Oceanography

Permanent URI for this collectionhttps://digital.lib.washington.edu/handle/1773/4950

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Deformation at Oceanic Plate Boundaries: Insights from Geophysical Observations
(2026-04-20) Kidiwela, Maleen Wijeratna; Wilcock, William S. D.
Studies of deformation along submarine plate boundaries are constrained by the difficulties associated with conducting seismic and geodetic measurements on the seafloor. This dissertation advances three geophysical methods (tomography, geodesy, and ambient noise interferometry) to investigate how deformation is accommodated within strain cycles across the principal tectonic systems of the Wilson Cycle: rifting, seafloor spreading, and subduction. At Orca Volcano in the Bransfield Basin, a new tomographic workflow incorporating secondary arrivals through a magma chamber. The tomographic models revealed a transition in rifting style controlled by variations in mantle hydration linked to a tear in the subducting Phoenix slab. At Axial Seamount on the Juan de Fuca Ridge, three years of horizontal acoustic ranging across the caldera demonstrated that inter-eruptive extension is primarily accommodated by volumetric inflation from two pressure sources at different depths, providing new constraints on magma storage geometry and the localization of eruptions. In the Cascadia subduction zone, a decade of ambient noise interferometry with novel denoising methods uncovered distinct regional variations in shallow megathrust dynamics, including evidence for slow slip on protothrusts and fluid migration. Across these three settings, two themes emerged: fluids exert a first-order control on crustal deformation at every stage of the plate tectonic cycle, and slab tears on different depths along the subducting plate influence crustal deformation in distinct ways. Together, these studies demonstrate the value of diverse geophysical methods for resolving deformation processes that remain largely hidden beneath the oceans.
Energetics, epigenetics, and memory as acclimation strategies of marine bacteria in subzero brines
(2026-02-05) Kanaan, Georges; Deming, Jody W
Memory is familiar to us all. Our memories structure our beings and inform how we respond to the present. The principle that memory alters an individual's response to a given stimulus structures the work conducted in this thesis. I ask: why do bacteria respond the way they do to environmental stressors in the Arctic? I set out to enable the study of memory in subzero brines and investigate its existence in a model sea-ice bacterium. As the Arctic transforms at an unprecedented pace, understanding memory in this ecosystem is urgent. Larger fluctuations in environmental conditions will select for organisms with well-suited acclimation mechanisms. Memory appears to be precisely such a mechanism, allowing organisms capable of encoding, storing, and recalling information about past conditions to be more fit in the face of change. Despite the diversity of functions, mechanisms, and timescales in bacterial memory, its ecological role remains obscure. Two Arctic ecosystems provide complementary natural laboratories to investigate the ecological function of memory: cryopeg brines and sea ice. Cryopeg brines are volumes of hypersaline subzero liquid water isolated in permafrost for millennia and relatively stable until the Anthropocene. Sea ice is shorter-lived and fluctuates significantly more. With respect to variability and timescale, they offer a natural contrast in which to study memory.In Chapter 1, I reconstructed the environmental history of heterotrophic bacterial communities in cryopeg brines by developing a model relating cell density, enzyme kinetics, energetic requirements, and available energy. I estimated cell-specific metabolic rates to be higher than those in marine sediments despite lower temperatures, challenging expectations. This high energy cost suggests substantial investment in producing extracellular enzymes to liberate organic carbon and synthesizing protective compounds for cryoprotection and osmoprotection. These results provide context for considering memory: if these bacteria possess memory of a more variable past, does that memory remain after 40,000 years of environmental stability? What are the implications for their capacity to acclimate as permafrost thaws? Such questions motivate an investigation of memory in these and related Arctic environments. The fluctuations experienced by sea ice, especially in a changing Arctic, make it a promising environment in which to begin searching for memory. In Chapter 2, I searched for bacterial memory in Colwellia psychrerythraea strain 34H, a model sea-ice bacterium. Culturing 34H in alternating salinity conditions showed acclimation to repeated stress evidenced by changes in growth rates and lag times, phenotypic evidence suggestive of bacterial memory. I used DNA sequencing to determine whether DNA methylation might serve as an underlying mechanism. DNA methylation clearly regulated gene expression in response to osmotic stress. However, DNA methylation did not clearly emerge as the mechanism for memory in 34H, though further investigation is warranted. Chapter 3 extended this work to the environment by studying DNA methylation patterns of entire sea-ice bacterial communities in situ. Comparing the thermally variable top ice with the more stable bottom ice, I found differential methylation across temperature and salinity gradients in various community members. DNA methylation served multiple roles: immune defense through restriction-modification systems, gene regulation across environmental gradients, and novel roles in prophage-host interactions. The abundance of orphan methyltransferases suggests that much of this methylation was serving purposes beyond classical immune defense. These chapters show the different acclimation mechanisms used by bacteria in subzero brines, from energetic strategies to memory. By understanding what allows bacteria to thrive in these extreme environments on Earth, we push the boundaries for what can be considered habitable, with implications for ice-bound brines on Europa, Enceladus, and Mars. This dissertation lays foundational work for further investigations of memory's ecological role in bacterial communities facing rapid environmental change.
Ecology and evolution of Prochlorococcus from oxygen-deficient zones
(2026-02-05) Kellogg, Natalie Ann; Ingalls, Anitra E.; Ribalet, Francois
Prochlorococcus—the most abundant photosynthetic organism in the global ocean—is central to carbon cycling and a key model for linking microbial diversity to ecological function. Yet the functional traits and ecological roles of its most deeply branching lineages, which inhabit the low-light, blue-shifted, nutrient-rich waters within the upper regions of oxygen-deficient zones (ODZs), remain largely uncharacterized. In this thesis, I integrated metabolomics, metatranscriptomics, comparative genomics, and cultivation-based physiology to characterize both the chemical landscape of ODZs and the traits of the deeply branching Prochlorococcus populations that inhabit them. I first showed that these Prochlorococcus lineages retain ancestral glycine betaine (GBT) synthesis, and that this labile metabolite forms a major organic currency linking primary production to SAR11 demethylation in the ODZ. I then isolated the first representatives of the Prochlorococcus clade AMZ II from ODZs and demonstrated that they retain complete phycobilisomes while synthesizing divinyl chlorophyll b, revealing a transitional light-harvesting state that bridges canonical Prochlorococcus and Synechococcus architectures. Next, I characterized their photophysiology, showing broad irradiance tolerance and strong blue-light specialization consistent with life at ODZ boundaries. Together, these findings clarify the metabolism, light-harvesting strategies, and environmental specialization of ancient Prochlorococcus lineages at the edges of the ocean’s least-oxygenated waters.
