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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 imp

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.

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

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 Biogeochemica

Datasets accompanying manuscript accepted for publication in Science of the Total Environment. Manuscript is titled: Implications of dietary carbon incorporation in fish carbonates for the global carbon cycle. Datasets include: 1. Mendeley-Ichthyocarbonate.csv: Presents ichthyocarbonate compositional characteristics, including stable carbon isotope values of the carbonate and associated organic matter, %TOC, and %carbonate (NM stands for not measured). 2. Mendeley-DaysPastFeeding-C.csv: Presents stable carbon isotope values of ichthyocarbonate measured in successive days since last meal, 3. Mendeley-Dietcsv: Presents compositional characteristics of diet fed to experimental fish, and 4. Mendeley-DaysPastFeeding.csv: Presents d-spacing and mol%MgCO3 calculated from results of XRD analyses.

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 biogeoche

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

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 dia

Harmful algal blooms (HABs) are a global concern in both freshwater and coastal systems; creating dire consequences for public health, water resources, and local economies. Thus, there is a focus among scientists and environmental managers on HAB prediction, prevention, and mitigation. Current chemical mitigation methods include algicides such as copper sulphate, chlorination, and hydrogen peroxide, which can have high financial costs and secondary pollution associated with them. The use of natural allelochemicals produced by plants and bacteria has received considerable attention as an alternative to synthetic algicides, as they can have negligible toxins, be highly selective, and easily degraded in the environment. This dissertation is a coalition of research looking into new sources of plant allelochemicals and whether natural levels of allelochemicals in the water column, can impact phytoplankton communities and the presence of toxin-producing algal species. The first objective focused on the use of the waste product: brewer’s spent grain (BSG), as a new control mechanism to inhibit the growth of toxic algae. BSG extract of doses higher than 250mg/L inhibited the growth of freshwater and marine toxin-producing cyanobacteria and dinoflagellate species (Microcystis aeruginosa and Karenia brevis), while not impacting the diatom and chlorophyte tested (Scenedesmus obliquus and Prorocentrum tricornutum). This same dosage of BSG caused cyanobacteria abundance in lake water to decline by 90% within 4 days and chlorophytes to dominate the community by day 6 during a microcosm study. However, an experiment controlling bacteria levels demonstrated that the decline of K. brevis growth was likely due to the increase in abundance or presence of certain types of bacteria growing with exposure to BSG extract rather than due to chemicals released from the BSG. The second and third objectives shifted focus to the New Jersey Pinelands and whether the chemicals released into the w

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 Californ

Estuarine environments are uniquely diverse coastal subsystems located at the land-river-ocean interface. Across different systems, carbon dioxide (CO2) parameters and anthropogenic inputs can vary greatly given the heterogeneity between individual estuarine systems, which makes it difficult to characterize coastal ocean systems as a whole. The Agua Hedionda Lagoon (AHL) is a tidal estuary located on the southern California coast, which supports a diverse ecosystem while serving numerous recreation activities, a marine fish hatchery, a shellfish hatchery (Carlsbad Aquafarm, CAF), and the largest desalination plant in the western hemisphere. This dissertation contains three main chapters. Chapter 1 provides the information about sampling design and instrumentation used for data collection at the AHL. The detailed steps and procedures required for quality control and processing of the data are also included. In Chapter 2, a one-year time series of carbon dioxide (CO2) data is used to establish baseline and seasonal average inorganic carbon conditions in the AHL. Based on a mass balance model of the lagoon, we propose that the outer lagoon of the AHL is a source of inorganic carbon to the adjacent ocean, through advective export, and a direct source of CO2 to the atmosphere. In Chapter 3, a time series from autonomous sensors deployed in AHL captured the effects of a massive red tide occurring along the Southern & Baja California coast during the spring of 2020. Biogeochemical data (pH and O2) were examined using an open-source model designed to filter out the influence of tides and estimate net ecosystem metabolism (NEM). Contemporaneous pH and O2 observations allowed simultaneous, independent evaluations of production, respiration and NEM.

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 so

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.

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.

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.

Estuarine environments are uniquely diverse coastal subsystems located at the land-river-ocean interface. Across different systems, carbon dioxide (CO2) parameters and anthropogenic inputs can vary greatly given the heterogeneity between individual estuarine systems, which makes it difficult to characterize coastal ocean systems as a whole. The Agua Hedionda Lagoon (AHL) is a tidal estuary located on the southern California coast, which supports a diverse ecosystem while serving numerous recreation activities, a marine fish hatchery, a shellfish hatchery (Carlsbad Aquafarm, CAF), and the largest desalination plant in the western hemisphere. This dissertation contains three main chapters. Chapter 1 provides the information about sampling design and instrumentation used for data collection at the AHL. The detailed steps and procedures required for quality control and processing of the data are also included. In Chapter 2, a one-year time series of carbon dioxide (CO2) data is used to establish baseline and seasonal average inorganic carbon conditions in the AHL. Based on a mass balance model of the lagoon, we propose that the outer lagoon of the AHL is a source of inorganic carbon to the adjacent ocean, through advective export, and a direct source of CO2 to the atmosphere. In Chapter 3, a time series from autonomous sensors deployed in AHL captured the effects of a massive red tide occurring along the Southern & Baja California coast during the spring of 2020. Biogeochemical data (pH and O2) were examined using an open-source model designed to filter out the influence of tides and estimate net ecosystem metabolism (NEM). Contemporaneous pH and O2 observations allowed simultaneous, independent evaluations of production, respiration and NEM.

