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'Deoxygenation Flagship': Ocean deoxygenation in Eastern Boundary Upwelling Systems

EUR-OCEANS organisation / funding

Description of Topic and Objectives

[Extract from proposal]

The issue of deoxygenation in the world ocean and its implications for ocean productivity, nutrient cycling, carbon cycling, and marine habitats is becoming an international scientific hot topic. It is one of the SOLAS Mid Term Strategy Initiative (http://solas, and as so, it is encouraging a series of important scientific meetings in order to define appropriate strategies and share expertise between the different communities that can help unraveling the processes responsible for the decrease of O2 content in the world ocean. Recently, an international Symposium took place last November 2010 in Peru on “Air-sea gas fluxes at Eastern Boundary Upwelling and Oxygen Minimum Zones (OMZs) systems”, a ‘brainstorming’ meeting on seawater deoxygenation, will take place on April 11 and 12, 2011 at the Royal Society in London, United Kingdom and finally a EUR-OCEANS Conference will occur in Toulouse, France, October 24-26 2011 on “Ocean deoxygenation and implications for marine biogeochemical cycles and ecosystems”. During the last ASLO conference in Puerto Rico in February 2011, several sessions were organized on this topic. It is important to mention here that the proponents either lead, co-organize or participate to these international initiatives.

A serious consequence of global warming that is increasingly gaining importance is indeed the decrease of the dissolved oxygen content of the world ocean. Deoxygenation and extension of the Oxygen Minimum Zones (OMZs), in particular in the Eastern Boundary Upwelling systems (hereafter EBUS), are predicted because oxygen is less soluble in warmer waters and also because the changing oceanic stratification and circulation are expected to reduce the supply of O2 to the ocean interior. However, the biogeochemical contribution due to the O2 consumed by the aerobic processes (e.g. remineralisation/respiration, nitrification) remains to be quantified. This deoxygenation of subsurface waters will have widespread consequences due to the role O2 and organic matter degradation plays in the biogeochemical cycling of carbon, nitrogen and other important elements such as P, Fe, Mn, S. Oxygen is essential to all aerobic life and sub-lethal and lethal O2 thresholds vary greatly between marine organisms. OMZs and associated upwelling regions are key areas where climatically relevant gases such as CO2, N2O, CH4, and halogenous compounds are released from the ocean to the atmosphere.

In order to develop innovative predictive management tools and strategies to resolve the dynamic interactions of climate change drivers, i.e. changes in ocean circulation, climate, ocean acidification, etc. on the structure and functioning of marine ecosystems in these vulnerable oceanic areas, we propose to employ a combination of data synthesis and numerical simulations. We will focus our efforts on the Oxygen Minimum Zone of the upwelling off Peru in the Eastern South Pacific and investigate changes on seasonal to decadal timescales.

The scientific questions we would like to address are the following:

  1. What is the origin of the low oxygen waters offshore the coast of Peru: physical O2 (or O2 deficit) advection/diffusion versus biological O2 consumption?
  2. Which coupled physical (wind-driven upwelling; equatorial Kelvin wave) and/or biogeochemical (organic matter remineralisation, nitrification, zooplankton respiration) mechanisms drive the interannual, seasonal and intraseasonal variability of hypoxia?
  3. What is the impact of physical changes (e.g. water mass characteristics) and of the biogeochemical feature (e.g. O2 availability, organic matter stoichiometry) on the marine N cycle concerning:
    - the nitrogen loss;
    - the joint venture (if any) between denitrification and anammox;
    - the greenhouse gas N2O air-sea flux in this coastal region?