Molecular mechanisms of microbial interactions in model systems and natural environments
(2026-02-05) Bartolek, Zinka; Armbrust, E. Virginia
Marine microbes are dominant life forms in the ocean and comprise dynamic populations of viruses, bacteria, archaea and single-celled eukaryotes. Interactions between marine microbes impact global biogeochemical cycles and form the base of marine food webs. Interactions range from symbiotic to parasitic, and are mediated through nutrient exchanges and chemical signals. In this dissertation, I focus on characterizing molecular mechanisms responsible for interactions within two groups of microorganisms, phytoplankton and bacteria. In Chapter 1, I studied how extracellular metabolites of an antagonistic bacterium Croceibacter atlanticus impact physiological and transcriptional changes in the model diatom Thalassiosira pseudonana through lab co-culture experiments. In response to extracellular bacterial metabolites, T. pseudonana showed inhibition of cell division, with transcriptional changes in cell cycle regulation, amino acid production and cell wall stability, suggesting that bacterial metabolites may modulate diatom metabolism in ways that support bacterial growth. In Chapter 2, I developed a new statistical method to detect microbial interactions and their transcriptional signatures from environmental metatranscriptome data collected in the North Pacific. Most consistent transcriptional interactions occurred in cross-kingdom pairs especially between diatoms and Proteobacteria, ranging from common functional mechanisms like cross-feeding and defense to species-specific mechanisms occurring through secondary metabolite exchanges, revealing molecular mechanisms of interactions directly in natural communities. In Chapter 3, I studied metabolic capabilities and interactions of 52 novel heterotrophic bacteria isolates capable of utilizing phytoplankton-derived organic matter from the Equatorial Pacific. I generated and analyzed closed genomes of novel strains, species and genus, and proposed potential metabolic exchanges between bacteria including cross-feeding of vitamins and growth factors that may influence interactions with phytoplankton hosts. In Chapter 4, I designed a course-based undergraduate research experience (CURE) that teaches students laboratory techniques and data analysis skills in genomics through exploration of the metabolism of marine bacteria. Novel Equatorial Pacific isolates and their genomes were used by students in their independent research projects to determine capacity of bacteria to grow on select phytoplankton metabolites and connect the growth phenotype to the genomic capability of the bacteria. This dissertation provides insights into the molecular mechanisms controlling interactions in marine microbial communities, from controlled lab studies to natural environments, and introduces novel methodologies to help advance our understanding of microbial interactions.
Insights from a changing ocean: Evolving biogeochemistry and its impacts on marine ecosystems and climate
(2025-10-02) Stoll, Mary Margaret; Carter, Brendan R.
Marine biogeochemistry integrates chemical, biological, geological, and physical processes that are fundamental to Earth's climate and ecosystems. As elements cycle through the ocean, atmosphere, and biosphere, they leave behind biogeochemical fingerprints that serve as proxies to track environmental change. Over the industrial era, anthropogenic CO2 emissions and other human activities have caused the oceans to change rapidly, perturbing this biogeochemical landscape. Characterizing biogeochemical shifts is critical to advance our understanding of climate-driven impacts, assess marine ecosystem health, and evaluate climate solutions. Recent advancements in biogeochemical tools and technologies have deepened our insights into oceanic change. The development of high-precision paleoproxies has extended records of ocean conditions into the pre-industrial era, while the Argo float array has enabled four-dimensional monitoring of biogeochemistry globally. High-resolution numerical modeling has also improved our ability to capture complex interactions at fine spatial and temporal scales, offering a holistic framework to understand anthropogenic impacts from past to future. Together, these technologies provide a comprehensive toolkit to characterize shifts in ocean biogeochemistry in unprecedented detail and advance our understanding of global environmental change. This thesis weaves together applications of novel biogeochemical tools to examine the drivers, impacts, and mitigation strategies of a rapidly changing ocean. Each chapter leverages diverse datasets and multiple tools to provide new insights on ocean change based on marine biogeochemistry. In Chapter 2, I combine boron-isotope measurements from cold-water corals with a biogeochemical model to reconstruct and investigate subsurface acidification trends over the industrial era in the California Current System. In Chapter 3, I combine Argo-based biogeochemical data products, archival tagging records, and machine learning methods to develop a four-dimensional species distribution model for an economically important fishery species, revealing biogeochemical constraints on its migration. In Chapter 4, I employ a high-resolution biogeochemical model of the Salish Sea to evaluate the detectability of ocean alkalinity enhancement, a marine carbon dioxide removal strategy for climate mitigation. These studies provide new frameworks and tools to investigate, monitor, and respond to a changing ocean.
The Ocean's Role in Air-Sea Interaction and Climate Predictability
(2025-10-02) Cohen, Jacob T.; Thompson, LuAnne
Ocean dynamics drive the memory of the climate system. Long-term predictions, therefore, rely on an understanding of the ocean processes that control climate variability, and the usefulness of these predictions requires an understanding of current models' predictive skill. Across three chapters, we study the influence of upper ocean dynamics influence on sea surface temperature variability, predictions of spatially coherent marine heatwave events, and predictions of seasonal-to-decadal ocean heat transport and sea ice. We first study the turbulent surface heat flux (Q) response to sea surface temperature (SST) anomalies and to mixed-layer heat content (HC) anomalies to understand where and when ocean processes control SST variability and air-sea interaction. From observational data of SST, HC, and Q, we use lagged covariances to define the feedback of SST to Q and the feedback of HC to Q. The feedback sensitivity, defined as the difference between SST-Q feedback and HC-Q feedback, illustrates the relative importance of ocean processes to atmospheric processes in controlling SST and Q variability. The regional and seasonal patterns of the sensitivity feedback demonstrate the varying pathways by which the ocean influences the surface heat flux feedback. Determining these patterns of ocean-dominated variability improves predictive understanding of the climate. We then evaluate how well climate models detect and predict spatially connected extreme SST events known as marine heatwaves (MHWs). Here, we evaluate a method of detecting and predicting spatially connected MHW objects. We apply object-based forecast verification to the CESM2 Seasonal-to-Multiyear Large Ensemble (SMYLE) experiment, a set of initialized hindcasts with 20-member ensembles of 24-month simulations initialized quarterly from 1970–2019. We demonstrate that SMYLE predicts MHWs that occur near observed MHWs with high skill at long lead times, but with errors in location, area, and intensity that grow with lead time. SMYLE exhibits improved skill in predicting the intensity of MHWs in December and January, and worse skill from August to October. This work illustrates the capacity to forecast connected MHW objects and to quantify the uncertainty in those forecasts with potential applications for future community use. The final chapter examines the prediction skill of Arctic sea ice and ocean heat transport (OHT) through the Pacific and Atlantic regions. Using the SMYLE dataset and a decadal prediction hindcast dataset (DP), we interrogate how the prediction skill of sea ice is related to the prediction skill of OHT across regions and timescales. We examine the co-occurrence of high OHT and sea ice prediction skill and evaluate the skill of DP in predicting the short-term tendency of the Arctic climate. We find high seasonal-to-decadal prediction skill and a strong relationship between the predictability of OHT and sea ice. This chapter demonstrates how ocean variability influences Arctic sea ice predictability. Together, the chapters in this dissertation contribute to our understanding of the ocean's role in climate variability and predictability.
