Biophysical modelling of marine organisms: fundamentals and applications to management of coastal waters: Chapter 3

Complicated coastlines along western continental margin at moderate and high latitude are suitable for developing sheltered finfish and shellfish aquaculture. Advection of Harmful Algal Blooms (HABs) generated offshore, and the transfer of pathogens and parasites has major negative impacts for coastal economic development. A tool with great potential for providing early warnings of these challenges for aquaculture communities is numerical modelling. This presents its own challenges in the prediction of hydrodynamics for regions of complex bathymetry and coastlines, and frequently changing weather pattern. In this chapter we present in detail a new regional numerical model (WSC-FVCOM) based on an unstructured finite volume approach, which provide adequate resolution of the hydrodynamic structure in this complex environment to simulate transport of particles (such as Kareania mikimotoi cells, sea-lice or larvae) within nearshore waters (our case study area being the west coast of Scotland). Assessment and validation tests demonstrate good agreement between our model system and observed tidal parameters as well as regional thermo-haline structure and current field. Lagrangian drifting buoy transport simulations and an individual-based biological (IBM) model for a bloom of K. mikimotoi demonstrate that the model system has substantial potential for HAB prediction. We also cover application of the model to understanding marine population connectivity, comparing different habitat structures found in the region. In the context of sea lice (a key aquaculture parasite), we investigate model prediction sensitivity to several aspects of model formulation. The model is under ongoing development, and since July 2015 essential progress was made towards a full operational setup.