Export of terrestrial carbon from land to sea is a globally important carbon flux that is poorly constrained and has implication for atmospheric carbon levels over modern and geologic timescales. Many factors control the fate of exported carbon and the subsequent impact on carbon budgets, including the timescales of export, the composition of organic matter, and degradation processes. This thesis uses biomarkers, bulk geochemical tools, and incubation studies to interrogate the factors controlling terrestrial carbon export and preservation in the marine environment. The thesis focuses on two globally important river systems that collectively deliver 25% of the total terrestrial carbon flux to the ocean, the Ganges-Brahmaputra (G-B) Rivers and the Amazon River. The first two chapters focus on the G-B Rivers, utilizing compound specific biomarker analysis within a high sedimentation rate (30 cm/yr) terrestrial archive in the Bay of Bengal, we interrogate (i) timescales of organic carbon export from land to sea, and (ii) basin-scale geochemical responses to rice agriculture expansion. These analyses utilize the radiocarbon ages and stable carbon-13 isotopic composition of lipids produced by Archaea and Bacteria. We identify that ca. 75% of these biomarkers experience millennial scale storage in the G-B basin, in agreement with previously assessed plant-derived compounds, highlighting that an overarching soil stabilization mechanism controls the age of exported terrestrial organic matter. Individual biomarkers and bulk geochemical analysis chronicle the change in methane-derived soil carbon within the basin due to rice paddy expansion, highlighting that 49% of Bangladesh’s methane emissions from 1990-2008 have been abated by soil storage. The last two chapters focus on the Amazon River, to examine the fate of terrestrial organic carbon in the marine environment, (iii) utilizing geochemical analysis of historical sediments and sediments from a field campaign in 2023, and (iv) utilizing terrestrial and marine endmembers in incubation experiments simulating the dynamic coastal environment. Sediment geochemical and biomarker analyses highlight the preservation of an isotopically distinct terrestrial endmember in the coastal sediments, which has led to at least 50% underestimation of the burial efficiency. Quantitative stable isotope probing incubations using 13C-lignin indicate the dual role of microbially-mediated and photo-degradation, and highlight that the microbial communities primarily responsible for lignin degradation in the marine environment are of terrestrial origin, and identify a new ecological role for Bathyarchaeota. This thesis integrates diverse biogeochemical techniques across the terrestrial-marine interface to examine important open questions in globally important carbon budgets, merging isotope geochemistry, microbiology and earth science. The findings contribute to our understanding of the modern carbon cycle and the impact of anthropogenic perturbations of the last decades and into the future.

Thesis

Abyssal benthonic foraminifera and the carbonate saturation of sea water and a benthonic foraminferal carbonate saturation history for the Cape Verde Basin for the last 550,000 years

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 1983-04) Bremer, Mary Lee

The distribution of certain Atlantic Ocean benthonic foraminifera is most consistently correlated with the degree of saturation of seawater with respect to calcium carbonate. The relative abundance of cibicidids, miliolids, Uvigerina and Globocassidulina subglobosa increases in saturate water and the relative abundance of Nuttlaides umbonifera increases in undersaturated water. It is suggested that this is a response of living benthonic foraminifera. Using this relationsship it is possible to recognize changes in the "paleosaturation" of deep and bottom water from fossil deep-sea benthonic foraminifera. The deepest water in the western Atlantic is barred from flowing into the eastern Atlantic by topographic barriers such as the Walvis Ridge and the mid-Atlantic Ridge. The major conduits of the depest and most dense water into the eastern Atlantic are the fracture zones on the ridge such as the Romanche, Chain ema Fracture Zones. The carbonate saturation of the Cape Verde Basin is very snsitive to the hydrography at these sill depths in the western Atlantic. The four cores studied range from 2471-4696m. They are relatively isolated from the influx of terrigenous detritus and have low sedimentation rates which vary between 0.5 and 0.7 cm/1000 years. They do no show the Atlanic Ocean low-carbonate glacial, high-carbonate interglacial cycles seen in other, higher sedimentation rate cores. This supports the contention of Broecker et al. (1958), Needham et al. (1969), Ruddiman (1971), Hays and Perruzza (1972) and Damuth (1977) that the cycles are produced by masking of carbonate by terrigenous detritus. The glacial-interglacial variability (in particular, increases in U. peregrina during glacial times) observed in higher latitude cores (Streeter and Shackleton, 1979; Schnitker, 1979; Croliss, in preparation) was not observed. A carbonate saturation history for the Cape Verde Basin for the last 550,000 years based on benthonic foraminifera shows that undersaturation in the Cape Verde Basin was as great or greater that it is today at 120,000-180,000 yr. B.P., 280,000 yr. B.P., 375-000-425,000 yr. B.P. and 525,000 yr. B..P. The inferred carbonate saturation changes could have been produced by a decrease of less than 1° C in bottom-water temperature at the sill depths of the Romanche, Chain and Vema Fracture Zones. The increases in undersaturation are no correlative with glacial-interglacial climate change. They are, in general, correlative with upward migrations of what is reinterpreted here to be the undersaturation biofacies at the Rio Grande Rise in the southwestern Atlantic (Lohmann, 1978) and in the southeastern Indian Ocean (Corliss, 1979). In both the southeastern Indian Ocean an in the Cape Verde Basin, the greatest increase in undersaturation occurs between 375,000-425,000 yr. B.P. These upward migrations are interpreted to represent shoaling of the deep-water bottom-water transition.