Future global warming informed by past emissions and mid-Pliocene climate sensitivity
(2025-10-02) Dvorak, Michelle; Armour, Kyle C
Warming over the next hundred years is almost certainly expected to differ from that of the next few decades, as evolving spatial patterns of sea surface temperatures modify the global radiative feedback and thus climate sensitivity. On much longer timescales, very slow feedbacks associated with the reduction of large ice sheets and changes in vegetation and biomes are expected to enhance the ultimate "Earth system" warming in response to greenhouse gas forcing. Present-day radiative feedbacks govern the modern geophysical climate commitment (i.e., the near-future warming that will occur from only past emissions), while past climate states, such as the mid-Pliocene, permit an examination of climate feedbacks operating on much longer timescales. In Chapter 1, I describe the framework of global mean radiation balance in the climate system and the separation of forcings and feedbacks central to this thesis. I then introduce the mechanisms by which spatial patterns of sea surface temperatures alter the global mean radiative feedback. Lastly, I introduce the mid-Pliocene Warm Period (mPWP) and its utility as an analogue of future climate. In Chapter 2, I use the framework of global energy balance to estimate the magnitude of global mean warming following an abrupt cessation of anthropogenic emissions -- a geophysical climate commitment -- both in the present-day and in the future, following realistic emissions pathways. I find that the probability of our past emissions committing us to surpassing 1.5°C of global warming, at least temporarily, is already greater than 40% (as of 2020), and increases to 66% by 2029. In Chapter 3, I estimate the forcings and feedbacks operating in the mid-Pliocene in a global climate model hierarchy. I find that the non-CO2 boundary conditions of the mPWP induce a spatial pattern of warming that results in a more sensitive climate relative to the modern-day, potentially reducing estimates of modern-day climate sensitivity that are constrained by mPWP warming. On long timescales, however, these feedbacks imply that Earth System Sensitivity may be higher than previously recognized. In Chapter 4, I separate the climate response to the loss of the West Antarctic Ice Sheet from northern hemisphere boundary condition changes on the sea surface temperature patterns of the mPWP in a coupled climate model. I find that increasing high latitude ocean heat transport results in gradual Southern Ocean warming in response to a loss of the West Antarctic Ice Sheet, driving the higher sensitivity of this paleoclimate state. The results suggest that a loss of the West Antarctic Ice Sheet could produce more future global warming than previously appreciated.
Constraining Drivers of the Southern Ocean Carbon Cycle with Autonomous Observations and Numerical Simulations
(2025-10-02) Sauvé, Jade; Gray, Alison R.; Riser, Stephen C.
The Southern Ocean plays a central role in the global carbon cycle, yet the processes that govern its air-sea carbon exchange remain incompletely understood. This dissertation advances our process-based understanding of dissolved inorganic carbon (DIC) variability, a key determinant of surface ocean pCO2 and air-sea carbon fluxes. A circumpolar DIC budget framework is developed and applied to both biogeochemical observations and global ocean models to quantify the drivers of mixed layer DIC variability. The approach is further refined through a closed budget analysis in a high-resolution, data-assimilating model, enabling more detailed process-level insight into the Southern Ocean carbon cycle. Chapter 2 constructs the first observation-based, monthly resolved mixed layer DIC budget for the circumpolar Southern Ocean, using six years of autonomous biogeochemical float data. Analysis of two regions, the Sea Ice Zone (SIZ) and the Antarctic Southern Zone (ASZ), shows that biological processes dominate seasonal DIC variability, with northward Ekman transport playing a secondary but important role. On annual scales, vertical mixing supplies DIC to the mixed layer in both regions, but the fate of this DIC diverges: in the ASZ it is either consumed by biological production or outgassed, while in the SIZ it is exported northward. This wind-driven DIC redistribution emerges as a key mechanism supporting carbon outgassing, with implications for future changes under reduced sea ice cover. The results also provide a robust observational benchmark for evaluating climate models. Chapter 3 extends the DIC budget framework to evaluate seasonal carbon fluxes across multiple models, including OMIP simulations, the B-SOSE data-assimilating model, and observations. All datasets identify vertical mixing as the primary DIC source and biological uptake as the main sink, but models consistently underestimate and delay the biological drawdown, leading to a negative entrainment flux, opposite in sign to observational estimates. Advective terms show the largest model spread, reflecting differences in simulated circulation. These results highlight that even models performing well in global metrics can misrepresent key seasonal processes, emphasizing the value of process-based diagnostics to improve model fidelity. Chapter 4 shifts focus to zonal variability, revealing that zonal asymmetries in the physical drivers of carbon flux are central to explaining spatial variability in Southern Ocean air-sea carbon exchange. Using a closed budget in the B-SOSE model, the analysis identifies carbon outgassing hotspots in the Indo-Pacific ASZ linked to intense vertical mixing downstream of topographic features. Zonal advection spreads this DIC eastward, sustaining outgassing further along the path of the ACC. Regional variation in mixing, entrainment, and advection explains much of the zonal variability in air-sea carbon exchange, underscoring the limitations of zonally averaged approaches and the necessity of resolving regional processes in both modelsand diagnostics. Across all chapters, this dissertation demonstrates that carbon fluxes in the Southern Ocean result from tightly coupled physical and biological processes whose variability plays out across both space and time. It highlights the importance of moving beyond global and annual averages to resolve seasonal and regional dynamics, which are critical for understanding and predicting carbon cycle behavior. Looking forward, extending the budget framework to additional float data, higher-resolution models, and climate projections will help clarify how DIC fluxes and carbon outgassing may evolve in a warming world. These advances are essential for improving Earth system models and supporting more reliable climate policy.
