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The physical processes driving the genesis of surface- and subsurface-intensified cyclonic and anticyclonic eddies originating from the coastal current system of the Mauritanian Upwelling Region are investigated using a high-resolution (~1.5 km) configuration of GFDL’s Modular Ocean Model. Estimating an energy budget for the boundary current reveals a baroclinically unstable state during its intensification phase in boreal summer and which is driving eddy generation within the near-coastal region. The mean poleward coastal flow’s interaction with the sloping topography induces enhanced anticyclonic vorticity, with potential vorticity close to zero generated in the bottom boundary layer. Flow separation at sharp topographic bends intensifies the anticyclonic vorticity, and submesoscale structures of low PV coalesce to form anticyclonic vortices. A combination of offshore Ekman transport and horizontal advection determined the amount of SACW in an anticyclonic eddy. A vortex with a relatively dense and low PV core will form an anticyclonic mode-water eddy, which will subduct along isopycnals while propagating offshore and hence be shielded from surface buoyancy forcing. Less contribution of dense SACW promotes the generation of surface anticyclonic eddies as the core is composed of a lighter water mass, which causes the eddy to stay closer to the surface and hence be exposed to surface buoyancy forcing. Simulated cyclonic eddies are formed between the rotational flow of an offshore anticyclonic vortex and a poleward flowing boundary current, with eddy potential energy being the dominant source of eddy kinetic energy. All three types of eddies play a key role in the exchange between the Mauritanian Coastal currents system and the adjacent eastern boundary shadow zone region.

Climate change is especially strong in the region of the Arctic Ocean, and will have an important impact on its thermo-haline structure. We analyze the results of a hindcast simulation of a new 3D ocean model of the Arctic and North Atlantic oceans for the period 1970–2019. We compared the time period 1970–1999 with the time period 2010–2019. The comparison showed that there is a decrease of stratification between the two periods over most of the shallow Arctic shelf seas and in the core of the Transpolar Ice Drift. Fresh water inputs to the ocean surface decline, and inputs of momentum to the ocean increase, which can explain the decrease in stratification. The comparison also showed that the mixed layer becomes deeper during winter, in response to the weakened stratification owing to increased vertical mixing. The comparison of summer mixed layer depths between the two time periods follows a deepening pattern that is less evident. Regional exceptions include the Nansen Basin and the part of the Canadian Basin bordering the Canadian Archipelago, where the mixed layer shoals. Trends of freshwater fluxes imply that the changes of haline stratification in these regions are also influenced by other processes, for example, horizontal advection of fresh water, increased mixing and changes in the underlaying water masses. Runoff increase toward the Arctic Ocean can locally decrease but also increase salinity, and has an impact on stratification which can be explained by coastal dynamics. The results emphasize the non-linear nature of Arctic Ocean dynamics.

An increasing number of dead zoning (hypoxia) has been reported as a consequence of declining levels of dissolved oxygen in coastal oceans all over the globe. Despite substantial efforts a quantitative description of hypoxia up to a level enabling reliable predictions has not been achieved yet for most regions of societal interest. This does also apply to Eckernförde Bight (EB) situated in the Baltic Sea, Germany. The aim of this study is to dissect underlying mechanisms of hypoxia in EB, to identify key sources of uncertainties, and to explore the potential of existing monitoring programs to predict hypoxia by developing and documenting a workflow that may be applicable to other regions facing similar challenges. Our main tool is an ultra-high spatially resolved general ocean circulation model based on a code framework of proven versatility in that it has been applied to various regional and even global simulations in the past. Our model configuration features a spacial horizontal resolution of 100 m (unprecedented in the underlying framework which is used in both global and regional applications) and includes an elementary representation of the biogeochemical dynamics of dissolved oxygen. In addition, we integrate artificial “clocks” that measure the residence time of the water in EB along with timescales of (surface) ventilation. Our approach relies on an ensemble of hindcast model simulations, covering the period from 2000 to 2018, designed to cover a range of poorly known model parameters for vertical background mixing (diffusivity) and local oxygen consumption within EB. Feed-forward artificial neural networks are used to identify predictors of hypoxia deep in EB based on data at a monitoring site at the entrance of EB. Our results consistently show that the dynamics of low (hypoxic) oxygen concentrations in bottom waters deep inside EB is, to first order, determined by the following antagonistic processes: (1) the inflow of low-oxygenated water from the Kiel

