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Anthropogenic emissions of carbon dioxide are warming, deoxygenating, and acidifying the global ocean. In coastal areas, these global trends are much more complicated. Climate change trends can be attenuated, exacerbated, or entirely overridden by local influences such as rivers, pollution, complex circulation patterns, or biological productivity. As such, climate stress in the coastal ocean is more accurately described as a mosaic of stress loci and refugia that shift in space and time. Capturing this complexity is difficult, but is critical for coastal resource managers tasked with sustaining local fisheries and ecosystems over small spatial and temporal scales. In this work, I investigate and identify regions of climate stress in two coastal ecosystems highly vulnerable to warming and acidification: the eastern Bering Sea and the California Current System. In the Bering Sea, I develop species distribution models for adult red king crab to evaluate the effectiveness of modeled oceanographic conditions to predict crab distributions. In the California Current System, I develop the largest synthesis of ocean acidification- and hypoxia-relevant coastal climate observations to date, then use my synthesis to evaluate spatial patterns of vulnerability to single and multiple stressors in four widely dispersed shellfish species. Throughout this work, I interrogate the utility of high-resolution maps to inform resource management decisions and find that, while spatially-explicit information about climate stresses is important, its utility for management is often undermined by uncertainty about species sensitivity to climate stress or distribution. In the California Current System, I also find that accounting for uncertainty shows where oceanographic observations versus better precision in species sensitivity metrics produces the biggest gains in information.

Climate dynamics are primarily forced by physical parameters such as insolation and ocean circulation; however, purely physical models fail to replicate the abrupt changes seen in climate records, implicating biogeochemical internal feedback mechanisms as important factors in the global climate system. Marine nutrient supply is a primary avenue that can potentially propagate climate signals to disparate parts of the globe; for example, a rapid response of the biological pump can both amplify signals and force further climate changes. Our current knowledge of paleo-biogeochemistry is limited by scant evidence and, often, low temporal resolution. This dissertation uses high-resolution marine sediments from the Subarctic and Subantarctic Pacific to reconstruct relationships between climate change, nutrient supply, and the biological pump.The Subarctic Pacific experienced a brief interval of extremely high primary productivity during the global transition from the glacial to the interglacial climate regimes. The cause of this high productivity has been debated, with both iron fertilization and reorganizations in Pacific circulation proposed: iron fertilization would suggest a strengthened biological pump, while circulation changes may indicate a weakened biological pump. Here, I reconstruct the diatom community response in terms of silicic acid utilization (single-genus silicon isotopes) and species composition, finding that silicic acid utilization was not enhanced, and that low-iron-adapted species were the primary responders to the high-productivity. These results suggest iron was the limiting nutrient during the high-productivity interval, consistent with the major reorganizations in Pacific circulation causing increased macronutrient supply and briefly releasing large amounts of CO2 to the atmosphere.Nutrient supply during the deglaciation is further explored via amino-acid-bound nitrogen isotopes from the same sediments from the Subarctic Pacific. This investigation finds that the high-productivity intervals carry an elevated signal of source δ15N (i.e., the δ15N of primary producers), corroborating a change in circulation. We also find high-productivity intervals have the lowest community Trophic Positions, indicative of shorter and more direct trophic chains, consistent with high macronutrient supply.Finally, I examine changes in sediment color in the Subantarctic Pacific across the glacial-interglacial transitions of marine isotope stages 7/8 and 17/18 and find that sediment color is strongly related to sediment composition. Interglacial intervals contain high weight percent calcium carbonate and glacial periods contain high weight percent nitrogen. This suggests the position of the Subantarctic Front was strongly linked to changes in climate, with cold periods characterized by northward expansion of high-silicate waters, favoring diatom production over coccolithophores, and strengthening the local biological pump.

Deoxygenation occurs along coastal environments and open ocean that affects ocean biogeochemistry and marine species. The causes of deoxygenation are multifaceted and can be influenced by various physical and biogeochemical properties in the ocean. The California Current System experiences deoxygenation along its coast and continental shelf, and effects sub-basins like the Santa Barbara Channel (SBC), located in the Southern California Bight. Here, oxygen concentrations can become hypoxic and anoxic, influencing the release of trace metals like iron from the sediment and the formation of sulfur-oxidizing bacteria mats in response to sulfide production in the sediment. Quantifying the impacts that deoxygenation has in the Santa Barbara Channel, will provide insights into ocean biogeochemistry locally, and in the California Current System more generally, along with guidance for broader ocean policies to advance regulations to combat ocean deoxygenation. In this dissertation, I will use data from two research expedition on R/V Atlantis in 2019 and 2023 to the Santa Barbara Channel and its basin, to quantify how benthic Fe flux affects phytoplankton growth along with the spatial and temporal distribution of oxygen in the basin; and extrapolate the impact of hypoxia and anoxia on basin-wide benthic Fe flux. Lastly, I developed a framework to determine the factors that can contribute to the implementation of deoxygenation policy into the Biodiversity Beyond National Jurisdiction Treaty. Since deoxygenation can affect marine biodiversity, fisheries management, and blue economies, it is important to determine the social-human environmental factors for governance and management as it relates to deoxygenation. Chapter 2. To investigate the influence of benthic Fe release from the oxygen-deficient deep basin on surface phytoplankton production, we combined benthic Fe flux measurements with numerical simulations using the Regional Ocean Model System coupled to the Biogeochemical Elemental Cycling model (ROMS-BEC). For this purpose, we updated the model Fe flux parameterization to include the new benthic flux measurements from the Santa Barbara Basin. Our simulations suggest that benthic Fe fluxes enhance surface primary production, supporting a positive feedback on benthic Fe release by decreasing oxygen in bottom waters. However, a reduction of phytoplankton Fe limitation by enhanced benthic fluxes near the coast may be partially compensated by increased nitrogen limitation further offshore, limiting the efficacy of this positive feedback.Chapter 3. While numerous studies have investigated the influence of hypoxia and anoxia on nutrient cycling and microbial activity in the sediment and water column of the SBC, studies that characterize the spatial distribution of dissolved oxygen in the channel, and its temporal variability, remain limited. I explored the spatial extent and temporal variability of dissolved oxygen in the SBC, with the goal of increasing our understanding of its dynamics and the consequences for the ocean biogeochemistry and phytoplankton productivity. To this end, I integrated historical observations of dissolved oxygen from California Cooperative Oceanic Fisheries Investigation (CalCOFI) and other programs with two highly spatially resolved oxygen surveys from recent cruises (AT42-19/2019 and AT50-11/2023) that deployed the Autonomous Underwater Vehicle (AUV) Sentry and the Remotely Operated Vehicle (ROV) Jason, equipped with oxygen sensors. This new data compilation provides the first spatially resolved characterization of dissolved oxygen across the SBC and in the bottom boundary layer.Chapter 4 Global deoxygenation is becoming an emerging issue in ocean policy that intersects with other ocean issues such as ocean acidification, climate impacts on marine species and marine conservation. However, deoxygenation has not appeared in international ocean policy even though the loss of oxygen transcends national and international jurisdiction. The Biodiversity Beyond National Jurisdiction Treaty (BBNJ) or “High Seas Treaty” provides an opportunity to implement deoxygenation for the High Seas. To do so we developed a framework for deoxygenation using scale and levels based on scientific understanding and consensus on the loss of oxygen that intersect with ocean governance. Our framework illustrates how ocean governance can advance ocean policy for deoxygenation that intersects with the initiative in BBNJ.