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 Californ

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 so

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

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 th

Marine dissolved organic matter (DOM) is a large, dynamic, and complex pool of carbon, comparable in size to the carbon dioxide pool in the atmosphere, yet it is arguably the least understood component of the global carbon cycle. DOM deriving from picocyanobacterial cells via situationally unique mechanisms, such as viral lysis and metazoan grazing, complicate the picture as the resident pool present reflects sequestration processes that occur at time scales ranging from days to hundreds of thousands of years. Recently virus induced cell lysis released from the globally distributed picocyanobacteria, such as Synechococcus and Prochlorococcus, have been shown to release optically active DOM known as Chromophoric DOM (CDOM) that closely matches the “humic-like” appearance of marine CDOM raising questions about our understanding of this carbon pool given the reliance on spectral measures to assess its composition. Hence, this thesis is seeking to understand CDOM released by lysed picocyanobacteria and to investigate the molecular chemical composition of picocyanobacteria-derived DOM in general. A special focus will be to confirm the refractory nature of chromophores released by lysed picocyanobacteria (Synechococcus) given the reliance on optical properties of recalcitrant DOM being used in the investigation of timescales of carbon storage and biological processing of carbon. As we consider the outcomes of the current global carbon inventory with a sizable error in flux, linking products of microbial processes to chromophore structures and spectrometry is a capstone in understanding the global carbon cycle for decades of research. This study offers a direct comparison of fluorescence signatures from the Bermuda Atlantic Time-Series (BATS) and the Hawai'i Ocean Time-series (HOT), observes optical and nutrient profiles tracking long-term incubation experiments of oligotrophic microbial communities amended with Synechococcus-derived DOM, and explores new techniques in DOM

This paper is based on a comparison of the carbon parameters at the western and eastern borders of the tropical Atlantic using data collected from 55 cruises. Oceanic and coastal data, mainly total alkalinity (TA), total dissolved inorganic carbon (CT), sea surface salinity (SSS) and sea surface temperature (SST), were compiled from different sources. These data were subdivided into three subsets: oceanic data, coastal data and adjacent to the Brazilian (western) and African coastal areas (eastern) data. Significant differences between the TA data (2099.4 ± 286.4 µmol kg−1) at the western and eastern edges (2198 ± 141.9 µmol kg−1) were observed. Differences in the CT values between the western edge (1779.6 ± 236.4 µmol kg−1) and eastern edge (1892.2 ± 94.2 µmol kg−1) were also noted. This pattern was due to the different variabilities in the carbon parameters between the eastern and western border coastal areas and to the biogeochemistry that drives these parameters. In the western coastal area, the physical features of the continental carbon and oceanic waters mixing with the freshwater that flows from the Amazon and Orinoco Rivers to the South American coast are different than the physical features of the water that flows from the Congo, Volta and Niger Rivers in the eastern region. Applying the TA empirical relationship to TA with values of SSS < 35 in the western and eastern regions leads to a higher root mean square error (rmse) in the eastern and western regions. Therefore, most of the existing TA empirical relationships are most useful at the regional scale due to the difference in the water properties of each region. The relationships of TA and CT determined in the western and eastern regions do not reproduce in situ data well, especially at the adjacent edges. This difference is explained by the difference between the African and Brazilian coasts in terms of their carbon parameter characteristics and processes responsible for their variation. Based on the m

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.

This paper is based on a comparison of the carbon parameters at the western and eastern borders of the tropical Atlantic using data collected from 55 cruises. Oceanic and coastal data, mainly total alkalinity (TA), total dissolved inorganic carbon (CT), sea surface salinity (SSS) and sea surface temperature (SST), were compiled from different sources. These data were subdivided into three subsets: oceanic data, coastal data and adjacent to the Brazilian (western) and African coastal areas (eastern) data. Significant differences between the TA data (2099.4 ± 286.4 µmol kg−1) at the western and eastern edges (2198 ± 141.9 µmol kg−1) were observed. Differences in the CT values between the western edge (1779.6 ± 236.4 µmol kg−1) and eastern edge (1892.2 ± 94.2 µmol kg−1) were also noted. This pattern was due to the different variabilities in the carbon parameters between the eastern and western border coastal areas and to the biogeochemistry that drives these parameters. In the western coastal area, the physical features of the continental carbon and oceanic waters mixing with the freshwater that flows from the Amazon and Orinoco Rivers to the South American coast are different than the physical features of the water that flows from the Congo, Volta and Niger Rivers in the eastern region. Applying the TA empirical relationship to TA with values of SSS < 35 in the western and eastern regions leads to a higher root mean square error (rmse) in the eastern and western regions. Therefore, most of the existing TA empirical relationships are most useful at the regional scale due to the difference in the water properties of each region. The relationships of TA and CT determined in the western and eastern regions do not reproduce in situ data well, especially at the adjacent edges. This difference is explained by the difference between the African and Brazilian coasts in terms of their carbon parameter characteristics and processes responsible for their variation. Based on the m

The decrease in delta C-13 of dissolved inorganic carbon (delta C-13(DIC)) owing to uptake of anthropogenic CO2 (the oceanic C-13 Suess effect) in the Southeastern Indian Ocean over the last decade was calculated using an extended multiparameter linear regression technique. Samples collected on the CROCCA-2S (Coring to Reconstruct Ocean Circulation and Carbon Dioxide Across 2 Seas) cruise in November-December 2018 were compared to samples from the CLIVAR (Climate and Ocean: Variability, Predictability, and Change) and OISO (Ocean Indien Service d'Observation) programs from 2007 to 2009. Surface ocean delta C-13(DIC) decreased by an average of -0.53 +/- 0.04 parts per thousand across this period, at an average rate of -0.053 +/- 0.004 parts per thousand per year. This rate of delta C-13(DIC) change is an increase from -0.021 +/- 0.024 parts per thousand per year between 1994 and 2008. We find that the interior water mass most impacted by the oceanic C-13 Suess effect between 2008 and 2018 was Subantarctic Mode Water (SAMW), within which delta C-13(DIC) decreased by -0.044 +/- 0.002 parts per thousand per year. Using previously published relationships between the oceanic C-13 Suess effect and anthropogenic carbon, we estimate the annual storage of anthropogenic carbon within SAMW in the southeastern Indian Ocean has increased from similar to 2.0 +/- 0.2 mu mol/kg per year between 1994 and 2008 to 5.5 +/- 0.6 mu mol/kg per year between 2008 and 2018.

