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The influence of chlorophyll shading on ocean dynamics has been usually disregarded in eastern boundary upwelling systems modeling studies in spite of their very high primary productivity. Here, we study how this effect impacts on the Peru upwelling system using a regional mesoscale-resolving physical biogeochemical coupled model. We show that the shading effect leads to a surface cooling of up to 1°C on the shelf due to subsurface cooling of the source waters during their transit toward the shelf. The shading effect leads to a more realistic subsurface stratification, a slowdown of the alongshore currents, and a shoaling of the oxycline. Impacts on the regional model biases show that the shading effect needs to be taken into account in both physical and coupled physical-biogeochemical regional models of upwelling systems.

The influence of the chlorophyll on the upper Tropical Atlantic Ocean is investigated with long-term (1979-2012) regional oceanic simulations with 1/48 horizontal resolution based on the NEMO3.6 model. The model solar radiation penetration scheme depends on the chlorophyll concentration. Simulations with time and spatially varying concentrations obtained from satellite ocean color observations are compared with a simulation forced with constant chlorophyll concentration of 0.05 mg m(-3), representative of chlorophyll depleted waters. Results indicate that regions of the Tropical Atlantic with chlorophyll concentrations larger than in the reference simulation (i.e., [chl] > 0.05 mg m(-3)) get warmer at the surface, with the exception of the main upwelling regions where high chlorophyll concentrations are associated with a significant cooling of the sea surface (similar to 1 degrees C in the Benguela upwelling). The analysis of the model heat balance shows that the biological differential heating causes negative temperature anomalies in subsurface source waters prior to their upwelling at the coast. The shallow mixed-layer in the eastern equatorial and tropical Atlantic favors the persistence of these subsurface anomalies and may explain why the Benguela is particularly sensitive to the biological differential heating. In spite of the presence of high chlorophyll concentrations in the upwelling regions, both the larger amount of shortwave radiation captured in the surface layers and the modifications of the horizontal and vertical advection at the coast are found to play a secondary role in the SST change in the upwelling region.

We used a coupled physical-biogeochemical model to investigate how the strong eddy activity typical of the Mozambique Channel affects biological production. A numerical experiment was carried out, in which mesoscale dynamics were suppressed by cancelling the nonlinear terms for horizontal momentum in the Naviers-Stokes equation. Mesoscale dynamics were found to be responsible for (1) increased offshore production in the Mozambique Channel as a result of net eddy-induced offshore transport of nutrient-rich coastal waters; (2) decreased shelf production along the central Mozambican and south-west Madagascar coast caused by a reduction in nutrient availability related to the net eddy-induced lateral transport of nutrients; (3) increased coastal production along the northern Mozambican coast caused by eddy-induced nutrient supply. The model results also showed an intensification and shallowing of the subsurface production, related to increased upper layer nutrient concentrations caused by eddy activity. In addition, by driving the detachment of the East Madagascar Current at the southern tip of the island, inertial processes intensify the southern Madagascar upwelling and causes offshore diffusion of the upwelled waters. These results emphasize the complex role played by eddy activity and, more generally, inertial processes on marine ecosystems in this region.

PISCES-v2 (Pelagic Interactions Scheme for Carbon and Ecosystem Studies volume 2) is a biogeochemical model which simulates the lower trophic levels of marine ecosystems (phytoplankton, microzooplankton and meso-zooplankton) and the biogeochemical cycles of carbon and of the main nutrients (P, N, Fe, and Si). The model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for short-term (seasonal, interannual) and long-term (climate change, paleoceanography) analyses. There are 24 prognostic variables (tracers) including two phytoplankton compartments (diatoms and nanophytoplankton), two zooplankton size classes (micro-zooplankton and mesozooplankton) and a description of the carbonate chemistry. Formulations in PISCES-v2 are based on a mixed Monod-quota formalism. On the one hand, stoichiometry of C/N/P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicon quotas are variable and the growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCES-v2, setting, for instance, the complexity of iron chemistry or the description of particulate organic materials. So far, PISCES-v2 has been coupled to the Nucleus for European Modelling of the Ocean (NEMO) and Regional Ocean Modeling System (ROMS) systems. A full description of PISCES-v2 and of its optional functionalities is provided here. The results of a quasi-steady-state simulation are presented and evaluated against diverse observational and satellite-derived data. Finally, some of the new functionalities of PISCES-v2 are tested in a series of sensitivity experiments.

