Chipemocs Biogeochemical modelling :
Introduction
To our knowledge, a global biogeochemical model taking into account the specific
processes which determine the OMZ formation does not exist. It is our goal within the
CHIPEMOCS program to develop such a model and to adapt it to the SEP zone. In order to
answer CHIPEMOCS objectives, it is necessary to develop an integrated model, which will
built from different elements developed by the different scientific teams involved in the
project. The strategy is the following i) to develop a process model dedicated to biochemical
processes specific to the OMZ, and to the interpretation of observations collected in the water
column and sediments, and ii) to develop an integrated three dimensional model coupling
dynamical processes in the SEP with biogeochemical processes important in the OMZ. These
2 steps are necessary to study the variability at the different time scales of interest for the
program. The 3D physical-biochemical model will benefit both from improvements in the
knowledge of biogeochemical processes of the OMZ and will be adapted to the SEP with
specific OMZ processes parameterizations. It will be used as an integrated tool to interpret the
data collected within the CHIPEMOCS program, at fixed long-term moorings as well as
during the CHIPEMOCS cruise.
The goal of this task is to create an integrated model that will describe the main
biogeochemical processes in the OMZ, from the surface layers to the sediments. Our
guideline is to use already existing model elements (surface ecosystem, particles model in the
water column, sediment model) that already function in a fully three dimensional, coupled,
integrated model. Indeed the PISCES ecosystem model we wish to use, has been run in a
three dimensional mode with two very different circulation models, OPA (developed at
LOCEAN, ex-LODYC) and ROMS (developed at UCLA, USA, and used by several IRD
scientists). Furthermore, the ecosystem model has been successfully coupled to a complex
water column model based on the work by Kriest and Evans (1999,2000), and to a sediment
model by Heinze et al.(1999) during the ORFOISE European project.
The main tasks of the modelling work will be to 1) adjust the parameters of the model
elements (surface, water column, sediment) using historical data and new data collected
during the chipemocs cruise, and 2) when necessary, introduce new parameterizations
dedicated to specific OMZ processes (denitrification in the surface model, role of OMZ
bacteria in the degradation of organic matter, ..etc, LIST OF PROCESSES TO BE
INTRODUCED ?).
The existing modelling tools
The model elements we are planning to use are the following:
1)
2)
Surface ecosystem model : The PISCES model
The characteristics of the model are:
- several macro- and micro-nutrients (NO3, PO4, NH4,SIO2, Fer)
- some of the redfield ratios vary ( Fe/C,Chl/C,SI/C in the phytoplankton groups). For all
species the ratios C/N/P/O2 are fixed.
- There are two size classes of phytoplankton, two size classes of zooplankton, two size
classes of non living sinking particles (sinking speed at 3 m/day, 50 m/day) in the standard
version of the PISCES model.
The water column model
a) Standard model
In the PISCES standard model, there is no specific, distinct, particles model, hence the
processes in the water column are the same as in the surface layers, except that there is no
photosynthesis. The processes are the following:
- Small and big particles sink with different velocities (7 m/day fro the organic matter, 50
m/day for the calcite and biogenic silica)
- Small and big particles aggregate due to micro-turbulence in the water colum. Presently,
micro-turbulence is parameterized in a crude manner, with fixed values in the mixed layer,
and below (micro turbulence is not linked to the vertical diffusion in the dynamical
model)
- Particles aggregate due to differential sinking velocities.
- Particles (big) are grazed by zooplankton. Grazing is inhibited when O2 concentration
falls below a certain threshold, as for instance in the OMZ core. This process is very
sensitive in the model as studied in the ORFOIS project (ORFOIS final Report,XXX).
- remineralisation by bacterial activity. It is modeled as a linear term proportional to the
concentration of particles ((T).C). The coefficient is a function of temperature as
bacterial activity increases with T. It is independent of the size of the particles.
b) More advanced water column spectral model
This a more advanced model particles model based on the work of Kriest and Evans
(1999, 2000) .
Model description : only one particle size class with two variables: C= concentration
(N/C/P)/l et N=number of particles/l
Main hypothesis : the size spectrum is in the form of a « power law »: N=f(R) with f a
fiunction of 2 parameters (to be completed).
This parameterization allows a continuous description of the aggregation and settling of
particles, an exact description of the size spectra.
Other hypotheses are implicitely made for the surface ecosystem: The size spectra of the
phytoplankton and zooplankton species are supposed to be known.
