Mussel dredging causes resuspension of sediment particles that reduce water clarity and potentially leads to reduced eelgrass growth. In order to study the impact of resuspension from mussel dredging on light conditions in the water column, field experiments were conducted at two sites in the Limfjorden. Light loggers were placed in two circular arrays around the dredge area. Vertical profiles of current velocity were measured by an ADCP and the sediment particle size composition was obtained from sediment core samples. The field data was used to force, calibrate and validate a sediment transport model developed in the FlexSem model system. Changes in sediment concentrations during and after mussel dredging were modeled for the two sites and for seven scenarios. We found that the distance and direction of the plume in the model was in good agreement with light logger data. The plume duration was less than 1 h, and the impact range was between 260-540 m. The scenarios showed that fishing intensity and current speeds were most important for shaping the sediment plumes. Changes in suspended sediment concentrations were 0.62-1.79 mg l −1 on median average and 1.22-11.61 mg l −1 for the upper quantile of the plume, which were on the same order of magnitude as background values in the Limfjorden. The amount of fishing days during the eelgrass growth season was 6-8% in Lovns Bredning and 16-35% in Løgstør Bredning and less than 1-2% of the total area was dredged per season. Even though there are substantial changes in the light conditions from the sediment plumes, the overall spatio-temporal impact in the study area is considered low. We recommend that management plans in other areas could sustain a shellfish fishery by limiting fishing intensity and frequency near eelgrass beds. The presented approach combines observational data, sediment transport modeling and reported fishing activity. It is a step forward within sediment transport modeling and could be incorporated into environmental impact assessments. The results have recently been used as scientific background for recommendations to improve the management plans according to the Danish Mussel Policy and relevant EU Directives.

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Fishery of blue mussels Mytilus edulis constitutes a very important economic activity in Denmark, whereas mussel farming on long-lines or nets is a new, growing sector. Spawning from natural mussel beds takes place during early summer, and larvae disperse via water currents before settling on the bottom or on spat collectors in the farms. In the present study, we coupled a 3D physical model system (FlexSem) with an agent-based model in order to examine the connectivity of this marine system in terms of mussel larval dispersal and settling potential. To address this question, we (1) estimated the dispersal and connectivity between 17 areas in the Limfjorden, (2) identified the main donor and receiver areas of mussel larvae and (3) identified possible dispersal barriers. The results show that the central narrow strait in the Limfjorden was the main donor area in all the studied years, and that the adjacent eastern areas were the main receiver areas. Towards the inner basins of the Limfjorden, isolation increased and limited connectivity was observed. The results from the cluster analysis grouped the Limfjorden into 3 to 5 clusters, but there was still some exchange of simulated larvae observed among these clusters. Analysis of molecular markers revealed no genetic differentiation between areas and supports the model results, indicating that despite distinguishable hydrographic boundaries, the mussel populations in the Limfjorden are well connected. This study demonstrates how connectivity modeling can be used to support site selection processes in aquaculture.

The improved understanding of complex interactions of marine ecosystem components makes the use of fully coupled hydrodynamic, biogeochemical and individual based models more and more relevant. At the same time, the increasing complexity of the models and diverse user backgrounds calls for improved user friendliness and flexibility of the model systems. We present FlexSem, a versatile and user-friendly framework for 3D hydrodynamic, biogeochemical, individual based and sediment transport modelling. The purpose of the framework is to enable natural scientists to conduct advanced 3D simulations in the marine environment, including any relevant processes. This is made possible by providing a precompiled portable framework, which still enables the user to pick any combination of models and provide user defined equation systems to be solved during the simulation. We here present the ideas behind the framework design, the implementation and documentation of the numerical solution to the Navier-Stokes equations in the hydrodynamic module, the surface heat budget model, the pelagic and benthic equation solvers and the Lagrangian movement of the agents in the agent based model. Five examples of different applications of the system are shown: 1) Hydrodynamics in the Disko Bay in west Greenland, 2) A biogeochemical pelagic and benthic model in the inner Danish waters, 3) A generic mussel farm model featuring offline physics, food levels and mussel eco-physiology, 4) Sediment transport in Clarion-Clipperton zone at the bottom of the Pacific and 5) Hydrodynamics coupled with an agent based model around Zanzibar in Tanzania. Hence we demonstrate that the model can be set up for any area with enough forcing data and used to solve a wide range of applications.

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