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See detailBenthic-Pelagic coupling in the Black Sea - A model Study
Capet, Arthur ULg; meysman, Filip; Soetaert, Karline

Conference (2013, May 15)

While benthic and sediment processes are now recognized as major components of the shelf iogeochemical budget, their representation in 3D biogeochemical model has for long been oversimplified [Soetaert et ... [more ▼]

While benthic and sediment processes are now recognized as major components of the shelf iogeochemical budget, their representation in 3D biogeochemical model has for long been oversimplified [Soetaert et al., 2000]. These oversimplified formulations of the bottom boundary onditions prevent to account for the response of diagenetic processes to the environment. The onsequent absence of spatial and temporal variability of benthic/pelagic fluxes may lead to mis- valuation of important terms in the biogeochemical budgets (e.g. Oxygen, Nitrogen, Carbon, hosphate). More importantly, feedbacks mechanisms within the ecosystem response to utrophication may be overlooked, such as, for instance, the sensitivity of benthic denitrification o the oxygen content in the bottom waters. The GHER-ECO 3D biogeochemical model is xtended ith a refined benthic component explicitly accounting for the effect of organic matter transport, eposition and resuspension and for the influence of the environmental conditions on the iagenetic pathways. A semi-empirical approach allows to reproduce the variability and feedbacks riven by benthic diagenesis without the computational burden of a vertically resolved sediment ayer. This simplification allows to use the coupled model for the long term runs (several ecades) required to appreciate the slow dynamics introduced by the accumulation of organic atter in the sediment layer during the years of high riverine discharge. The extended model has een implemented for the Black Sea North western shelf [Capet et al., 2012]. After a presentation f the main assumptions used to construct the benthic module, results are analyzed with a focus n (1) spatial and seasonal variability of benthic diagenesis and consequent benthic/pelagic xchanges, (2) comparison to in-situ estimates of benthic/pelagic dissolved fluxes, (3) implication n biogeochemical budgets and eutrophication issue. Inherent limitations of the semi-empirical pproach are discussed in the perspective of the current challenges addressed to biogeochemical odels. [less ▲]

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See detailIntroducing dynamic benthic fluxes in 3D biogeochemical model : an application on the Black Sea North-Western shelf
Capet, Arthur ULg; Meysman, Filip; Soetaert, Karline et al

Conference (2013, April 15)

While benthic and sediment processes are now recognized as major components of the shelf iogeochemical budget, their representation in 3D biogeochemical model has for long been oversimplified [Soetaert et ... [more ▼]

While benthic and sediment processes are now recognized as major components of the shelf iogeochemical budget, their representation in 3D biogeochemical model has for long been oversimplified [Soetaert et al., 2000]. These oversimplified formulations of the bottom boundary onditions prevent to account for the response of diagenetic processes to the environment. The onsequent absence of spatial and temporal variability of benthic/pelagic fluxes may lead to mis- valuation of important terms in the biogeochemical budgets (e.g. Oxygen, Nitrogen, Carbon, hosphate). More importantly, feedbacks mechanisms within the ecosystem response to utrophication may be overlooked, such as, for instance, the sensitivity of benthic denitrification o the oxygen content in the bottom waters. The GHER-ECO 3D biogeochemical model is xtended ith a refined benthic component explicitly accounting for the effect of organic matter transport, eposition and resuspension and for the influence of the environmental conditions on the iagenetic pathways. A semi-empirical approach allows to reproduce the variability and feedbacks riven by benthic diagenesis without the computational burden of a vertically resolved sediment ayer. This simplification allows to use the coupled model for the long term runs (several ecades) required to appreciate the slow dynamics introduced by the accumulation of organic atter in the sediment layer during the years of high riverine discharge. The extended model has een implemented for the Black Sea North western shelf [Capet et al., 2012]. After a presentation f the main assumptions used to construct the benthic module, re- sults are analyzed with a focus n (1) spatial and seasonal variability of benthic diagenesis and con- sequent benthic/pelagic xchanges, (2) comparison to in-situ estimates of benthic/pelagic dissolved fluxes, (3) implication n biogeochemical budgets and eutrophication issue. Inherent limitations of the semi-empirical pproach are discussed in the perspective of the current challenges addressed to biogeochemical odels. [less ▲]

