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The Arctic is warming at a rate twice that of other global ecosystems and changing climate conditions in the Arctic are mobilizing long frozen permafrost stores of organic carbon. In regions of extensive ground ice, thawing permafrost can cause land subsidence, and the creation of thermokarst features. The Peel Plateau, Northwest Territories, Canada has extensive thermokarst features exposing early Holocene age paleo-thaw layers and Pleistocene age glaciogenic material deposited by the Laurentide Ice Sheet. This study aimed to see if unique permafrost thermokarst inputs could be readily observed in streams across six diverse thermokarst features via optical and ultrahigh-resolution mass spectrometry. Samples from within thermokarst slump features, and downstream of thermokarst inputs exhibited higher dissolved organic carbon concentrations and lower aromaticity as evidenced by optical parameters (e.g. declining SUVA254, increasing S275-295) and FT-ICR MS metrics (e.g. lower AImod and nominal oxidation state of carbon) versus upstream of thermokarst inputs. Increases in the relative abundances of assigned heteroatomic molecular formulae (e.g. CHON, CHOS, CHONS) were also greater within and downstream of thermokarst features. The unique molecular formulae present in permafrost thermokarst inputs were determined (n=1,844) and subsequently tracked downstream. These permafrost marker formulae were enriched in aliphatics and H/C as well as heteroatoms and exhibited low aromaticity. A portion of the unique molecular signatures persisted downstream, highlighting the potential to not only assess thermokarst inputs but also to follow these inputs and their fate downstream throughout the aquatic network.

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.

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.

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.

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.

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.

Methylmercury (MeHg) is a neurotoxin that bioaccumulates to potentially harmful concentrations in Arctic marine wildlife and in those that consume them. Monitoring and modeling MeHg bioaccumulation and biogeochemical cycling in the ocean requires understanding of the mechanisms behind net mercury (Hg) methylation. The key functional gene for Hg methylation, hgcAB, is widely distributed throughout ocean basins and spans multiple microbial phyla. While multiple microbially-mediated anaerobic pathways for Hg methylation are known, in the ocean, the majority of hgcA homologs have been found in oxic subsurface waters, in contrast to other ecosystems. In particular, microaerophilic Nitrospina, a genera of nitrite-oxidizing bacteria containing a hgcA-like sequence, has been proposed as a potentially important Hg methylator in upper ocean waters. The objective of this work was therefore to examine the potential of nitrifiers as Hg methylators and quantify total Hg and MeHg across three Arctic Seas (the Gulf of Alaska, the Bering Sea and the Chukchi Sea) in regions where Nitrospina are likely present. In Spring 2021, samples for Hg analysis were obtained from all sites with a trace metal clean rosette. Hg methylation rates were quantified in concert with nitrification rates using on-board incubation experiments with Hg and 15NH4+ stable isotope additions. A significant correlation between Hg methylation and nitrification was observed across all sites, with the strongest correlation in the Chukchi Sea. Nitrospina-specific hgcA-like genes were detected at all sites. This study, linking Hg methylation and nitrification in oxic seawater, furthers understanding of MeHg cycling in these high latitude waters and the ocean in general. Furthermore, these studies inform predictions of how climate and human interactions could influence MeHg concentrations in the Arctic region in the future.

The Southern Ocean (SO) is one of the most productive oceanic regions in the world. Despite a high abundance of macronutrients such as nitrate and phosphorus, some areas have a surprisingly low amount of phytoplankton biomass. These areas are known as high nutrient low chlorophyll regions (HNLC) and are often limited by the micronutrient iron (Fe). The influx of Fe to the surface Southern Ocean has varied over geological timescales and is expected to change further in a future climate. Additionally, climate change will alter surface ocean mixing depth which can constrain phytoplankton productivity. To identify and understand the effects of Fe and light availability on phytoplankton, this study assessed ecophysiological and photophysiological responses of two SO phytoplankton species: the haptophyte Emiliania huxleyi (E. hux.) and the diatom Fragilariopsis cylindrus (F. cyl.). The species were grown under saturating and sub-saturating Fe conditions and different light conditions. A dynamic light treatment mimicked natural light variability in different mixed layer depths, inducing either light limitation, saturation and/or short-term high light stress while a continuous light environment for F. cyl. also simulated conditions in the Antarctic higher latitude summer. In all treatments, ecophysiological parameters such as growth, elemental ratios, and cellular chlorophyll a were measured. Photophysiology was examined using Fast Repetition Rate fluorometry (FRRf) over a diurnal cycle. For both species, the results indicated a clear reduction in chlorophyll a, growth rate and cellular POC under Fe limitation with weaker effects attributed to light intensity. Fe limitation reduced photochemical efficiency (photosynthetic quantum yield (Fv/Fm)) and resulted in a reduced reoxidation rate of the photosystem (τ). Light affected photophysiological parameters mainly during peak light in the dynamic lighting environment. Irrespective of Fe availability, light adaptation strategies differed between species. E.hux primarily adjusted its photosystem to become less effective in capturing photons under high light (lower low light utilization (α)) while F. cyl primarily adapted to high light by increasing non-photochemical quenching (NPQ) during peak light in the dynamic lighting acclimation. Data on E. hux. productivity and photophysiology indicate that this haptophyte has a high light tolerance, even when Fe depleted, and is capable of acclimating to the full range of environmental stressors applied. F. cyl was less effective at adapting to the Fe-limited conditions. Here a major decrease in productivity was observed under Fe limitation. The overall results of this experiment highlight that Fe is the major driver in changes to cellular energetics with light being a secondary influence.