Thesis

Adaptive robotic search and sampling of sparse natural phenomena

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-06) Todd, Jessica Eve ; Yoerger, Dana R.

Autonomous robots are increasingly being used in the field of scientific exploration and data acquisition. Intelligent autonomous robots, capable of online adaptive planning, are seeing wide use in underwater field mapping and agricultural monitoring. The majority of these approaches produce maps of easily observable and widely dispersed phenomena such a temperature, salinity or tree coverage. However underwater and planetary science can often involve phenomena that are ‘expensive’ to observe, discrete, and sparsely distributed. For example, coral disease can only be visually detected by an underwater robot when hovering close to the reef, due to light attenuation underwater, putting the robot at risk of collision with obstacles or organisms. Similarly, subsurface water on Mars can only be detected from a landed system on the surface, due to the short range of the detectors. When the operating conditions are resource-constrained, such as a limited battery life, expensive sensing actions can consume the resource budget, limiting the range of area that can be explored. The tension between needing to act intelligently to find and measure sparse phenomena, and needing to operate within resource constraints, leads to challenges for the robot’s autonomous decision making process in choosing what to sense, where, and when. This thesis aims to address this challenge by combining semantic ‘substrates’ in the environment with hierarchical probabilistic modelling which maps substrate distributions to the underlying phenomena of interest. By using substrates that are detectable over a wide field of view, and correlated with sparser and harder to find phenomena, a robot can be guided to regions known to be associated with the phenomena of interest. This problem can be formulated as a partially-observable Markov decision process (POMDP) referred to as the Discrete Search and Sample problem. This thesis proposes two algorithmic contributions to the field of adaptive path planning to address two scenarios within this framework. In the first scenario, we assume the robot has prior knowledge about the expected density of discrete targets in the various substrates, however is operating without prior knowledge of substrate distributions. We develop a novel multi-altitude planning method, the Sparse Adaptive Search and Sample (SASS) for seeking out targets by mixing low-altitude observations of discrete targets with high-altitude observations of the surrounding substrates. By using the prior information about the distribution of targets across substrate types in combination with belief modelling over these substrates in the environment, high-altitude observations provide information that allows SASS to quickly guide the robot to areas with high target densities. In our second scenario, the a priori assumption of substrate-target correlation models is relaxed and the robot is now operating without strong prior knowledge of target density, or the relationship between target and substrate. Drawing inspiration from the Species Distribution Modelling community, an hierarchical probabilistic model is developed using the Integrated Nested Laplace Approximation framework, that enables online inference about expected target hotspots using predicted substrate distributions. Model parameters are learned online to build a prediction over the discrete targets, and the model is integrated into an anytime online planner to enable adaptive path planning. Both algorithms are extensively evaluated with both synthetic and real-world datasets. Additionally, through the course of addressing these two scenarios, two novel generative species-substrate model were developed that enable rapid simulation of synthetic worlds, with properties derived from real-world data. The development of these simulators allow the testing of path planners that aim to exploit natural correlations in spatial distributions that occur in the real world.

Thesis

Vertical distributions of megafauna on inactive vent sulfide features correspond to their feeding modes

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-09) Meneses, Michael J. ; Mullineaux, Lauren S.