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See detailCarbon and nitrogen flows during a bloom of the coccolithophore Emiliania huxleyi: Modelling a mesocosm experiment
Joassin, Pascal ULg; Delille, Bruno ULg; Soetaert, Karline et al

in Journal of Marine Systems (2011), 85

A dynamic model has been developed to represent biogeochemical variables and processes observed during experimental blooms of the coccolithophore Emiliania huxleyi induced inmesocosms over a period of 23 ... [more ▼]

A dynamic model has been developed to represent biogeochemical variables and processes observed during experimental blooms of the coccolithophore Emiliania huxleyi induced inmesocosms over a period of 23 days. The model describes carbon (C), nitrogen (N), and phosphorus (P) cycling through E. huxleyi and the microbial loop, and computes pH and the partial pressure of carbon dioxide (pCO2) from dissolved inorganic carbon (DIC) and total alkalinity (TA). The main innovations are: 1) the representation of E. huxleyi dynamics using an unbalanced growthmodel in carbon and nitrogen, 2) the gathering of formulations describing typical processes involved in the export of carbon such as primary production, calcification, cellular dissolved organic carbon (DOC) excretion, transparent exopolymer (TEP) formation and viral lyses, and 3) an original and validated representation of the calcification process as a function of the net primary production with a modulation by the intra-cellular N:C ratio mimicking the effect of nutrients limitation on the onset of calcification. It is shown that this new mathematical formulation of calcification provides a better representation of the dynamics of TA, DIC and calcification rates derived from experimental data compared to classicaly used formulations (e.g. function of biomass or of net primary production without anymodulation term). In a first step, the model has been applied to the simulations of present pCO2 conditions. It adequately reproduces the observations for chemical and biological variables and provides an overall view of carbon and nitrogen dynamics. Carbon and nitrogen budgets are derived from the model for the different phases of the bloom, highlighting three distinct phases, reflecting the evolution of the cellular C:N ratio and the interaction between hosts and viruses. During the first phase, inorganic nutrients are massively consumed by E. huxleyi increasing its biomass. Uptakes of carbon and nitrogen are maintained at a constant ratio. The second phase is triggered by the exhaustion of phosphate (PO4 3−). Uptake of carbon and nitrogen being uncoupled, the cellular C:N ratio of E. huxleyi increases. This stimulates the active release of DOC, acting as precursors for TEP. The third phase is characterised by an enhancement of the phytoplankton mortality due to viral lysis. A huge amount of DOC has been accumulated in the mesocosm. [less ▲]

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See detailCarbon, nitrogen, oxygen and sulfide budgets in the Black Sea: A biogeochemical model of the whole water column coupling the oxic and anoxic parts
Grégoire, Marilaure ULg; Soetaert, Karline

in Ecological Modelling (2010)

Carbon, nitrogen, oxygen and sulfide budgets are derived for the Black Sea water column from a coupled physical-biogeochemical model. The model is applied in the deep part of the sea and simulates ... [more ▼]