Sinking particles transport organic carbon produced in the surface ocean to the ocean interior, leading to net storage of atmospheric CO2 in the deep ocean. The rapid growth of in situ imaging technology has the potential to revolutionize our understanding of particle flux attenuation in the ocean; however, estimating particle flux from particle size and abundance (measured directly by in situ cameras) is challenging. Sinking rates are dependent on several factors, including particle excess density and porosity, which vary based on particle origin and type. Additionally, particle characteristics are transformed while sinking. We compare optically-measured particle size spectra profiles (Underwater Vision Profiler 5, UVP) with contemporaneous measurements of particle flux made using sediment traps and 234Th:238U disequilibrium on six process cruises from the California Current Ecosystem (CCE) LTER Program. These measurements allow us to assess the efficacy of size-flux relationships for estimating fluxes from optical particle size measurements. We find that previously published parameterizations that estimate carbon flux from UVP profiles are a poor fit to direct flux measurements in the CCE. This discrepancy is found to result primarily from the important role of fecal pellets in particle flux. These pellets are primarily in a size range (i.e., 100 – 400 µm) that is not well-resolved as images by the UVP due to the resolution of the sensor. We develop new, CCE-optimized parameters for use in an algorithm estimating carbon flux from UVP data in the southern California Current (Flux = ∑_(i=1)^x▒〖n_i A〖d_i〗^B ∆d_i 〗), with A = 15.4, B = 1.05, d = particle diameter (mm) and Flux in units of mg C m-2 d-1. We caution, however, that increased accuracy in flux estimates derived from optical instruments will require devices with greater resolution, the ability to differentiate fecal pellets from low porosity marine snow aggregates, and improved sampling of rapidly sinking fecal pellets. We also find that the particle size-flux relationships may be different within the euphotic zone than in the shallow twilight zone and hypothesize that the changing nature of sinking particles with depth must be considered when investigating the remineralization length scale of sinking particles in the ocean.

On a global scale, peatlands contain 530 ± 160 Pg carbon, which is equivalent to >50% of the atmospheric pool. The fate of this enormous C reservoir could significantly impact the climate trajectory. Yet, two puzzling phenomena persist regarding C cycling dynamics in Sphagnum-rich peatlands ("bogs"): (1) their extraordinarily slow C mineralization rates; and (2) their high (relative to predicted) CO2:CH4 production ratios. This dissertation investigates three mechanisms thought to contribute to one or both phenomena. It also investigates the effects of temperature on C cycling dynamics within peat bogs and assesses the ability for incubation experiments to predict peatland climate responses. The first mechanism that we investigated involves interactions between phenolic compounds and enzymes. We hypothesized that these interactions would significantly limit C mineralization rates in bogs given that (1) these interactions cause enzyme immobilization and decreased C mineralization rates; and (2) bogs are postulated to contain an abundance of phenolics. The second mechanism that we investigated, "non-enzymatic browning", consists of a series of abiotic reactions involving a metabolite of Sphagnum spp. (galacturonic acid). Given its propensity to expel CO2 and limit bio-available nitrogen, we hypothesized that non-enzymatic browning would elevate CO2:CH4 production ratios and suppress overall decomposition rates in peat bogs. The third mechanism that we investigated, "organic matter hydrogenation", involves the addition of H2 (a biproduct of fermentation) to organic matter. As organic matter hydrogenation has a higher energy yield than methanogenesis (which also uses H2), we hypothesized that this mechanism would elevate bog CO2:CH4 production ratios (via methane inhibition). Using a combination of incubation experiments and field measurements, we determined that the extraordinarily slow C mineralization rates associated with bogs are influenced by both phenolic-enzyme interactions (mechanism 1)—which inhibited CO2 and CH4 production rates by 62 ± 16% and 54 ± 19, respectively—and non-enzymatic browning (mechanism 2)—which caused changes to the dissolved organic matter pool consistent with bioavailable N sequestration. We determined that non-enzymatic browning could also account for the high (relative to other peatland habitats) CO2:CH4 production ratios frequently observed in bogs—as evidenced by our observation that abiotic bog incubations with minimal hydrolytic enzyme content yielded CO2 production rates equivalent to ~8% of control treatments (bioactive) at 23℃. We demonstrated a positive and significant correlation between inferred indicators of organic matter hydrogenation (mechanism 3; based on analyses of dissolved organic carbon) and CO2:CH4 production ratios. While this finding is consistent with the hypothesis that organic matter hydrogenation elevates CO2:CH4 production ratios in bog peat, further research regarding our methodology is necessary for this hypothesis to be thoroughly assessed. Using a series of temperature-controlled incubation experiments, we determined that production rates of CO2 and CH4 increase exponentially with temperature across a range of 1-26°C. Combining these results with seven years of field CH4 flux measurements, we assessed the extent to which soil temperature, alongside basic field data (water table position and permafrost depth), could accurately model CH4 emissions. The model produced yearly estimates that were within 5-60% of all measured values, or 5-34% when excluding two outlier years. These findings suggests that (1) three variables currently undergoing significant change—temperature, water table position, and permafrost depth— have a collectively significant effect on methane fluxes; (2) incubations can serve as useful tools for understanding this interplay; and (3) understanding the impact of additional variables (other than temperature, water table position, and permafrost depth) on methane fluxes could lead to improved model performance.