This thesis uses a variety of natural abundance isotope measurements to expand our understanding of nitrogen and organic carbon cycling within the ocean. Chapters 2 & 3 use stable isotopes of nitrate to investigate recent trends in nitrogen cycling in the southern California Current System (sCCS). In Chapter 2 we show that surface ocean warming during the 2015-2016 El Niño event led to reduced nitrate supply and increased reliance on recycled nitrate produced via euphotic zone nitrification. We also identified spatial and temporal variability in euphotic zone nitrate utilization associated with iron limitation of phytoplankton. Chapter 3 uses a time series of stable isotopes of nitrate along with other physical and chemical measurements to examine recent biogeochemical changes in a partially isolated marine basin off the coast of California, whose bottom waters become deoxygenated between annual flushing events. Our data confirm an unprecedented increase in water column denitrification in basin bottom waters in recent years that was likely caused by a long-term trend of decreasing oxygen concentrations outside the basin. Chapter 4 uses a variety of chemical and isotopic measurements to characterize organic matter across oxygen gradients in the eastern tropical North Pacific (ETNP). This work describes unique organic matter dynamics along the oxycline and shows that optical properties of dissolved organic matter effectively identify locations where intense oxic remineralization takes place, whereas most other bulk measurements of organic matter do not provide insight into unique processes within these environments. We also document the impact of a passing hurricane on water column properties. Chapter 5 uses thermal oxidation in conjunction with a chemical processing method to show that the current paradigm of marine DOC cycling needs revision. Our results show that even the most 14C-depleted DOC fraction exhibits a vertical radiocarbon gradient, suggesting the ad

As pH measurement technologies evolve and are increasingly used to study the ocean’s CO2 system, there is a need to assess the uncertainty of seawater pH measurements, particularly those based on the spectrophotometric method using an indicator dye, which is used to calibrate alternative pH measurement methods, including autonomous pH sensors. In this dissertation, I investigated methodological and instrumental contributions to uncertainty in spectrophotometric pH measurements, developed tools for their quality control, and evaluated their likely quality based on their consistency with other seawater CO2 parameters. The accuracy of seawater pH measurements has been questioned due to observations from open ocean cruises of a significant pH-dependent discrepancy between measured pH and pH calculated from dissolved inorganic carbon (CT) and total alkalinity (AT), using a thermodynamic model of seawater acid-base systems. Based on an analysis of high quality CO2 measurements on four open ocean cruises, I showed that a combination of plausible biases in the constants and assumptions used to calculate pH can explain the observed inconsistencies and that there is likely an unaccounted, possibly organic, contribution to the AT measured in the open ocean. Next, I developed methods for analyzing spectra to identify and possibly correct instrumental contributions to spectrophotometric pH measurement error, such as those that may arise from degradation of the spectrophotometer lamp. In another chapter, laboratory and chemical modeling experiments were conducted to evaluate how adjustments for effect of the indicator addition on the sample pH contribute to uncertainty in the final pH result. Assumptions about the indicator’s behavior can result in error in the pH correction, but is minor, except when using high dye concentrations in short pathlength cells. Finally, I evaluated the performance of pH measurements using impure m-cresol purple, which contains absorbing impurities th

The nearshore environment is an extremely dynamic seascape that is difficult to characterize with high spatial and temporal resolution. Here, I utilize a novel sensor package, the WavepHOx, to spatially depict the signature of the seawater reverse osmosis (SRWO) byproduct plume emanating from the outfall of the Carlsbad Desalination plant (CDP) over the course of 60 days and 10 different surveys with a human powered watercraft equipped with a global positioning system (GPS). Subsurface and surface measurements detected areas of seawater at the mouth of the desalination plant’s outlet into the ocean with properties 1.5% higher salinity (RMS = ±0.17%) and 7.7% (±0.20%) higher temperature than nearby ambient values (~33.4 on the Practical Salinity scale and ~14 ⁰C respectively) and similar surface values as far as 600 m from the outfall. This brine-induced gravity current tended to propagate latitudinally southward parallel to shore, consistent with the encompassing Oceanside Littoral Cell. Possible explanations for vertical distributions of the plume are also discussed. These observations provide a pathway for a new method to map the nearshore environment’s physical and biogeochemical processes.

Dissolved organic carbon (DOC) is the largest exchangeable pool of organic carbon in the ocean, and is similar in size to atmospheric carbon. DOC is formed during surface ocean primary production by marine phytoplankton and can survive on average >6000 14C years in the deep ocean. This residence time greatly exceeds that of dissolved inorganic carbon (DIC), and indicates that a majority of DOC is refractory, or unreactive. Even though previous estimates of refractory DOC (RDOC) abundance is ~95% of total DOC, the mechanisms that facilitate its formation, cycling, and sinks are still poorly understood. A better understanding of these mechanisms is important because the ocean’s role in the global carbon cycle, and global physical climate, may link closely to the strength of the biological pump and DOC storage. This dissertation research characterizes the stable and radiocarbon isotopic compositions (13C and ∆14C) of solid-phase extracted DOC (SPE-DOC), which is representative of RDOC. First, the mass and isotopic composition of extraneous carbon (Cex) in the SPE method is analyzed. This study identifies that one SPE resin commonly used to extract DOC from seawater (Bond Elut PPL) elutes SPE-DOC with isotopic heterogeneity. Incomplete elution may exclude terrestrial-like organic matter that elutes later. An updated protocol including an extended elution is developed to ensure no fractionation of SPE-DOC occurs. This updated protocol is used to characterize SPE-DOC 13C and ∆14C values at the highest latitudinal resolution to date, using samples from three GO-SHIP Repeat Hydrography Cruises spanning the central and eastern Pacific Ocean and a portion of the western Indian Ocean. SPE-DOC 13C and ∆14C values are significantly lower than those for total DOC. Low 13C values relative to total DOC indicate preferential respiration of large biomolecules with high 13C values. An additional product of this heterotrophic respiration is carboxy-rich alicyclic matter, which