Carbon, nitrogen, oxygen and sulfide budgets are derived for the Black Sea water column from a coupled physical-biogeochemical model. The model is applied in the deep part of the sea and simulates processes over the whole water column including the anoxic layer that extends from ~ 115 m to the bottom (~ 2000 m). The biogeochemical model involves a refined representation of the Black Sea foodweb from bacteria to gelatinous carnivores. It includes notably a series of biogeochemical processes typical for oxygen deficient conditions with, for instance, bacterial respiration using different types of oxidants (i.e denitrification, sulfate reduction), the lower efficiency of detritus degradation, the ANAMMOX (ANaerobic AMMonium OXidation) process and the occurrence of particular redox reactions. The model has been calibrated and validated against all available data gathered in the Black Sea TU Ocean Base and this exercise is described in Gregoire et al., (2008). In the present paper, we focus on the biogeochemical flows produced by the model and we compare model estimations with the measurements performed during the R.V. KNORR expedition conducted in the Black Sea from April to July 1988 (Murray and the Black Sea Knorr Expedition, 1991). Model estimations of hydrogen sulfide oxidation, metal sulfide precipitation, hydrogen sulfide formation in the sediments and water column, export flux to the anoxic layer and to the sediments, denitrification, primary and bacterial production are in the range of field observations. With a simulated Gross Primary Production (GPP) of 7.9 molC m-2 yr-1 and a Community Respiration (CR) of 6.3 molC m-2 yr-1, the system is net autotrophic with a Net Community Production (NCP) of 1.6 molC m-2 yr-1. This NCP corresponds to 20 % of the GPP and is exported to the anoxic layer. In order to model Particulate Organic Matter (POM) fluxes to the bottom and hydrogen sulfide profiles in agreement with in-situ observations, we have to consider that the degradation of POM in anoxic conditions is less efficient that in oxygenated waters as it has often been observed (see discussion in Hedges et al., 1999). The vertical POM profile produced by the model can be fitted to the classic power function describing the oceanic carbon rate (CR=Z-) using an attenuation coefficient  of 0.36 which is the value proposed for another anoxic environment (i.e. the Mexico Margin) by Devol and Hartnett, (2001). Due to the lower efficiency of detritus degradation in anoxic conditions and to the aggregation of particles that enhanced the sinking, an important part of the export to the anoxic layer (i.e. 33 %, 0.52 molC m-2 yr-1) escapes remineralization in the water column and reaches the sediments. Therefore, sediments are active sites of sulfide production contributing to 26 % of the total sulfide production. In the upper layer, the oxygen dynamics is mainly governed by photosynthesis and respiration processes as well as by air-sea exchanges. ~ 71 % of the oxygen produced by phytoplankton (photosynthesis + nitrate reduction) is lost through respiration, ~ 21 % by outgasing to the atmosphere, ~ 5 % through nitrification and only ~ 2 % in the oxidation of reduced components (e.g. Mn2+, Fe2+, H2S). The model estimates the amount of nitrogen lost through denitrification at 307 mmolN m-2 yr-1 that can be partitioned into a loss of ~ 55 % through the use of nitrate for the oxidation of detritus in low oxygen conditions, ~ 40 % in the ANAMMOX process and the remaining ~ 5% in the oxidation of reduced substances by nitrate. In agreement with data analysis performed on long time series collected since the 1960's (Konovalov and Murray, 2001), the sulfide and nitrogen budgets established for the anoxic layer are not balanced in response to the enhanced particle fluxes induced by eutrophication: the NH4 and H2S concentrations increase. [less ▲]

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See detailA mathematical modelling of bloom of the coccolithophore Emiliania huxleyi in a mesocosm experiment
Joassin, Pascal ULg; Delille, Bruno ULg; Soetaert, Karline et al

Poster (2008, July 23)

A dynamic model has been developed to represent biogeochemical variables and processes observed during a bloom of Emiliania huxleyi coccolithophore. This bloom was induced in a mesocosm experiment during ... [more ▼]

A dynamic model has been developed to represent biogeochemical variables and processes observed during a bloom of Emiliania huxleyi coccolithophore. This bloom was induced in a mesocosm experiment during which the ecosystem development was followed over a period of 23-days through changes in various biogeochemical parameters such as inorganic nutrients (nitrate, ammonium and phosphate), total alkalinity (TA), dissolved inorganic carbon (DIC), partial pressure of carbon dioxide (pCO2), dissolved oxygen (O2), photosynthetic pigments, particulate organic carbon (POC), dissolved organic carbon (DOC), Transparent Exopolymer Particles (TEP), primary production, and calcification. This dynamic model is based on unbalanced algal growth and balanced bacterial growth. In order to adequately reproduce the observations, the model includes an explicit description of phosphorus cycling, calcification, TEP production and an enhanced mortality due to viral lysis. The model represented carbon, nitrogen and phosphorus fluxes observed in the mesocosms. Modelled profiles of algal biomass and final concentrations of DIC and nutrients are in agreement with the experimental observations. [less ▲]

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See detailNumerical modeling of the deep Black Sea ecosystem functioning during the late 80’s (eutrophication phase)
Grégoire, Marilaure ULg; Raick, Caroline ULg; Soetaert, Karline

in Progress in Oceanography (2008), 76(9), 286-333

A one-dimensional coupled physical–biogeochemical model has been developed to simulate the ecosystem of the central Black Sea at the end of the 1980s when eutrophication and invasion by gelatinous ... [more ▼]