The discovery of inactive hydrothermal vent sulfide features located off the ridge axis in the 9°50'N region of the East Pacific Rise provides an opportunity to investigate knowledge gaps in the distribution and feeding ecology of communities inhabiting this type of deep-sea habitat. Previous seafloor imaging studies indicate that megafaunal taxa on inactive sulfides are not endemic to these features, but their assemblages differ from other deep-sea habitats. I investigated the influence of environmental conditions on megafaunal distributions using highresolution imagery of two inactive sulfide features, Lucky's Mound and Sentry Spire, to determine how taxonomic composition and feeding traits vary with vertical position on the features. A total of 51 morphotypes, each categorized to feeding mode, was identified from three levels of the features (spire, apron, and base) and a section of the surrounding flat oceanic rise. Quantitative image analysis showed that passive suspension feeders were more abundant on the spires of the sulfide features than the base or surrounding rise. Deposit feeders were more abundant on the base of Lucky’s mound and the oceanic rise, than on the spire or apron, but were unexpectedly abundant on the spire of Sentry Spire. These distributions correspond generally to the expected availability of suspended organic particles and detritus on the seafloor that serve, respectively, as food for these two feeding modes, and indicate a potential role for physical attributes of the sulfide feature to influence their faunal assemblages. Distinct differences in community composition between the two inactive sulfide features, however, suggest that other, feature-specific processes, perhaps including local chemoautotrophic production, may also play a role.

Thesis

Modeling sandbar effects on nearshore waves and morphological change using SWAN

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-09) Murman, Charles E. ; Raubenheimer, Britt

Numerical model simulations (Delft3D SWAN) are used to examine the impact of small alongshore variations in the bathymetry of an outer sandbar (in about 5-m water depth) on the nearshore wave field as the shallow (< 3 m) bathymetry changes from near alongshore uniform to strongly spatially variable to understand wave driven morphologic evolution. Waves were observed at Duck, NC with an array of 14 pressure gages between 1- and 3-m water depth spread over 250 meters alongshore. Bathymetry was measured between the dune toe and about 8-m water depth on September 26 and October 2, 2013. The bathymetry evolved from roughly alongshore uniform on September 26 to strongly alongshore variable on October 2. Between these dates incident significant wave heights ranged from 0.5 meters to 2.3 meters, with incident angles from 20 degrees north to 5 degrees south of shore normal. Simulations were run with observed bathymetry for both the outer bar and inner shallow bathymetry, with smoothed outer bar and observed shallow bathymetry, and with digital elevation model bathymetry to determine the effects of outer bar and shallow bathymetry on wave evolution.

Thesis

Movement and energetics of swimming marine mollusks

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-09) Cones, Seth F. ; Mooney, T. Aran

Mollusks constitute a significant proportion of marine animal biomass and fulfill essential ecosystem functions. Yet, our knowledge of their behavior and energy output in natural environments remains elusive. This key knowledge gap stems from our inability to quantify their positions and movements for appreciable time-scales, and thus we know extremely little about how abundant mollusks that are pervasive in all ocean biomes respond to naturally varying and anthropogenically-induced changes. In this thesis, I adapted emerging biologging sensor technology, traditionally designed for large robust vertebrates, for two key mollusk taxonomic groups (squid and scallops) to quantify and characterize movements at fine-temporal scales. In Chapter 2, I collected the first high-resolution (> 1 Hz) in situ movement data for any squid species. These novel data elucidated fundamental swimming behaviors such as swim direction, postures, and environmental extents of ecologically-vital diel vertical migration. In Chapter 3, I linked lab-calibrated bioenergetic models and field observations to map energy output and necessary caloric intake of natural behaviors in the wild. These data revealed dynamic gait use on seconds time scales. Next, in Chapters 4 and 5, I quantified the behavioral disruption and the metabolic cost of a prominent anthropogenic stressor, sound pollution. Squid and scallops elicited drastically different ecophysiological responses to field-simulated offshore windfarm construction. Squid elicited dramatic behavioral responses coinciding with the onset of construction, although animals habituated rapidly. Contrarily, scallops’ behavioral responses were moderate but consistent, and surprisingly there was no evidence of habituation across second, minutes, and daily time scales. Extended behavioral changes manifested as heightened metabolic rates and weakened antipredator responses, suggesting prolonged and potential population-level impacts on a key fishery. This thesis provides new insight in marine invertebrate movement ecology and eco-physiology, demonstrating the utility of coupling biologging and physiological experiments to reveal how key ocean animals behave and expend energy.