Brief description of Joint Programme of Activities

[Extract from proposal]

To adequately answer these fundamental questions, we will adopt a modelling approach in combining a high resolution 3D physical model, the Regional Ocean Modelling System (ROMS) with a hierarchy of biogeochemical models of increasing structural complexity, which have been evaluated with respect to their ability to reproduce global patterns of oxygen and nutrient concentrations, and which are currently refined specifically for OMZs areas (Kriest et al., 2010). These models encompass the biogeochemical status of the Peru OMZ, namely oxygen, sulphur cycle, denitrification and the anammox reaction (Gutknecht et al., 2011, Le Vu et al., 2011). Current coupled modeling similations in this region exhibit significant biased in oxygen conditions (although they simulated realistic productivity; Albert et al., 2010), which stresses on the limitations of the parametrizations used in these models and calls for testing other approach and models. For the biogeochemical models, a special focus will be addressed to the parameterization of the bacterial processes which consume O2 and produce N2 and N2O, taken into account the O2 vertical OMZ structure and the organic matter input (e.g. stoichiometry: Paulmier et al., 2009).

The oceanic model has been implemented for the Humboldt system at 1/6° resolution in previous studies (Penven et al., 2005; Montes et al., 2010; Echevin et al., 2010; Cambon et al., 2011). Recent efforts have been dedicated to sensitivity studies to the atmospheric boundary conditions in order to reduce biases of the key elements of the physical environment. Whereas atmospheric wind stress forcing can be provided through statistical downscaling (Goubanova et al., 2010), a new dynamical downscaling approach with WRF (Weather Research and Forecasting Model) (cf. Goubanova et al. 2011) allows assessing realistic heat flux forcing at an appropriate resolution for the oceanic experiments. The latter allows for a significant reduction of the SST biases in the 1/6° ROMS configuration compared to experiments using downscaled wind stress only (heat flux being derived from low-resolution global model outputs).

We will benefit from these improvements for the higher resolution version (1/9°; and 1/18° at a later time) to be used within this project. This new ROMS configuration at a higher resolution is being configured for the Peru domain. It will be coupled to the biogeochemical models taking advantage of earlier works over the Benguela upwelling (Gutknecht et al., 2011, Le Vu et al., 2011). Atmospheric forcing conditions will be provided through dynamical downscaling with WRF. In particular a control run experiment has been performed within the CORDEX -IPSL project (Goubanova et al., 2011). It consists in the downscaling of the ERA Interim atmospheric Reanalysis (1989-2010) over the South American continent, which encompasses the study domain over sea. This atmospheric model outputs will be used for the long-term experiments planned within the current project. In collaboration with IGP and IMARPE, higher-resolution atmospheric model outputs could be used over some peculiar periods of time, which will allow testing the sensitivity of the results to the characteristics (spatial and temporal resolution) of the atmospheric forcing. Ocean boundary conditions will be provided by MERCATOR which has been shown to provide realistic equatorial Kelvin wave forcing (Dewitte et al., 2007; Mosquera et al., 2011).

The configuration (physical component only) will be run in a hindcast mode over the period 1990 to 2010 and in situ observations collected over the years in the area off Peru will be used to ensure a proper and rigorous validation of the model. The coupled model will then be run for specific periods of time corresponding to contrasted mean conditions for interannual variability (i.e. 1997/98 El Niño and 2009/10 Modoki El Niño and 1998/2000 La Niña conditions) and intraseasonal Kelvin wave activity (cf. Dewitte et al., 2008). Either conceptual projections (corresponding to cold or warm conditions) or realistic climate scenarii will be achieved depending on time availability.

We plan to offer a post-doctoral position on this topic and seek here the financial support from the EUR-OCEANS Consortium for a one year funding (55 KEuros). The post-doctoral fellow will share his (her) time between LEGOS in Toulouse, IFM GEOMAR in Kiel and IMARPE in Lima.
The overall duration of the Flagship on Ocean deoxygenation in Eastern Boundary Upwelling Systems will be 2 full years. A tentative timeline is described below.