A one-dimensional coupled physical–biogeochemical model has been developed to simulate the ecosystem of the central Black Sea at the end of the 1980s when eutrophication and invasion by gelatinous organisms seriously affected the stability and dynamics of the system. The physical model is the General Ocean Turbulence Model (GOTM) and the biogeochemical model describes the foodweb from bacteria to gelatinous carnivores through 24 state variables including three groups of phytoplankton: diatoms, small phototrophic flagellates and dinoflagellates, two zooplankton groups: micro- and mesozooplankton, two groups of gelatinous zooplankton: the omnivorous and carnivorous forms, an explicit representation of the bacterial loop: bacteria, labile and semi-labile dissolved organic matter, particulate organic matter. The model simulates oxygen, nitrogen, silicate and carbon cycling. In addition, an innovation of this model is that it explicitly represents processes in the anoxic layer. Biogeochemical processes in anaerobic conditions have been represented using an approach similar to that used in the modeling of diagenetic processes in the sediments lumping together all the reduced substances in one state variable [Soetaert, K., Herman, P., 1996. A model of early diagenetic processes from the shelf to abyssal depths. Geochimica et Cosmochimica Acta 60 (6) 1019–1040]. In this way, processes in the upper oxygenated layer are fully coupled with anaerobic processes in the deep waters, allowing to perform longterm simulations. The mathematical modeling of phytoplankton and zooplankton dynamics, detritus and the microbial loop is based on the model developed by Van den Meersche et al. [Van den Meersche, K., Middelburg, J., Soetaert, K., van Rijswijk P.H.B., Heip, C., 2004. Carbon–nitrogen coupling and algal–bacterial interactions during an experimental bloom: Modeling a 13c tracer experiment. Limnology and Oceanography 49 (3), 862–878] and tested in the modeling of mesocosm experiments and of the Ligurian sea ecosystem [Raick, C., Delhez, E., Soetaert, K., Gregoire, M., 2005. Study of the seasonal cycle of the biogeochemical processes in the Ligurian sea using an 1D interdisciplinary model. Journal of Marine Systems 55 (3–4) 177–203]. This model has been extended to simulate the development of top predators, the aggregation of detritus as well as the degradation and chemical processes in suboxic/anoxic conditions (e.g. denitrification, anoxic remineralization, redox reactions). The coupled model extends down to the sediments (’2000 m depth) and is forced at the air–sea interface by the 6 hourly ERA-40 reanalysis of ECMWF data. The model has been calibrated and validated using a large set of data available in the Black Sea TU Ocean Base. The biogeochemical model involves some hundred parameters which are first calibrated by hand using published values. Then, an identifiability analysis has been performed in order to determine a subset of identifiable parameters (i.e. ensemble of parameters that can be together estimated from the amount of data we have at our disposal, see later in the text). Also a subset of 10 identifiable parameters was isolated and an automatic calibration subroutine (Levenberg Marquart) has been used to fine tune these parameters. Additionally, in order to assess the sensitivity of model results to the parameterization of the two gelatinous groups, Monte Carlo simulations were performed perturbing all the parameters governing their dynamics. In order to calibrate the particle dynamics and export, the chemical model was run off-line with the particle and microbial loop model in order to check its capacity of simulating anoxic waters. After a 104 year run, the model simulated NH4 and H2S profiles similar to observations but steady state was not reached suggesting that the Black Sea deep waters are not at steady state. The fully coupled model was then used to simulate the period 1988–1992 of the Black Sea ecosystem. The model solution exhibits a complex dynamics with several years of transient adjustment. This complexity is imparted by the explicit modeling of top predators. The integrated chlorophyll and phytoplankton biomasses, the maximum concentration and depth of maximum, mesozooplankton biomass, depth of oxycline, primary production, bacterial production, surface concentrations of nutrients and plankton simulated by the model and obtained from available data analysis were compared and showed a satisfactory agreement. Also, as in the data, the model shows a continuous development of phytoplankton throughout the year, with an intense spring bloom dominated by diatoms and a fall bloom dominated by dinoflagellates. Dinoflagellates dominate from summer until late fall while small phototrophic flagellates are never dominant in terms of biomass, but are present almost throughout the year except in winter. The model simulates an intense silicate removal associated to increased diatoms blooms which were promoted by increased nutrient conditions, and by the presence of gelatinous zooplankton. This silicate pumping leads to silicate limitation of diatoms development in summer allowing the development of dinoflagellates. [less ▲]