Marine particles are an essential component of the marine biological pump (BP). The BP transfers particulate organic matter (POM) produced by phytoplankton at the surface into the ocean interior and exerts a primary control on the atmospheric CO2 level (Volk & Hoffert, 1985). This classic view of POM transport vertically has dominated our view of particle cycling in the ocean. It has long been known, however, that marine particles are complicated matrixes consisting of phases beyond POM (e.g., Lam et al., 2015), and the transport of particles can be both horizontal and vertical (e.g., Honjo et al., 2010). A limited number of particle concentration and composition measurements globally, however, remain one of the main barriers to understanding the biogeochemical cycling of marine particles and their associated elements and isotopes. This dissertation examines the sources, sinks, and transport of marine particles in recent U.S. GEOTRACES cruises in three ocean basins: the Western Arctic, the South Pacific, and the North Atlantic. Measurements of particle composition and metal chemical speciation are used to investigate the importance of lateral transport of particles and diel cycles of particulate manganese (Mn) in the Western Arctic Ocean, respectively. Enhancements in Mn oxides in the halocline and high lithogenic particles in the deep ocean point to the significance of lateral transport throughout the water column, while the contrasting difference in particulate Mn average oxidation states during the day and at night suggests rapid redox variations of Mn in the surface Western Arctic Ocean. The Western Arctic Ocean is characterized by the lowest particle flux of the three cruises. Our data with higher spatial and depth resolution show that there are ballast minerals present in particles in the Western Arctic Ocean, unlike what was observed by Honjo et al. (2010) using a handful of ice-tethered sediment traps. The low export fluxes found in the Western Arctic Oc

The decrease in delta C-13 of dissolved inorganic carbon (delta C-13(DIC)) owing to uptake of anthropogenic CO2 (the oceanic C-13 Suess effect) in the Southeastern Indian Ocean over the last decade was calculated using an extended multiparameter linear regression technique. Samples collected on the CROCCA-2S (Coring to Reconstruct Ocean Circulation and Carbon Dioxide Across 2 Seas) cruise in November-December 2018 were compared to samples from the CLIVAR (Climate and Ocean: Variability, Predictability, and Change) and OISO (Ocean Indien Service d'Observation) programs from 2007 to 2009. Surface ocean delta C-13(DIC) decreased by an average of -0.53 +/- 0.04 parts per thousand across this period, at an average rate of -0.053 +/- 0.004 parts per thousand per year. This rate of delta C-13(DIC) change is an increase from -0.021 +/- 0.024 parts per thousand per year between 1994 and 2008. We find that the interior water mass most impacted by the oceanic C-13 Suess effect between 2008 and 2018 was Subantarctic Mode Water (SAMW), within which delta C-13(DIC) decreased by -0.044 +/- 0.002 parts per thousand per year. Using previously published relationships between the oceanic C-13 Suess effect and anthropogenic carbon, we estimate the annual storage of anthropogenic carbon within SAMW in the southeastern Indian Ocean has increased from similar to 2.0 +/- 0.2 mu mol/kg per year between 1994 and 2008 to 5.5 +/- 0.6 mu mol/kg per year between 2008 and 2018.

Accurately measuring the marine CO2 system is imperative to assess the effect of oceanic uptake of anthropogenic CO2 and the consequences for marine biogeochemical processes. CO2 in the ocean is both a gas and an acid, so it is necessary to measure at least two parameters describing its chemistry, where two of the most commonly used parameters being pHT and total alkalinity (AT). While both are fairly straight forward to measure and have a long history in oceanography, they have unique challenges that can greatly reduce their quality for use in CO2 system calculations. For pHT measurements, especially electrometric methods involving a liquid junction, it is crucial to calibrate the measurement using a buffer prepared in a solution similar to seawater. Chapter 2 of this dissertation describes a method to prepare 0.04 mol kg-H2O−1 equimolar buffer 2-amino-2-hydroxymethyl-1,3-propanediol (TRIS)-TRIS·H+ in synthetic seawater. Its point of success is using a simple methodology that is also reproducible, and produces a buffer with a pHT within 0.006 of the assigned value 8.094 (at 25 °C). The measurement of AT and even its definition is simple, being the balance between bases and acids in seawater and measured by titration with acid. To use AT in CO2 system calculations, it is necessary to account for the non-carbonate alkalinity components. While most if not all inorganic bases and acids have been identified and can be accounted for, for decades there has been evidence for unidentified, likely organic, bases present at significant levels. Little advance has been made in understanding the alkalinity contribution from component “X” (AX) due to a lack of an unambiguous measurement. Chapter 3 describes an unambiguous, open-cell titration method to measure AX, which includes an uncertainty assessment informed both by ancillary measurements and by titration simulations using a custom chemical equilibrium model. Chapter 4 shows the success of this this titration method using a

The cycling of iron in the ocean is intimately tied to whole ecosystem processes and other biogeochemical cycles. While ocean basin surveys of iron concentration have revealed important sources to the ocean, questions remain regarding the controls on supply of this critical micronutrient to productive planktonic ecosystems. Using a combination of oceanographic-scale observations and mechanistic experiments, work in this thesis seeks to advance our understanding of controls of new and regenerated iron supply to coastal polar and temperate ecosystems and microbially-mediated cycling in such marine environments.In Chapter 2 we comprehensively characterized the cryospheric inputs of iron to Andvord Bay, a cold glaciomarine fjord located on the west Antarctic Peninsula. Iron content and speciation were measured to characterize inter-seasonal changes in the water column, a subglacial meltwater plume and glacial ice, fjord sediments, including a first assessment of iron-binding organic ligands in a highly productive fjord environment. We utilized multi-elemental analyses to understand the cycling of iron sources. Results from a high-resolution numerical model revealed episodic atmospheric forcing events are important for supplying subglacial meltwater to the surface, and for the export of surface meltwater and associated iron away from the coast. In Chapter 3 we characterize iron supply and cycling in a coastal upwelling filament, a mesoscale feature which commonly occurs during times of intensified along-shore winds in eastern boundary current systems, such as the southern California Current. We used a Lagrangian framework to capture the biogeochemical evolution of a filament, including: the development of iron-limitation of the phytoplankton community, assessment of in situ geochemical proxies of iron stress, and impacts of diminishing iron flux on phytoplankton allometric ratios, namely the biogenic silica-to-organic carbon content of diatoms. We have determined filamen

Throughout most of the world’s oceans, the bioavailability of marine dissolved organic nitrogen (DON) acts to limit marine primary production and thus is a key control on marine biogeochemical cycles and carbon sequestration. Understanding the processes that control marine DON cycling and availability, and by extension long-term carbon storage in the ocean, are thus of vital importance. Nevertheless, despite significant research, the mechanisms that lead to the accumulation of refractory DON (RDON) largely remain an enigma. In this thesis, I address this knowledge gap by investigating the source and degradation processes of traditionally studied younger, high molecular weight (HMW) DON and, for the first time, directly isolated older, low molecular weight (LMW) solid phase extracted (SPE) DON. I used a range of novel proxies and analytical approaches, including a new suite of D-amino acids and the first compound-specific specific amino acid measurements across the DON age/size spectrum. These powerful molecular level proxies for proteinaceous marine DON source and cycling allowed me to posit a new theory for bacterial control of RDON production. Finally, I pair these analyses with broader advanced solid state NMR techniques to present new information regarding overall marine DON chemical composition. Together, I use these data to propose a novel theory regarding production of the most refractory nitrogen containing molecules in the ocean, suggesting a fundamental paradigm shift in our understanding of the marine DON pool.