The rise of oxygen in the early Earth atmosphere allowed for a vast expansion of life, including the proliferation of animal life, that could utilize this powerful electron acceptor for new metabolisms. This oxygen requirement has left many organisms vulnerable to oxygen-depleted conditions (i.e., anoxia). These anoxic events in Earth’s aquatic environments allow for free iron (ferruginous) or free sulfide (euxinic) conditions to develop. While much research has been done on the past and present of aquatic anoxia, transiently deoxygenated systems that cycle annually between oxygenated and anoxic states are underexplored. Questions about these cycles of aquatic redox state abound; for example, 1) if benthic sulfur-oxidizing bacteria promote free sulfide at the sediment-water interface in transiently deoxygenated systems 2) if these cycles of anoxia can promote a loss of free iron from the benthic marine environment and 3) if sulfate reducing bacteria are quickly established in lacustrine waters after anoxia develops. The first and second questions will be addressed in this dissertation through a suite of investigations in the transiently deoxygenated Santa Barbara Basin. Porewater geochemistry, sulfate reduction rates, and benthic flux measurements were collected between 2019-2023 under varying oxygen concentrations. We found that sulfur-oxidizing bacterial mats in the basin are associated with high rates of dissimilatory nitrate reduction to ammonium and require an elevation of the sulfate reduction zone to the sediment-water interface in order to proliferate. Mat proliferation also requires an exhaustion of iron oxides in the surface sediment. Mat formation is also associated with extremely high fluxes of iron into the water column. This free iron is potentially lost from the basin through bottom water currents that carry mid-waters upslope during the anoxic events.The third question will be addressed in this dissertation by several geochemical and ex-situ sulfate reduction measurements taken in the Salton Sea between 2020-2023 under a variety of water column redox conditions. We found that sulfate reduction is present in waters that contained oxygen, most likely occurring inside organic particles in the water. We also found that sulfate reduction is quickly established after the onset of anoxia in the lake.

Monomethylmercury (MeHg, CH3Hg+) is a neurotoxin that bioaccumulates in the food web. Previous investigations have found eutrophication to be associated with both increases and decreases in MeHg accumulation. We embarked on a time series study at Younger Lagoon Reserve, adjacent to agricultural fields, to investigate the influence of anthropogenic nitrate on MeHg production in a local lagoon. Our work hints at why it is possible for dichotomous results to exist, and also again demonstrates that sulfur is an important control on MeHg production. MeHg production in soils has received less attention than wetland and marine environments, yet agricultural soils such as vineyards are of interest as they receive elemental sulfur applications. Our research reveals the results of a first inquiry into the fate of sulfur in vineyards and its implications for potential methylation.

Coastal oceans are among the most dramatic, engaging, and dynamic locations the Earth has to offer. The Southern California Bight (SCB) is among those locations, full of iconic coastlines, economically important fisheries, marine protected areas, ports and shipping lanes, a national park, and a massive tourism industry. The SCB homes a diverse array of ecosystem types, ranging from rocky inner-tidal reef systems to giant kelp forests. The SCB also supports a coastal population of 23 million, making this a region of high human influence. Wastewater, rivers, and other sources of anthropogenic nutrients-enter this coastline in impressive quantities daily, heavily influencing the nutrient balance of coastal ecosystems. This dissertation provides a comprehensive analysis of anthropogenic nutrient influence in the context of micro and macro algae, first through a study of wastewater distribution, then through the impacts of kelp health through a nutrient stressed event. We also explore which regions would be most ideal to support kelp farming operations, amidst this anthropogenic influence.In Chapter 2, we present a mechanistic analysis of components of oceanic wastewater discharge in the SCB. Our goal was to understand productivity in the nearshore coastal area (0-15 km of coastline) and examine how it changes with and without chemical and physical components of the major wastewater plumes. We accomplish this by using five different scenarios of a wastewater model examining the mechanisms of buoyancy and inorganic nitrogen composition of outfall plumes. In this Chapter I demonstrate that the primary factors within treated wastewater that influence the productivity are the form of dissolved inorganic nitrogen and the buoyancy of the emitted plume. I show that the effects of increased buoyancy and nutrients on biomass are non-additive. Furthermore we identify a highly seasonal cycle in the influence of outfall scenarios on biomass in the surface ocean, with the largest impacts on NPP seen in the winter, when stratification in the water column is minimal.In Chapter 3, we illuminate the influence of anthropogenic nutrient inputs on the recovery and growth of giant kelp forests in the SCB. To do this we examine kelp forests before and amidst the 2014-2016 marine heat wave (MHW) an event which caused a large loss of kelp forest area. From this study we identify a significant positive relationship of anthropogenic nutrients and kelp forest area maintained through the 2014-2016 MHW. Additionally, we find that during this period there are large portions of the SCB that would be nutrient limited if not for anthropogenic inputs.In Chapter 4, we highlight the optimal locations in the SCB to cultivate giant kelp, and analyze the anthropogenic nutrient influence in these optimal locations. As demand for aquaculture, and in particular macroalgal cultivation, grows in the SCB, so has need for siting optimal locations. Our suitability analysis utilizes highly resolved biogeochemical models to find optimal nutrient (DIN), sunlight (PAR), and water temperature, as well as locational factors such as distance to port and depth in a rigorous spatial analysis framework, which builds upon others from this region. Our suitability results identifies highly suitable regions in the Santa Monica Bay and the Santa Barbara Channel. We find that of these two regions those located in Santa Monica Bay have the least potential interference with current kelp forest areas.