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See detailA dynamic model of an experimental bloom of coccolithophores Emiliania huxleyi
Joassin, Pascal ULg; Borges, Alberto ULg; Chou, Lei et al

Conference (2007, November 27)

A dynamic model has been developed to represent biogeochemical events observed during an experimentally induced bloom of coccolithophores Emiliania huxleyi. This bloom occurred in a mesocosm experiment ... [more ▼]

A dynamic model has been developed to represent biogeochemical events observed during an experimentally induced bloom of coccolithophores Emiliania huxleyi. This bloom occurred in a mesocosm experiment (Bergen 2001 experiment) during which ecosystem development was followed over a 23-days period through changes of the stocks of inorganic nutrients (nitrate, ammonium and phosphate), dissolved inorganic carbon and pCO2, O2 concentration, pigments, particulate organic carbon and nitrogen, dissolved organic carbon, the production of Transparent Exopolymeric Particles (TEP), primary production, alkalinity, calcification and particulate inorganic carbon. The dynamic model is based on unbalanced algal growth and balanced growth for bacteria as described in Van den Meersche et al. (2004). In addition, in order to adequately reproduce the observations, the model has been extended by including an explicit description of calcification, T.E.P production and an enhanced mortality due to viruses. This last process, based on a critical promiscuity between cellular hosts and viral agents, successfully contributed to reproduce the bloom extinction as observed in the mesocosm experiment. This model will be implemented in a coupled physical-biogeochemical model of the Black Sea ecosystem in the framework of the EU Sesame project and in the Gulf of Biscay in the frame of the Belgian PEACE project. [less ▲]

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See detailCan principal component analysis be used to predict the dynamics of a strongly non-linear marine biogeochemical model?
Raick, Caroline ULg; Beckers, Jean-Marie ULg; Soetaert, Karline et al

in Ecological Modelling (2006), 196(3-4), 345-364

In the framework of model complexity reduction, we investigate the ability of the principal component analysis technique to represent in a compact form the dynamics of a coupled physical-ecosystem model ... [more ▼]

In the framework of model complexity reduction, we investigate the ability of the principal component analysis technique to represent in a compact form the dynamics of a coupled physical-ecosystem model. The biogeochemical model describes the evolution in time and depth of the partly decoupled nitrogen and carbon cycles of the pelagic food web in the Ligurian Sea (North Western Mediterranean Sea) through 19 biogeochemical state variables. The GHER hydrodynamic model (1D version) is used to represent the physical forcings. The coupled model presents a high variability in time and space that can be decomposed in modes by principal component analysis. To investigate the possibility of being represented in a compact form, the model is constrained to evolve in a reduced space spanned by its most dominant modes of variability that are the empirical orthogonal functions (EOFs). Different orthogonal bases (formed by 1D and OD EOFs) are used to investigate the performance and realism of the method. 1D vertical EOFs show a tendency to impose a spatial structure to model results according to the most dominant EOFs. In the case of OD EOFs, results of the reduced model can be very close to the original one, but it requires a large number of modes. (c) 2006 Elsevier B.V. All rights reserved. [less ▲]

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See detailModel complexity and performance: How far can we simplify?
Raick, Caroline ULg; Soetaert, Karline; Grégoire, Marilaure ULg

in Progress in Oceanography (2006), 70(1), 27-57

Handling model complexity and reliability is a key area of research today. While complex models containing sufficient detail have become possible due to increased computing power, they often lead to too ... [more ▼]

Handling model complexity and reliability is a key area of research today. While complex models containing sufficient detail have become possible due to increased computing power, they often lead to too much uncertainty. On the other hand, very simple models often crudely oversimplify the real ecosystem and can not be used for management purposes. Starting from a complex and validated 1D pelagic ecosystem model of the Ligurian Sea (NW Mediterranean Sea), we derived simplified aggregated models in which either the unbalanced algal growth, the functional group diversity or the explicit description of the microbial loop was sacrificed. To overcome the problem of data availability with adequate spatial and temporal resolution, the outputs of the complex model are used as the baseline of perfect knowledge to calibrate the simplified models. Objective criteria of model performance were used to compare the simplified models' results to the complex model output and to the available data at the DYFAMED station in the central Ligurian Sea. We show that even the simplest (NPZD) model is able to represent the global ecosystem features described by the complex model (e.g. primary and secondary productions, particulate organic matter export flux, etc.). However, a certain degree of sophistication in the formulation of some biogeochemical processes is required to produce realistic behaviors (e.g. the phytoplankton competition, the potential carbon or nitrogen limitation of the zooplankton ingestion, the model trophic closure, etc.). In general, a 9 state-variable model that has the functional group diversity removed, but which retains the bacterial loop and the unbalanced algal growth, performs best. (C) 2006 Elsevier Ltd. All rights reserved. [less ▲]

