A highly spatially resolved ecosystem model for the North West European Continental Shelf

A three-dimensional mechanistic model of Prorocentrum minimum blooms in eutrophic Chesapeake Bay

Planktonic Prorocentrum, common harmful dinoflagellate, are increasing in frequency, duration, and magnitude globally, as exemplified by the number of blooms of P. minimum in Chesapeake Bay that have nearly doubled over the past 3 decades. Although the dynamics of transport and seasonal occurrence of this species have been previously described, it has been challenging to predict the timing and location of P. minimum blooms in Chesapeake Bay. We developed a new three-dimensional mechanistic model of this species that integrates physics, nutrient cycling and plankton physiology and embedded it within a coupled hydrodynamic-biogeochemical model originally developed for simulating water quality in eutrophic estuarine and coastal waters. Hindcast simulations reproduced the observed time series and spatial distribution of cell density, in particular capturing well its peak in May in the mid-to-upper part of the estuary. Timing and duration of the blooms were mostly determined by the temperature-dependent growth function, while mortality due to grazing and respiration played a minor role. The model also reproduced the pattern of overwintering populations, which are located in bottom waters of the lower Bay, and are transported upstream in spring by estuarine flow. Blooms develop in the mid-upper parts of the estuary when these transported cells encounter high nutrient concentrations from the Susquehanna River and favorable light conditions. Diagnostic analysis and model-sensitivity experiments of nutrient conditions showed that high nitrogen:phosphorus conditions favor bloom development. The model also captured the observed interannual variations in the magnitude and spatial distribution of P. minimum blooms.

A generic framework for individual-based modelling and physical-biological interaction

The increased availability of high-resolution ocean data globally has enabled more detailed analyses of physical-biological interactions and their consequences to the ecosystem. We present IBMlib, which is a versatile, portable and computationally effective framework for conducting Lagrangian simulations in the marine environment. The purpose of the framework is to handle complex individual-level biological models of organisms, combined with realistic 3D oceanographic model of physics and biogeochemistry describing the environment of the organisms without assumptions about spatial or temporal scales. The open-source framework features a minimal robust interface to facilitate the coupling between individual-level biological models and oceanographic models, and we provide application examples including forward/backward simulations, habitat connectivity calculations, assessing ocean conditions, comparison of physical circulation models, model ensemble runs and recently posterior Eulerian simulations using the IBMlib framework. We present the code design ideas behind the longevity of the code, our implementation experiences, as well as code performance benchmarking. The framework may contribute substantially to progresses in representing, understanding, predicting and eventually managing marine ecosystems.

Individual-based modelling of the development and transport of a Karenia mikimotoi bloom on the North-west European continental shelf

In 2006, a large and prolonged bloom of the dinoflagellate Karenia mikimotoi occurred in Scottish coastal waters, causing extensive mortalities of benthic organisms including annelids and molluscs and some species of fish (Davidson et al., 2009). A coupled hydrodynamic-algal transport model was developed to track the progression of the bloom around the Scottish coast during June-September 2006 and hence investigate the processes controlling the bloom dynamics. Within this individual-based model, cells were capable of growth, mortality and phototaxis and were transported by physical processes of advection and turbulent diffusion, using current velocities extracted from operational simulations of the MRCS ocean circulation model of the North-west European continental shelf. Vertical and horizontal turbulent diffusion of cells are treated using a random walk approach. Comparison of model output with remotely sensed chlorophyll concentrations and cell counts from coastal monitoring stations indicated that it was necessary to include multiple spatially distinct seed populations of K. mikimotoi at separate locations on the shelf edge to capture the qualitative pattern of bloom transport and development. We interpret this as indicating that the source population was being transported northwards by the Hebridean slope current from where colonies of K. mikimotoi were injected onto the continental shelf by eddies or other transient exchange processes. The model was used to investigate the effects on simulated K. mikimotoi transport and dispersal of: (1) the distribution of the initial seed population; (2) algal growth and mortality; (3) water temperature; (4) the vertical movement of particles by diurnal migration and eddy diffusion; (5) the relative role of the shelf edge and coastal currents; (6) the role of wind forcing. The numerical experiments emphasized the requirement for a physiologically based biological model and indicated that improved modelling of future blooms will potentially benefit from better parameterisation of temperature dependence of both growth and mortality and finer spatial and temporal hydrodynamic resolution.

Challenges and difficulties in assessing the environmental status under the requirements of the Ecosystem Approach in North African countries, illustrated by eutrophication assessment

Marine ecosystems provide many ecosystem goods and services. However, these ecosystems and the benefits they create for humans are subject to competing uses and increasing pressures. As a consequence of the increasing threats to the marine environment, several regulations require applying an ecosystem-based approach for managing the marine environment. Within the Mediterranean Sea, in 2008, the Contracting Parties of the Mediterranean Action Plan decided to progressively apply the Ecosystem Approach (EcAp) with the objective of achieving Good Environmental Status (GES) for 2018. To assess the environmental status, the EcAp proposes 11 Ecological Objectives, each of which requires a set of relevant indicators to be integrated. Progress towards the EcAp entails a gradual and important challenge for North African countries, and efforts have to be initiated to propose and discuss methods. Accordingly, to enhance the capacity of North African countries to implement EcAp and particularly to propose and discuss indicators and methods to assess GES, the aim of this manuscript is to identify the practical problems and gaps found at each stage of the environmental status assessment process. For this purpose, a stepwise method has been proposed to assess the environmental status using Ecologic Objective 5-Eutrophication as example.

Modeling the dynamics of continental shelf carbon

Continental margin systems are important contributors to global nutrient and carbon budgets. Effort is needed to quantify this contribution and how it will be modified under changing patterns of climate and land use. Coupled models will be used to provide projections of future states of continental margin systems. Thus, it is appropriate to consider the limitations that impede the development of realistic models. Here, we provide an overview of the current state of modeling carbon cycling on continental margins as well as the processes and issues that provide the next challenges to such models. Our overview is done within the context of a coupled circulation-biogeochemical model developed for the northeastern North American continental shelf region. Particular choices of forcing and initial fields and process parameterizations are used to illustrate the consequences for simulated distributions, as revealed by comparisons to observations using quantitative statistical metrics.

Diagnostic monitoring of a changing environment: an alternative UK perspective

Adaptive management of the marine environment requires an understanding of the complex interactions within it. Establishing levels of natural variability within and between marine ecosystems is a necessary prerequisite to this process and requires a monitoring programme which takes account of the issues of time, space and scale. In this paper, we argue that an ecosystem approach to managing the marine environment should take direct account of climate change indicators at a regional level if it is to cope with the unprecedented change expected as a result of human impacts on the earth climate system. We discuss the purpose of environmental monitoring and the importance of maintaining long-term time series. Recommendations are made on the use of these data in conjunction with modern extrapolation and integration tools (e.g. ecosystem models, remote sensing) to provide a diagnostic approach to the management of marine ecosystems, based on adaptive indicators and dynamic baselines.