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 main goal of this work will be to have a modeling system robust enough in order to:
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 (www.mohid.com). 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.
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.
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