There are adjustable parameters related to the masse (M) and sinking velocity (w) of
particles as a function of their size (presently M  (R ) , with =2.28, and w  (R ) ,
with =1.18). Presently the sinking velocity does not take into account the variation of
density due to the different Redfield ratios and hence density of the particles, but this can
also be introduced.
3) Sediment model
a) Simple standard « sediment » model
Presently there is no specific sediment model in PISCES. The particles sediment to the
bottom of the ocean and are remineralized in the same way as in the water column during
their fall.Part of the matter that reach the bottom of the ocean is sucked out of the system
(buried into the earth), to close a budget and compensate with the inputs from rivers and
atmospheric dust.
b) An « Archer type » sediment model based on Heinze et al. (1999)
Within the framework of the european ORFOIS model, a more sophisticated sediment
model has been coupled to PISCES by scientists from LSCE (M. Gehlen, N. Emprin, L.
Bopp).
It contains several compartments: clay,organic matter, Si, CaCO3, dissolved
compartments (DIC, Alcalinity, nutrients, O2).
Anoxic processes are described but crude except denitrification.
Specific OMZ processes to be introduced
The biogeochemical processes associated to the OMZs are not well known. The single
model which represents nitrification/denitrification processes associated with OMZ
(Anderson et al., 1982) does not reproduce the low oxygen concentrations observed in the
SEP OMZ (Paulmier, personal communication), as it is based on processes taking place in the
OMZ core, and it does not focus on the most active zone in the OMZ, the oxycline. To
evaluate what and how biogeochemical processes create and maintain the OMZ, a model with
the following characteristics must be developed:
i)
specific processes of the OMZ and oxycline must be parameterized, such as
productivity, denitrification, nitrification, and remineralization of organic
matter in different oxygen conditions (oxic, suboxic and anoxic).
Parameterisations of all these processes will be calibrated with data obtained
from laboratory experiments and in situ fixed point measurements during
the SHOC cruise, will allow to develop the MINOC model.
ii)
interactions between photosynthesis processes linked to the OMZ biomass
and C and Si fluxes will be parameterised taking into account the vertical
gradient of oxygen concentration.
iii)
remineralisation of organic matter will be parameterized for the OMZ. It
will allow representation of the thickening of the OMZ in response to an
increase of primary production and to euphotic layer fertilizing due to
mineralisation. Remineralization of organic matter in the OMZ will be
modelled theoretically at first, based on results from the literature and
existing data. This parameterization will be adjusted with the data provided
by both sediment traps and fixed point experiments.
This work will be done at LBCM (A. Paulmier, M. Graco, C. Bonhomme ?, O.
Aumont ?). One scientist from IMARPE will spend a stay at LBCM to collaborate in the
implementation of the model. The parametrizations will then be introduced in the 3D model.
1D coupled model: integrated sediments-water column-surface layer model
This part has not been modified, initially Diana wrote it ! Does it stay
as such? Who can be in charge of it ? (not me .. V.E.)
The objective of this modelling task is twofold :
i)
to interpret fluxes variability of POM and main biogeochemical elements (C,
N, Si) as well as fluxes of other organic and inorganic tracers observed by
sediment traps.
ii)
to link surface observations (in which the present time signal is contained) to
sediments observations (in which the signal from the past is contained) in
order to help for the calibration of proxies.
Such models have been developed at LBCM and used in a forced mode (Dadou et al.,
2001). The 1D integrated model is composed of three models, an ecosystem surface layer
model PISCES, a deep water column model (PISCES standard and/or PISCES+Kriest and
Evans ?) and a benthic HNLO (High Nutrient Low Oxygen) process model (Graco,2002) or
the sediment model developed in ORFOIS project. Currently, the integrated model couples
carbon and nitrogen cycles, but specific processes of the OMZ are not represented.
In order to interpret the flux variability at the sediment traps and to calibrate the
proxies, the water column model will be adapted:
i)
an oxycline-dependant parameterization of the remineralisation will be
introduced in the particle model. This model will focus on elements
measured in sediment traps (C, N, Si, 13C, 15N ?) and this will lead to an
improvement of the parameterization of remineralisation processes in the
water column.
ii)
processes linked to the silicate cycle, which are necessary in order to
restitute the carbon export from the opal accumulation, will be introduced
following approaches from the ORFOIS project (O. Ragueneau). To be
developped by Ragueneau
For sediments and benthic processes at the water-sediment interface, a model adapted to low
oxygen conditions and taking into account nitrification/denitrification is needed. Such a
model is currently being developed (M. Graco, LBCM, in collaboration with C. Rabouille,
LSCE)/or the sediment model used in ORFOIS ?.