Insights from Automated and Untargeted Marine Microbial Metabolomics
(2025-10-02) Kumler, William; Ingalls, Anitra E
Metabolomics is the study of small molecules that are the product of cellular metabolism. Most commonly done with mass spectrometry (MS), this field involves the characterization and quantification of the many small, bioactive molecules that serve as building blocks for life. In the marine environment, this gives us a powerful lens with which to view the forms of material and energy as well as the fluxes they undergo in a dynamic ecosystem dominated by microbial life. This dissertation applies metabolomics to the marine ecosystem to determine how the marketplace of metabolites is an integral part of the ocean's productivity. It also includes novel tools for metabolomics that were developed alongside these environmental analyses to streamline access to MS data because the existing frameworks were often fragile black boxes lacking reproducibility and scaling poorly across larger file sizes and sample sets. In Chapter 2, I developed an R package that reads the open-source mzML and mzXML file types into a tidy in-memory object for easy extraction and visualization of data subsets such as ion chromatograms. In Chapter 3 I extend this framework into the storage of MS data in on-disk databases to avoid the major memory constraints. I then contrast those databases with several alternative MS data storage methods and find that the simpler, on-disk methods result in performance improvements of 10-100x in query speed without much size penalty. In Chapter 4 I use this tool to improve the peak-picking performance of one of the most common untargeted mass-spectrometry tools and show that metabolites from the North Pacific Subtropical Gyre have a wide variety of patterns with depth in the ocean but most follow biomass. Chapter 5 expands upon this dataset by investigating how mesoscale eddy features affect the abundance of those same metabolites, with clear trends in metabolite abundance mirroring those in the biogeochemistry and community. Finally, in Chapter 6 I use isotope tracing to investigate how the open ocean euphotic community uses various forms of nitrogen. I determine that ammonia is highly bioavailable at the surface while nitrate's use is restricted to a subset of organisms. Organic nitrogen, on the other hand, is used slowly and steadily with equal utility at the surface and base of the euphotic zone. In sum, this thesis contains novel insights into marine metabolites with unprecedented detail through the use of new tools and provides a framework for future investigation into marine microbial ecosystems.
Metabolomes are an emergent property of marine microbial systems
(2025-08-01) Sacks, Joshua Scott; Ingalls, Anitra E.
Microbial communities underpin ocean biogeochemical cycles and form the basis of marine ecosystems. Microbes use and maintain pools of small, organic molecules called metabolites as the core intermediates and building blocks of their metabolisms and as currencies in the exchanges of nutrients, energy, and information. Microbes also use metabolites to adapt to environmental conditions such as osmotic pressure and oxidative stress. Metabolomics, or the measurement of all metabolites in a system (the metabolome), is a powerful tool for characterizing microbial systems in the marine environment. Metabolomics studies have revealed the role of taxonomy and physiochemical factors in controlling marine microbial metabolite pools. However, microbial ecosystems are also shaped by the myriad of biological and chemical interactions that occur among their component parts, leading to the emergence of new dynamics at the community level not predictable from studying a single organism. In this dissertation, I employ metabolomics to characterize the metabolite pools of marine microbial communities at an unprecedented scale and investigate the roles of a diverse suite of interactions in shaping metabolic processes. In Chapter 2, I developed a novel extraction approach for separating dissolved metabolites from seawater, enabling the first measurement of many dissolved compounds in marine samples. In Chapter 3, I used metabolomics and transcriptomics to characterize viral infection of the globally important cyanobacterium Prochlorococcus, revealing extensive metabolic remodeling and demonstrating the importance of viral infection in shaping marine metabolite dynamics. In Chapter 4, I used uptake experiments to quantify the cycling of two metabolites, glycine betaine and homarine, and show that the uptake rates and standing stocks of these compounds is dependent on the concentrations of other metabolites present in the system. Finally, in Chapter 5, I measured pools of osmolytes inside and outside of cells at the basin scale in the North and Equatorial Pacific Ocean and the Salish Sea. I found that the composition of osmolyte pools was largely conserved at the community level despite vast changes in microbial biomass, community composition, nutrient status, and productivity. Taken together, these projects demonstrate that the composition and fluxes of marine metabolite pools are an emergent property that stem from a wide range of interactions across scales in microbial ecosystems.
Mixing, exchange, and residence times in estuaries with complex bathymetry
(2025-05-12) Broatch, Erin Morgan; MacCready, Parker
Circulation in estuaries is complicated by irregular bathymetric features such as branching basins, constrictions, islands, river mouths distributed along the coastline, multiple entrances, and shallow sill areas. This dissertation examines the dynamics within complex fjord-type estuaries and their exchange with the coastal ocean. A combination of realistic and idealized numerical models is used to provide descriptive results and generalizable insights. In Chapter 2, output from a realistic numerical ocean model is used to study mixing in the Salish Sea. Salinity variance budgets are used to quantify the mixing in different regions within the estuary and to evaluate the importance of numerical mixing in the model. The timing of mixing in the Salish Sea is found to be tightly coupled to the river flow, and mixing hotspots are located at the river mouths. A simple approximation based on the river flow and the estuarine exchange flow salinities is shown to predict the total mixing in the Salish Sea and Puget Sound with good accuracy. Over a long time average, the exchange flow salt transport can also be used to estimate mixing in Puget Sound. In Chapters 3 and 4, an ensemble of idealized models is used to study the effects of varying sill length and its ratio to the tidal excursion. Five idealized estuary models are developed with geometry loosely based on Puget Sound and its entrance sill at Admiralty Inlet, with sill lengths ranging from 5 km to 80 km. Chapter 3 seeks to characterize the mechanisms driving the estuarine exchange flow in estuaries with long and short sills. Three different salt transport decompositions are applied at cross sections along the sill in the idealized estuary models. The behavior of salt transport over the spring-neap cycle is used to identify the dominant mechanism of exchange as either gravitational circulation or tidal pumping. At the ends of the sill, tidal pumping is found to be important regardless of sill length, whereas the middle of the sill develops a stronger gravitational circulation in the long sill models. A momentum balance analysis also supports these results. A transition from tidally-driven to gravitationally-driven exchange is shown to occur when the sill length exceeds the tidal excursion. Chapter 4 investigates the relationship between sill length and estuarine residence times. The idealized model ensemble is used to conduct particle tracking experiments and construct box models of different regions of the estuary. Both approaches are used to calculate transport time scales representing retention in the estuary, as well as reflux coefficients, which quantify subtidal recirculation on the sill. Longer sills are found to produce greater retention in the inner basin of the estuary due to increased reflux and reentry from the sill region. The fate of particles on the sill is shown to be linked to the tidal cycle and the ratio of the sill length to the tidal excursion.