Tentative timeline:
Months 0-5: LEGOS, Toulouse, France
Set up of coupling of the BIOBUS biogeochemical model in ROMS (1/9°) over the OMZ off Peru, climatological 15 years long simulation in fully coupled mode.
Months 6-8: IMARPE, Lima, Peru
Complete coupled model validation with IMARPE climatological data bases, and other data base (CARS09, WOA, etc...). Study processes in the climatological run (physical control of seasonal hypoxia, O2 consumption, N cycle and N20)
Months 9-18: IFM-Geomar, Kiel, Germany
Add phosphorus cycle to the model and implement the optimality based N:P uptake kinetics “chain model” (Pahlow and Oschlies, 2009) that allows for non-Redfield dynamics. Include a similar, optimality-based model of switching from DIN uptake to N2 fixation (Pahlow, pers. comm.) and investigate the role of biogeochemical feedbacks between denitrification and nitrogen fixation (Deutsch et al., 2007; Landolfi et al., in prep) in the presence of non-Redfield dynamics (Mills and Arrigo, 2010). Perform a fully coupled run with interannual forcing (1990-2010).
Months 19-20: IMARPE, Lima, Peru
Complete coupled model validation with IMARPE interannual cruises data bases over 1990-2010. Study processes based on the model simulation (impact of the intra to inter-annual Kelvin waves on hypoxic events; Interannual variability of O2 consumption and of N, N20; quantification of greenhouse air-sea fluxes)
Months 21-24: LEGOS, Toulouse, France
Interannual present scenario (1990-2010) for coupled BIOBUS/ROMS models and complete coupled model validation with IMARPE interannual cruises data bases over 1990-2010 and process studies.


  • Albert A, Echevin V, Lévy M, Aumont O (2010) Impact of nearshore wind stress curl on coastal circulation and primary production in the Peru upwelling system, J Geophys Res 115, C12033, doi:10.1029/2010JC006569.
  • Cambon G., B. Dewitte, P. Marchesiello and K.Goubanova, 2011: Assessing the impact of downscaled atmospheric winds on the regional ocean model simulation of the Humboldt system (1992-2000). Ocean Modelling, to be submitted
  • Deutsch, C., J. L. Sarmiento, D. M. Sigman, N. Gruber, and J. P. Dunne (2007), Spatial coupling of nitrogen inputs and losses in the ocean, Nature, 445, 163-167.
  • Dewitte B., M. Ramos, O. Pizarro and G. Garric, 2007: Connexion between the equatorial Kelvin wave and the extra-tropical Rossby wave in the South Eastern Pacific in the Mercator Ocean POG05B simulation: a case study for the 1997/98 El Niño. Mercator Ocean Quaterly Newsletter, July 2007 issue, 34-44.
  • Dewitte B., S. Purca, S. Illig, L. Renault and B. Giese, 2008: Low frequency modulation of the intraseasonal equatorial Kelvin wave activity in the Pacific ocean from SODA: 1958-2001. J. Climate, 21, 6060-6069.
  • Echevin V., K. Goubanova, A. Belmadani and B. Dewitte, 2011: Sensitivity of the Humboldt Current system to global warming: A downscaling experiment of the IPSL-CM4 model, Clim. Dyn., revised
  • Goubanova K., V. Echevin, B. Dewitte, F. Codron, K. Takahashi, P. Terray et M. Vrac, 2010: Statistical downscaling of sea-surface wind over the Peru-Chile upwelling region: diagnosing the impact of climate change from the IPSL-CM4 model. Clim Dyn., DOI 10.1007/s00382-010-0824-0.
  • Goubanova K. et al., 2011: ENSO impact on upwelling favourable winds off the coast of Peru/Chile in a downscalling experiments with WRF over 1989-2010. In preparation.
  • Gutknecht , E. I. Dadou, B. Le Vu, G. Cambon, J. Sudre1, V. Garçon1, E. Machu, T. Rixen, A. Kock, A. Flohr, A. Paulmier, and G. Lavik, 2011, Nitrogen transfer and air-sea N20 fluxes in the upwelling off Nambia within the oxygen minimum zone: a 3-D model approach, Biogeosciences, submitted.
  • Kriest, I., S. Khatiwala, and A. Oschlies (2010), Assessment of simple global marine biogeochemical models of increasing complexity, Progr. Oceanogr., 86, 337-360.
  • Landolfi, A., H. Dietze, and A. Oschlies, The more you fix, the more you lose: On the nitrogen fixation paradox. In preparation.
  • Le Vu, B., Gutkencht E., Machu, E., Sudre,J., Dadou, I., and Garçon, V. 2011, Physical and biogeochemical processes maintaining the Oxygen Minimum Zone in the Benguela Upwelling System using an eddy resolving model, In preparation.
  • Mills, M. M. and K. R. Arrigo (2010), Magnitude of oceanic nitrogen fixation influenced by the nutrient uptake ratio of phytoplankton, Nature Geoscience, 3, 412-416.
  • Montes, I., F. Colas, X. Capet, and W. Schneider (2010), On the pathways of the equatorial subsurface currents in the eastern equatorial Pacific and their contribution to the Peru‐Chile undercurrent, J Geophys Res 115, C09003, doi:10.1029/2009JC005710.
  • Mosquera, K. B. Dewitte, S. Illig and G. Garric, 2011: Equatorial waves sequence during the 2002-03 Modoki El Niño and their impact on SST. Advance in Geoscience, submitted.
  • Pahlow, M., and A. Oschlies (2009), Chain model of phytoplankton P, N and light colimitation, Mar. Ecol. Prog. Ser., 376, 69-83.
  • Paulmier, A., Kriest, I., and A. Oschlies (2009) Stoichiometries of remineralisation and denitrification in global biogeochemical coupled ocean models. Biogeosciences 6, 923-935,
  • Penven P, Echevin V, Pasapera J, Colas F, Tam J (2005) Average circulation, seasonal cycle, and mesoscale dynamics of the Peru Current System: A modeling approach. J Geophys Res 110, C10, C1002110.1029/2005JC002945.