Pelagic biogeochemical models (BGCMs) have matured into generic components of Earth System Models. BGCMs mimic the effects of marine biota on oceanic nutrient, carbon and oxygen cycles. They rely on parameters that are adjusted to match observed conditions. Such parameters are key to determining the models’ responses to changing environmental conditions. However, many of these parameters are difficult to constrain and constitute a major source of uncertainty in BGCM projections. Here we use, for the first time, variance-based sensitivity analyses to map BGCM parameter uncertainties onto their respective local manifestation in model entities (such as oceanic oxygen concentrations) for both contemporary climate and climate projections. The mapping effectively relates local uncertainties of projections to the uncertainty of specific parameters. Further, it identifies contemporary benchmarking regions, where the uncertainties of specific parameters manifest themselves, thereby facilitating an effective parameter refinement and a reduction of the associated uncertainty. Our results demonstrate that the parameters that are linked to uncertainties in projections may differ from those parameters that facilitate model conformity with present-day observations. In summary, we present a practical approach to the general question of where present-day model fidelity may be indicative for reliable projections.

The ecosystem of the Baltic Sea is endangered by eutrophication. This has triggered expensive international management efforts. Some of these efforts are impeded by natural processes such as nitrogen-fixing cyanobacteria blooms that add bioavailable nitrogen to the already over-fertilized system and thereby enhance primary production, export of organic matter to depth, and associated oxygen consumption. Controls of cyanobacteria blooms are not comprehensively understood, and this adds to the uncertainty of model-based projections into the warming future of the Baltic Sea. Here we review our current understanding of cyanobacteria bloom dynamics. We summarize published field studies and laboratory experiments and dissect the basic principles ingrained in state-of-the-art coupled ocean–circulation biogeochemical models.

Nitrogen fixers, or diazotrophs, play a key role in the carbon and nitrogen cycle of the world oceans, but the controlling mechanisms are not comprehensively understood yet. The present study compares two paradigms on the ecological niche of diazotrophs in an Earth System Model (ESM). In our standard model configuration, which is representative for most of the state-of-the-art pelagic ecosystem models, diazotrophs take advantage of zooplankton featuring a lower food preference for diazotrophs than for ordinary phytoplankton. We compare this paradigm with the idea that diazotrophs are more competitive under oligotrophic conditions, characterized by low (dissolved, particulate, organic and inorganic) phosphorous availability. Both paradigms are supported by observational evidence and lead to a similar good agreement to the most recent and advanced observation-based nitrogen fixation estimate in our ESM framework. Further, we illustrate that the similarity between the two paradigms breaks in a RCP 8.5 anthropogenic emission scenario. We conclude that a more advanced understanding of the ecological niche of diazotrophs is mandatory for assessing the cycling of essential nutrients, especially under changing environmental conditions. Our results call for more in-situ measurements of cyanobacteria biomass if major controls of nitrogen fixation in the oceans are to be dissected.

Controlled manipulation of environmental conditions within large enclosures in the ocean, so-called pelagic mesocosms, has become a standard method to explore potential responses of marine plankton communities to anthropogenic change. Among the challenges of interpreting mesocosm data is the often uncertain role of vertical mixing, which usually is not observed directly. To account for mixing nonetheless, two pragmatic assumptions are common: either that the water column is homogeneously mixed or that it is divided into two water bodies with a horizontal barrier inhibiting turbulent exchange. In this study, we present a model-based reanalysis of vertical turbulent diffusion in the mesocosm experiments PeECE III and KOSMOS 2013. Our diffusivity estimates indicate intermittent mixing events along with stagnating periods and yield simulated temperature and salinity profiles that are consistent with the observations. Here, we provide the respective diffusivities as a comprehensive data product in the Network Common Data Format (NetCDF). This data product will help to guide forthcoming model studies that aim at deepening our understanding of biogeochemical processes in the PeECE III and KOSMOS 2013 mesocosms, such as the CO2-related changes in marine carbon export. In addition, we make our model code available, providing an adjustable tool to simulate vertical mixing in any other pelagic mesocosm. The data product and the model code are available at https://doi.org/10.1594/PANGAEA.905311 (Mathesius et al., 2019).