Constraining Antarctic polynya formation and sea ice and snow evolution using autonomous observations and modeling
(2025-05-12) Campbell, Ethan Chen; Riser, Stephen C
This dissertation focuses on resolving key uncertainties in Southern Ocean sea ice and snow processes using under-ice autonomous ocean observations and modeling techniques in a Lagrangian, or flow-following, framework. After an introduction to the region and relevant processes (Chapter 1), the first portion of this work (Chapter 2) investigates the periodic appearance of large sea ice openings offshore of Antarctica, known as open-ocean polynyas. The rarity of these intermittent events in the 50-year satellite record has prevented oceanographers from pinpointing the factors that initiate polynyas and fully characterizing the vigorous cycle of ocean mixing and heat exchange believed to sustain them. Fortuitously, two Argo profiling floats, which are free-drifting robotic instruments that can collect ocean measurements beneath sea ice, were present during unexpected polynya events that occurred over Maud Rise in the Weddell Sea in 2016 and 2017. By placing their ocean measurements in context of meteorological data and past hydrographic and satellite records, we conclude that these sea ice openings were preconditioned by reduced upper-ocean salinity stratification and triggered by storms. Identifying links between these conditions and fluctuations in the primary mode of Southern Hemisphere climate variability, the Southern Annular Mode, yields a robust explanation for why polynyas have appeared at this location in some years but not others. These first in situ ocean observations also confirm that the anomalous openings were maintained by deep convective mixing, as long suspected. Antarctic sea ice thickness and overlying snow depth are important climate variables due to their strong influence on freshwater fluxes, ocean-atmosphere heat exchange, and momentum transfer. Yet monitoring their evolution from satellites has proven challenging, partly due to a sparsity of in situ measurements for validation purposes. The next portion of this work (Chapter 3) presents a newly developed numerical model that reconstructs the daily evolution of snow deposited on Antarctic sea ice along satellite-observed Lagrangian ice drift trajectories. Atmospheric reanalysis input data and parameterizations of key snow accumulation, erosion, and transformation processes are calibrated using autonomous snow buoy measurements. The resulting model reconstruction from 2003 to 2024 offers constraints on the annual mass budget of snow intercepted by sea ice in the Southern Ocean, including the magnitude and timing of freshwater release to the ocean. This represents a substantially larger flux than previously diagnosed, with implications for water mass transformation and vertical mixing. Snow-ice formation is inferred by comparing the simulated snow accumulation with satellite-observed snow depths, and trends in the reconstruction estimates are assessed. In the third portion of this work (Chapter 4), Antarctic sea ice formation and melt rates are directly estimated by calculating mixed layer salinity budgets along the wintertime drift trajectories of over 300 under-ice Argo profiling floats in the Southern Ocean. All except one budget term can be constrained using the float measurements and auxiliary data sources, leaving sea ice-induced fluxes from brine rejection during ice formation and freshwater release during ice melt to be inferred as the large budget residual. The seasonal cycle of sea ice exhibits a pronounced asymmetry with a prolonged net growth phase that slows in mid-winter before the initiation of rapid melt in fall. A circumpolar climatology of sea ice growth and melt rates within the Antarctic seasonal ice zone show net annual sea ice production near the Antarctic continent that switches to net annual melt at around 65°S. However, sea ice freezing and melt rates estimated from the float observations are found to be highly sensitive to uncertainties in the magnitude and timing of freshwater fluxes from snow. This float-based methodology highlights the potential to reconstruct climatological Antarctic sea ice thickness using autonomous ocean measurements. The final portion of this dissertation (Chapter 5) highlights a retrospective study on an undergraduate Python programming and ocean data analysis course that was co-developed and taught remotely in 2020 with another graduate student. Our teaching integrated evidence-based teaching practices—a flipped structure, activities infused with active learning, an individualized final research project, and efforts to center accessibility. A mixed-methods approach is used to evaluate the efficacy of the instructional design using data from surveys, online teaching platforms, student work, assessments, and a focus group. We find that the course elements bolstered student engagement and learning, allowing students with less or no prior coding experience to achieve similar success as peers with more experience.
Investigating the effects of environmental stress on coastal zooplankton populations: from mechanistic drivers to trophic impacts
(2025-01-23) Wyeth, Amy C; Keister, Julie; Grunbaum, Daniel
Environmental stressors, such as hypoxia and acidification, are increasing in intensity, duration, and extent in coastal waters and estuaries. Environmental stressors are known to affect a wide range of marine species, including zooplankton. Zooplankton are a critical link in marine food webs, connecting phytoplankton to higher trophic levels such as economically important fish, and are thought to be informative indicators of ecosystem change. For this reason, increased attention has been paid to understanding the mechanisms shaping zooplankton populations. Previous studies have shown that zooplankton exhibit both lethal and sublethal responses to changes in dissolved oxygen and pH. However, there is a range of species-specific responses to stressors. Different responses across species alter zooplankton community composition and spatial distributions, directly impacting predator-prey interactions and the trophic dynamics in coastal environments. This dissertation integrates laboratory experiments, in situ observations, and field work to understand how environmental stressors affect coastal zooplankton populations and nearshore food webs. In Chapter 1, I conducted laboratory experiments to investigate whether the copepod, Calanus pacificus, showed behavioral responses to stressors, and whether these responses lead to changes in vertical population distributions. Our laboratory experiments demonstrated significant effects of bottom water hypoxia and acidification on behavioral avoidance, swimming statistics, and apparent mortality rates in C. pacificus. In Chapter 2, I used a remote camera system to quantify in situ behavioral responses of zooplankton to stressors, using results from Chapter 1 to generate hypotheses about observations in the field. Our in situ videos revealed that copepods in stressful conditions exhibited significantly slower swimming speeds than copepods in non-stressful conditions, while amphipods showed significantly decreased abundances within stressful conditions. Finally, in Chapter 3, I collected zooplankton net tows in an intertidal estuary to investigate the transport of pelagic species into eelgrass beds and the role of eelgrass beds as potential sinks of pelagic zooplankton over the tidal cycle, potentially due to predation by juvenile fish. We found evidence of transport of pelagic species into intertidal habitats and measured large spatial and temporal variability, highlighting the need for sampling programs that can capture small-scale variability. This dissertation provides insight into the mechanisms that link the effects of environmental stressors across individual responses to population, community, and ecosystem level scales and suggests novel methodologies to help advance our understanding of changing zooplankton dynamics.