Leading scientists and institutions

  • Dr Aurélien PAULMIER, IRD/LEGOS, Lima, Peru
  • Pr Andreas OSCHLIES, IFM-GEOMAR, Kiel, Germany
  • Dr Michelle GRACO, IMARPE and LMI DISCOH, Lima, Peru

Other scientists and institutions involved in the JPA

  • Dr Boris DEWITTE (IRD), Dr Serena ILLIG (IRD), Dr Katerina GOUBANOVA (CNES post-doc fellow), Dr Véronique GARCON (CNRS) all at LEGOS/UMR5566, and within LMI DISCOH, IRD/CNRS/CNES/UPS, 18 Avenue Edouard Belin, 310401 Toulouse Cedex 9, France,
  • Dr Vincent ECHEVIN (IRD, LOCEAN, Paris), also within LMI DISCOH.
  • Dr Iris KRIEST, Dr. Olaf DUTEIL, both at IFM-GEOMAR, Kiel, Germany
  • Dr Sara PURCA, Ing. L. VASQUEZ, Dr Dimitri GUTIERREZ and Ing. Jesus LEDESMA, IMARPE and LMI DISCOH, Lima, Peru
  • Dr. Ken TAKAHASHI, Ms. Kobi MOSQUERA, Ms. Julio QUIJANO, IGP and LMI DISCOH, Lima, Peru

Planned outputs

  • Regional high-resolution (1/9°) analysis (1990-2010) for oceanic and biogeochemical parameters over Peru (based on the ROMS/BioBUS model);
  • Comparison between Redfield-type and variable-stoichiometry models;
  • Comparison of results of the ROMS model with a high-resolution regional z-level model (NEMO) developed within the SFB 754 by the Kiel group. Both the comparison of different stoichiometries and different vertical grid architectures should serve for designing future model experiments dedicated to the study of the impact of climate change on the Peru ecosystem;
  • Two scientific publications in peer reviewed journals.
Activity leader(s): 
•Dr Aurélien PAULMIER, IRD/LEGOS, Lima, Peru •Pr Andreas OSCHLIES, IFM-GEOMAR, Kiel, Germany •Dr Michelle GRACO, IMARPE and LMI DISCOH, Lima, Peru
Financial support: 
47.5 k€ from EO
Start date: 
End date: 

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