Climate change is dramatically altering the global carbon cycle. The warming caused by climate change is approximately twice the global average in Arctic and contiguous northern high-latitude regions, which are thus especially susceptible to ecosystem shifts (e.g. permafrost thaw, wetland drying/wetting cycle exacerbation). Rivers process and transport organic matter (OM) from land where warming is destabilizing previously stabilized carbon stocks to the ocean. This dissertation examines how fluvial OM in northern high latitudes responds to climate change, and how the fate of such OM may influence the global carbon cycle. Specifically, it focuses on how the source and processing of dissolved and particulate organic matter (DOM and POM) interact to dictate OM fate. To do so, Fourier-transform ion cyclotron resonance mass spectrometry, carbon isotopes (Δ14C, δ13C), and data on OM concentrations and carbon to nitrogen (C:N) ratios are used. Across the pan-Arctic (Chapters 2 and 3) and northeast Pacific coastal temperate rainforest (NPCTR; Chapters 4 and 5), sources appear to influence the fate of DOM (Chapters 2, 4, and 5) and POM (Chapter 3). Both landscape-scale factors like permafrost or agricultural extent (Chapters 2 and 3) and watershed slope and wetland extent (Chapters 3, 4, and 5), as well as specific source types like tree canopy or bark and soil layer (Chapters 4 and 5) impact OM molecular, isotopic, and elemental compositions and thus processing. Further, seasonality varies between the pan-Arctic watershed (Chapters 2 and 3) and the NPCTR (Chapters 4 and 5), leading to differential timing of the strongest terrestrial carbon source impacts on the system.In large pan-Arctic rivers, spring freshet contains DOM primarily sourced from terrestrial material but also includes a latent high-energy subsidy that explains the historical paradox of freshet DOM's bulk terrestrial composition but apparent high biolability. Winter riverine DOM is mostly sourced from old, microbially degraded groundwater DOM. This work uncovered a stable core Arctic riverine fingerprint (CARF) present in all samples from six years. The CARF may contribute to a carbon sink of aged DOM that appears to persist in the global ocean. Further, this dissertation uses a decade of compositional data on POM to untangle multiple allochthonous and autochthonous pan-Arctic and watershed-specific POM endmembers sourced from literature (for the full list of literature values used in endmembers, see supplementary file "Table B5.csv"). The three tracers used (C:N ratio, δ13C, and Δ14C) appear to reveal a substantial, previously overlooked aquatic biomass signal in POM (~53% of the annual pan-Arctic POM flux which averages 4391 Gg/y of exported particulate organic carbon). Splitting soil endmember values into shallow and deep soil pools (mean ± standard deviation: -228 ± 211 v. -492 ± 173‰) rather than the less representative traditional active layer and permafrost categories (-300 ± 236 v. -441 ± 215‰) also improved endmember resolution. In the NPCTR, dissolved organic carbon concentrations as high as 167 mgCL-1 were found in tree DOM (which proved highly biolabile in this study; >50%). Since the NPCTR is hypermaritime, tree DOM fluxes may be substantial. Condensed aromatic formulae comprised as much as 38% relative abundance of spruce and hemlock bark leachate DOM. Coniferous trees could thus be major condensed aromatic sources. Soil wetness determined DOM composition and response to microbial processing. Source-specific marker formulae were discovered in multiple soil and tree sources, and though the majority were consumed during bioincubations certain marker formulae persisted. All of these source-specific marker formulae (of which >90% were from spruce stemflow) were then located downstream in the watershed demonstrating that tree DOM may escape biodegradation. Summertime in the NPCTR yields the most terrestrial DOM, which then appears to degrade during the colder, wetter, fall-spring period. Despite these seasonal trends two metrics of fresh terrestrial DOM contribution (marker formulae and modified aromaticity index) did not show any significant relationships with hydrologic or temperature variables. Antecedent conditions (rather than precipitation alone) thus seems to control molecular terrestrial connectivity. Climate change is modifying both the sources and seasons that this dissertation shows to influence DOM composition and fate in northern regions. Increasing precipitation intensity in the NPCTR may tighten land-ocean linkages, while warming, permafrost thaw, and increasing CO2 concentrations could enhance allochthonous and autochthonous POM fluxes and the contribution of old, microbially processed, stable DOM to the Arctic Ocean. This work shows that an improved understanding of current controls on OM composition and fate will be necessary to predict future changes in northern high-latitude ecosystem carbon cycling and its role in furthering global climate change.

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.

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.

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.

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.

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.

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.

Peatlands cover a small percentage of the earth surface, but the exact mechanisms of how a third of the Earths global soil carbon is sequestered is not yet resolved. Therefore, this thesis aims to explore the relationship between the chemical composition of peat soils and organic matter and their response to various physical and environmental stimuli in three standalone projects, so that we may be able to better understand the fate of the carbon currently stored in peatland systems. (1) We analyzed peat samples from the Spruce and Peatland Responses Under Changing Environments (SPRUCE) project to explore ecosystem-scale warming effects on peatland carbon storage in vegetative organic matter using Fourier Transform Infrared spectroscopy (FTIR). We found that the depth of the sample had a larger effect than the amount of in situ heat the sample was exposed to. (2) Wooden blocks were positioned at pre-determined depths within the peat soil horizon in a bog in tropical Borneo and incrementally removed at different time points, with the last blocks being removed after eight years in situ. By taking dimensional data from the blocks, and using FTIR to observe any shift in chemical composition, we found that the blocks mechanically decayed before large trends in chemistry emerged. Depth of the blocks and exposure to aerobic conditions were important drivers in the rate of decay in this bog system. (3) To observe how carbohydrate content drives the rate of CO2, CH4 production in anoxic peatland systems, we created incubations from peat samples representing a range of latitudes and parent vegetation. We found that the carbohydrate content positively drove the rate of CO2, CH4 production; but this was only true for samples that were not from habitats that primarily consist of Sphagnum moss. Results from our projects suggest that the current store of carbon in peatlands are compositionally stable under stress from a changing climate, at least on the timescale of this experiment. Further work is needed to fully understand the processes that govern controls on carbon storage in peatland systems as our findings raise questions that the scope of our studies do not answer.

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 is known to be extremely recalcitrant (C-rich and low in oxygen and hydrogen). These low SPE-DOC 13C and ∆14C values point to the microbial carbon pump (MCP) as a major driver of the marine carbon cycle through the removal of biomolecules with high 13C, and addition of refractory products that resist degradation. This increases DOC residence time and drives low ∆14C values. The large meridional span in this ∆14C dataset also allows for the first regional estimates of RDOC abundance. These estimates match the simple yet powerful “two-pool” model of DOC cycling proposed in 1987, in which the deep ocean is a well-mixed pool of old RDOC, and the surface is a mixture of RDOC from depth and labile DOC from recent photosynthesis. Although the importance of the MCP, and the two-pool model are not new ideas, sampling has been spatially and temporally sparse. This dissertation research provides a high-resolution isotopic perspective from under-sampled regions in the open ocean that supports these concepts.

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 Ocean result from this basin having the smallest particle sizes, lowest particle concentrations and most viscous water. Overall, this dissertation contributes to the growing body of literature on the distribution and biogeochemistry of marine particles in the global ocean.

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 combination of well-characterized simple salt solutions and a simple seawater solution, by themselves and with the addition of one or two simple organic, proving that the system is capable of measuring AX at 3.4 micromol kg–1.

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 filaments are not likely significant sources of dissolved iron to the open ocean, yet their importance for advecting particulate iron remains to be tested. Coincident with the development of iron-limitation of the phytoplankton community we observed greater biogenic silica-to-organic carbon ratios and enhanced export efficiency to depth. In Chapter 4, within microcosm a field experiment, we examined the production of organic iron-binding ligands during remineralization – an important process supplying iron regenerated from phytoplankton blooms. As a part of this work we developed an improved data processing methods for multiple analytical windows electrochemical iron ligand titration data, enabling more robust detection of distinct pools of iron-binding ligands produced by heterotrophic bacteria and in diverse oceanic waters.Together, this work examines the processes involved in the flux of new iron to the ocean, and internal transformations affecting its fate within the water column. We hope this work results in an improved understanding of the controls on modern iron supply and ties to the marine biogeochemical cycles of macronutrients.