Coastal waters connect the terrestrial and marine carbon cycles and are the location of a large portion of the organic carbon (OC) burial in the ocean. Anthropogenic activity has affected the carbon (C) cycling in these waters. However, the heterogeneity of these systems makes generating global estimates challenging. Thus, detailed information about the mechanisms and long-term trends of C fluxes and storage are needed to assess past and future changes to the coastal C cycle. This dissertation examines the mixing of multiple pools of C in coastal waters using C isotopes (13C and 14C). First, we performed a series of laboratory experiments that examined whether sorption of riverine dissolved OC to sediments could be isotopically selective. We found that compounds with higher ∆14C values and lower ?13C values were selectively sorbed by the sediments. Lignin phenols and black C were suspected as possible sorbed compounds. Second, we report a timeseries of ∆14C and ?13C values from dissolved inorganic C at the Newport Beach Pier, CA. This record showed a steady decrease in the ∆14C and ?13C values over the study period that indicates an increasing quantity of fossil fuel derived CO2 dissolved in the surface waters. Third, we compare the magnitude and composition of particulate OC and sedimentary OC from the Santa Clara River Estuary during periods of extreme precipitation and extreme drought. The results mirror the change in the C isotope values of atmospheric CO2 and show that even in low precipitation years, significant quantities of eroded petrogenic OC are exported by this watershed. The amount of recently produced plant- and algae-derived OC is highly variable in the estuary while the amount petrogenic OC is relatively stable over the study period. Together, these studies enhance our understanding of the processes that control C cycling within coastal waters.

Dissolved organic matter (DOM) sustains microbial activity and structures ecological interactions. The composition of DOM, in terms of quality and quantity, shapes microbial communities, subsequently affecting global biogeochemical cycles. Beyond contributing nutrient, organic molecules can also function as communication signals and, in certain scenarios, engage in chemical warfare. Therefore, a molecular-level study of DOM is necessary for a more thorough understanding of its role in aquatic environments. However, DOM exists as a very complex mixture in seawater, and its individual components' concentrations are extremely small relative to salts. This complicates the analysis of DOM and as a result, the true chemical diversity within DOM has remained elusive. To address this, innovative analytical and data processing techniques are essential. Chapter 2 introduces the analytical framework developed in this thesis. By employing untargeted metabolomics—specifically, liquid chromatography paired with high-resolution tandem mass spectrometry—and utilizing cutting-edge cheminformatic tools, I was able to illuminate the chemical dark matter of DOM. Using molecular networking and in silico annotation tools, I assigned molecular formulas and predicted structures and compound class affiliations for thousands of chemical features, representing most detectable compounds. I then used this established methodological workflow to explore the role of DOM in ecosystems vulnerable to global change, such as harmful algal blooms, coral reefs, and oxygen-deficient zones. Toxin-producing marine microalgae, Pseudo-nitzschia sp. thrive in upwelling coastal ecosystems, and their harmful blooms are increasing in frequency and intensity in the face of ecosystem changes due to global warming and eutrophication. In Chapter 3, I showed that these algae have species-specific microbiomes that appear to be interacting with unique metabolites, particularly compounds containing diverse nitrogen functional groups. This research provides an in-depth cataloging of chemical classes in algal culture, enhancing our understanding of microbial interactions. Oxygen-deficient zones (ODZs) occur naturally in coastal upwelling regions, but studies suggest they may expand due to climate change. In Chapter 4, I examined DOM in the ODZ of the Eastern Tropical North Pacific. I used specific compounds to trace organic matter inputs to the ODZ and highlighted potential reasons for DOM accumulation in these low-oxygen waters. The results suggest selective preservation of DOM, which could lead to carbon sequestration, altering the local carbon cycle. Coral reefs are among the world's most impacted ecosystems, threatened by global warming, ocean acidification, and pollution. In Chapter 5, I investigated the dynamics of DOM, which is critical to coral reefs' health, productivity, and function. Using a Lagrangian sampling approach and following the biogeochemical changes in water flowing over a rapidly flushed reef in Mo'orea, French Polynesia, I was able to provide new insights into nutrient recycling, metabolite production by benthic primary producers, and DOM removal processes over the reef. Together, the chapters of this dissertation establish a robust methodological foundation for molecular-level DOM analysis. By applying this approach to specific environments, I demonstrated the profound impact of DOM on ecosystems vulnerable to global change, underscoring its broader implications for marine biogeochemistry in a changing world.