This thesis uses a variety of natural abundance isotope measurements to expand our understanding of nitrogen and organic carbon cycling within the ocean. Chapters 2 & 3 use stable isotopes of nitrate to investigate recent trends in nitrogen cycling in the southern California Current System (sCCS). In Chapter 2 we show that surface ocean warming during the 2015-2016 El Niño event led to reduced nitrate supply and increased reliance on recycled nitrate produced via euphotic zone nitrification. We also identified spatial and temporal variability in euphotic zone nitrate utilization associated with iron limitation of phytoplankton. Chapter 3 uses a time series of stable isotopes of nitrate along with other physical and chemical measurements to examine recent biogeochemical changes in a partially isolated marine basin off the coast of California, whose bottom waters become deoxygenated between annual flushing events. Our data confirm an unprecedented increase in water column denitrification in basin bottom waters in recent years that was likely caused by a long-term trend of decreasing oxygen concentrations outside the basin. Chapter 4 uses a variety of chemical and isotopic measurements to characterize organic matter across oxygen gradients in the eastern tropical North Pacific (ETNP). This work describes unique organic matter dynamics along the oxycline and shows that optical properties of dissolved organic matter effectively identify locations where intense oxic remineralization takes place, whereas most other bulk measurements of organic matter do not provide insight into unique processes within these environments. We also document the impact of a passing hurricane on water column properties. Chapter 5 uses thermal oxidation in conjunction with a chemical processing method to show that the current paradigm of marine DOC cycling needs revision. Our results show that even the most 14C-depleted DOC fraction exhibits a vertical radiocarbon gradient, suggesting the ad

Dissolved organic carbon (DOC) is the largest exchangeable pool of organic carbon in the ocean, and is similar in size to atmospheric carbon. DOC is formed during surface ocean primary production by marine phytoplankton and can survive on average >6000 14C years in the deep ocean. This residence time greatly exceeds that of dissolved inorganic carbon (DIC), and indicates that a majority of DOC is refractory, or unreactive. Even though previous estimates of refractory DOC (RDOC) abundance is ~95% of total DOC, the mechanisms that facilitate its formation, cycling, and sinks are still poorly understood. A better understanding of these mechanisms is important because the ocean’s role in the global carbon cycle, and global physical climate, may link closely to the strength of the biological pump and DOC storage. This dissertation research characterizes the stable and radiocarbon isotopic compositions (13C and ∆14C) of solid-phase extracted DOC (SPE-DOC), which is representative of RDOC. First, the mass and isotopic composition of extraneous carbon (Cex) in the SPE method is analyzed. This study identifies that one SPE resin commonly used to extract DOC from seawater (Bond Elut PPL) elutes SPE-DOC with isotopic heterogeneity. Incomplete elution may exclude terrestrial-like organic matter that elutes later. An updated protocol including an extended elution is developed to ensure no fractionation of SPE-DOC occurs. This updated protocol is used to characterize SPE-DOC 13C and ∆14C values at the highest latitudinal resolution to date, using samples from three GO-SHIP Repeat Hydrography Cruises spanning the central and eastern Pacific Ocean and a portion of the western Indian Ocean. SPE-DOC 13C and ∆14C values are significantly lower than those for total DOC. Low 13C values relative to total DOC indicate preferential respiration of large biomolecules with high 13C values. An additional product of this heterotrophic respiration is carboxy-rich alicyclic matter, which

Marine particles are an essential component of the marine biological pump (BP). The BP transfers particulate organic matter (POM) produced by phytoplankton at the surface into the ocean interior and exerts a primary control on the atmospheric CO2 level (Volk & Hoffert, 1985). This classic view of POM transport vertically has dominated our view of particle cycling in the ocean. It has long been known, however, that marine particles are complicated matrixes consisting of phases beyond POM (e.g., Lam et al., 2015), and the transport of particles can be both horizontal and vertical (e.g., Honjo et al., 2010). A limited number of particle concentration and composition measurements globally, however, remain one of the main barriers to understanding the biogeochemical cycling of marine particles and their associated elements and isotopes. This dissertation examines the sources, sinks, and transport of marine particles in recent U.S. GEOTRACES cruises in three ocean basins: the Western Arctic, the South Pacific, and the North Atlantic. Measurements of particle composition and metal chemical speciation are used to investigate the importance of lateral transport of particles and diel cycles of particulate manganese (Mn) in the Western Arctic Ocean, respectively. Enhancements in Mn oxides in the halocline and high lithogenic particles in the deep ocean point to the significance of lateral transport throughout the water column, while the contrasting difference in particulate Mn average oxidation states during the day and at night suggests rapid redox variations of Mn in the surface Western Arctic Ocean. The Western Arctic Ocean is characterized by the lowest particle flux of the three cruises. Our data with higher spatial and depth resolution show that there are ballast minerals present in particles in the Western Arctic Ocean, unlike what was observed by Honjo et al. (2010) using a handful of ice-tethered sediment traps. The low export fluxes found in the Western Arctic Oc

