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Abstract. The trace metal iron (Fe) is an essential micronutrient that controls phytoplankton productivity, which subsequently affects organic matter cycling with feedback on the cycling of macronutrients. Along the continental margin of the US West Coast, high benthic Fe release has been documented, in particular from deep anoxic basins in the Southern California Borderland. However, the influence of this Fe release on surface primary production remains poorly understood. In the present study from the Santa Barbara Basin, in situ benthic Fe fluxes were determined along a transect from shallow to deep sites in the basin. Fluxes ranged between 0.23 and 4.9 mmol m−2 d−1, representing some of the highest benthic Fe fluxes reported to date. To investigate the influence of benthic Fe release from the oxygen-deficient deep basin on surface phytoplankton production, we combined benthic flux measurements with numerical simulations using the Regional Ocean Modeling System coupled to the Biogeochemical Elemental Cycling (ROMS-BEC) model. 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 in phytoplankton Fe limitation by enhanced benthic fluxes near the coast may be partially compensated for by increased nitrogen limitation further offshore, limiting the efficacy of this positive feedback.

 

Abstract. Nitrogen (N) plays a central role in marine biogeochemistry by limiting biological productivity in the surface ocean; influencing the cycles of other nutrients, carbon, and oxygen; and controlling oceanic emissions of nitrous oxide (N2O) to the atmosphere. Multiple chemical forms of N are linked together in a dynamic N cycle that is especially active in oxygen minimum zones (OMZs), where high organic matter remineralization and low oxygen concentrations fuel aerobic and anaerobic N transformations. Biogeochemical models used to understand the oceanic N cycle and project its change often employ simple parameterizations of the network of N transformations and omit key intermediary tracers such as nitrite (NO2-) and N2O. Here we present a new model of the oceanic N cycle (Nitrogen cycling in Oxygen Minimum Zones, or NitrOMZ) that resolves N transformation occurring within OMZs and their sensitivity to environmental drivers. The model is designed to be easily coupled to current ocean biogeochemical models by representing the major forms of N as prognostic tracers and parameterizing their transformations as a function of seawater chemistry and organic matter remineralization, with minimal interference in other elemental cycles. We describe the model rationale, formulation, and numerical implementation in a one-dimensional representation of the water column that reproduces typical OMZ conditions. We further detail the optimization of uncertain model parameters against observations from the eastern tropical South Pacific OMZ and evaluate the model's ability to reproduce observed profiles of N tracers and transformation rates in this region. We conclude by describing the model's sensitivity to parameter choices and environmental factors and discussing the model's suitability for ocean biogeochemical studies. 

Eddies play a crucial role in shaping ocean dynamics by affecting material transport, and generating spatio‐temporal heterogeneity. However, how eddies at different scales modulate biogeochemical transformation rates remains an open question. Applying a multi‐scale decomposition to a numerical simulation, we investigate the respective impact of mesoscale and submesoscale eddies on nutrient transport and biogeochemical cycling in the California Current System. First, the non‐linear nature of nutrient uptake by phytoplankton results in a 50% reduction in primary production in the presence of eddies. Second, eddies shape the vertical transport of nutrients with a strong compensation between mesoscale and submesoscale. Third, the eddy effect on nutrient uptake is controlled by the covariance of temperature, nutrient and phytoplankton fluctuations caused by eddies. Our results shed new light on the tight interaction between non‐linear fluid dynamics and ecosystem processes in realistic eddy regimes, which remain largely under‐resolved by global Earth system models.

 

Oceanic emissions of nitrous oxide (N₂O) account for roughly one‐third of all natural sources to the atmosphere. Hot‐spots of N₂O outgassing occur over oxygen minimum zones (OMZs), where the presence of steep oxygen gradients surrounding anoxic waters leads to enhanced N₂O production from both nitrification and denitrification. However, the relative contributions from these pathways to N₂O production and outgassing in these regions remains poorly constrained, in part due to shared intermediary nitrogen tracers, and the tight coupling of denitrification sources and sinks. To shed light on this problem, we embed a new, mechanistic model of the OMZ nitrogen cycle within a three‐dimensional eddy‐resolving physical‐biogeochemical model of the Eastern Tropical South Pacific (ETSP), tracking contributions from remote advection, atmospheric exchange, and local nitrification and denitrification. The model indicates that net N₂O production from denitrification is approximately one order of magnitude greater than nitrification within the ETSP OMZ. However, only ∼32% of denitrification‐derived N₂O production ultimately outgasses to the atmosphere in this region (contributing ∼36% of the air‐sea N₂O flux on an annual basis), while the remaining is exported out of the domain. Instead, remotely produced N₂O advected into the OMZ region accounts for roughly half (∼57%) of the total N₂O outgassing, with smaller contributions from nitrification (∼7%). Our results suggests that, together with enhanced production by denitrification, upwelling of remotely derived N₂O contributes the most to N₂O outgassing over the ETSP OMZ.

 

Abstract. Eastern boundary upwelling systems (EBUSs) are physically and biologically active regions of the ocean with substantial impacts on ocean biogeochemistry, ecology, and global fish catch. Previous studies have used models of varying complexity to study EBUS dynamics, ranging from minimal two-dimensional (2-D) models to comprehensive regional and global models. An advantage of 2-D models is that they are more computationally efficient and easier to interpret than comprehensive regional models, but their key drawback is the lack of explicit representations of important three-dimensional processes that control biology in upwelling systems. These processes include eddy quenching of nutrients and meridional transport of nutrients and heat. The authors present the Meridionally Averaged Model of Eastern Boundary Upwelling Systems (MAMEBUS) that aims at combining the benefits of 2-D and 3-D approaches to modeling EBUSs by parameterizing the key 3-D processes in a 2-D framework. MAMEBUS couples the primitive equations for the physical state of the ocean with a nutrient–phytoplankton–zooplankton–detritus model of the ecosystem, solved in terrain-following coordinates. This article defines the equations that describe the tracer, momentum, and biological evolution, along with physical parameterizations of eddy advection, isopycnal mixing, and boundary layer mixing. It describes the details of the numerical schemes and their implementation in the model code, and provides a reference solution validated against observations from the California Current. The goal of MAMEBUS is to facilitate future studies to efficiently explore the wide space of physical and biogeochemical parameters that control the zonal variations in EBUSs. 

Global change is leading to warming, acidification, and oxygen loss in the ocean. In the Southern California Bight, an eastern boundary upwelling system, these stressors are exacerbated by the localized discharge of anthropogenically enhanced nutrients from a coastal population of 23 million people. Here, we use simulations with a high-resolution, physical–biogeochemical model to quantify the link between terrestrial and atmospheric nutrients, organic matter, and carbon inputs and biogeochemical change in the coastal waters of the Southern California Bight. The model is forced by large-scale climatic drivers and a reconstruction of local inputs via rivers, wastewater outfalls, and atmospheric deposition; it captures the fine scales of ocean circulation along the shelf; and it is validated against a large collection of physical and biogeochemical observations. Local land-based and atmospheric inputs, enhanced by anthropogenic sources, drive a 79% increase in phytoplankton biomass, a 23% increase in primary production, and a nearly 44% increase in subsurface respiration rates along the coast in summer, reshaping the biogeochemistry of the Southern California Bight. Seasonal reductions in subsurface oxygen, pH, and aragonite saturation state, by up to 50 mmol m⁻³, 0.09, and 0.47, respectively, rival or exceed the global open-ocean oxygen loss and acidification since the preindustrial period. The biological effects of these changes on local fisheries, proliferation of harmful algal blooms, water clarity, and submerged aquatic vegetation have yet to be fully explored.