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.

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 that can bias pH measurements. Calibrated impure dye measurements can still be inconsistent with purified dye measurements depending on the assumptions about the impurity absorption behavior or the purity of the reference dye. This dissertation contributes to understanding of the uncertainty of spectrophotometric pH measurements and our ability to use ocean pH data to characterize the CO2 system.

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.

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 addition and removal of DOC from this reservoir on shorter timescales than current models predict. We propose a new hypothesis for marine DOC cycling that would revise the water column lifetime of marine DOC to only 2,300 years, approximately doubling the estimated flux of carbon through the deep ocean.

Climate change is radically altering the Arctic. These alterations are expected to have immense and cascading implications on the carbon cycling of the region. In particular, our interest lies in the Kolyma River (KR) as it is the largest Arctic watershed entirely lined below with continuous organic-rich permafrost and is equally subject to shrubification. On one hand, it appears that permafrost is predicted to thaw with the potential to release large quantities of ancient organic carbon. On the other hand, nutrient liberation, increased moisture, and warming allow vegetation to colonize more effectively increasing modern sources of organic carbon. The decomposition of permafrost soil organic matter has been postulated to release permafrost-derived dissolved organic matter (DOM) into stream and riverine networks that is exceptionally old and aliphatic in nature. We aimed to improve the evaluation of permafrost dissolved organic carbon (DOC) inputs and fate by implementing ramped pyrolysis oxidation (RPO) and isotopic analysis coupled with ultrahigh-resolution mass spectrometry. Bioincubation analyses were fundamental in replicating the transformations that occur to DOM during riverine transport. We found that highly aliphatic molecular formulae identified in undegraded permafrost DOM contrasts with the comparatively aliphatic-poor composition of KR DOM, suggesting that limited quantities of undegraded permafrost DOM are present in the KR. RPO radiocarbon analysis of KR DOC fractions exhibited no “hidden” aged component indicative of permafrost influence. Consistent with radiocarbon results, thermostability analysis indicated limited biodegraded permafrost DOC in the KR. A mixing model allowed us to estimate permafrost inputs to the KR DOC. Ultimately, our findings highlight that export of modern terrestrial DOM is currently overwhelming any permafrost DOM signature in the KR. This emphasizes the important ramifications of vegetation changes on the composition and biolability of transported DOM in this region with increasing shrubs dominance over herbaceous vegetation and bare ground. To investigate this, we subjected leachates of representative vegetation and soils both to biodegradation incubations and analysis using ultrahigh-resolution mass spectrometry. Biolability was seen to primarily be driven by lower relative abundances of highly unsaturated and phenolic compounds and higher relative abundances of aliphatic compounds and an overall low nominal oxidation state of carbon. In particular, DOC derived from shrubs has a lower biolability when compared to non-woody vegetation, containing on average nearly half as much %BDOC. This indicates that this DOC may persist in the water column which may have large implications as we continue attempts to quantify a permafrost DOC flux. It may be that studies will need to appraise the role vegetation cover plays in altering the age and composition of DOM of a region before investigating inputs of aged sources.

Dissolved organic phosphorus (DOP) in the surface ocean has a dual role as both the product of primary production and as a phosphorus substrate for phytoplankton when inorganic forms of phosphorus (P) are scarce. DOP has increasingly been recognized as an important source of P, especially in oligotrophic gyres, where recent modeling work suggests it may support 8% of net primary production and 33% of biological nitrogen (N2) fixation. However, there are few DOP concentration measurements in the global ocean, especially compared to measurements of dissolved organic carbon (DOC) and dissolved organic nitrogen (DON). In particular, there are few DOP concentration measurements from the Indian Ocean and South Pacific Ocean. Consequently, a robust understanding of the role of DOP in supporting primary production and N2 fixation remains data-limited. Here, I present 365 DOP concentration measurements from the 2016 GO-SHIP I08S and I09N cruise in the Eastern Indian Ocean, 199 DOP concentration measurements from the 2017 GO-SHIP P06 cruise in the South Pacific Ocean, and 188 DOP concentration measurements from the 2016 P18 GO-SHIP cruise in the Eastern Pacific Ocean. Additional DOP concentration measurements were made in the Gulf of Alaska (n = 36), South Atlantic (n = 20) and Eastern Tropical South Pacific Ocean (n=115). Together with nitrate+nitrite (NO3−), phosphate (PO43−), and dissolved organic carbon and nitrogen concentration measurements made in same samples, I evaluate trends in surface ocean DOP concentrations to identify regions of net DOP accumulation and loss. I find that upper 50 m ocean DOP stocks are positively correlated with surface ocean chlorophyll a concentration and negatively correlated with iron stress in the Eastern Pacific Ocean, indicating a region of net DOP accumulation. In contrast, the upper 50 m ocean DOP stocks are negatively correlated with surface ocean chlorophyll a concentrations and positively correlated with surface ocean iron stress in the Eastern Indian, Western Tropical South Pacific, and Atlantic Oceans, indicating net DOP loss in these regions when iron stress is alleviated. Additionally, DOP concentration is significantly negatively correlated with subsurface NO3−:PO43− concentration ratios, indicating that PO43− availability plays a key role in regulating surface ocean DOP stocks. Together, these findings significantly expand the global surface ocean DOP dataset and provide a mechanism to explain DOP distributions, with primary roles for DOP accumulation and loss in the context of phosphate and iron stress.

