Modelling benthic fauna in coastal and estuarine systems: North Sea

S. Saraiva, Prof. Dr. J. van der Meer, Prof. Dr. S. A. L. M. Kooijman ,


Bivalves are a main component of the benthic fauna in marine and estuarine systems, even when densities are not enhanced by mariculture activities (Dame, 1996). They provide unique habitats with generally higher biodiversity than the surrounding sediments, exert a major influence on overlying primary producers, are important in the biogeochemical cycling of minerals, nutrients and energy within the system and are a major food resource for many other species (Beadman et al., 2002).

It is well established that the growth of cultures of bivalve species depends on the environmental conditions found at a particular site. However, high densities of suspension feeding bivalves may also alter the prevailing environmental conditions (Dowd, 1997). Filtration of phytoplankton, detritus and inorganic seston from the water column often leads to a depletion of the benthic boundary layer (Prins et al., 1998; Beadman et al., 2002). In turn, bivalves output faeces and pseudofaeces that enrich the surrounding sediments, where the nutrients are re-mineralized by microbial activity (Dame, 1996). This provides a potential feedback mechanism whereby bivalve cultures can influence its supporting ecosystem, and ultimately the growth rate of its own population (Dowd, 1997).

Historically bivalves have been extensively researched and this knowledge base has no doubt influenced the extensive range of modelling approaches used to study their ecology (Gosling, 1992). Each model is developed from a particular perspective and with a particular set of objectives in mind (Beadman et al., 2002). Models range from the simple filtration model, where feeding and excretions are the main processes involved (e.g. Saraiva et al. 2006), to more complex models (e.g. Dowd, 1997, Scholten and Smaal, 1998; Ren and Ross, 2001; Hawkins et al., 2002; Pouvreau et al., 2006;) where processes like filtration, particle rejection and selection, absorption efficiency related to different types of food and reproduction can be described as a function of the environmental conditions.

The complexity of the model can also be increased when the population dynamics is considered (e.g. Bacher and Gangnery, 2006). In the last years the potential of the dynamic energy budgets (DEB) approach to describe mechanistically the bivalves activity have been recognized and several models can be found (including some referenced before), varying in terms of their physiological complexity, accuracy of prediction of individual bivalves growth and ability to predict bivalve population production most of the models (Beadman et al., 2002).

The commercial exploitation of bivalves has led to both increased and decreased abundance in many coastal waters, thereby raising questions about management and carrying capacity of the ecosystem (Smaal et al., 2001). Decision making with respect to sustainable exploitation of areas for shellfish culture requires knowledge of the complex relations between the bivalve species and their environment. Reconciling environmental objective (eutrophication abatement, conservation of biodiversity) with a sustainable shellfish harvest is not a simple balance and it requires analysis and modelling of these complex interactions.

At the ecosystem level models can also have various levels of complexity, and the focus of the models can be oriented more on (i) eco-physiology, models with complex biogeochemical and/or biological models coupled with simple reference to physical processes, e.g. ERSEM (Baretta and Ruardij, 1988) or (ii) physical transport processes, complex physical models where simple formulations for biogeochemical/biological processes where introduced, for example GOTM (e.g. Burchard and Bolding, 2002; Maar et al., 2007) and MOHID Water Modelling System (e.g. Neves, 1985; Martins et al., 2001). However if the model aims to simulate the dynamics of nutrients, phytoplankton, organic matter and bivalves production in an estuary/coastal area, with good comparison with field data in several conditions and in several systems, it must use physical and biogeochemical/biological formulations complex and detailed enough to describe the main processes.

Modelling the different components of the system (hydrodynamics, nutrients, phytoplankton and organic matter, bivalves) in a fully coupled modelling system, where the interactions between the different compartments (pelagic and benthic) are described, can be useful as it is an efficient way of compiling knowledge about different processes, and also an important tool in predicting the system behaviour in response to environmental changes.