Anthropogenic emissions of greenhouse gases such as CO2 and N2O impinge on the Earth system, which in turn modulates atmospheric greenhouse gas concentrations. The underlying feedback mechanisms are complex and, at times, counterintuitive. So-called Earth system models have recently matured to standard tools tailored to assess these feedback mechanisms in a warming world. Applications for these models range from being targeted at basic process understanding to the assessment of geo-engineering options. A problem endemic to all these applications is the need to estimate poorly known model parameters, specifically for the biogeochemical component, based on observational data (e.g., nutrient fields). In the present study, we illustrate with an Earth system model that through such an approach biases and other model deficiencies in the physical ocean circulation model component can reciprocally compensate for biases in the pelagic biogeochemical model component (and vice versa). We present two model configurations that share a remarkably similar steady state (based on ad hoc measures) when driven by historical boundary conditions, even though they feature substantially different configurations (parameter sets) of ocean mixing and biogeochemical cycling. When projected into the future the similarity between the model responses breaks. Metrics such as changes in total oceanic carbon content and suboxic volume diverge between the model configurations as the Earth warms. Our results reiterate that advancing the understanding of oceanic mixing processes will reduce the uncertainty of future projections of oceanic biogeochemical cycles. Related to the latter, we suggest that an advanced understanding of oceanic biogeochemical cycles can be used for advancements in ocean circulation modules.

Recent advances in the development of compute hardware have pushed the explicit resolution of mesoscale (and, using nesting approaches, even sub-mesoscale) processes in global coupled ocean-circulation biogeochemical models within reach. This adds realism to the models in that previously-parameterized processes can now be explicitly resolved. Analogous reasoning suggests that this also adds to the realism of model-based projections. Using examples of our modeling work in the Baltic Sea, the subtropical North Atlantic, the Southern Ocean and off Mauretania we will put the latter hypothesis to the test.

Ocean eddies can both trigger mixing (during their formation and decay) and effectively shield water encompassed from being exchanged with ambient water (throughout their lifetimes). These antagonistic effects of eddies complicate the interpretation of synoptic snapshots typically obtained by ship-based oceanographic measurement campaigns. Here we use a coupled physical–biogeochemical model to explore biogeochemical dynamics within anticyclonic eddies in the eastern tropical South Pacific Ocean. The goal is to understand the diverse biogeochemical patterns that have been observed at the subsurface layers of the anticyclonic eddies in this region. Our model results suggest that the diverse subsurface nutrient patterns within eddies are associated with the presence of water masses of different origins at different depths.

Conventional integration of Earth system and ocean models can accrue considerable computational expenses, particularly for marine biogeochemical applications. "Offline" numerical schemes in which only the biogeochemical tracers are time stepped and transported using a pre-computed circulation field can substantially reduce the burden and are thus an attractive alternative. One such scheme is the "transport matrix method" (TMM), which represents tracer transport as a sequence of sparse matrix–vector products that can be performed efficiently on distributed-memory computers. While the TMM has been used for a variety of geochemical and biogeochemical studies, to date the resulting solutions have not been comprehensively assessed against their "online" counterparts. Here, we present a detailed comparison of the two. It is based on simulations of the state-of-the-art biogeochemical sub-model embedded within the widely used coarse-resolution University of Victoria Earth System Climate Model (UVic ESCM). The default, non-linear advection scheme was first replaced with a linear, third-order upwind-biased advection scheme to satisfy the linearity requirement of the TMM. Transport matrices were extracted from an equilibrium run of the physical model and subsequently used to integrate the biogeochemical model offline to equilibrium. The identical biogeochemical model was also run online. Our simulations show that offline integration introduces some bias to biogeochemical quantities through the omission of the polar filtering used in UVic ESCM and in the offline application of time-dependent forcing fields, with high latitudes showing the largest differences with respect to the online model. Differences in other regions and in the seasonality of nutrients and phytoplankton distributions are found to be relatively minor, giving confidence that the TMM is a reliable tool for offline integration of complex biogeochemical models. Moreover, while UVic ESCM is a serial code, the TMM