North Atlantic Deep Water is found in much of the deep Atlantic Ocean, and its formationin the Labrador and Nordic Seas and subsequent southward export are a vital part of globalocean circulation and Earth’s climate system. The overarching goal of this dissertation is tobetter understand the processes controlling variability of North Atlantic Deep Water formation,properties, and transport in the Atlantic Ocean.Chapter 1 uses data from the central Labrador Sea during winter to estimate the uptake of oxygenassociated with deep convection in 2014–15. The results show that intense air-sea exchangeresults in an uptake of 29.1 ± 3.8 mol m^−2 during the convective season, with much of the fluxbeing associated with injection of air bubbles. Chapter 2 looks at lateral fluxes of carbon, oxygen,and nitrate from the Labrador Sea’s boundary current into the center of the basin during thesummertime productive season. Lateral fluxes are found to play an important role for the carbonand nitrate budgets immediately below the mixed layer, with respiration rates underestimated byup to 50% if they are ignored.In chapter 3, gravity measurements from satellites are used to investigate variability in oceancirculation. After trends in the data are validated using independent measurements, they are usedto study decadal circulation changes of North Atlantic Deep Water in the North Atlantic Ocean.The analysis reveals a strengthening of the interior branch of North Atlantic Deep Water flow,with transport increasing by 13.9 ± 3.7 Sv (1 Sv = 10^6 m^3 s^−1 ), balanced by a weaker southwardflow in the Deep Western Boundary Current.A twenty-year record of mooring data is analyzed in chapter 4 to investigate changes in NorthAtlantic Deep Water transport at 16 ◦ N. Multi-decadal variability is observed in the transport timeseries, and is largely associated with density changes in the lower half of the North Atlantic DeepWater layer, which in turn appear to be caused by changes in the source region. The data are alsocompared to another transport time series at 26 ◦ N, and similarities and differences are discussed.

The 13C/12C ratio of stable carbon isotopes in dissolved inorganic carbon (DIC) can provide insight into carbon cycle variability and trends in the surface ocean. Measurements of δ13C-DIC when combined with DIC can be used to estimate anthropogenic carbon uptake and marine productivity and can contribute to our understanding of the role that the ocean plays in the global carbon cycle. This dissertation describes surface ocean time-series measurements near Bermuda (S-BATS) and Hawaii (HOT) of δ13C-DIC, DIC, and alkalinity (ALK) as a part of the Scripps Seawater Program, focusing on δ13C-DIC. Prior to this study, there was a hiatus in seawater δ13C-DIC measurements at Scripps, while samples continued to be collected and archived for future analysis. This dissertation details the resumption of these measurements along with the calibration and methodology used for Scripps measurements of δ13C-DIC. We quantify the calibration contributions to uncertainty in the context of consistency between newer and older measurements. In addition, we introduce and document the stability of three new seawater secondary standards, including a method based on CO2 in compressed N2 gas. In these time-series records of nearly three decades, we show that the long-term trends and seasonal cycles in sDIC and δ13C-DIC at both S-BATS and HOT are consistent with earlier studies and independent time-series records. From the full record we find no long-term changes in the seasonal cycle of sDIC, δ13C-DIC, or computed pCO2. Consistent to some earlier studies we find significant correlations at S-BATS with the North Atlantic Oscillation and at HOT with the Pacific Decadal Oscillation (PDO). We also find correlations at HOT that were not previously noted including the PDO with sea surface temperature and mixed layer depth (MLD), as well as El Nino Southern Oscillation (NINO3.4) with sDIC and MLD. Lastly, we use a combination of observations and CESM hindcast simulations to explore upper ocean carbon variability in subtropical gyres. This allows us to examine the time-series in a broader geographic context, showing coherent patterns of variability across the North Atlantic and North Pacific subtropical gyres and illustrating key differences in the controls of variability at BATS and HOT.

Ocean acidification (OA), the decrease in surface ocean pH and seawater saturation state with respect to carbonate minerals (Ω), is expected to increase carbonate mineral dissolution. However, the influence of OA on carbonate dissolution has been largely neglected despite evidence that it is more sensitive to OA than calcification. Increases in the rate of carbonate dissolution could have severe impacts for ecosystems such as coral reefs, which rely on the accumulation of carbonate structures and substrates to exist. At present, dissolution rates of bulk shallow biogenic carbonate sediments are largely unknown and laboratory dissolution rates exceed in situ rates by orders of magnitude. The goal of this study was to develop a better understanding of the drivers and controls of bulk carbonate sediment dissolution in coral reef environments. Based on results from in situ benthic chambers and laboratory free-drift experiments of bulk biogenic carbonate sediments from global locations, dissolution rates were found to be primarily controlled by organic matter decomposition, but significantly influenced by the overlying seawater carbonate chemistry and the solubility of the most soluble mineral phase in the sediments. Shallow carbonate dissolution will therefore be enhanced via ocean acidification, increased respiration, or a combination of these processes. The sensitivity of bulk sediment dissolution rates to changes in Ω was not related to median grain size or mineralogy, but may be attributed to organic coatings on sediment grains. Dissolution rates in bulk sediments increased ~2-3-fold when these coatings were removed, suggesting that they act as a protective barrier that limits direct interaction of seawater with the mineral surface, thus inhibiting dissolution. On the ecosystem scale, carbonate dissolution was inferred from calcium anomalies measured using a novel spectrophotometric titration system and confirms seasonal and inter-annual trends in reef biogeochemical processes based on parallel alkalinity measurements. However, calcium measurements may be best employed in environments where multiple processes significantly influence alkalinity or Mg-calcites are precipitating and dissolving. Although many questions remain, this work has elucidated certain key drivers and controls of shallow carbonate sediment dissolution and how they may respond to a rapidly changing ocean.

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 trends, but did not scale with net primary production, perhaps due to enhanced grazing nearshore. Furthermore, the observed temperature control of bacterial production was a proxy for the role of upwelling and substrate production, not metabolic rate. Strong bottom-up controls and weak temperature controls observed during the 2014 warm anomaly suggest future warming and stratification within the sCCS could be rapidly experienced by the bacterial community.