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See detailStudy of the seasonal cycle of the biogeochemical processes in the Ligurian Sea using a ID interdisciplinary model
Raick, Caroline ULg; Delhez, Eric ULg; Soetaert, Karline et al

in Journal of Marine Systems (2005), 55(3-4), 177-203

A one-dimensional coupled physical-biogeochemical model has been built to study the pelagic food web of the Ligurian Sea (NW Mediterranean Sea). The physical model is the turbulent closure model (version ... [more ▼]

A one-dimensional coupled physical-biogeochemical model has been built to study the pelagic food web of the Ligurian Sea (NW Mediterranean Sea). The physical model is the turbulent closure model (version I D) developed at the GeoHydrodynamics and Environmental Laboratory (GHER) of the University of Liege. The ecosystem model contains 19 state variables describing the carbon and nitrogen cycles of the pelagic food web. Phytoplankton and zooplankton are both divided in three size-based compartments and the model includes an explicit representation of the microbial loop including bacteria, dissolved organic matter, nano-, and microzooplankton. The internal carbon/nitrogen ratio is assumed variable for phytoplankton and detritus, and constant for zooplankton and bacteria. Silicate is considered as a potential limiting nutrient of phytoplankton's growth. The aggregation model described by Kriest and Evans in (Proc. Ind. Acad. Sci., Earth Planet. Sci. 109 (4) (2000) 453) is used to evaluate the sinking rate of particulate detritus. The model is forced at the air-sea interface by meteorological data coming from the "Cote d'Azur" Meteorological Buoy. The dynamics of atmospheric fluxes in the Mediterranean Sea (DYFAMED) time-series data obtained during the year 2000 are used to calibrate and validate the biological model. The comparison of model results within in situ DYFAMED data shows that although some processes are not represented by the model, such as horizontal and vertical advections, model results are overall in agreement with observations and differences observed can be explained with environmental conditions. (c) 2004 Elsevier B.V. All rights reserved. [less ▲]

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See detailModeling the nitrogen cycling and plankton productivity in the Black Sea using a three-dimensional interdisciplinary model
Grégoire, Marilaure ULg; Soetaert, Karline; Nezlin, Nikolay Pavlovich et al

in Journal of Geophysical Research. Oceans (2004), 109(C5),

[1] A six-compartment ecosystem model defined by a simple nitrogen cycle is coupled with a general circulation model in the Black Sea so as to examine the seasonal variability of the ecohydrodynamics ... [more ▼]

[1] A six-compartment ecosystem model defined by a simple nitrogen cycle is coupled with a general circulation model in the Black Sea so as to examine the seasonal variability of the ecohydrodynamics. Model results show that the annual cycle of the biological productivity of the whole basin is characterized by the presence of a winter-early spring bloom. In all the regions this bloom precedes the onset of the seasonal thermocline and occurs as soon as the vertical winter mixing decreases. Phytoplankton development starts in winter in the central basin, while in coastal areas ( except in the river discharge area) it begins in early spring. In the Danube's discharge area and along the western coast, where surface waters are almost continuously enriched in nutrient by river inputs, the phytoplankton development is sustained during the whole year at the surface. The seasonal variability of the northwestern shelf circulation induced by the seasonal variations in the Danube discharge and the wind stress intensity has been found to have a major impact on the primary production repartition of the area. In the central basin the primary production in the surface layer relies essentially on nutrients being entrained in the upper layer from below. Simulated phytoplankton concentrations are compared with satellite and field data. It has been found that the model is able to reproduce the main characteristics of the space-time evolution of the Black Sea's biological productivity but underestimates the phytoplankton biomass especially in regions extremely rich in nutrients such as the Danube discharge area. [less ▲]

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