Observational estimates of ocean energy from Argo floats
(2025-01-23) Christensen, Katy; Gray, Alison R; Riser, Stephen C
This dissertation investigates energy in the ocean interior, focusing on the baroclinic conversion pathway between Eddy Available Potential Energy (EAPE) and Eddy Kinetic Energy (EKE), as well as the reservoir of EKE itself. This topic is explored using observational data from the global Argo float array, compared to using the classic approach in ocean energy analysis of examining model output. A major component of this dissertation is the development of methodology for estimating energy from observational data, which requires the consideration of numerous steps of quality control, spatial averaging techniques, and merging multiple sources of data.Because the baroclinic conversion pathway is driven by vertical motion, I show the novel method for estimating mesoscale vertical velocities from Argo float data at 1,000 m. We find that the distribution of vertical velocities in the ocean is highly non-Gaussian, with a large number of small values near zero and a small number of large values up to the order of 10−4 m s-1. The spatial variability of vertical velocity is linked to the ocean depth, where the largest values of vertical velocity appear to occur as horizontal flow interacts with topographic features. Due to the small magnitudes and high spatial variability, these estimates are amongst the first for vertical velocity across wide swaths of the interior ocean. Using these estimates of vertical velocity, I include here the result of computing the baroclinic conversion in the Southern Ocean. Using a local least-squares spatial regression for mapping, we find the anomaly components for vertical velocity and density that drive the conversion of energy by converting the EAPE in sloping isopycnals into EKE. We find that the largest values of baroclinic conversion occur in the ACC as it flows over large topographic features. The magnitude ranges from −5 to 5 Ã 10−5 kg m−1 s−3 but is positively skewed meaning that potential energy is being converted into eddy kinetic energy. This is found to agree well with model estimates of baroclinic conversion. To further understand ocean energy, I also explore estimates of EKE throughout the water column using the horizontal velocity field from the surface to 2,000 m estimated by Argo float profiles. To examine the vertical structure in the EKE, we use the square of the Rossby wave vertical modes and apply two different boundary conditions: a flat bottom and a rough bottom. Comparing the proportion of variance in the EKE explained by the different regimes, we find that the flat-bottom boundary condition accounts for a greater proportion of the variance in fewer modes; however, this result is spatially variable where the rough-bottom modes are better suited for estimating the vertical structure of EKE where there are topographic features present. The final part of this dissertation branches away from scientific research on ocean energy and into science education, where I discuss an introductory Python programming course for oceanographic data methods. Working collaboratively with another graduate student, we used evidence-based teaching practices and a constructivist approach to redesign a course to include a flipped structure, activities infused with active learning, an individualized final research project, and a focus on creating an accessible learning environment. By analyzing quantitative and qualitative data from surveys, online learning platforms, student work, assessments, and a focus group, we conclude that the instructional design facilitated learning and supported self-guided scientific inquiry. Students with less or no prior exposure to coding achieved similar success as peers with more experience, an outcome likely mediated by higher engagement with course resources. The result of this dissertation is an examination of one branch of energy in the ocean from an observational standpoint and an in-depth description of effective science communication in the classroom. Capturing the structure of EKE and the pathway that contributes to it is fundamental for understanding the effects of a changing system on climate and carbon.
Constraining cycles of deformation at submarine plate boundaries using cabled ocean bottom seismometers
(2025-01-23) Krauss, Zoe; Wilcock, William S.D.
The processes that reorganize the Earth’s crust occur primarily beneath our oceans, where it is difficult to make observations. Much of our knowledge of deformation at mid-ocean ridges and subduction zones is therefore limited to large events that can be recorded on land, including dike emplacements and moderate to large earthquakes. Although these large deformation events are thought to relieve most of the strain built up by plate motions, some fault slip can occur in the interim. Close seafloor observation of seismic signals at mid-ocean ridges and subduction zones between large events is needed to properly constrain how fault slip varies across frictional conditions and to address hazards associated with offshore faults. In this dissertation, I leverage novel cabled ocean bottom seismometer (OBS) datasets, which provide the first long-term (> 10 year) time series of seafloor seismic activity, to constrain deformational behavior between large events at submarine plate boundaries. In Chapter 2, I combine cabled OBS data from the Endeavour segment of the Juan de Fuca ridge with past autonomous OBS datasets to create an earthquake catalog that tracks how activity evolves between dike emplacements in relation to regional tectonics, magmatism, and hydrothermal fluid circulation. In Chapter 3, I show how just one cabled OBS can be used to constrain earthquake rates at the Endeavour segment, which allows the earthquake catalog to be extended by five years and supports that seismicity rates remain relatively low for most of the spreading cycle. In Chapter 4, I investigate multiplet earthquakes, groups of earthquakes with highly similar waveforms, at the Endeavour segment. I show that they represent a range of fault slip types, including fluid-induced earthquake swarms and repeating earthquakes, which provide the first direct evidence for aseismic slip at a mid-ocean ridge. Finally, in Chapter 5, I develop a new approach to search for tectonic tremor, a signal associated with slow fault slip, on individual OBSs. Application of this approach to cabled seismometers in the Cascadia subduction zone finds potential tectonic tremor signals that suggest localized shallow slow slip may occur near the deformation front.