The objective of this doctoral program is to develop an individual-based population/community model of various North Sea benthic species, which will subsequently be coupled to a 3D hydrodynamic/biogeochemical model (MOHID Water Modelling System). An integrated modeling tool will be created in order to simulate the ecosystem dynamics in a coastal and estuarine environment with large areas of cultivated shellfish: (i) seasonal and spatial patterns of nutrients and organic matter and (ii) production of bivalves and its influence in the ecological status of the system.

The main goal of this work will be to have a modeling system robust enough in order to:

  1. study the influence of different climate scenarios (in terms of temperature, wind/air pressure, fresh water and nutrient input, boundary conditions) in the production of different bivalve species
  2. study the influence of bivalve activity in the water column properties evolution in large areas of cultivated shellfish
Combining the good description of a physical and biogeochemical/ecological model with the good description of a bivalves' population/community model, one can aim at the direct comparison between the model and field data and expect better agreements, and thus the validation of the model. Hence, there is a higher degree of confidence in terms of predicting the systems behaviour under different environmental scenarios, creating the base for an effective ecosystem management tool by enabling the determination and quantification of important indexes such as the carrying capacity of the system, vulnerability under competition from foreign species or environmental changes related with climate changes.

Detailed Description

Bivalves live in a highly dynamic physical environmental, resulting in a large variability in terms of quantity and quality of the available food. For example, the temporal and spatial variability of suspended matter (that serves as their food) induced by tidal flow can be as important as seasonal changes, due to advective processes, ressuspension and wind-induced wave action (Prins et al., 1998), with consequences in terms of bivalve growth and production. High culture biomass may result in a negative impact on local environment through an increase of organic loading and consequent increased oxygen demand beneath culture leases, phytoplankton biomass reduction and increased nutrient turnovers (Prins et al,. 1998; Smaal et al. 2001), compromising the sustainability of the cultures environment. On the other hand, bivalve growth may assist in eutrophication control through nitrogen and phosphorus removal from the water column (Prins et al. 1998; Shpigel, 2005 in Duarte et al. 2008). The mechanisms for this control depend on the interaction between physical factors (currents, turbulence, mixing), biogeochemistry and the biology of the organisms.

The main challenge in this thesis lies in the design and implementation of a modelling tool that could at the same time simulate the main physical, chemical and biological processes occurring in coastal and estuarine systems with large cultivated areas of shellfish. This includes the development of an individual-based population/community model of various bivalve species, based on the Dynamic Energy Budget theory. This model will be developed as new module in the MOHID Water Modelling System ( This doctoral program is a joint exercise of the Royal NIOZ - Dept. Marine Ecology, Free University Amsterdam - Theoretical Biology, and the Technical University of Lisbon - Instituto Superior Técnico - Dept. Mechanical Engineering.

Mohid Water Modelling System

MOHID Water Modelling System is a three-dimensional (3D) water modelling system developed since the middle eighties at Instituto Superior Técnico (IST), Technical University of Lisbon, in close cooperation with Hidromod Lda, by several generations of post-graduation students and researchers with background in Engineering, Physics and Biology and with contribution of other research groups. MOHID has been largely used to simulate estuarine systems and consists in a set of coupled models, based on the finite volume concept. The system includes modules describing hydrodynamics, eulerian and lagrangian transport, sediment transport and biogeochemical/ecological processes (nutrients, phytoplankton, zooplankton and macroalgae).

The model has been applied to several coastal and estuarine areas in the framework of research and consulting projects and it has showed its ability to simulate complex flow features. The model results have been well compared with field and remote sensing data and in different estuarine and coastal systems (Braunschweig et al., 2003; Coelho et al., 2002; Leitão et al., 2005; Trancoso et al., 2005; Saraiva et al., 2007).

Concerning modelling bivalve activity, MOHID has already implemented a simple filtration/accumulation/excretion model which has been applied in the framework of EU MaBenE project in the Oosterschelde (The Netherlands) and Ria de Vigo (Spain). However the ability of the model to compute and quantify bivalve production is limited due to the simplified representation of the organisms' physiology, thus creating the necessity of developing a more detailed model following an individual-based population/community approach.