Thesis

The origins of the East Greenland Coastal Current on the Northeast Greenland Shelf: a comparison of two reanalysis products

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-09) Vianco, Sara L. ; Foukal, Nicholas P. ; Mahadevan, Amala

The East Greenland Coastal Current (EGCC) carries some of the freshest outflow from the Arctic southward along the East Greenland Shelf and into the Nordic Seas and subpolar North Atlantic. How this fresh water initially flows onto the Northeast Greenland Shelf (NEGS) and feeds the EGCC is not well known due in part to the lack of observations in the region. In this thesis, I use two ocean reanalyses, the Regional Arctic Ocean/sea-ice Reanalysis (RARE) and Global Ocean Physics Reanalysis (GLORYS) to explore the structure and dynamics of the ocean circulation on the NEGS. To validate the use of these products in the region, I compare the reanalysis products to the Fram Strait Arctic Outflow Observatory for the period of 2003-2019. In the mean, RARE is too warm and salty compared to the moorings, while the properties in GLORYS track more closely to the observations. However, the observed velocity field is better represented in RARE than GLORYS. From there, I analyze the cross-shelfbreak flow from 74°N to 81.5°N in the two reanalysis products, and conclude that transport onto the NEGS of waters fresher than 34 salinity is driven by an Ekman circulation that arises from along-shelfbreak winds and a widening shelf south of 81.5°N. The enhanced transport of fresh water also shifts the isohalines across the shelfbreak, directing a geostrophic flow onshelf between 81°N and 79°N. The convergence of fresh water on the NEGS initiates the EGCC as an identifiable and distinct feature around 80°N in RARE, uniting the EGCC along the southwest coast of Greenland and its northern counterpart, the Polar Surface Water (PSW) Jet. In GLORYS, the EGCC is not present throughout the domain, though there is a weak net southward flow on the NEGS. The EGCC in RARE is primarily buoyancy-driven, though the along-coast winds likely play a major role in maintaining the density front that supports the EGCC. Results from this thesis have implications for the transport and fate of Arctic and Greenland-sourced fresh water, and stratification in the high latitude North Atlantic and Nordic Seas.

Thesis

Cross-shelf exchange driven by dense flow down a canyon

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-09) Mier, Christian M. ; Cenedese, Claudia

Laboratory experiments investigated the dynamics controlling the cross-shelf exchange in a prograde sloping canyon induced by dense shelf water descending into the canyon. This thesis is motivated by the dispersal of dense water generated by polynyas on the Arctic and Antarctic continental shelves. Laboratory results corroborate prior numerical results suggesting that canyons are hotspots of cross-shelf exchange. When the dense water descends a canyon, it induces an onshore return flow of offshore water into the canyon. This return flow is initially driven by the dense water eddies descending the canyon and acting like a bucket brigade. At later times, another mechanism may also be at play where large dense cyclonic (anticlockwise) eddies on the northern continental shelf may pull more dense water out of the canyon producing a region of low pressure, near the canyon head, which induces an increase in ambient flow into the canyon. The Burger number (Rossby radius of deformation/canyon width) and the dense water source location with respect to the canyon head affect the offshore ambient water velocity up the canyon. Additionally, as the offshore water reaches the canyon head, the offshore water volume flux becomes larger than the dense water volume flux, possibly due to the low pressure region described above. Understanding these dynamics in the Antarctica region is of global significance for two main reasons: 1. The offshore flowing dense water forms Antarctic Bottom Water and thus affects the global meridional circulation; 2. The onshore heat transport induced by the return flow drives glacial ice melt and therefore contributes to sea level rise.

Thesis

Analyzing remote sensing-derived normal difference vegetation index to predict coastal protection by Spartina alterniflora

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-09) Garber, Samantha C. ; Nepf, Heidi M.

Coastal vegetation can provide protection to the coastline through its root structures, which reduce soil erosion, and its stem structures, which dissipate wave energy. The drag a plant induces could be used to quantify the amount of coastal protection that is provided. This study combined field measurements and drone surveys to develop methods for quantifying vegetation drag, focusing on Spartina alterniflora (S. alterniflora), a smooth cordgrass native to the study site: Waquoit Bay National Estuarine Research Reserve. The drag of a single plant is proportional to frontal area. The drag per bed area is proportional to the drag of a single plant and the number of stems per bed area. This study collected plant samples over the growing season to generate allometric relationships between tiller height and individual plant biomass and frontal area, which provides a way to translate remotely-sensed measures of biomass into stem count and frontal area per bed area. The frontal area was measured through digital imaging of individual plants. The elastic modulus of the stem was also measured using an Instron testing machine. For sixteen 1m x 1m test plots, Normalized Difference Vegetation Index (NDVI) extracted from drone multispectral imagery was compared to measured stem count and estimated biomass. The study compared two different years and three time points within a growing season [August 2022; June, August, October 2023). In addition, at three plots the stem count was manually altered by cutting out 50% and 100% of the plants. This study found that while NDVI can be used to determine the abundance of S. alterniflora, there are several limitations that cause the correlations to be case-specific. Limitations to NDVI-S. alterniflora correlations included: (1) saturation, (2) species in-homogeneity of the area tested, (3) shoot density inhomogeneity of the area tested, and (4) environmental conditions.