Accurately measuring the marine CO2 system is imperative to assess the effect of oceanic uptake of anthropogenic CO2 and the consequences for marine biogeochemical processes. CO2 in the ocean is both a gas and an acid, so it is necessary to measure at least two parameters describing its chemistry, where two of the most commonly used parameters being pHT and total alkalinity (AT). While both are fairly straight forward to measure and have a long history in oceanography, they have unique challenges that can greatly reduce their quality for use in CO2 system calculations. For pHT measurements, especially electrometric methods involving a liquid junction, it is crucial to calibrate the measurement using a buffer prepared in a solution similar to seawater. Chapter 2 of this dissertation describes a method to prepare 0.04 mol kg-H2O−1 equimolar buffer 2-amino-2-hydroxymethyl-1,3-propanediol (TRIS)-TRIS·H+ in synthetic seawater. Its point of success is using a simple methodology that is also reproducible, and produces a buffer with a pHT within 0.006 of the assigned value 8.094 (at 25 °C). The measurement of AT and even its definition is simple, being the balance between bases and acids in seawater and measured by titration with acid. To use AT in CO2 system calculations, it is necessary to account for the non-carbonate alkalinity components. While most if not all inorganic bases and acids have been identified and can be accounted for, for decades there has been evidence for unidentified, likely organic, bases present at significant levels. Little advance has been made in understanding the alkalinity contribution from component “X” (AX) due to a lack of an unambiguous measurement. Chapter 3 describes an unambiguous, open-cell titration method to measure AX, which includes an uncertainty assessment informed both by ancillary measurements and by titration simulations using a custom chemical equilibrium model. Chapter 4 shows the success of this this titration method using a

The cycling of iron in the ocean is intimately tied to whole ecosystem processes and other biogeochemical cycles. While ocean basin surveys of iron concentration have revealed important sources to the ocean, questions remain regarding the controls on supply of this critical micronutrient to productive planktonic ecosystems. Using a combination of oceanographic-scale observations and mechanistic experiments, work in this thesis seeks to advance our understanding of controls of new and regenerated iron supply to coastal polar and temperate ecosystems and microbially-mediated cycling in such marine environments.In Chapter 2 we comprehensively characterized the cryospheric inputs of iron to Andvord Bay, a cold glaciomarine fjord located on the west Antarctic Peninsula. Iron content and speciation were measured to characterize inter-seasonal changes in the water column, a subglacial meltwater plume and glacial ice, fjord sediments, including a first assessment of iron-binding organic ligands in a highly productive fjord environment. We utilized multi-elemental analyses to understand the cycling of iron sources. Results from a high-resolution numerical model revealed episodic atmospheric forcing events are important for supplying subglacial meltwater to the surface, and for the export of surface meltwater and associated iron away from the coast. In Chapter 3 we characterize iron supply and cycling in a coastal upwelling filament, a mesoscale feature which commonly occurs during times of intensified along-shore winds in eastern boundary current systems, such as the southern California Current. We used a Lagrangian framework to capture the biogeochemical evolution of a filament, including: the development of iron-limitation of the phytoplankton community, assessment of in situ geochemical proxies of iron stress, and impacts of diminishing iron flux on phytoplankton allometric ratios, namely the biogenic silica-to-organic carbon content of diatoms. We have determined filamen

Throughout most of the world’s oceans, the bioavailability of marine dissolved organic nitrogen (DON) acts to limit marine primary production and thus is a key control on marine biogeochemical cycles and carbon sequestration. Understanding the processes that control marine DON cycling and availability, and by extension long-term carbon storage in the ocean, are thus of vital importance. Nevertheless, despite significant research, the mechanisms that lead to the accumulation of refractory DON (RDON) largely remain an enigma. In this thesis, I address this knowledge gap by investigating the source and degradation processes of traditionally studied younger, high molecular weight (HMW) DON and, for the first time, directly isolated older, low molecular weight (LMW) solid phase extracted (SPE) DON. I used a range of novel proxies and analytical approaches, including a new suite of D-amino acids and the first compound-specific specific amino acid measurements across the DON age/size spectrum. These powerful molecular level proxies for proteinaceous marine DON source and cycling allowed me to posit a new theory for bacterial control of RDON production. Finally, I pair these analyses with broader advanced solid state NMR techniques to present new information regarding overall marine DON chemical composition. Together, I use these data to propose a novel theory regarding production of the most refractory nitrogen containing molecules in the ocean, suggesting a fundamental paradigm shift in our understanding of the marine DON pool.

The nearshore environment is an extremely dynamic seascape that is difficult to characterize with high spatial and temporal resolution. Here, I utilize a novel sensor package, the WavepHOx, to spatially depict the signature of the seawater reverse osmosis (SRWO) byproduct plume emanating from the outfall of the Carlsbad Desalination plant (CDP) over the course of 60 days and 10 different surveys with a human powered watercraft equipped with a global positioning system (GPS). Subsurface and surface measurements detected areas of seawater at the mouth of the desalination plant’s outlet into the ocean with properties 1.5% higher salinity (RMS = ±0.17%) and 7.7% (±0.20%) higher temperature than nearby ambient values (~33.4 on the Practical Salinity scale and ~14 ⁰C respectively) and similar surface values as far as 600 m from the outfall. This brine-induced gravity current tended to propagate latitudinally southward parallel to shore, consistent with the encompassing Oceanside Littoral Cell. Possible explanations for vertical distributions of the plume are also discussed. These observations provide a pathway for a new method to map the nearshore environment’s physical and biogeochemical processes.

As pH measurement technologies evolve and are increasingly used to study the ocean’s CO2 system, there is a need to assess the uncertainty of seawater pH measurements, particularly those based on the spectrophotometric method using an indicator dye, which is used to calibrate alternative pH measurement methods, including autonomous pH sensors. In this dissertation, I investigated methodological and instrumental contributions to uncertainty in spectrophotometric pH measurements, developed tools for their quality control, and evaluated their likely quality based on their consistency with other seawater CO2 parameters. The accuracy of seawater pH measurements has been questioned due to observations from open ocean cruises of a significant pH-dependent discrepancy between measured pH and pH calculated from dissolved inorganic carbon (CT) and total alkalinity (AT), using a thermodynamic model of seawater acid-base systems. Based on an analysis of high quality CO2 measurements on four open ocean cruises, I showed that a combination of plausible biases in the constants and assumptions used to calculate pH can explain the observed inconsistencies and that there is likely an unaccounted, possibly organic, contribution to the AT measured in the open ocean. Next, I developed methods for analyzing spectra to identify and possibly correct instrumental contributions to spectrophotometric pH measurement error, such as those that may arise from degradation of the spectrophotometer lamp. In another chapter, laboratory and chemical modeling experiments were conducted to evaluate how adjustments for effect of the indicator addition on the sample pH contribute to uncertainty in the final pH result. Assumptions about the indicator’s behavior can result in error in the pH correction, but is minor, except when using high dye concentrations in short pathlength cells. Finally, I evaluated the performance of pH measurements using impure m-cresol purple, which contains absorbing impurities th