The marine carbon cycle is a major driver of global climate. Reliable marine carbon cycle proxies are required to study the relationship between life in the ocean and climate in the past and to predict how the marine carbon cycle may change in the future. Pelagic barite in marine sediments is a valuable marine carbon cycle proxy. However, many aspects of pelagic barite dynamics are poorly constrained. Important questions remain regarding how and where pelagic barite forms, what factors influence pelagic barite dissolution in the water column, and which aspects of the marine carbon cycle the pelagic barite proxy captures. This dissertation presents observational studies and laboratory experiments that shed light on these questions and thus advance the ability of the pelagic barite proxy to provide insights into earth’s history. Chapter 1 presents a quantitative visual analysis of 5481 barite microcrystals from the Eastern Pacific water column. This extensive dataset provides new evidence for the role of organic matter aggregates in barite formation and suggests that barite records are influenced by water column dissolution and spatially heterogeneous formation. Chapter 2 uses laboratory experiments to constrain physical and chemical conditions during pelagic barite formation. These findings suggest that pelagic barite forms in marine organic matter aggregate microenvironments that are short-lived, moderately supersaturated with respect to barite, and rich in soy phospholipids. Chapter 3 uses laboratory incubations to constrain plausible water column pelagic barite dissolution rates under a range of seawater conditions. These experiments suggest that organic matter aggregates play a vital role in shielding pelagic barite from dissolution, which implies that the pelagic barite proxy captures the arrival of organic matter to the sediment-water interface. Chapter 4 presents preliminary findings regarding how pelagic barite size, abundance, and morphology vary within sediment core tops and across the sediment water interface over an offshore gradient off the coast of Southern California. This early work suggests differential dissolution of very small barite crystals at the sediment-water interface, and the data and samples acquired for this investigation are available for potential collaborators interested in pursuing the topic further. Together, these chapters increase our confidence in the barite proxy by shedding light on pelagic barite formation, dissolution, and preservation. This work advances the accurate and reliable interpretation of barite records to gain insight into past ocean conditions.

In contrast to other biogeochemical tracers, nitrogen in the ocean exists in a myriad of chemical forms, each with its own distinct properties and reactivity. These diverse chemical forms of nitrogen, including organic and inorganic compounds, are collectively involved in a unique and dynamic microbially-mediated cycle which is tightly intertwined with the overall functioning of marine ecosystems and has significant implications for the global cycles of carbon, phosphorous, and oxygen. While nitrogen is predominantly cycled between bioavailable forms in the ocean, additional anaerobic metabolic pathways emerge when the concentration of dissolved oxygen drops to suboxic or anoxic levels within the ocean's oxygen-minimum-zones (OMZs). These pathways produce gaseous dinitrogen (N2) and nitrous oxide (N2O), a potent greenhouse agent and contributor to ozone depletion, which together lead to a loss of bioavailable nitrogen from the oceans to the atmosphere. This dissertation provides a comprehensive analysis of these microbial pathways in OMZs, and further explores their sensitivity to both physical and biogeochemical variability.In Chapter 2, we describe the development of a general algorithm used to expand the observational record of a special class of subsurface, predominantly anticyclonic oceanic eddies known as submesoscale coherent vortices (SCVs). These eddies have been shown to play an oversized role in propagating water masses in the intermediate and deeper parts of the ocean, and were recently identified as hot-spots of N2 and N2O production. By applying the algorithm to the global Argo float array, we detect nearly 4000 new global observations of these eddies. Furthermore, we demonstrate that their formation takes place in regional hot-spots, allowing us to quantify their contributions to local heat and salt anomalies due to their formation and propagation.In Chapter 3, we incorporate a new model of the oceanic nitrogen cycle into an eddy-resolving 3D regional ocean model of the Eastern Tropical South Pacific, an upwelling region and hot-spot of nitrogen loss and N2O outgassing. The model accurately simulates both aerobic and anaerobic transformations responsible for N2 and N2O production, and provides a realistic representation of the large scale physical circulation. By decomposing the N2O tracer in the 3D model, we are able to attribute contributions from local biogeochemical sources and sinks, explore the role of the physical circulation in supplying N2O to the region, and ultimately quantify the drivers of N2O outgassing to the atmosphere.Finally, Chapter 4 builds upon the findings of Chapter 3. Specifically, we deploy a higher resolution version of the 3D model to explore how mesoscale-driven heterogeneity governs the production of N2 and N2O in the Eastern Tropical South Pacific. By filtering biogeochemical tracer fields into ``mean'' and ``eddy'' components (e.g., fields governed by low/high frequency and large/small spatial scales, respectively), we demonstrate that oxygen variability induced by ephemeral eddies and filaments stimulates nitrogen loss to the atmosphere, but by preferential producing N2 at the expense of N2O consumption. These findings reveal that the mesoscale circulation plays a critical role in regulating N2O production, and further implies that coarse-grained biogeochemical models may overestimate the fluxes to the atmosphere from these regions.