Thesis

Characterization of microbial primary and secondary metabolism in the marine realm

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-09) Geller-McGrath, David ; Edgcomb, Virginia P.

This thesis applies meta-omics data analysis to elucidate the ecological roles of marine microorganisms in diverse habitats and includes the development of new bioinformatics tools to enhance these analyses. In my second chapter, I applied genome mining tools to analyze the gene content and expression of biosynthetic gene clusters (BGCs). The analysis of BGCs through largescale genome mining efforts has identified diverse natural products with potential applications in medicine and biotechnology. Many marine environments, particularly oxygen-depleted water columns and sediments, however, remain under-represented in these studies. Analysis of BGCs in free-living and particle-associated microbial communities along the oxycline water column of the Cariaco Basin, Venezuela, revealed that differences in water column redox potential were associated with microbial lifestyle and the predicted composition and production of secondary metabolites. This experience set the stage for my third chapter, in which I developed MetaPathPredict, a machine learning-based tool for predicting the metabolic potential of bacterial genomes. This tool addresses the lack of computational pipelines for pathway reconstruction that predict the presence of KEGG modules in highly incomplete prokaryotic genomes. MetaPathPredict made robust predictions in highly incomplete bacterial genomes, enabling more accurate reconstruction of their metabolic potential. In my fourth chapter, I performed metagenomic analysis of microbial communities in the hydrothermally-influenced sediments of Guaymas Basin (Gulf of California, Mexico). Previous studies indicated a decline in microbial abundance and diversity with increasing sediment depth. Analysis revealed a distribution of MAGs dominated by Chloroflexota and Thermoproteota, with diversity decreasing as temperature increased, consistent with a downcore reduction in subsurface biosphere diversity. Specific archaeal MAGs within the Thermoproteota and Hadarchaeota increased in abundance and recruitment of metatranscriptome reads towards deeper, hotter sediments, marking a transition to a specialized deep biosphere. In my fifth chapter, I developed MetaPathPredict-E, a deep learningpowered extension of MetaPathPredict for eukaryotic metabolism predictions. Eukaryotic metabolism is diverse, reflecting varied lifestyles across eukaryotic kingdoms, but the complexity of eukaryotic genomes presents challenges for assembly and annotation. MetaPathPredict-E was trained on diverse eukaryotic genomes and transcriptomes, demonstrating a robust performance on test datasets, thus advancing the study of eukaryotic metabolic potential from environmental samples.

Thesis

Decoding divergence in marine protistan communities: from strain diversity to basin biogeography

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-09) Krinos Quinn, Arianna I. ; Follows, Michael J. ; Alexander, Harriet

Protists (microbial eukaryotes) in the global ocean are critical components of primary productivity and nutrient recycling. Protists are genetically diverse and have distinctive ecological niches based on genetically-driven differences in physiological fitness. A deeper understanding of which dimensions of protistan genetic diversity translate to measurable phenotypic variation is needed to predict the impact of protists on marine biogeochemistry and protists’ environmental change sensitivity. I cultured twelve strains of the coccolithophore Gephyrocapsa huxleyi across temperatures, which revealed strain-specific differences in thermal optima and niche widths. I used traits measured during the experiments to design a Darwin ecosystem model simulation, which demonstrated basin-specific biogeography of thermal optima and niche widths (Chapter 2). For seven of the twelve strains, I sequenced transcriptomes at 3-5 temperatures to assess gene expression variation. Using the RNAseq data, I developed a regression modeling approach to identify proteome allocation model parameters. Combining differential expression analysis, gene abundance normalization, and the regression model to explore the proteome allocation model parameter space, I probed differences in modeled strategies of G. huxleyi strains in response to temperature (Chapter 3). Scalable workflows highlight the challenge and promise of meta-omic data to link community structure to physiology. I developed a pipeline for metatranscriptome analysis and taxonomic annotation to address the lack of tools built specifically for microbial eukaryotes, and created mock communities to assess recovery success in protistan metatranscriptome analysis workflows (Chapters 4 and 5). I applied these tools to a three-year metatranscriptomic dataset from Cape Cod Bay to investigate a recent emergence of a summer occolithophore population in the 20-year time series, tracking shifts in nutrient physiology to identify potential bottom-up controls (Chapter 6). This dissertation advances approaches to constrain the protistan taxonomic diversity that underlies shifts in global primary productivity and nutrient turnover. Specifically, strains of a single phytoplankton species revealed diversity relevant to a global ecosystem model. Future work will clarify variability in protistan gene content and expression that may underpin both protists’ present ecological niches and their future climate change response.