Coupled Spatial Variability in the Sea Ice-Ocean System: From Ice Growth to Internal Waves
(2025-01-23) Crews, Laura Jean; Lee, Craig M.; Rainville, Luc
Changes in the extent, thickness, drift speed, and phenology of sea ice are altering atmosphere-ice-ocean interactions with the potential to modify climate feedback mechanisms. This thesis shows how spatial heterogeneities of the sea ice pack and the ocean mixed layer affect the coupled evolution of both media. Chapter 2 demonstrates how lateral variability in mixed layer properties feeds back into ice growth during the autumn freeze-up. Chapter 3 and Chapter 4 examine how sea ice variability impacts inertial oscillation development and internal wave generation. In Chapter 2, we used observations from autonomous vehicles, remote sensing, and a mixed layer model to show how advected sea ice meltwater cooled and restratified the mixed layer, causing earlier freeze-up than in adjacent waters. By demonstrating how melt-related temperature and stratification anomalies precondition freeze-up in predictable ways, our results can improve freeze-up forecasting. Chapter 3 used moored velocity observations, remote sensing, and an idealized ice-ocean slab model to demonstrate how sea ice lead opening permitted inertial oscillation development in winter despite persistently high ice concentrations, whereas an unfractured ice pack selectively filtered out near-inertial motions. Our results indicate that wintertime near-inertial motion predictions should account for the lateral scales of ice fracturing and cannot rely on free-drift proxies like ice concentration. Chapter 4 investigated ways in which sea ice affected the fate of energy contained in mixed layer inertial oscillations, including near-inertial internal wave generation. Moored observations, drifting buoys, and ice floe tracking in satellite imagery were used to quantify the spatial coherence scales of inertial oscillations in the marginal ice zone. Our results support the hypothesis that sea ice properties can promote spatially divergent inertial oscillations, resulting in internal wave generation. This research demonstrated reciprocal impacts between spatial variability in the sea ice and the ocean. In addition to the process-level conclusions described above, this dissertation also contributed methods for integrating data from distributed observational platforms, remote sensing, and simple models to generate system-level understanding of the coupled evolution of the atmosphere-ice-ocean system.
Seeps, slip, and subduction: A geochemical investigation of subduction zone hydrogeology and its links to megathrust slip behavior
(2025-01-23) Aylward, Irita; Solomon, Evan A
Subduction zone faults host a range of modes of slip spanning the spectrum from aseismic creep to devastating earthquakes. Hydrogeologic processes and conditions at the plate boundary and in surrounding sediments of the outer forearc have profound impacts on geomechanical processes in these convergent margins. Specifically, fluid production, permeability and fluid migration pathways, and pore fluid pressures, are thought to impact the nature and timing of slip behavior. While direct measurements of these properties are rare and limited to depths and locations only accessible by scientific ocean drilling, seafloor seeps hosted by deep-reaching faults provide a unique opportunity to assess the nature and efficiency of fluid flow through the system, informing on the state of pore fluid overpressure, the permeability structure, and the overall water budget of the outer forearc. This dissertation comprises three studies in which visual, geophysical, and chiefly geochemical methods are employed at sites of focused and diffuse flow (i.e., seeps and non-seeps, respectively) to investigate and advance our understanding of the interrelationships between mechanical and hydrogeologic processes at subduction zones.Chapters 2 and 3 target active seafloor seeps and diffuse flow sites spanning the continental slope at the northern and southern Hikurangi margin, offshore of the North Island of New Zealand. Using pore water from sediment cores and heat flow measurements, Chapter 2 provides direct constraints on the source and flow rate of fluids traveling through the accretionary wedge. Results suggest that fluids are not efficiently draining from the plate boundary or surrounding sediments to the seafloor along fault zones. This implies that splay fault permeability at depth is low in the offshore forearc, likely contributing to the accumulation of pore fluid overpressure in the region of slow slip at northern Hikurangi. Chapter 3 reports continuous fluid flow rates measured by benthic fluid flow meters deployed at seeps and non-seep locations over a 2-year period. Early in the deployment period, a large slow slip event (SSE) occurred beneath the instrument array offshore northern Hikurangi. Net flow polarities at non-seep locations are consistent with creeping on the shallow megathrust and locking in the slow slip source region in the inter-SSE period; flow transients reflect local volumetric strain induced by the slow slip event. At seep sites, flow transients additionally reflect gas-driven processes and possibly a shallow permeability response to the SSE, but convincing evidence of wide-spread fault-valving is not observed. Chapter 4 presents a detailed examination of a single seep site called Pythia’s Oasis, which is located ~20 km landward of the deformation front on the central Cascadia margin. The composition of the venting fluid suggests a fluid source within the subducting sediment section, at source temperatures of ~170 ˚C – 250 ˚C. Highly altered fluid compositions, along with anomalously high heat flow and rapid flow rates observed at Pythia’s Oasis, are consistent with focused, long-range water flow along the Alvin Canyon fault in the mid-slope region. High permeability conditions along the Alvin Canyon fault and/or high pore fluid pressures in the central Cascadia outer wedge likely permit sustained, high-volume discharge at Pythia’s Oasis. These hydrogeologic conditions may play an important role in the reduced locking, increased seismicity, and other changes in margin characteristics that occur in this region. Solute fluxes at Pythia’s Oasis resulting from the rapid, long-distance fluid transport are comparable to those at both high- and low-temperature hydrothermal discharge sites, indicating that subduction zone seeps may be more important for marine geochemical cycles than previously considered.