Past studies in paleoenvironmental reconstruction have set out to bridge the gap that limits our understanding of the biogeochemical controls in the past oceans by developing redox proxies based on trace metal content, iron speciation, and pyrite formation. Many of those studies have relied on broad-scale temporal assumptions about ocean redox conditions inferred from idealized chemical processes and classifying past oceans into either oxygenated, ferruginous, or euxinic. The redox threshold values associated with these proxies can vary considerably among depositional systems and, for this reason, geochemical proxies should be scrutinized in multiple modern deposition systems of variable redox characteristics (stable and dynamic). This dissertation applies various geochemical tools to understand the biogeochemical controls on carbon, iron, and sulfur reaction rates during early diagenesis. Specifically, I test, refine, and expand the use of pyrite as a paleoredox proxy by expanding our understanding on the controls on pyrite formation and the incorporation of trace elements in pyrite during early diagenesis by investigating those relationships in modern marine depositional systems. First, I explore the early diagenetic processes occurring in marine sediments with emphasis on the carbon, iron, and sulfur cycle–the three main components in sedimentary pyrite formation. This effort is made by measuring nutrients, organic carbon, and iron and sulfur mineralogical characterization and coupling with reactive-transport diagenetic modelling to understand the diagenetic reactions that lead to iron-sulfide precipitation within the sedimentary profile. Two geographically distinct locations are studied in detail: (1) The Santa Monica Basin (SMB), an exceptionally iron dominated system, and (2) Saanich Inlet, BC, Canada, a fjord with high redox variability and transient euxinic bottom waters. Then, I explore the relationships between the chemical signatures in syngenetic and diagenetic framboidal pyrite and the bulk chemistry of the sediments and bottom waters from Saanich Inlet, to understand the mechanisms of sulfur fractionation and trace metal incorporation in pyrite during formation. In Chapter 1, I explore the cryptic biogeochemical reactions that inhibit the formation of pyrite in the Santa Monica Basin. We find that this persistently hypoxic basin experiences limited bottom water O2 fluctuations that enables strong Fe redox cycling. This in turn enhances the formation of iron oxides bounded to organic matter (Fe[III]-OM complexes), limiting the reactivity of organic matter and iron oxides. The result is an extended ferruginous zone (dominated by iron oxides and dissolved Fe2+) and the suppression of a sulfidic zone in anoxic marine sediments. This study highlights key local controls on Fe availability in marginal basins and describes an intricate biogeochemical carbon-iron-sulfur cycling in modern and possibly ancient marine systems with important implications for Fe availability in the marine realm.Chapter 2 investigates the influence of bottom water and sediment (early diagenetic) influence on framboidal pyrite trace element incorporation under a highly redox variable system in Saanich Inlet. The nonsteady-state diagenetic nature, defined by rapid sedimentation rate, sediment reworking, and transient euxinic conditions, produce a restricted diagenetic system evident from 34S enriched sulfur isotopic signatures in the sulfidic species (H2S, FeS, FeS2). I explore the viability for trace element content in syngenetic and early-diagenetic pyrite towards capturing the first-degree redox chemistry of the ocean. To determine if pyrite reveals biogeochemical properties obscured by bulk analyses, I compare in-situ trace metal content (LA-ICP-MS technique) from framboidal pyrite grains with bulk sediment and porewater trace metal content from Saanich Inlet. Following, Chapter 3 focuses on machine-learning approaches for classifying pyrite into formation types, based on in-situ sulfur isotopes and trace metal content, and the implications for pyrite as a biosignature. Finally, the final chapter is a collection of concluding remarks on implications of using pyrite as a proxy of past environmental conditions and as a possible biosignature for ancient life.

Carbon in the earth system has gained immense relevance to modern society, and understanding the controls on and impacts of rising carbon dioxide (CO2) in the atmosphere is central to humans’ social well-being in the years to come. Predicting future changes requires both global-level knowledge of sources and sinks of CO2 to the atmosphere and local-level information about individual ecosystems’ responses to changes in environmental conditions thus far. This dissertation addresses three components of the greater effort to understand and predict impacts on the earth system of rising CO2. In the first chapter I explore whether the atmospheric CO2 record since 1900 can be used to better estimate the source of CO2 from land use and land cover change to the atmosphere when accounting for uncertainties in the other global sources of sinks of CO2 (e.g., fossil fuel emissions, terrestrial and marine drawdown and release of CO2) thus far. I show that the atmospheric CO2 record favors land use and land cover change CO2 flux estimates with lower decadal variability and can potentially highlight erroneous features in some published estimates. Further, we resolve a downward correction to the land use flux mean since 1900 across 20 published estimates of 0.35 PgC year−1 to 1.04 ± 0.57 PgC year−1. The second chapter combines observations of seawater organic and inorganic carbon in two coral reef ecosystems to add resolution to our snapshot of two coral reef systems’ biogeochemistry under current climatic conditions. The study presents the first inorganic carbon isotope measurements collected on a coral reef in Okinawa and finds that the reef has a community fractionation factor between -13.4 and -11 ‰ during organic matter fractionation. Finally, the third chapter presents the framework for a method to make fast and precise measurements of seawater dissolved inorganic carbon, which is one of the primary parameters used to quantify changes in the ocean stemming from marine biogeochemical processes and rising atmospheric CO2. This chapter shows that the developed method is capable of achieving high-precision measurements and can be calibrated, and the chapter identifies possible limitations to overall measurement precision.

The abundance and size distribution of marine organic particles are two major factors controlling biological carbon sequestration in the ocean. These quantities are the result of complex physical-biological interactions that are difficult to observe, and their spatial and temporal patterns remain uncertain. This dissertation describes our analysis of particle size distributions (PSD) and the resulting export, from a global compilation of \textit{in situ} Underwater Vision Profiler 5 (UVP5) optical measurements. In Chapter 2, we demostrate the ability to extrapolate sparse UVP5 observations to the global ocean from well-sampled oceanographic variables, using a machine learning algorithm. We reconstruct global maps of the biogenic PSD parameters (biovolume and slope) for particles at the base of the euphotic zone. These reconstructions reveal consistent global patterns, with high chlorophyll regions generally characterized by high particle biovolume and flatter PSD slope, i.e., a high relative abundance of large vs. small particles. The resulting negative correlations between particle biovolume and slope further suggest amplified effects on sinking particle fluxes. Our approach and estimates provide a baseline for understanding the export of organic matter from the surface ocean. Chapter 3 describes how applying a simple empirical relationship to our reconstructions of the PSD, we can calculate the total export. In this Chapter, we explore the seasonal and spatial patterns of carbon export. Taking advantage of the high vertical resolution of the UVP5, we quantify the export from the surface using two previously established depth horizons. We identify a larger export from the Southern Ocean than most other models of export. Similarly, we find the lower part of the euphotic zone to be dominated by heterotrophy, rather than autotrophy. Being able to reconstruct the PSD and particle flux at multiple depths allows for further exploration of the full 3-dimensional particle field. Chapter 4 describes a full 3-D model, where depth specific export is calculated, highlighting significant deviations from idealized flux profiles and quantify the efficiency of the biological pump globally. Our results reveal the primary drivers of carbon storage and sequestration and highlight the importance of transport by diel vertical migration of marine animals. These estimates of the global particle field serve as a baseline for future model-based estimates of particulate flux, and as an independent estimate of the efficiency of organic matter storage in the ocean.