The decrease in delta C-13 of dissolved inorganic carbon (delta C-13(DIC)) owing to uptake of anthropogenic CO2 (the oceanic C-13 Suess effect) in the Southeastern Indian Ocean over the last decade was calculated using an extended multiparameter linear regression technique. Samples collected on the CROCCA-2S (Coring to Reconstruct Ocean Circulation and Carbon Dioxide Across 2 Seas) cruise in November-December 2018 were compared to samples from the CLIVAR (Climate and Ocean: Variability, Predictability, and Change) and OISO (Ocean Indien Service d'Observation) programs from 2007 to 2009. Surface ocean delta C-13(DIC) decreased by an average of -0.53 +/- 0.04 parts per thousand across this period, at an average rate of -0.053 +/- 0.004 parts per thousand per year. This rate of delta C-13(DIC) change is an increase from -0.021 +/- 0.024 parts per thousand per year between 1994 and 2008. We find that the interior water mass most impacted by the oceanic C-13 Suess effect between 2008 and 2018 was Subantarctic Mode Water (SAMW), within which delta C-13(DIC) decreased by -0.044 +/- 0.002 parts per thousand per year. Using previously published relationships between the oceanic C-13 Suess effect and anthropogenic carbon, we estimate the annual storage of anthropogenic carbon within SAMW in the southeastern Indian Ocean has increased from similar to 2.0 +/- 0.2 mu mol/kg per year between 1994 and 2008 to 5.5 +/- 0.6 mu mol/kg per year between 2008 and 2018.

The decrease in delta C-13 of dissolved inorganic carbon (delta C-13(DIC)) owing to uptake of anthropogenic CO2 (the oceanic C-13 Suess effect) in the Southeastern Indian Ocean over the last decade was calculated using an extended multiparameter linear regression technique. Samples collected on the CROCCA-2S (Coring to Reconstruct Ocean Circulation and Carbon Dioxide Across 2 Seas) cruise in November-December 2018 were compared to samples from the CLIVAR (Climate and Ocean: Variability, Predictability, and Change) and OISO (Ocean Indien Service d'Observation) programs from 2007 to 2009. Surface ocean delta C-13(DIC) decreased by an average of -0.53 +/- 0.04 parts per thousand across this period, at an average rate of -0.053 +/- 0.004 parts per thousand per year. This rate of delta C-13(DIC) change is an increase from -0.021 +/- 0.024 parts per thousand per year between 1994 and 2008. We find that the interior water mass most impacted by the oceanic C-13 Suess effect between 2008 and 2018 was Subantarctic Mode Water (SAMW), within which delta C-13(DIC) decreased by -0.044 +/- 0.002 parts per thousand per year. Using previously published relationships between the oceanic C-13 Suess effect and anthropogenic carbon, we estimate the annual storage of anthropogenic carbon within SAMW in the southeastern Indian Ocean has increased from similar to 2.0 +/- 0.2 mu mol/kg per year between 1994 and 2008 to 5.5 +/- 0.6 mu mol/kg per year between 2008 and 2018.

Methane (CH4) is a potent greenhouse gas and its concentration has been increasing in the atmosphere. While natural emissions from inland water bodies are known to be important, there is large uncertainty in the amount of methane released from lakes to the atmosphere, especially from Northern latitudes. Part of this is due to limited sampling in these systems during dynamic periods, such as ice-over and ice-melt. To better understand these temporal dynamics, I used autonomous, continuous samplers (OsmoSamplers) to collect lake water year-round over two years (2015-2017). Lake water was collected at a fine temporal resolution to provide time-integrated (~1 week) samples from multiple Arctic lakes within the Mackenzie Delta. The Mackenzie Delta is a lake-rich, productive environment that is expected to be a significant source of methane to the atmosphere. Lakes spanning the central delta and outer delta were sampled for methane concentration and stable carbon isotope ratio (δ13C-CH4) changes, ion concentrations, and water column characteristics were measured with continuous sensor data (temperature, water pressure, conductivity, light, and dissolved oxygen). These unique time-series datasets show lakes exhibit a close coupling of dissolved oxygen, and other electron acceptors, with the timing of methane increasing during ice-cover. The increase in methane concentrations is primarily from diffusion out of sediments and possibly water-column methanogenesis. One lake in the outer delta exhibited thermogenic gas bubble dissolution that contributed to under-ice methane concentration increases. Following ice-melt, lake depth appears to impact methane release to the atmosphere. Shallower lakes exhibit rapid fluxes followed by significant microbial methanotrophy. Deeper lakes in the central delta are connected to groundwater, though it does not appear groundwater transports methane. This is the first study of dissolved methane and gas bubble 14C-age in the Mackenzie Delta and

The southern CCS (sCCS), part of the California Current Ecosystem (CCE), is home to the California Cooperative Oceanic Fisheries Investigation (CalCOFI) survey program and the California Current Ecosystem Long Term Ecological Research (CCE-LTER) program. CalCOFI, begun in 1949, was designed as a survey program, sampling the same stations each quarter; whereas, the CCE-LTER program was designed to study interactions between various physical perturbations and ecosystem processes using Lagrangian cycles. The goal of this thesis was to examine microbial dynamics within these two programs and present a model for carbon fluxes into and out of the bacterial compartment. Chapter 1 ‘binned’ findings from CCE-LTER cruises into the relevant CalCOFI climatology and hydrography allowing the mechanistic studies into microbial dynamics enabled by the CCE-LTER program to be interpreted in the context of long-term observations. For example, the underlying mechanism of the enhanced microbial loop hypothesis, originally based on CalCOFI data, was supported using bacterial production data from CCE-LTER cycles in 2017. Additionally, the picoplankton community responded to broad climate variability with increased abundances and shifts in spatial distribution following a switch to the positive phase of the Pacific Decadal Oscillation at the end of 2013. Using the binned oceanic regions designated in Chapter 1, Chapter 2 showed that including the bacterial component in the food web strengthened previous conclusions that the nearshore is net autotrophic, providing excess carbon available to be laterally exported to the offshore. Examination of the westward propagating 2017 Morro Bay filament supported the hypothesis that lateral transport of organic material could support offshore, net heterotrophic communities. Bacterial production was strongly correlated to organic carbon pools, as observed in Chapter 3. Bottom-up control of bacterial production across the CCE was comparable to global tre

