J. Icarus Allen

Skill assessment for coupled biological/physical models of marine systems

Coupled biological/physical models of marine systems serve many purposes including the synthesis of information, hypothesis generation, and as a tool for numerical experimentation. However, marine system models are increasingly used for prediction to support high-stakes decision-making. In such applications it is imperative that a rigorous model skill assessment is conducted so that the models capabilities are tested and understood. Herein, we review several metrics and approaches useful to evaluate model skill. The definition of skill and the determination of the skill level necessary for a given application is context specific and no single metric is likely to reveal all aspects of model skill. Thus, we recommend the use of several metrics, in concert, to provide a more thorough appraisal. The routine application and presentation of rigorous skill assessment metrics will also serve the broader interests of the modeling community, ultimately resulting in improved forecasting abilities as well as helping us recognize our limitations.

End-To-End Models for the Analysis of Marine Ecosystems: Challenges, Issues, and Next Steps

Abstract There is growing interest in models of marine ecosystems that deal with the effects of climate change through the higher trophic levels. Such end-to-end models combine physicochemical oceanographic descriptors and organisms ranging from microbes to higher-trophic-level (HTL) organisms, including humans, in a single modeling framework. The demand for such approaches arises from the need for quantitative tools for ecosystem-based management, particularly models that can deal with bottom-up and top-down controls that operate simultaneously and vary in time and space and that are capable of handling the multiple impacts expected under climate change. End-to-end models are now feasible because of improvements in the component submodels and the availability of sufficient computing power. We discuss nine issues related to the development of end-to-end models. These issues relate to formulation of the zooplankton submodel, melding of multiple temporal and spatial scales, acclimation and adaptation, behavioral movement, software and technology, model coupling, skill assessment, and interdisciplinary challenges. We urge restraint in using end-to-end models in a true forecasting mode until we know more about their performance. End-to-end models will challenge the available data and our ability to analyze and interpret complicated models that generate complex behavior. End-to-end modeling is in its early developmental stages and thus presents an opportunity to establish an open-access, community-based approach supported by a suite of true interdisciplinary efforts.

Extraction of a weak climatic signal by an ecosystem

The complexity of ecosystems can cause subtle and chaotic responses to changes in external forcing. Although ecosystems may not normally behave chaotically, sensitivity to external influences associated with nonlinearity can lead to amplification of climatic signals. Strong correlations between an El Niño index and rainfall and maize yield in Zimbabwe have been demonstrated; the correlation with maize yield was stronger than that with rainfall. A second example is the 100,000-year ice-age cycle, which may arise from a weak cycle in radiation through its influence on the concentration of atmospheric CO2 (ref. 5). Such integration of a weak climatic signal has yet to be demonstrated in a realistic theoretical system. Here we use a particular climatic phenomenon—the observed association between plankton populations around the UK and the position of the Gulf Stream—as a probe to demonstrate how a detailed marine ecosystem model extracts a weak signal that is spread across different meteorological variables. Biological systems may therefore respond to climatic signals other than those that dominate the driving variables.

Biomass changes and trophic amplification of plankton in a warmer ocean

Ocean warming can modify the ecophysiology and distribution of marine organisms, and relationships between species, with nonlinear interactions between ecosystem components potentially resulting in trophic amplification. Trophic amplification (or attenuation) describe the propagation of a hydroclimatic signal up the food web, causing magnification (or depression) of biomass values along one or more trophic pathways. We have employed 3-D coupled physical-biogeochemical models to explore ecosystem responses to climate change with a focus on trophic amplification. The response of phytoplankton and zooplankton to global climate-change projections, carried out with the IPSL Earth System Model by the end of the century, is analysed at global and regional basis, including European seas (NE Atlantic, Barents Sea, Baltic Sea, Black Sea, Bay of Biscay, Adriatic Sea, Aegean Sea) and the Eastern Boundary Upwelling System (Benguela). Results indicate that globally and in Atlantic Margin and North Sea, increased ocean stratification causes primary production and zooplankton biomass to decrease in response to a warming climate, whilst in the Barents, Baltic and Black Seas, primary production and zooplankton biomass increase. Projected warming characterized by an increase in sea surface temperature of 2.29 ± 0.05 °C leads to a reduction in zooplankton and phytoplankton biomasses of 11% and 6%, respectively. This suggests negative amplification of climate driven modifications of trophic level biomass through bottom-up control, leading to a reduced capacity of oceans to regulate climate through the biological carbon pump. Simulations suggest negative amplification is the dominant response across 47% of the ocean surface and prevails in the tropical oceans; whilst positive trophic amplification prevails in the Arctic and Antarctic oceans. Trophic attenuation is projected in temperate seas. Uncertainties in ocean plankton projections, associated to the use of single global and regional models, imply the need for caution when extending these considerations into higher trophic levels.

A computational model of the digestive gland epithelial cell of marine mussels and its simulated responses to oil-derived aromatic hydrocarbons.

