12.3. Biogeochemical models

CROCO comes with series of biogeochemical (BGC) models of increasing complexity, from relatively simple 5- or 7-component NPZD (Gruber et al., 2006, 2011) and N2P2Z2D2 BioEBUS model (Gutknecht, 2013) that proved well suited to upwelling regions to 24-component PISCES (Aumont et al., 2005).

BioEBUS is a nitrogen-based model (Fig. 1) derived from a N2P2Z2D2 evolution of ROMS NPZD model (Gruber et al., 2006, 2011) and accounting for the main planktonic communities in upwelling ecosystems associated oxygen minimum zones (OMZs). It is validated in Gutknecht et al. (2013) using available satellite and in situ data in the northern part of the Benguela upwelling system. In this model, phytoplankton and zooplankton are split into small (PS and ZS: flagellates and ciliates, respectively) and large (PL and ZL: diatoms and copepods, respectively) organisms. Detritus are also separated into small and large particulate compartments (DS and DL). A semi-labile dissolved organic nitrogen (DON) compartment was added since DON can be an important reservoir of OM and can potentially play an important role in supplying nitrogen or carbon from the coastal region to the open ocean (Huret et al., 2005). The pool of dissolved inorganic nitrogen is split into nitrate (NO3-), nitrite (NO2-) and ammonium (NH4+) species to have a detailed description of the microbial loop: ammonification/nitrification processes under oxic conditions, and denitrification/anammox processes under suboxic conditions (Yakushev et al., 2007). These processes are directly oxygen dependent, so an oxygen (O2) equation was also introduced in BioEBUS with the source term (photosynthesis), sink terms (zooplankton respiration, bacteria re-mineralisation) and sea–air O2 fluxes following Pena et al. (2010) and Yakushev et al. (2007). To complete this nitrogen-based model, nitrous oxide (N2O) was introduced using the parameterization of Suntharalingam et al. (2000, 2012). It allows determining the N2O production under oxygenated conditions and at low-oxygen levels, mimicking the N2O production from nitrification and denitrification processes. The SMS terms of BioEBUS and parameter values are described in detail in Gutknecht et al. (2013).

PISCES was developed for NEMO (the French ocean climate model). It was implemented in CROCO for its supposed suitability for a wide range of oceanic regimes. PISCES currently has five modeled limiting nutrients for phytoplankton growth: Nitrate and Ammonium, Phosphate, Silicate and Iron. Phosphate and nitrate+ammonium are linked by constant Redfield ratios but the nitrogen pool undergoes nitrogen fixation and denitrification. Four living compartments are represented: two phytoplankton size-classes/groups corresponding to nanophytoplankton and diatoms, and two zooplankton size classes which are micro-zooplankton and mesozooplankton. For phytoplankton, prognostic variables are total biomass, the iron, chlorophyll and silicon contents. This means that the Fe/C, Chl/C and Si/C ratios of both phytoplankton groups are fully predicted by the model. For zooplankton, only the total biomass is modeled. For all species, the C/N/P/O2 ratios are supposed constant and are not allowed to vary. The Redfield ratio O/C/N/P is set to 172/122/16/1. In addition, the Fe/C ratio of both zooplankton groups is kept constant. No silicified zooplankton is assumed. The bacterial pool is not yet explicitly modeled. There are three non-living compartments: semi-labile dissolved organic matter, small and big sinking particles. The iron, silicon and calcite pools of the particles are explicitly modeled and their ratios are allowed to vary. The sinking speed of the particles is not altered by their content in calcite and biogenic silicate (”The ballast effect”). The latter particles are assumed to sink at the same speed as big organic matter particles. All the non-living compartments experience aggregation due to turbulence and differential settling. In addition to the ecosystem model, PISCES also simulates dissolved inorganic carbon, total alkalinity and dissolved oxygen. The latter tracer is also used to define the regions where oxic or anoxic remineralization takes place. see Aumont et al. (2005) in the documentation section for details.

Related CPP options:


Activate 24-component PISCES biogeochemical model


Activate 5-component NPZD type model


Activate 7-component NPZD type model


Activate 12-component NPZD type model

Preselected options:

# ifdef BIOLOGY
# undef PISCES
# define BIO_NChlPZD
# undef BIO_N2ChlPZD2
# undef BIO_BioEBUS
# endif