The deep sea is often thought of as removed from terrestrial and nearshore processes. Despite imaginaries of discontinuity, connecting seemingly separate systems informs us on how best to relate to far, or not easily accessible, regions. Such expansive views of interconnections aid in the holistic understanding of whether and how to manage areas both far and near. Toward this, I first illuminate the surface-deep connections through the biogeochemical history of deep sea coral organic skeletons off of North-Central California that reflect overlying surface water processes over the past century. I then investigate the chemical oceanographic changes of the overlying surface waters within the past decade, and attend to the accelerating geopolitical tensions of the deep sea due to demands on land. I document a shift in coral isotopic signatures over the 20th century and modified surface and subsurface waters over the past decade. I present evidence for changes in upwelling with implications for both deep water communities and surface ocean acidification during marine heatwaves. Lastly, I will show the utility of incorporating multiple perspectives to inform 1) the contextualization of deep sea mining, 2) ongoing deep sea mining discussions, and 3) the selection of the overarching goal i.e. centering climate justice rather than green futures.

Microbial sulfate reduction (MSR) is the predominant pathway of organic matter (OM) degradation for half of all microbial cells in the ocean. However, measuring the rate and magnitude of MSR using well established radiotracer 35S-SO42- is limited logistically in the field by regulations on radioactive substances. This study lays the framework for the use of novel stable minor isotope 33S labeled sulfate for in situ measurements of MSR and fractionations. The first stage of this study compares sulfate reduction rates of 33SO42- to those of 35SO42- by pure culture Desulfovibrio vulgaris Hildenborough (DvH) in parallel bottle incubations. The second half of this study focuses on parallel incubations of 33SO42- and 3SO42- in sediment cores from the sub-oxic Santa Barbara Basin (SBB) to examine SRR and model sulfur isotope compositions of newly formed sulfides at the surface where microbial activity and pyrite formation are most active. The conclusions of these two studies pave the way for the eventual use of 33SO42- for in situ experiments where MSR is occurring rapidly and in large magnitudes.

Halogenated organic compounds (HOCs) are a diverse groups of both environmentally interesting and challenging compounds. With both natural and anthropogenic sources and a wide range of toxicities, predictions of their environmental transport and fate are not always straightforward. This dissertation includes four chapters that explore HOCs in the environment. The first chapter introduces HOCs and what is currently known about their sources and environmental transport and fate and is followed by two research chapters and a summary chapter.Chapter 2 describes the development of a nontargeted approach to catalogue the accumulative HOCs in environmental samples. A mass spectral library was constructed of 327 persistent and bioaccumulative compounds identified in blubber from two ecotypes of common bottlenose dolphins (Tursiops truncatus) sampled in the Southern California Bight. The abundance of compounds whose structures could not be fully elucidated highlights the prevalence of undiscovered HOCs accumulating in marine food webs. Eighty-six percent of the identified compounds are not currently monitored, including 133 known anthropogenic chemicals. Compounds related to dichlorodiphenyltrichloroethane (DDT) were the most abundant. Natural products were, in some cases, detected at abundances similar to anthropogenic compound abundances. This nontargeted analytical framework has generated a comprehensive list of HOCs that may be characteristic of the region, and its application within monitoring surveys may suggest new chemicals for evaluation.Chapter 3 investigated the abundance, distribution, and ecological relevance of the dimethyl (DMBPs) and methyl bipyrroles (MBPs) present in coastal- and offshore-dwelling ecotypes of common bottlenose dolphins (Tursiops truncatus) stranded within the Southern California Bight and examined pyrrole distributions and compositions across the available datasets using a lens that considers the possible sources of these compounds and their cycling once released into the environment. The fully halogenated DMBP and MBP congeners have been detected the most frequently, specifically DMBP-Br4Cl2 and MBP-Cl7 (Q1). The D/MBP concentrations vary over large ranges, and the levels of D/MBP isomers detected in the environment do not appear to follow the trend predicted by their bioconcentration factors. Overall, the offshore dolphins sampled contained more abundant and diverse D/MBPs than the coastal dolphins. The analyses illustrate that the bioaccumulation of these compounds is not necessarily straightforward in all environments. To guide future investigations, a representative suite of Q1, MBP-Cl6, MBP-Br6, DMBP-Cl6, DMBP-Br6, and DMBP-Br4Cl2 could serve as an indicator of this compound class, with differences in this fingerprint potentially related to the sample location.