Seawater CO2-chemistry in the Southern California Bight (SCB) has been well characterized at seasonal resolution over the past several decades by multiple research expeditions. However, the near-shore environment (0-2 km) has largely been absent from these surveys and the drivers of seawater CO2-chemistry variability in this region remain to be fully characterized. In particular, the role of variable upwelling intensity is poorly known, and could have important implications for near-shore habitats sensitive to low pH and ΩAr conditions. Here, I present near-shore seawater CO2-chemistry data based on monthly transects between March 2017 and September 2018 at four stations extending from the Scripps Pier to the 60 m depth contour (~2 km offshore). Seawater samples were analyzed for seawater CO2-chemistry parameters and were paired with autonomous sensors deployed at 18 m depth. The results showed that during fall and winter, pH and ΩAr values ranged from 7.9-8.1 and 1.8-2.9 along the transect, respectively. During spring and summer, intensified upwelling transported low pH and ΩAr seawater to the near-shore region reaching values as low as 7.69 and 0.95, respectively, at depths less than 20 m and within 1 km of the shoreline. The low pH and ΩAr conditions typically persisted for several months from April to July. The magnitude of change in pH and ΩAr was correlated with the density of the water, i.e., the higher the density the lower the pH and ΩAr, but did not show direct correlation with the total amount of water that was upwelled.

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 demonstrating direct iron limitation of this community with consequences for downstream carbon processing. Together, this work sheds light on the role of heterotrophic bacteria at multiple points within the marine iron cycle, from the incorporation of iron into the marine environment to controlling the balance between the export and recycling of iron and macronutrients. It is our hope that this work results in an improved mechanistic understanding of marine iron biogeochemical cycling.

Geochemical analysis was carried out on samples of environmental phases (water, sediments, and soils) from La Barra de Santiago estuary (El Salvador, Central America) and adjacent streams to understand the dynamics and possible environmental and health effects of heavy metals, nutrient and sulfate concentrations in the ecosystem. Physiochemical parameters such as nutrient concentration (Nitrate and Phosphate), oxidation reduction potential (ORP), dissolved oxygen (DO), conductivity, total dissolved solids (TDS), pH, temperature, Chloride, Iodide and sulfate concentrations were determined using spectrophotometric methods, while heavy metal analysis was carried out using ICP-MS. Multivariate statistical methods, including correlation analysis (CA) and principal component analysis (PCA) were applied to define the mutual relationships between these parameters. Low concentration of sulfate in the water and sediments suggest it is unlikely that sulfur contamination due to the eruption of Santa Ana volcano in 2005 could be causing the lack of macroinvertebrates in the region. Phosphate in sediments and soil samples has low variability in concentration probably due to buffering by the solubility of phosphate minerals, whereas Nitrate concentration in the sediment is higher than in soil samples. High nutrient concentration and chloride in the region with low DO (symptoms of eutrophication) suggest hypernutrification could be the driver for the lack of macroinvertebrates in the estuary. The statistically significant relationships between Sr, Rb and Cl, and between Sr, Rb and SO4, suggest a chemical contribution from marine sources for these elements, while correlation between Fe, Cu, Cd, Zn, Cr, Ce, Co and Al indicates inland input into the ecosystem for these metals. Lastly, results from sediment quality assessments using several pollution indices such as geoaccumulation index (Igeo), mean-ERM quotient, concentration factor (CF), pollution load index (PLI), and contamination Factor (Cf) shows the presence of high Ni and Cr concentration in the ecosystem which could be responsible for the lack of macroinvertebrates in the estuary. The present study serves as the first insight into the environmental quality assessment of La Barra de Santiago estuary and its adjacent rivers and raises awareness for immediate response towards conservation and protection of this biodiversity rich ecosystem.

In the spring of 2010, the MC 252 Deepwater Horizon well blow out lead to nearly five million barrels of Gulf of Mexico light sweet crude to be released into the northern Gulf at a depth of 1500 meters. Dispersant injected into the plume at the wellhead helped little to keep the oil below the surface. This dispersant inefficiency, coupled with the limited effectiveness of sea surface mitigation, allowed an estimated 150,000 barrels to impact the shores of the Northern Gulf of Mexico, from East Texas to the Western Florida Panhandle. Nearly half of the impacted coastline is comprised of permeable sandy beaches. The surface oil took several months to reach the shore, and over that time it was degraded by heat, UV light, oxygen, and microbes. The weathered oil final reached the shores of Pensacola Beach, Florida on June 22, 2010. In the surf zone, the weathered oil was mixed with sand to form Sediment-Oil-Aggregates (SOA) that sank in the swash zone between the beach and longshore bar. This SOA material was transported with longshore currents, and repeatedly buried and exhumed. The weathered oil also came ashore at the same time as Tropical Storm Lee, whose increased wave action cause some of the SOA material to be deposited and buried into the dry beach sediment above the high-water line. The goal of this dissertation is to investigate the fate of MC252 crude oil from the Deepwater Horizon accident on Northern Gulf of Mexico permeable sandy beaches. Sampling trips to Santa Rosa Island, Florida were performed monthly from July 2010 to July 2011, where sediment cores from the dry beach above the high-water line were taken. These cores were sectioned and incubated to measure microbial activity in response to the buried oil, using oxygen as a proxy, over the year after the oil came ashore. On these trips, SOA material on the beach and in the surf was collected, homogenized, and use for lab incubations to investigate the role of microbes, temperature, and mechanical stress due to wave action, on the degradation of SOA material in the surf zone. Column experiments were also performed to investigate the aerobic decomposition of SOA material in the coastal water column and permeable sediments. The time series incubations showed that clearly oiled sections of sediment had significantly higher oxygen consumption rates, compared to sections that were visibly clean. In October of 2010, beach cleaning crews used heavy machinery to exhume the top meter of beach, sieve out the large SOAs, and in the process homogenized the smaller oil particles throughout the top meter of beach sand, increasing the surface area available to microbes for degradation. By April of 2011, a clearly oiled layer in the beach was no longer visible. Along with decreasing visible oil in the dry sediment, SOA material in the swash zone also decreased during the year. In laboratory incubations, it was found that microbes play a large part in the degradation of the SOA material, with microbes accounting for 80% of the oxygen consumption in SOA incubations. Higher temperatures increased the rate of oxygen consumption, with warmer summer temperatures causing a 4-fold increase in oxygen consumption rates over winter temperatures. The mechanical stress of wave action also causes the SOA material to quickly fall apart. In incubations, SOA material was rotated at 0.5rpm, and SOAs were disintegrated within 24 hours. In column experiments, it was found that increased fluid front velocity increased the oxygen consumption rates of sediment with artificially weathered crude oil. In columns amended with SOA material, there was no difference in oxygen consumption compared to sediment with no SOA material. There was also very little DOC release in SOA columns where the water was amended with Corexit 9500®, suggesting that the small surface area to volume ratio of larger, intact SOAs buried in the sediment develop a tough crust of highly degraded hydrocarbons, protecting the more labile inside from microbial degradation. This research shows the importance of microbial activity, wave action, and temperature on the degradability of the Deepwater Horizon oil. The wave energy of the environment, coupled with the permeable sandy sediments and warm temperature of the Florida summer, all contributed to the rapid degradation of the oil.