Dynamic Energy Budget model

The Dynamic Energy Budget (DEB) theory aims to describe the physiological response of an organism's assimilation and utilization of energy for maintenance, growth and reproduction to changes in aspects of its environment. The theory uses a set of assumptions and principles to translate functional description of the organisms in to differential equations and assumes that the various energetic processes, such as assimilation rate and maintenance, are dependent either on surface area or on body volume (Kooijman, 2000). Several DEB models have been developed in recent years aiming to describe bivalves' production and the similarity between patterns obtained with the models and observed data suggest that this theory should be considered valid for this organisms (Ren and Ross, 2001; Beadman et al., 2002). In the late 1980s Kooijman (1986) published the so-called kappa-rule DEB theory and over the years this theory has been successfully applied in describing the energy allocation to growth and reproduction in a variety of species (van der Veer et al., 2006). The effects at the population level can be modelled using the concept of cohorts where the dynamics of each cohort is reproduced by simulating the growth trajectories of numerous individuals. Standing stock is obtained by summing up individual masses and the size distribution of individuals will reproduce the real size distribution (Bacher and Gangnery, 2006).


The work will proceed with the following steps:
  1. Study the influence of bivalve activity in coastal and estuarine systems An extensive study in terms of the main processes involved in bivalves activity and its modeling approach will be performed. Particular emphasis will be given to coupling hydrodynamics/biogeochemical models and bivalve production models as well as the inclusion of population dynamics effect on the systems conditions.
  2. Compilation and analysis of the existing data available The available sets of data obtained by different authors in the last years (in field and in laboratory) will be at this stage compiled and analyzed. The objective is to prepare the data to be used in the model simulations (parameters and processes description) and data that would be further used for the model validation (main properties dynamics: temperature, nutrients, chlorophyll, organic matter and bivalves abundance).
  3. Development of an individual based model for bivalves production Based on DEB theory, an individual based model for bivalve production will be developed. The model requirements will be: (i) include main processes related with bivalves activity (filtration, ingestion, assimilation, excretion, reproduction, shell construction) and (ii) enable the simulation of different species of bivalves. The model code will be written in FORTRAN 95, as a 0D model following the structure used in MOHID Water Modeling System, enabling the coupling with a 3D hydrodynamic-biogeochemical model. This module will be tested in a stand-alone project in order to verify its consistency.
  4. Development of the population/community model A population/community model will be designed and programmed, based on the concept of different cohorts. Each cohort will have a number of organisms associated and the population distribution will than be represented by the organisms abundance in the different cohorts.
  5. Consistency tests Consistency tests, comprising parameters estimation and model calibration, will be performed using the module created in a stand-alone project. At this stage, the model results (at a 0D scheme) should be in agreement with the bivalve activity described in the literature.
  6. Coupling to MOHID Water Modelling System In this step, the objective is to fully couple the new module to MOHID Water Modelling System. Specific changes, in some of the main modules of the system must be performed in order to simulate the influence of the bivalve in the environment and vice-versa, namely Module WaterProperties (eulerian transport module), Module Interface SedimentWater (benthic boundary layer module) and Module Interface (module responsible with coupling 3D physics with the 0D biogeochemical models).
  7. Implementation of the model in a schematic scenario The correct coupling of the models would be firstly tested in a schematic estuary, in order to verify consistency. The model simulations can be compared with data obtained in specific experiments in order to evaluate its capability in reproducing the results.
  8. Abiotic factors influence in different species bivalve production Different simulations will be performed in order to understand the effect of abiotic factors in bivalves' activity and production. The model results will be as much as possible compared with real data under different abiotic conditions (in terms of temperature, wind/air pressure, fresh water and nutrient inputs, boundary conditions). The inter-species relations between different bivalve species will also be analyzed. The model will be implemented in the North Sea (first following a 1D scheme) in order to be confronted with real data, and different climate scenarios will be examined. The possibility of a fully 2D/3D MOHID implementation in the North Sea will be evaluated. After the validation of the model results several studies can be done in order to better understand the system behavior and the influence of bivalves' cultures in the system, using all the capabilities of the model.


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