Past model studies have projected a global decrease in marine net primary production (NPP) over the 21st century, but these studies focused on the multi-model mean rather than on the large inter-model differences. Here, we analyze model-simulated changes in NPP for the 21st century under IPCC's high-emission scenario RCP8.5. We use a suite of nine coupled carbon–climate Earth system models with embedded marine ecosystem models and focus on the spread between the different models and the underlying reasons. Globally, NPP decreases in five out of the nine models over the course of the 21st century, while three show no significant trend and one even simulates an increase. The largest model spread occurs in the low latitudes (between 30° S and 30° N), with individual models simulating relative changes between −25 and +40 %. Of the seven models diagnosing a net decrease in NPP in the low latitudes, only three simulate this to be a consequence of the classical interpretation, i.e., a stronger nutrient limitation due to increased stratification leading to reduced phytoplankton growth. In the other four, warming-induced increases in phytoplankton growth outbalance the stronger nutrient limitation. However, temperature-driven increases in grazing and other loss processes cause a net decrease in phytoplankton biomass and reduce NPP despite higher growth rates. One model projects a strong increase in NPP in the low latitudes, caused by an intensification of the microbial loop, while NPP in the remaining model changes by less than 0.5 %. While models consistently project increases NPP in the Southern Ocean, the regional inter-model range is also very substantial. In most models, this increase in NPP is driven by temperature, but it is also modulated by changes in light, macronutrients and iron as well as grazing. Overall, current projections of future changes in global marine NPP are subject to large uncertainties and necessitate a dedicated and sustained effort to improve the

Here we test the hypothesis that winds have an important role in determining the rate of exchange of CO2 between the atmosphere and ocean through wind stirring over the Southern Ocean. This is tested with a sensitivity study using an ad hoc parameterization of wind stirring in an ocean carbon cycle model, where the objective is to identify the way in which perturbations to the vertical density structure of the planetary boundary in the ocean impacts the carbon cycle and ocean biogeochemistry. Wind stirring leads to reduced uptake of CO2 by the Southern Ocean over the period 2000–2006, with a relative reduction with wind stirring on the order of 0.9 Pg C yr−1 over the region south of 45° S. This impacts not only the mean carbon uptake, but also the phasing of the seasonal cycle of carbon and other ocean biogeochemical tracers. Enhanced wind stirring delays the seasonal onset of stratification, and this has large impacts on both entrainment and the biological pump. It is also found that there is a strong reduction on the order of 25–30% in the concentrations of NO3 exported in Subantarctic Mode Water (SAMW) to wind stirring. This finds expression not only locally over the Southern Ocean, but also over larger scales through the impact on advected nutrients. In summary, the large sensitivity identified with the ad hoc wind stirring parameterization offers support for the importance of wind stirring for global ocean biogeochemistry through its impact over the Southern Ocean.

In high-nutrient low-chlorophyll waters of the western Atlantic sector of the Southern Ocean, an intense phytoplankton bloom is observed annually north of South Georgia. Multiple sources, including shallow sediments and atmospheric dust deposition, are thought to introduce iron to the region. However, the relative importance of each source is still unclear, owing in part to the scarcity of dissolved iron (dFe) measurements in the South Georgia region. In this study, we combine results from a recently published dFe data set around South Georgia with a coupled regional hydrodynamic and biogeochemical model to further investigate iron supply around the island. The biogeochemical component of the model includes an iron cycle, where sediments and dust deposition are the sources of iron to the ocean. The model captures the characteristic flow patterns around South Georgia, hence simulating a large phytoplankton bloom to the north (i.e. downstream) of the island. Modelled dFe concentrations agree well with observations (mean difference and root mean square errors of ~0.02 nM and ~0.81 nM) and form a large plume to the north of the island that extends eastwards for more than 800 km. In agreement with observations, highest dFe concentrations are located along the coast and decrease with distance from the island. Sensitivity tests indicate that most of the iron measured in the main bloom area originates from the coast and very shallow shelf-sediments (depths < 20 m). Dust deposition exerts almost no effect on surface chlorophyll a concentrations. Other sources of iron such as run-off and glacial melt are not represented explicitly in the model, however we discuss their role in the local iron budget.

The impact of mesoscale activity on phytoplankton and nutrient distribution in the Mozambique Channel was simulated by coupling a biogeochemical model (PISCES) with a regional oceanic model (ROMS). Examples of the effects of eddies on the biogeochemistry of the Mozambique Channel are presented to illustrate the complexity of the system. In the model, several cyclonic eddies were found with low concentrations of chlorophyll at their cores, which contrasts with previous studies in the open ocean. In addition, several anticyclonic eddies were simulated with high concentrations of chlorophyll at their cores. Phytoplankton growth within these mesoscale features (both cyclonic and anticyclonic eddies) occurred in response to nutrient injection into the euphotic zone by advection, and subsequent retention of surrounding nutrient-rich waters within eddies. Offshore nutrient distributions depended strongly on lateral advection of nutrient-rich water from the coastal regions, induced by eddy interaction with the shelf. The environmental conditions at the locations where eddies were generated had an important effect on nutrient concentrations within these structures.