Dynamic Green Ocean Project

PlankTOM Model

Biogeochemical model: The PlankTOM series of models are being developed from the the PISCES-T ocean biogeochemistry model which represents ecosystem dynamics based on Plankton Functional Types, the full cycles of P, Si, C, O2 and simplified Fe and a representation of particle ballasting based on Stokes' law. PISCES-T stems from the original PISCES model of Aumont et al. (2003) modified by Buitenhuis et al. (2006) to improve the representation of meso-zooplankton processes and the temperature-dependance of particle remineralization. We pay considerable attention to the use of data for model parameterization and evaluation. We welcome collaborations with external researchers particularly for the use of observations in the modelling of the ecosystem dynamics. The results available on this web site correspond to the simulation where nutrient fields were not restored below the mixed layer.

PlankTOM is a global model with one global set of parameters, but it can also be used for local and regional applications. Prognostic variables are the three dimensional tracer concentrations. Depending on the version, there are 22-39 prognostic variables describing the C, N, Si, P and Fe cycles and phytoplankton chlorophyll.

PlankTOM is under constant development. The model equations and can be found on the Modelling Shopping Tool developed by Eur-Oceans Work Package 3.1.

  • PISCES-T is no longer under development, but is used as a benchmark. (view PISCES structure and equations Developer E. Buitenhuis).
  • PlankTOM5.0 includes silicifiers, calcifiers and mixed phytoplankton, proto-zooplankton and mesozooplankton.
  • PlankTOM5.1 PlankTOM5 with addition of an explicit DMS cycle; select PlankTOM, Developer M. Vogt.
  • PlankTOM6 PlankTOM5 with addition of N2-fixers; select PlankTOM, Developer N.Stephens .
  • PlankTOM10 in addition includes pico-heterotrophs, pico-autotrophs, DMS-producers, and macro-zooplankton; select PlankTOM10, Developer C. Le Quéré .
    See the paper by Le Quéré et al. (2005) for a full description of the research plan.

    Physical model: PlankTOM5 is embedded into the OPA-ORCA general circulation model (GCM); additional information on transport can be found in the OPA 8.1 tracer transport model reference manual . The OPA physical model is a fully prognostic OGCM based on primitive equations (Madec et al., 1999). The model has a horizontal resolution of 2 degrees; latitudinal resolution is enhanced to 0.5 degree at the equator and at the poles. The vertical eddy diffusivity and viscosity coefficients are calculated using a 1.5 order turbulent closure scheme which explicitely calculates mixed layer depth and produces a minimum of diffusion in the thermocline. OPA is coupled to a thermodynamical and prognostic sea-ice model - LIM (Timmermann et al 2005). It is possible to couple the PlankTOM5 to other GCMs.

    Forcing and Initialization: The model is forced with NCEP daily winds and fluxes. We initialise the biogeochemical fields with observations from the World Ocean Atlas.

    Output: PISCES-T was included in two model intercomparisons by McKinley et al (2006) and Carr et al (2006). The oceanic CO2 sink is 2.17 PgC/yr averaged over 1991-2002, which is fully consistent with independent observations of atmospheric O2/N2 changes.

    References

    • Aumont,O., E. Maier-Reimer, S. Blain and P. Pondaven, 2003, An ecosystem model of the global ocean including Fe, Si, P co-limitations, Global Biogeochem. Cycles, 17, doi:10.1029/2001GB001745.
    • Buitenhuis, E. T., C. Le Quéré, O. Aumont, A. Bunker, A. Hirst, T. Ikeda, T. O'Brien, S. Piontkovski. 2006, Biogeochemical fluxes through mesozooplankton. Global Biogeochemical Cycles Vol. 20, GB2003, doi: 10.1029/2005GB002511.
    • Carr, M-E., A.M. Friedrichs, M. Schmeltz, M.N. Aita, D. Antoine, K.R. Arrigo, I Asanuma, O. Aumont, R. Barber, M. Behrenfeld, R. Bidigare, E.T. Buitenhuis, J. Cambell, A. Ciotti, H. Dierssen, M. Dowell, J. Dunne, W. Esaias, B. Gentili, W. Gregg, S. Groom, N. Hoepffner, J. Ishizaka, T. Kameda, C. LeQuéré, S. Lohrenz, J. Marra, F. Mélin, K. Moore, A. Morel, T.E. Reddy, J. Ryan, M. Scardi, T. Smyth, K. Turpie, G. Tilstone, K. Waters, Y. Yamanaka (2006) A comparison of global estimates of marine primary production from ocean color. Deep Sea Research II 533, 741770 doi:10.1016/j.dsr2.2006.01.028.
    • Le Quéré, S.P. Harrison, I.C. Prentice, E.T. Buitenhuis, O. Aumont, L. Bopp, H. Claustre, L. Cortrim da Cunha, R. Geider, X. Giraud, C. Klaas, K.E. Kohfeld, L. Legendre, M. Manizza, T. Platt, R.B. Rivkin, S. Sathyendranath, J. Uitz, A.J. Watson and D. Wolf-Gladrow. 2005, Ecosystem dynamics based on plankton functional types for global ocean biogeochemistry models. Global Change Biology, Vol. 11, 2016-2040, doi:10.1111/j.1365-2486.2005.01004.x.
    • Madec, G., P. Delecluse, M. Imbard and C. Lévy, 1999, OPA 8.1 Ocean General Circulation Model Reference Manual, Laboratoire d`Océanographie Dynamique et de Climatologie, Paris, France.
    • McKinley, G.A., T. Takahashi, E. Buitenhuis, F. Chai, J.R. Christian, S.C. Doney, M.-S Jiang, C. LeQuéré I. Lima, K. Lindsay, J.K. Moore, R. Murtugudde, L. Shi, P. Wetzel (2006) north Pacific carbon cycle response to climate variability on seasonal to decadal timescales. J. Geophys. Res., doi:10.1029/2005JC003173
    • R. Timmermann et al., 2005. On the representation of high latitude processes in the ORCA-LIM global coupled sea ice-ocean model, Ocean Modelling 8, 175-201