Eastern Boundary Upwelling Systems (EBUS) are highly productive biomes, which provide benefit to society and support local ecosystems. Although EBUS total area is small when compared to other pelagic ecosystems, a growing body of literature demonstrate that climate impacts on EBUS will have disproportionately large consequences for human society. Like other EBUS, the California Current System (CCS) is experiencing a number of inextricably linked stressors: acidification, oxygen stress (hypoxia), altered food webs, and warming temperatures. Each stressor has the potential to change species interactions; alter the abundance and distribution of organisms; and can even result in mortality for certain organisms. Wind forcing and freshwater input drive change in the coastal zone, and result in heterogeneous expression of multiple stressors in time and space. River-flow and winds are both anticipated to change in magnitude and timing due to human- and climate-induced changes, which drive associated impacts to physical and biogeochemical processes in estuaries and continental shelves. A step towards better understanding drivers of multiple stressor interactions includes analysis of subsurface observations to identify relationships and trends in shelf waters. In this work we focus on the physical dynamics which influence dissolved oxygen (DO) over the shelf off northern California and Washington, to better understand the physical dynamics that influence hypoxia. In the CCS, and other EBUS, high productivity is supported by coastal wind-driven upwelling that supplies the shelf with nutrient-rich waters. However, high rates of productivity in the coastal zone may operate at the expense of (1) decreasing aragonite and calcite saturation states and decreasing dissolved oxygen (DO) concentrations because the water that is upwelled to the continental shelf also has reduced DO levels, lower pH, and higher concentrations of dissolved inorganic carbon (DIC); and (2) high productivity maintains a high standing stock of particulate organic carbon (POC), which builds a respiration signal in the water column and at the sediment/water interface and results in a decline in DO. These are two mechanisms that make EBUS, including the CCS, prone to hypoxia and acidification, which threaten ecosystems and the communities they support. The coastal waters of Washington (and southern British Columbia) have the highest primary productivity in the CCS, but this high productivity is not co-located with the strongest upwelling-favorable alongshore winds (which occur off northern California). This mismatch has been explored (e.g, by Hickey and Banas 2008), and results point to additional mechanisms that facilitate the region's high productivity beyond the traditional focus of the coastal wind field. The work presented in this dissertation, to explore the physical dynamics which influence DO over the shelf in two regions of the CCS, was motivated by (1) the link between productivity and hypoxia (and the mismatch of productivity/wind forcing); (2) reports of extreme low DO observed off Washington in the summers of 2017 - 2019; and (3) a lack of subsurface DO time-series observations off northern California (where peak upwelling wind stress occurs). Two chapters of this dissertation focus on the central CCS (off northern California), a region for which which DO time-series are scarce; and one chapter addresses the northern CCS (off Washington) and is comprised of an analysis of a 10-year record of DO, temperature and salinity at multiple sites along with wind and river discharge data to better understand the timing and severity of shelf hypoxia. Although the CCS is one of the most highly observed ocean regions in the world, there has been comparatively limited research on subsurface DO and carbonate system parameters in the central CCS off northern California (from 37°N to 42°N). Since long time-series of subsurface DO are relatively scarce, management decisions are made without a proper understanding of regional risk. Scientifically we are left wondering: (1) what DO levels occur in a section of the CCS that experiences the strongest upwelling favorable winds (~8x stronger than the Pacific Northwest)?; and (2) how DO levels respond to upwelling and relaxation events in this subregion? We collected time-series mooring data (temperature, salinity and DO), which are used to describe patterns and timing of hypoxia, and explore how DO levels respond to upwelling and relaxation events in the northern California coastal upwelling region. A deeper, mid-shelf site (~54m) is located in the Gulf of the Farallones, offshore San Francisco Bay, and within the more stratified upwelling shadow south of Point Reyes. The lowest DO concentrations and most persistent hypoxia were present at the mid-shelf site. At the shallower sites, (~18 and 30m), results show highly variable DO values with brief hypoxic events outside the core upwelling season (i.e., strongest winds and coldest water did not associate with the lowest DO levels). At the deeper, mid-shelf site, two distinct modes of variability were observed. During the first mode, upwelling events related to DO decline and relaxation events to increasing DO. During the second mode, the opposite occurs: upwelling related to an increase in DO and relaxation events to declining DO. At the shallower inner-shelf sites, and for the entire time-series, upwelling generally relates to DO decline and relaxation events to increasing DO. The importance of source water is clear during the first half of the mid-shelf deployment, and the overall trend and second half shows the importance of local drawdown. We also explored the seasonality of DO over a submarine bank (Cordell Bank) located at the shelf-break off northern California. Results show a recurrent seasonal cycle in temperature and DO. The similarity of seasonal patterns of temperature across years (2014 - 2018) is interesting, especially given the diverse set of oceanographic conditions the CCS experienced from 2014 – 2019. Although the coolest water occurs over the bank early in the upwelling season, the DO minimum occurs later, towards the end of the upwelling season and often during the relaxation season. Deviations from the seasonal trend observed are likely attributed to a combination of physical and biogeochemical processes working together. Specifically, we hypothesize that the interplay of wind-driven mixing and surface productivity can explain internanual differences, but additional work is needed to fully understand the role of these drivers. At Cordell Bank, DO concentrations were often below the threshold of mild hypoxia (2.45 ml/L), but only one instance of intermediate hypoxia was observed (1.4 to 2.45 ml/L) during the relaxation season (July 2017). Overall DO off northern California appears higher (fewer hypoxic events) than those observed in the northern CCS, but the upwelling favorable winds are also eight times stronger off northern California. Finally, observed DO is also lower than predicted using two source waters (PEW and PSUW) thus pointing to the likely importance of local drawdown (and potentially presence of more than two source water masses).We focused on the physical dynamics which influence shelf DO in the northern CCS (off Washington), in attempt to better understand the physical dynamics that influenced the extreme low DO observed in the summers of 2017 - 2019. Mooring data (2011 - 2020) are used to describe the timing and severity of hypoxia off Washington. River and winds data (1991 - 2020) are also used to better understand the coastal environment and drivers of low DO. From this work we found significant interannual variability in DO. The 2016-2019 low DO period is statistically associated with spicier water, suggesting a link between source waters impacted by the El Niño, very, very low North Pacific Gyre Oscillation Index, marine heat wave presence and low DO over the shelf. When compared to historical DO records, summertime hypoxic exposure appears to have worsened on the Washington shelf. However, 2011 – 2020 shows significant interannual variability without a clear downward trend. We also observed a north-south trend with lower DO in the south, which can be explained by several hypotheses, ranging from shelf width to canyons to stratification. However, the relationship between stratification, surface salinity and DO is complex. Within periods with similar surface salinity, more stratification is related to lower DO, but overall higher stratification is caused by lower surface salinity and is associated with higher DO. This likely demonstrates a complex relationship between the presence of river water advected northward by downwelling-favorable winds and vertical mixing driven by downwelling. Additional work to further assess the impact of timing of the Columbia and Fraser Rivers relative to wind events is important to understand DO and carbonate chemistry off Washington, and help make predictions for future climate conditions.