Calibration of proxies
This part has not been modified, initially Diana wrote it ! Does it stay
as such? Who can be in charge of it ? (not me .. V.E.)
The calibration of proxies is a complex task because of the various coupled processes from
the surface to the bottom which modify the tracers used for the reconstructions. Numerical
modelling is suggested in SHOC to de-convoluate these processes. To this aim, two new
aspects will be introduced in the benthic model:
i)
parametrizations associated to the most important proxies (isotopic tracers:
15
N, 13C, and organic biomarkers) in the OMZ and resurgence areas will be
integrated in the coupled model.
ii)
the analytic model of Mangini et al. (2001) will be used to study the potential
impact of authigenic molybden and uranium remobilization in the sediments.
This model is able to characterize the front produced by the reduced oxygen
conditions at depth as a function of O2 concentration, organic flux and
sedimentation. The model will be adapted in order to take into account the
impact of low oxygen values in the SEP.
Coupling of the three models (surface-water column-sediments) will be performed within the
SHOC program, and will be used to interpret present time observations (from sediment traps
in the water column) and past observations (from the sediments). This work will be done at
LBCM (A. Paulmier, M. Graco, D. Ruiz-Pino).
The 3D coupled model dynamical-biogeochemical model.
The main objective for developing a three-dimensional coupled model adapted to the
SEP zone is the ability to describe and to understand space and time evolution of the oxygen
concentration, and to evaluate the impact of various dynamical processes (e.g. local wind
forcing versus remote forcing by coastal waves) on biogeochemical processes linked to the
OMZ. The model will also be useful for interpretation of the spatial variability of
biogeochemical measurements obtained during the CHIPEMOCS program.
We will use the PISCES (Aumont et al., 2003) model, coupled to a particle model and
a sediment model, with adapted OMZ parametrizations. The following tasks will be done:
i)
the biogeochemical model in its present form will be coupled to the ROMS
coastal circulation model in order to study the impact of the mean and
variability of the circulation on the OMZ mean structure and variability.
ii)
it will be adapted to take into account processes in the OMZ using the new
specific parameterisations.
iii)
the coupled model will require to be calibrated, validated and improved, and
data obtained during the whole CHIPEMOCS project will be used to this end.
The numerical experiments:
After the parametrisations of OMZ biogeochemical processes are improved and introduced in
the 3D model, the coupled model (ROMS + PISCES) will be run over the CHIPEMOCS
cruise period and over the period 1992-2004 to study interannual variability of the OMZ.
.The output of the model will be validated against available satellite (SeaWifs, POLDER)
observations and in situ observations collected during the SHOC cruise (oxygen
measurements, nutrients, sediment traps).
The mean state and the variability of the simulated chlorophyll concentration will be studied
and compared to satellite (SeaWIFS, POLDER) and in situ data. The mean state and
variability of nutrients and oxygen will be compared to data from IMARPE and COPAS. The
mean state and the variability of the OMZ at intraseasonal to interannual time scales in
response to the various dynamical forcings (large scale, mesoscale, vertical mixing) will be
studied.
The numerical experiments and their analysis will be performed by V. Echevin, O.
Aumont (IRD/LOCEAN). Parameterisation, calibration and analysis of the results will be
performed by V. Echevin, O. Aumont, C. Bonhomme (Thesis LOCEAN), O. Ulloa (COPAS),
Jorge Tam, (IMARPE).
People implicated in this part of the project :
- Olivier Aumont (IRD) : 50% over 3 years after mid-2005 on the them of interannual
variability in the OMZ
- Vincent Echevin (IRD) : <50% (50% on dynamical modelling) : impact of the
dynamical variability on the surface productivity in the SEP, impact of the wind
forcing short scales.
- Céline Bonhomme (Thesis 2005-2007) : 100%: parameterization of OMZ processes in
the ecosystem and in the particle model in PISCES
- Sédiments : Olivier Ragueneau ? % ?
Michelle Graco ? % ? which model ?
Aurélien Paulmier ? post-doc ?
People to contact : Laurent Bopp (LSCE, particle and sediment
modelling in ORFOIS), Lars Stemman (particle model?)
Références :
Aumont O., PISCES reference guide, draft, 2004.
ORFOIS final report, LSCE contribution, 2004.