Mid-water oceanic depths in coastal upwelling regions often contain oxygen deficient waters, called oxygen minimum zones (OMZs). These hypoxic (< 60 �M O2) conditions can have adverse effects on ecosystems, as many organisms cannot survive in low O2 conditions. This study investigated the OMZ in the topographically isolated Santa Monica Basin (SMB), California, a recipient of high nutrient input. The last survey of this area ~35 years ago, reported a pervious 350 year expansion of the SMB OMZ. In order to assess the OMZ since the last evaluation, sediment cores from 12 stations were retrieved by a multicorer from O2-ventilated (>60 μM O2) to near-anoxia (~4 μM O2) regions along two depth-transects ranging from water depths between 71 and 907 m. The sediment porewater and supernatant water of the cores were analyzed for sulfate (SO42-), nitrate (NO3-), phosphate (PO43-), ammonium (NH4+), total sulfide, dissolved iron (Fe (II)), total alkalinity (TA) and bacterial sulfate reduction. The two deepest stations (907 and 893 meters, ~5 �M O2) exhibited down-core accumulation of NH4+ and TA, while also displaying enhanced rates of sulfate reduction close to the sediment surface; these patterns are all evidence of low oxygen conditions in the overlying water column. Shallower stations upslope (starting at 777 m water depth) featured increasing signs of bioturbation and bioirrigation effects in the geochemical profiles of NH4+, TA, PO43- and Fe (II). Low sulfate reduction rates (areal rates range from 0.13–0.86 mmol m-2 d-1) were detected at all stations. These results were compared with data separate from this thesis, including: 210Pb lamination analyses, the presence and activity of macrofauna at the seafloor, and iron speciation analyses. According to the stations sampled, we could not identify a definite spreading or reduction of the OMZ at the seafloor since the last survey of the SMB was done ~35 years ago.

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

Methane is a major greenhouse gas and a key component of global biogeochemical cycles. Its emissions are largely governed by microbial production and oxidation of methane. While the mechanisms and isotope effects of these processes have been extensively studied, important questions continue to arise. These include (1) the clumped isotope effects associated with microbial methane metabolisms in anoxic environments, specifically anaerobic oxidation of methane (AOM) and methanogenesis, and (2) the environmental controls on the electron acceptors involved in AOM.

The first question is addressed through a combination of laboratory microbial incubations and methane samples from natural environments. We found that with high metabolic reversibility of methanogenesis and AOM, the distribution of carbon and hydrogen isotopes among methane molecules is consistent with thermodynamic equilibrium. These near-equilibrium methane isotopologue signatures result from isotope exchange operating under conditions of near-threshold free energy, catalyzed by the methyl-coenzyme M reductase enzyme. When the thermodynamic driving force is elevated, methanogenesis and AOM can generate more negative and positive isotopologue signatures, respectively. We propose that clumped isotopes of methane provide a proxy for characterizing the bioenergetics of environments for methane production and consumption. Together, these observations demonstrate clumped isotopes of methane as a powerful tool to better understand the relation between methane metabolisms and the energy landscape in natural environments. We further applied this approach to track coupled hydrocarbon biodegradation and secondary methanogenesis in terrestrial mud volcanoes.

The second question is addressed through comprehensive porewater and solid-phase geochemical analyses, along with microbial radiotracer incubations, in hypersaline coastal wetland sediment. We demonstrate that, despite the high concentrations of sulfate, AOM is not associated with sulfate reduction but is instead coupled with the reduction of an unconventional electron acceptor—iron oxides—in subsurface sediment. This finding highlights the role of wetland sediments enriched in iron oxides as an effective sink for the greenhouse gas methane. Iron-dependent AOM in sulfate-free sediments has been extensively studied. Extending these observations into sulfate-rich sediments significantly advances the earlier observations and hypotheses, while suggesting that iron-AOM is an under-considered sink for methane in wetlands.

Methane is the simplest form of organic matter on Earth, the most abundant organic molecule in the atmosphere where it is a potent greenhouse gas, an important source of energy, and considered to be a signature of life on other worlds. Methane’s genesis and its fate can occur abiotically and biotically in various atmospheric, geologic, and geographic settings. Investigations into the porewater and solid phase geochemistry, metabolic ex-situ activity and stable isotope compositions have brought considerable insight into distinguishing and tracking the microbial footprints of methane production and consumption. However, questions remain pertaining to, for example, 1) the potential for geomicrobiological communities to simultaneously produce and consume methane in sedimentary environments and, 2) the biological signatures of rare methane clumped isotopologues that indicate whether methane has been altered by oxidation.ii The first question will be addressed in this dissertation, using a newly adapted radiotracer method to show the cryptic, simultaneous methane production and consumption by biological activity in coastal wetland and marine sediment. Radiotracer analysis of the sediment from within the top 15-20 cm, collected from a coastal wetland and a marine environment revealed the cryptic, simultaneous methane production and consumption by biological activity. The findings strongly suggest that this cryptic methane cycling was overlooked by previous studies and must be considered in sediment within other wetland and marine settings. The second issue will be addressed by using the latest technological advancements in high resolution mass spectrometry to elucidate the rare methane isotopologue signatures of microbial methane oxidation in bacterial pure cultures, enzyme extracts, in environmental methane-bearing natural fluids, and in sediment slurries. Laboratory experiments that induced methane oxidation by biological activity revealed that the residual methane have distinct methane clumped isotopologue signatures in a two-dimensional space. The experimental data were applied to open and closed system models, which not only revealed that methane clumped isotopologue signatures of various microbial methane oxidation pathways are distinct from each other but also distinct from methane sources. The findings have furthered the utility of the methane clumped isotopologues in a two-dimensional space to distinguish source and process.

The rise of oxygen in the early Earth atmosphere allowed for a vast expansion of life, including the proliferation of animal life, that could utilize this powerful electron acceptor for new metabolisms. This oxygen requirement has left many organisms vulnerable to oxygen-depleted conditions (i.e., anoxia). These anoxic events in Earth’s aquatic environments allow for free iron (ferruginous) or free sulfide (euxinic) conditions to develop. While much research has been done on the past and present of aquatic anoxia, transiently deoxygenated systems that cycle annually between oxygenated and anoxic states are underexplored. Questions about these cycles of aquatic redox state abound; for example, 1) if benthic sulfur-oxidizing bacteria promote free sulfide at the sediment-water interface in transiently deoxygenated systems 2) if these cycles of anoxia can promote a loss of free iron from the benthic marine environment and 3) if sulfate reducing bacteria are quickly established in lacustrine waters after anoxia develops.

The first and second questions will be addressed in this dissertation through a suite of investigations in the transiently deoxygenated Santa Barbara Basin. Porewater geochemistry, sulfate reduction rates, and benthic flux measurements were collected between 2019-2023 under varying oxygen concentrations. We found that sulfur-oxidizing bacterial mats in the basin are associated with high rates of dissimilatory nitrate reduction to ammonium and require an elevation of the sulfate reduction zone to the sediment-water interface in order to proliferate. Mat proliferation also requires an exhaustion of iron oxides in the surface sediment. Mat formation is also associated with extremely high fluxes of iron into the water column. This free iron is potentially lost from the basin through bottom water currents that carry mid-waters upslope during the anoxic events.

The third question will be addressed in this dissertation by several geochemical and ex-situ sulfate reduction measurements taken in the Salton Sea between 2020-2023 under a variety of water column redox conditions. We found that sulfate reduction is present in waters that contained oxygen, most likely occurring inside organic particles in the water. We also found that sulfate reduction is quickly established after the onset of anoxia in the lake.