As a scarce but essential micronutrient for microbial growth in the marine environment, iron plays a critical role in supporting marine primary productivity and is tightly coupled to the cycling of carbon and additional macronutrients. While significant progress in recent years has been made in understanding the distribution of iron and iron-binding ligands in the marine environment, many questions remain regarding the mechanistic processes underlying these distributions.Heterotrophic bacteria serve as the primary drivers of the turnover of organic matter in the marine environment and have a significant cellular iron requirement, making them an important link between iron and carbon biogeochemical cycles. The work presented in this dissertation aims to improve our understanding of the molecular mechanisms by which heterotrophic marine bacteria acquire iron from their surroundings and the subsequent effects of their metabolic activities on both iron and carbon biogeochemical cycling. We have first developed Alteromonas macleodii ATCC 27126 as a model marine organism for the study of iron acquisition by heterotrophic bacteria. This has allowed us to characterize outer membrane TonB-dependent transporters for organically complexed forms of iron across the genus Alteromonas. This work revealed that a high diversity of iron-ligand compounds in the marine environment are potentially bioavailable. We have also utilized Alteromonas macleodii ATCC 27126 as a model organism for studying the functional role of siderophore production in iron acquisition in the marine environment. Through the insertional inactivation of the petrobactin biosynthetic pathway, we have determined that siderophore production increases the bioavailability of non-labile iron sources such as particulate minerals. Finally, in microcosm field experiments, we examined the transcriptional response of natural heterotrophic bacterial communities in the southern California Current System to iron additions demo

The southern CCS (sCCS), part of the California Current Ecosystem (CCE), is home to the California Cooperative Oceanic Fisheries Investigation (CalCOFI) survey program and the California Current Ecosystem Long Term Ecological Research (CCE-LTER) program. CalCOFI, begun in 1949, was designed as a survey program, sampling the same stations each quarter; whereas, the CCE-LTER program was designed to study interactions between various physical perturbations and ecosystem processes using Lagrangian cycles. The goal of this thesis was to examine microbial dynamics within these two programs and present a model for carbon fluxes into and out of the bacterial compartment. Chapter 1 ‘binned’ findings from CCE-LTER cruises into the relevant CalCOFI climatology and hydrography allowing the mechanistic studies into microbial dynamics enabled by the CCE-LTER program to be interpreted in the context of long-term observations. For example, the underlying mechanism of the enhanced microbial loop hypothesis, originally based on CalCOFI data, was supported using bacterial production data from CCE-LTER cycles in 2017. Additionally, the picoplankton community responded to broad climate variability with increased abundances and shifts in spatial distribution following a switch to the positive phase of the Pacific Decadal Oscillation at the end of 2013. Using the binned oceanic regions designated in Chapter 1, Chapter 2 showed that including the bacterial component in the food web strengthened previous conclusions that the nearshore is net autotrophic, providing excess carbon available to be laterally exported to the offshore. Examination of the westward propagating 2017 Morro Bay filament supported the hypothesis that lateral transport of organic material could support offshore, net heterotrophic communities. Bacterial production was strongly correlated to organic carbon pools, as observed in Chapter 3. Bottom-up control of bacterial production across the CCE was comparable to global tre

As a scarce but essential micronutrient for microbial growth in the marine environment, iron plays a critical role in supporting marine primary productivity and is tightly coupled to the cycling of carbon and additional macronutrients. While significant progress in recent years has been made in understanding the distribution of iron and iron-binding ligands in the marine environment, many questions remain regarding the mechanistic processes underlying these distributions.Heterotrophic bacteria serve as the primary drivers of the turnover of organic matter in the marine environment and have a significant cellular iron requirement, making them an important link between iron and carbon biogeochemical cycles. The work presented in this dissertation aims to improve our understanding of the molecular mechanisms by which heterotrophic marine bacteria acquire iron from their surroundings and the subsequent effects of their metabolic activities on both iron and carbon biogeochemical cycling. We have first developed Alteromonas macleodii ATCC 27126 as a model marine organism for the study of iron acquisition by heterotrophic bacteria. This has allowed us to characterize outer membrane TonB-dependent transporters for organically complexed forms of iron across the genus Alteromonas. This work revealed that a high diversity of iron-ligand compounds in the marine environment are potentially bioavailable. We have also utilized Alteromonas macleodii ATCC 27126 as a model organism for studying the functional role of siderophore production in iron acquisition in the marine environment. Through the insertional inactivation of the petrobactin biosynthetic pathway, we have determined that siderophore production increases the bioavailability of non-labile iron sources such as particulate minerals. Finally, in microcosm field experiments, we examined the transcriptional response of natural heterotrophic bacterial communities in the southern California Current System to iron additions demo

Coral skeletal Sr/Ca is a widely applied proxy indicator for tropical sea surface temperature (SST) because the elemental ratio in coral aragonite is influenced by both SST and seawater Sr/Ca. Application of the methodology assumes that seawater Sr/Ca is a constant in coral reef environments, and the ratio can be used to solve for paleotemperatures based upon an established coral Sr/Ca – SST relationship. This study tests that assumption by documenting seawater Sr/Ca variability in the Florida Keys and in the U.S. and British Virgin Islands using continuous osmotic pumps. Samples are analyzed for Sr/Ca using a novel method via Inductively Coupled Plasma – Atomic Emission Spectrometry. While mean seawater Sr/Ca did not vary significantly between sites, all sites exhibited significant annual variability (~0.5 – 0.1 mmol/mol), with the greatest variability observed in locations most impacted by freshwater discharge. These findings correspond to large temperature offsets (>2 degrees Celsius) in standard coral Sr/Ca-based SST reconstructions.