Northern high-latitude regions are undergoing rapid changes as the Arctic warms at about twice the rate of mid-latitudes. Climate change is causing permafrost thaw, vegetation and hydrologic shifts, and the increased incidence of wildfire, all of which have major implications for regional and global carbon (C) cycling. In this study, I evaluate dissolved organic matter (DOM) composition across temporal and spatial gradients using chromophoric DOM (CDOM), the biomarker lignin phenol, and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The goal of this dissertation was to improve spatial and temporal understanding of DOM composition and cycling across aquatic gradients by improving spatial (Chapter 1) and temporal (Chapter 2) coverage of DOM composition, and using space for time gradients to understand the seasonal and landscape scale controls on DOM composition in lakes and rivers (Chapters 3 and 4, respectively) and how they may change into the future. Finally, an overarching theme of these studies were the utilization of optical measurements to estimate dissolved organic carbon (DOC) concentration and DOM composition for future applications for in situ and remote sensing technology. By including an understudied, mid-sized watershed in pan-Arctic flux estimates as a model for the unsampled portion of the pan-Arctic watershed (i.e. not encompassed in the major six Arctic rivers from which historic estimates are extrapolated) DOC flux estimates were increased from 27 Tg C to 34 Tg C annually to the Arctic Ocean. Additionally, the residence time of lignin and thus terrestrial DOM was further constrained from previous studies to 0.5 to 1.8 years. This refinement of the pan-Arctic flux estimate and terrestrial DOM residence time is important for the accurate assessment of land-ocean C fluxes and their implications for future change. Temporal DOM dynamics were also evaluated in both rivers and lakes. Diel lake sampling revealed that seasonal variability accounted for the greatest changes in DOM composition and underscored the need to sample lakes seasonally while regular diel trends were not observed. Finally, using space for time transitions in both lakes and rivers the seasonal and landscape drivers of DOM composition were evaluated to allow future projections in a changing Arctic. In lakes that were relatively hydrologically disconnected there was lower CDOM compared to hydrologically connected lakes and a strong decoupling of DOC from CDOM. Further evidence showed that DOM in these lakes was driven by autochthony and that a future drier climate is unlikely to cause browning in these lakes as suggested by recent research. In rivers, where hydrologic connectivity is high, the watershed relief, soils and vegetation played an important role in determining DOM composition. Lower DOC yields and more aliphatic DOM were mobilized in watersheds underlain by continuous permafrost compared to discontinuous permafrost. Together these studies show the utility of space for time gradients to project future change and the use of CDOM parameters as a proxy for DOC concentration and DOM composition. Taken together these results allow us to make projections for boreal and arctic change, as well as allow future studies to improve spatial and temporal resolution via CDOM parameters.

This dissertation explores the role that organic ligands play in controlling copper speciation in a range of oceanic and coastal environments, using voltammetric methods. Chapter 1 details the analysis of samples collected on the 2013 U.S. GEOTRACES cruise in the Equatorial Pacific from Peru to Tahiti (GP16). This represents one of the largest copper speciation datasets to date, covering 22 full ocean depth profiles. Results demonstrate that copper ligands follow a similar pattern to dissolved copper of increasing concentrations with increasing depth. Free copper ion concentrations ([Cu2+]) also increase with depth. This dataset provides insight into the impact of large-scale ocean circulation and water mass aging with respect to copper speciation, with increasing Cu2+ and decreasing excess ligand concentrations in the oldest waters of the deep Pacific.In Chapter 2, copper speciation from select samples in the GP16 data set is analyzed via a novel processing protocol that enables competitive ligand exchange titrations at multiple competition strengths to be analyzed as a unified dataset. This method utilizes publicly available processing tools to determine a unified sensitivity for the data set as a whole. In this way the full spectrum of the copper-binding ligand pool can be most accurately characterized at a range of analytical windows, revealing both weak and strong ligands. For GP16 samples, this analysis reveals two classes of copper-binding ligands present throughout the oceanic water column, with the weaker L2 ligands present at higher concentrations. Strong L1 ligands are present at or above dissolved copper concentrations, dominating copper speciation especially in surface waters where L1 concentrations exceed that of dissolved copper.Copper binding ligands play a vital role in maintaining low concentrations of the Cu2+ ion in coastal environments, which helps buffer such systems from copper toxicity. In Chapter 3, the processing method developed in Chapter 2 is applied to an assessment of the ligand pool and free copper ion levels in San Diego Bay, an impacted urban environment with high concentrations of recreational watercraft coated with copper-based antifouling paint. Sampling campaigns at 7 locations within the Bay took place in Summer 2015, Spring 2016 and Fall 2016. Samples for total dissolved copper and copper speciation were collected, as well as samples for Synechococcus concentrations as a biological indicator of copper toxicity. Results from the three samplings show elevated levels (30 –120 nM) of dissolved copper throughout the Bay and a ligand pool capable of buffering most of the locations within the Bay from reaching toxic levels of the free copper ion. Shelter Island Yacht Basin, however, was consistently found to contain toxic levels of Cu2+, results that show a relationship with the lowest Synechococcus concentrations in two out of the three samplings. Findings of this study are relevant for ongoing remediation and regulation efforts in San Diego Bay.