The Neogene (~23.0 – 2.6 million years ago) is the current climate analogue used in predictive scenario modeling, as it is characterized as having similar biota, geography, and environments when compared to present-day. Parameters that cannot be directly measured from the past can be estimated by stable isotope analysis measurements from proxies. Unlike most marine proxies, shark teeth provide ‘snapshots’ of environmental conditions during formation. Shark teeth can be used to calculate sea temperatures the teeth formed in after measuring δ18O of phosphate (PO4) and carbonate (CO3) within the enameloid and using δ18O of seawater (δ18Osw) estimates. Here, we model δ18OPO4 and δ18OCO3 from published linear regression equations to assess the fidelity of local T and δ18Osw being recorded in modern shark teeth. We also developed a Bayesian regression model to estimate the probability of T and δ18Osw for basins using δ18OPO4 of fossilized Neogene shark teeth from our collection and published datasets. Modern empirical δ18O and predictive δ18O* values indicate that carbonate (mean = 27.4 ± 1.5‰) is not a reliable recorder and therefore should not be considered as a paleothermometer until further constrained, but phosphate (mean = 23.5 ± 0.7‰) δ18OPO4 values were similar between taxa at localities and suggest a latitudinal temperature gradient. Variation within and between taxa may be due to species specific migration and mesothermy. Neogene T and δ18Osw estimates reflect a warmer climate, and salinity and temperature differences between the Miocene and Pliocene epochs.

Eastern boundary upwelling systems (EBUSs) are among the most ecologically diverse and productive regions in the ocean. EBUSs account for approximately 1\% of the global ocean by area, but yields nearly 20\% of the global fish catch. Thus, consequences to changes in productivity in EBUSs anticipated under climate change span from regional socioeconomic stability to global food security. Ecological responses to wind-driven upwelling in EBUSs have long been studied, yet questions still remain on the controls of the cross-shore (zonal) ecosystem composition. Previous studies indicate that large plankton contribute to a majority of the biomass near the coast, where upwelling supports high levels of productivity, whereas small plankton account for most of the biomass in offshore regions with low productivity. However, little is known about the variations in zonal ecosystem composition with respect to perturbations in the large-scale physical forcing. In this thesis, I present a new quasi-2D, idealized physical model of EBUSs and a size structured ecosystem model, in which an organism’s size is chosen to represent ecological diversity. With this coupled physical-biogeochemical model, we characterize the zonal ecosystem composition and its responses to perturbations. These results are an important step toward understanding the sensitivities of plankton communities and higher food-web structure in EBUSs.

Our understanding of the ocean historically has moved forward in parallel with our ability to make observations. In the thesis, high-resolution observations of the California Current System made by Spray underwater gliders are used to discuss extreme events, eddy across-shore transport, and the annual cycle of dissolved oxygen in the upper ocean. The time scales covered in the thesis include annual to interannual changes while the spatial scales are mesoscale and larger. The availability of high-resolution ocean glider data for over 13 years provides the backbone to conduct analyses over these time and spatial scales. The thesis starts by examining temperature and salinity extremes from 2014-2019 in the California Current System and its source waters. The 2014-2019 period was anomalously warm. In addition, a salinity anomaly from 2017-2019 in the California Current System was found to have formed in the North Pacific Subtropical Gyre in 2015 and subsequently advected into the source waters of the California Current. Next, the thesis examines the offshore propagation of subthermocline eddies from the coast. Subthermocline eddies are observed to propagate at near the local first baroclinic Rossby wave speed. It is estimated that the subthermocline eddies are important to the salt budget in the California Current System and are difficult to track with surface observations alone. The thesis next discusses dissolved oxygen observations collected from 2017 to 2020. First, the thesis considers the procedure to correct for drift in the optical sensors used to make dissolved oxygen observations. A model is fit to changes in the gain correction coefficient over time and predicts the drift for 5 years after sensor calibration. Second, the thesis describes the annual cycle of dissolved oxygen in the upper 500 m of the central and southern California Current System. A subsurface dissolved oxygen maximum is described in the oligotrophic region on the offshore edge of the California Current System. During seasonal coastal upwelling, heave of isopycnals is the primary mechanism that deoxygenates the water column, while mixing and biological sources and sinks also cause changes. Evidence of ventilation is found along sloping isopycnals which oxygenates the ocean above 300 m. The collection of work in the thesis is relevant to extreme climate events and climate change in the oceans, including impacts to the biological environment. The thesis also touches on basic research questions related to geostrophic turbulence. The discoveries in the thesis are made possible by the high-resolution ocean data collected by autonomous Spray gliders used together in a network to create sustained observations of a regional ocean.

The glacial fjords that connect the Greenland Ice Sheet to the North Atlantic control ocean heat transport toward the ice sheet and the downstream fate of glacier meltwater. This thesis builds on a growing body of research into Greenland fjord dynamics, focusing on aspects of glacier-fjord systems that are especially challenging to observe: sub-annual ocean variability beneath a floating ice tongue; iceberg meltwater properties and distribution; and the distribution and cycling of environmental mercury.Ice discharge to the ocean can be moderated by ice tongues, floating extensions of glaciers that buttress the upstream ice flow. In Chapter 3, an ice-tethered mooring record from beneath the 79 North Glacier ice tongue shows that ocean warming observed on the continental shelf is advected into the fjord and reaches the glacier grounding line within 6 months, indicating that basal melt of the ice tongue is sensitive to regional ocean variability. Icebergs calved from tidewater glaciers are a major component of fjord freshwater and heat budgets in fjords, but there are few observations to constrain iceberg melt models. In Chapter 4, meltwater plume intrusions are identified based on their temperature and salinity properties in two surveys of a large iceberg in Sermilik Fjord in southeast Greenland. The intrusions are distributed around the iceberg between 80-250 m depth and drive upwelling over vertical scales averaging 15-50 m, with the plume height primarily controlled by stratification. A standard melt plume model does not recreate the observed melt concentrations even with adjustments to the model coefficients, suggesting that more substantial modifications to the model physics are needed to accurately simulate iceberg melt and upwelling.In Chapter 5, results from a recent survey in Sermilik Fjord show that glacially modified waters are depleted in the toxic trace element mercury relative to regional ocean waters, indicating that glacier melt is not a significant source of environmental mercury in that system. We hypothesize that mercury is removed from the water column in the ice melange region near the glacier terminus through scavenging and settling of suspended sediments from iceberg melt and runoff.