Thesis

Dynamics and implications of ROS in marine systems

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-09) Taenzer, Lina ; Hansel, Colleen M. ; Wankel, Scott

The reactive oxygen species (ROS), superoxide and hydrogen peroxide, play critical roles across diverse marine ecosystems, influencing redox chemistry and organismal health. The distribution and concentration of these compounds in the oceans may serve as important controls for various biogeochemical cycles. The contrasting physiological nature of ROS, serving as both integral compounds for cellular processes such as signaling and growth while inducing oxidative cell damage at elevated concentrations, has made interpretation of their roles in organismal and ecosystem health challenging. Despite the potential for these ROS to provide unique insights into the intricate interactions occurring at the interface between life and its surrounding environment, critical gaps in our understanding of these compounds in marine systems exist. In this thesis I explored two aspects of marine ROS. The first part is focused on advancing our understanding of the distribution of superoxide in the sea. As part of a multidisciplinary team, I developed a submersible chemiluminescent sensor (SOLARIS) capable of measuring ROS in situ to ocean depths greater than 4,000 meters. With the use of SOLARIS, I discovered that a broad diversity of sponges and corals are local hotspots of superoxide at depth. Then, I studied the distribution of superoxide in the stratified water column of the Baltic Sea and found large subsurface maxima in the aphotic zone. In the second part of this thesis, I probed the use of hydrogen peroxide as a monitoring agent of organismal health. I measured hydrogen peroxide and bromoform production by two seaweed species exposed to different stressors. An analysis of these signals suggests that hydrogen peroxide could serve as a non-invasive chemical signature for stress in seaweed meadows and farms. Lastly, I characterized hydrogen peroxide associated with different coral species during a Stony Coral Tissue Loss Disease transmission experiment. I determined that hydrogen peroxide does not predict infection before lesions are visible, thus hindering its utility as an early-stage signature of disease within corals. Altogether, this thesis extends our perspective on the distribution and controls on ROS in various marine systems and provides a baseline for using ROS dynamics to monitor organismal health.

Thesis

Quantifying the effects of sunlight on the fate of oil spilled at sea

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-09) Freeman, Danielle Haas ; Ward, Collin P.

Oil spilled at sea is transformed by sunlight-driven photochemical reactions. The transformed oil has different properties and behavior in the environment compared to the fresh oil, resulting in different fates and effects. My work in this thesis was to put numbers on these changes, with the goal of better predicting where oil goes and how it behaves in diverse spill scenarios. First, I focused on how sunlight generates water-soluble compounds from oil, which can lead to the dissolution of oil-derived compounds in seawater (photo-dissolution; Chapter 2). To find out whether photo-dissolution could be an important fate process during an oil spill, I used a combination of experiments and photochemical rate modeling to calculate photo-dissolution rates for the 2010 Deepwater Horizon spill (DwH) in the Gulf of Mexico (GoM). I found that photodissolution likely converted ~8% of the floating surface oil to dissolved organic carbon during DwH, a fraction similar in magnitude to other well-recognized fate processes. Moving beyond DwH, I evaluated the sensitivity of oil photo-dissolution and photochemically-altered oil physical properties to temperature. I found that if a spill like DwH had occurred in 5°C water rather than the exceptionally warm 30°C water of the GoM, 7x less oil could have dissolved via photodissolution and the viscosity of the remaining insoluble oil could have been 16x higher, resulting in lower entrainment of oil into the water column as small droplets (Chapter 3). The net result is that more oil would stay at the sea surface in a cold-water spill. Finally, I determined photodissolution rates for diverse oil products beyond the light crude that spilled during DwH (Chapter 4). I found that oil photo-reactivity could be predicted from oil chemical composition. I also found that photo-dissolution likely affects oil mass balance in spills of light oils forming thin slicks but not in spills of light or heavy oils forming thick slicks. Overall, this work advances our understanding of how oil changes in the environment upon sunlight exposure. This information can be applied to better predict, evaluate, and mitigate the effects of oil spilled at sea on marine ecosystems, including humans.

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