Ferromanganese (FeMn) crusts are of interest and clear importance both as a unique paleoceanographic archive of seawater chemistry and as a potential resource for valuable and critical metals. Presently, there is a need to shift FeMn crust research from purely exploration-based studies to more targeted expeditions that can precisely locate FeMn crusts with characteristics of interest for scientific research and resource evaluation. Understanding the influence of general oceanographic conditions on FeMn crust formation is key to defining permissive regions. This thesis investigates variations in the geochemistry of FeMn crusts from the west-central Pacific that are associated with regional oceanographic conditions, including proximity to the oxygen minimum zone and high biological productivity maintained at the equator, as well as water depth controls and the effects of diagenetic phosphatization. Chemical analysis of over 60 FeMn crusts reveals that the oxygen minimum zones in the northern and southern tropics in the west Pacific exhibit strong controls on the composition of recent FeMn crust growth as well bulk FeMn crusts. Manganese contents are increased near the oxygen minimum zones, which is shown quantitatively for a broad region in this thesis for the first time. Iron is instead enriched in deeper waters where oxidation of iron is increased, which may be caused by higher carbonate ion concentrations and pH at depth and the availability of deep sources of iron. High biological productivity in the equatorial upwelling zone enriches iron, magnesium, and barium in FeMn crusts that are forming below this zone due to increased efficiency of the biological pump. Diagenetic phosphatization is commonly observed in crusts from depths above 2000 meters, but does not exceedingly dilute manganese oxides or elements of economic interest. Synchrotron analyses of phosphatized FeMn crust layers indicate that phosphatization does not change the speciation of lead as hypothesized based on previous sequential leaching studies. Overall, is it shown that the general oceanographic parameters studied here influence FeMn crust composition based on their geographic location and water depth, and these parameters can help create criteria for future crust exploration.

This study of an upwelling cross-shore filament in the California Current System attempts to follow a parcel of water from upwelling source to offshore in order to characterize changes in silica cycling and associated impacts on carbon cycling under the influence of iron limitation. Water column samples were collected throughout the euphotic zone in conjunction with sediment traps following the filament in Lagrangian fashion (cycles); additional samples were taken across the filament (transects). The filament progressed from iron-replete to iron-limited throughout the study, identified by low silicic acid to nitrate ratios (Si:N) and elevated nitrate to iron (N:Fe) ratios in situ. Increases in biogenic silica to POC ratios (bSi:POC) in the water column were apparent with increasing iron limitation of the diatom-dominated community. The Lagrangian nature of the study improves overall understanding of the dynamics of biogenic silica as an upwelling filament develops to iron-limited, low Si:N water conditions. This work builds upon and adds context to previous studies which have shown that iron limitation affects silicic acid to carbon (Si:C) and silicic acid to nitrate (Si:N) uptake ratios in marine diatoms. These ratios have potential implications for both carbon and silica cycling in the ocean, impacting uptake and export of these elements. The filament was shown to transport biogenic silica laterally away from the coast, and enhanced silica ballasting was shown to be associated with increased export efficiency offshore.

Anthropogenic environmental change threatens the ability for many coral reefs to maintain the calcium carbonate structures that provide shoreline protection, fisheries provision, and tourism revenue to human populations worldwide. Rigorous quantification of the rates and drivers of coral and coral reef net ecosystem calcification (NEC) represents a significant challenge but is tantamount for understanding how these services to humanity may be affected by environmental change. This challenge is addressed here by leveraging a combination of field observations, numerical models, and statistical analyses. The major findings showed that extremely large NEC errors of –91% to +1000% can be driven by interacting ±83% uncertainties in the difficult to measure seawater depth and residence time parameters used to calculate NEC. Confidence in NEC rates can nonetheless be improved by leveraging multiple NEC methods as evidenced by the agreement between chemistry and census-based NEC calculated for Hog Reef, Bermuda. Analysis of the environmental drivers of coral and reef-scale calcification at Hog Reef and Crescent Reef, Bermuda showed that temperature was the strongest driver of coral and reef-scale calcification rates with little influence by the other environmental parameters studied. This suggests that reduced warming rates driven by lower global carbon dioxide emissions pathways could maintain Bermudan coral calcification through the twenty-first century. However, more rapid warming can cause coral bleaching that reduces NEC as evidenced by the observation of zero NEC during the fall 2015 coral bleaching event in Kāne'ohe Bay, Hawai'i. The subsequent recovery to pre-bleaching NEC rates by the following summer highlights the capacity of coral reef NEC to rapidly recover in the absence of continued stressors. Conversely, the cumulative effects of 20 years of disturbances on coral calcification capacity (CCC) across the main Hawaiian Islands, Mo'orea, Florida Keys reef tract, and St. John revealed disturbance-driven reductions in CCC and community-level shifts in contributions to CCC from competitive to weedy corals that may increase CCC resilience to future disturbances. This dissertation collectively improves projections for how the Anthropocene may change reef structures and the services they provide humanity by advancing our understanding of the rates and drivers of coral and coral reef calcification.

Marine dissolved organic matter (DOM) is the largest pool of actively cycling organic carbon and nitrogen in the ocean. Despite the importance of DOM in biogeochemical cycles, understanding of its composition and cycling is limited, in part due to difficulty in isolating representative material. Here we present a new approach to DOM isolation via a sequential combination of ultrafiltration and solid phase extraction, which allowed the selective isolation of two fractions with different compositions and reactivities. By limiting the influence of reactivity mixtures, we were able to directly investigate the composition and cycling of both labile and refractory DOM. Measurements of bulk isotopic (Δ14C, δ13C, δ15N) and compositional (C/N ratio, 13C and 15N NMR) parameters confirmed the uniqueness of the two fractions. The ultrafiltered high molecular weight (HMW) fraction was younger and dominated by carbohydrate-like and protein-like molecules. In contrast, the low molecular weight (LMW) fraction was older and dominated by alicyclic carbon and heterocyclic nitrogen containing molecules. Spectroscopic studies have shown that the nitrogen-containing fraction of DOM (DON) is dominated by labile proteinaceous material. Despite this, other evidence suggests that a large fraction of DON is resistant to degradation. However, the paradigm of DON composition is based on measurements of HMW DON alone. Measurements of isotopic (δ15N, AA-Δ14C) and compositional (15N NMR, AA-D/L ratios) parameters of LMW DON provided a new perspective on the composition and cycling of DON in the ocean. Amino acids in LMW DON had both old radiocarbon ages and high D/L ratios, suggesting a bacterial mechanism capable of preserving proteinaceous material on millennial timescales. NMR analysis and nitrogen isotopic ratios demonstrated that LMW DON is dominated by heterocyclic nitrogen-containing molecules likely with intrinsically refractory molecular structures. These observations present a new paradigm for marine DON composition and suggest a mechanism for its long-term persistence.