Virus-microbe interactions in marine environments determined by DNA proximity linkages
(2024-09-09) Rathwell, Christina Renee; Rocap, Gabrielle
Microbial processes in the ocean drive global biogeochemical cycles and within microbial communities the most abundant entities are viruses. Viruses in the marine environment can alter microbial community composition and genomic potential when they interact with host and non-host microbes. However, because many host microbes are not yet in culture, traditional methods of culturing viruses cannot yet be undertaken for most viruses. A key component of interpreting data collected about virus presence and abundance across the world’s oceans is determining with which microbes they can interact and under what conditions. In this thesis, I apply the DNA linkage method known as Hi-C sequencing to map out virus-host interactions in three different environments. In Chapter 1, I used this method to determine the impact and interaction of viruses with hosts in both particle-associated and free-living microbial communities at a depth below the euphotic zone in a shallow coastal fjord. I inferred that infected cells on particles were likely delivered to greater depths by particle flux and that viruses moved into new environments where host cells are sparse may interact with non-host organisms. In Chapter 2, I used Hi-C sequencing to analyze viral activity within the deep chlorophyll maximum of the Eastern Tropical North Pacific. Viruses were linked across multiple phytoplankton populations. I obtained evidence of viral auxiliary metabolic genes (AMGs) within Synechococcus cells at the time of sampling. Hi-C links also provided evidence of a known Phycodnaviridae, as well as a Mimivirus infecting a Bathycoccus prasinos at the time of sampling. Furthermore, a CrAss-like phage was shown to be interacting with a Planctomycetes of the Pirellulales order, a novel host in the marine environment for the Crassvirales family. In Chapter 3, I analyzed virus-microbe interactions in an oxygen deficient zone (ODZ), in the Eastern Tropical North Pacific, from which few microbes have been cultivated. The majority of organisms at this depth are prokaryotic and live amongst a diverse and unique community of viruses that have remained difficult to characterize. Hi-C links enhanced microbial binning and resulted in 268 medium-to-high quality bins with genomic potential for a range of methane, sulfur and nitrogen cycling metabolisms in the sample examined. We associated 75 viral genomes with microbial metagenomes in one sample and identified 19 virus-host interactions with high virus per host cell values. Though some virus-host interactions were predicted with computational software, the majority of viruses linking with hosts by Hi-C were not predicted computationally and these were statistically more abundant within the metagenome. Summarily, Hi-C method applied in this thesis revealed virus-microbe activity that other tools at our disposal could not, increasing our understanding of the complex path viral DNA may travel in marine environments, suggesting unique influences on biogeochemical cycling and potential genetic diversity.
Investigating blue and fin whale populations through passive acoustic monitoring using ocean bottom seismometers
(2024-09-09) Hilmo, Rose; Wilcock, William S.D.
Many large baleen whale species are endangered due to decades of commercial whaling before its international ban in the 1980s. Monitoring the recovery of their populations is difficult to study with traditional animal survey methods. Visual transect methods using ships and planes cover only small portions of baleen whales’ vast migratory ranges that span thousands of kilometers and are incomplete because they only record surfacing whales. GPS tagging studies are invaluable for studying behavior but are limited to small numbers due to cost. Passive acoustic monitoring (PAM), which detects whale presence through recording calls, is a complementary method that is not sight-limited and can provide long-term continuous data on a large spatial scale. Ocean bottom seismometers (OBSs), geophysical instruments used to study earthquakes through recording ground motion, are opportunistic PAM sensors that record large baleen whale calls. There are large amounts of publicly available OBS data, but these datasets have so far been underutilized as tool to study whales. This dissertation develops new methodologies for PAM using OBSs and highlights their utility for characterizing populations and studying behaviors of fin and blue whales. In Chapter 2, I develop, implement, and evaluate a method for ranging to fin whales using multipath reflected arrivals of calls on solitary OBSs deployed in different regions of the abyssal ocean. I demonstrate how to account for various site properties and discuss how the method might be implemented in different environments. In Chapter 3, I employ the multipath ranging method and point-transect distance sampling methods to estimate fin whale call densities using OBSs deployed in the Marianas region. This chapter demonstrates the utility of single-OBS ranging for estimating populations through PAM. In Chapter 4, I employ a previously developed acoustic localization algorithm to track calling northeast Pacific (NEP) blue whales with a pair of large OBS networks off the Pacific Northwest coast. I characterize the behavior of an understudied subpopulation of NEP blue whales that skip southward migration to investigate how they are using the temperate habitat while they overwinter. Behavioral metrics indicate that overwintering whales likely forage off the coast of Washington and Vancouver Island throughout the fall and early winter.
On Coastlines and Climate: How Basin Geometry Shapes Ocean Circulation and Global Climate
(2024-04-26) Ragen, Zho; Armour, Kyle C
This dissertation investigates the role of ocean basin geometry in the circulation of the ocean, of the atmosphere, and in shaping the global climate system as a whole. To explore this topic, a major component of this dissertation is the development of a novel coupled climate model with configurable bathymetry, orography, and coastline geometry. Here I developed an ocean--atmosphere--sea-ice model that allows the testing of different theories for the development of major hemispheric asymmetries in the climate system. The model can be configured with a wide range of continental configurations. When configured with two ocean basins -- one that is narrow and Atlantic-like and one wide and Pacific-like -- and forced with zonally uniform atmospheric conditions in an ocean-only setup, the pole-to-pole, cross-equatorial meridional overturning circulation (MOC) and associated northern high latitude deep water formation localizes to the narrower of two ocean basins. This is similar to the ocean circulation in the real world, characterized by an Atlantic meridional overturning circulation (AMOC) and neither deep water formation nor cross equatorial overturning circulation in the Pacific. Widening the narrow basin increases the strength of the overturning circulation, in contrast to previous idealized geometry ocean-only studies. Also, the shape with which the basin widens matters for the magnitude and pattern by which the MOC strengthens. For instance, maintaining straight, meridional coastlines and widening the ocean basins results in different changes to ocean circulation than widening the ocean basin by creating slanted coastlines. I show that adding an atmosphere and a land model to form a fully-coupled model reveals vastly different results. Coupling the ocean--sea-ice model to an atmosphere--land model yields a surprising result of cross-equatorial MOC and northern deep water formation in the wide basin. MOC occurs in the wide basin, where negative surface buoyancy fluxes in the northern high latitudes allows for water transformation and deep water formation. Adding a subsurface zonal sill across the basin cuts off dense isopycnals that outcrop in the southern ocean from returning to the surface in the northern wide basin, forcing watermass transformation and deep sinking into the narrow basin. Idealized continental configurations as explored in this dissertation also allow for the study of meridional heat transport by the ocean and the atmosphere. Differences in top of atmosphere radiation between different continental geometries drive different partitioning of poleward heat transport between the ocean and the atmosphere. The total climate system heat transport also can adjust, due to changes in planetary albedo driven by cloud distribution responses to ocean circulation changes. We conclude that idealized modeling studies can illuminate key features of ocean and atmosphere circulation. These findings suggest that ocean basin geometry is of primary importance for ocean circulation and setting the mean climate state.

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