This paper describes a computational model of digestive gland epithelial cells (digestive cells) of marine mussels. These cells are the major environmental interface for uptake of contaminants, particularly those associated with natural particulates that are filtered from seawater by mussels. Digestive cells show well characterised reactions to exposure to lipophilic xenobiotics, such as oil-derived aromatic hydrocarbons (AHs), which accumulate in these cells with minimal biotransformation. The simulation model is based on processes associated with the flux of carbon through the cell. Physiological parameters such as fluctuating food concentration, cell volume, respiration, secretion/excretion, storage of glycogen and lipid, protein/organelle turnover (autophagy/resynthesis) and export of carbon to other tissues of the mussel are all included in the model. The major response to AHs is induction of increased autophagy in these cells. Simulations indicate that the reactions to AHs and food deprivation correspond well with responses measured in vivo.

A first appraisal of prognostic ocean DMS models and prospects for their use in climate models

Ocean dimethylsulfide (DMS) produced by marine biota is the largest natural source of atmospheric sulfur, playing a major role in the formation and evolution of aerosols, and consequently affecting climate. Several dynamic process-based DMS models have been developed over the last decade, and work is progressing integrating them into climate models. Here we report on the first international comparison exercise of both 1D and 3D prognostic ocean DMS models. Four global 3D models were compared to global sea surface chlorophyll and DMS concentrations. Three local 1D models were compared to three different oceanic stations (BATS, DYFAMED, OSP) where available time series data offer seasonal coverage of chlorophyll and DMS variability. Two other 1D models were run at one site only. The major point of divergence among models, both within 3D and 1D models, relates to their ability to reproduce the summer peak in surface DMS concentrations usually observed at low to mid- latitudes. This significantly affects estimates of global DMS emissions predicted by the models. The inability of most models to capture this summer DMS maximum appears to be constrained by the basic structure of prognostic DMS models: dynamics of DMS and dimethylsulfoniopropionate (DMSP), the precursor of DMS, are slaved to the parent ecosystem models. Only the models which include environmental effects on DMS fluxes independently of ecological dynamics can reproduce this summer mismatch between chlorophyll and DMS. A major conclusion of this exercise is that prognostic DMS models need to give more weight to the direct impact of environmental forcing (e.g., irradiance) on DMS dynamics to decouple them from ecological processes.

Lysosomal and Autophagic Reactions as Predictive Indicators of Environmental Impact in Aquatic Animals

The lysosomal-autophagic system appears to be a common target for many environmental pollutants as lysosomes accumulate many toxic metals and organic xenobiotics, which perturb normal function and damage the lysosomal membrane. In fact, lysosomal membrane integrity or stability appears to be an effective generic indicator of cellular well-being in eukaryotes: in bivalve molluscs and fish, stability is correlated with many toxicological and pathological endpoints. Prognostic use of adverse lysosomal and autophagic reactions to environmental pollutants has been explored in relation to predicting cellular dysfunction and health in marine mussels, which are extensively used environmental sentinels. Derivation of explanatory frameworks for prediction of pollutant impact on health is a major goal; and we have developed a conceptual mechanistic model linking lysosomal damage and autophagic dysfunction with injury to cells and tissues. This model has also complemented the creation of a cell-based computational model for molluscan hepatopancreatic cells that simulates lysosomal, autophagic and other cellular reactions to pollutants. Experimental and simulated results have also indicated that nutritional deprivation - induced autophagy has a protective function against toxic effects mediated by reactive oxygen species (ROS). Finally, coupled measurement of lysosomal-autophagic reactions and modelling is proposed as a practical toolbox for predicting environmental risk. Addendum to: Environmental Prognostics: An Integrated Model Supporting Lysosomal Stress Responses as Predictive Biomarkers of Animal Health Status M.N. Moore, J.I. Allen and A. McVeigh Mar Environ Res 2005; In press

Advective controls on primary production in the stratified western Irish Sea: An eddy‐resolving model study

[1] The Proudman Oceanographic Laboratory Coastal Ocean Modelling System and the European Regional Seas Ecosystem Model are applied at eddy-resolving (∼1.8 km) scales to the stratified region of the western Irish Sea to investigate the effects of advective transport processes on the ecosystem. We find currents can transport nutrient-rich water into the otherwise nutrient-depleted surface layer of the stratified region, fueling intermittent production throughout the summer. The currents involved fall into three classes: large-scale wind and density-driven circulation, smaller-scale eddies, and tidally mediated dispersive phenomena; all appear to play a role in this area. A model experiment without ecosystem advection does not show the intermittent surface production; summer growth only occurs at the thermocline. This experiment gives a significantly lower total annual production of 110 ± 26 g C m -2 yr -1 , compared with 150 ± 40 g C m -2 yr -1 for the full model, which is in better agreement with observational estimates of 140 g C m-2 yr -1 . We calculate summer averages of the terms in the scalar transport equation, which show that advective transport of all nutrients dominates over vertical diffusion above the thermocline in most of the stratified region. The transport of nitrate, ammonia, and phosphate is significantly greater than the transport of silicate. This can be attributed to the lack of silicate recycling in the pelagic ecosystem. Only limited and anecdotal observational evidence exists to support these model results, which points to a need for observations of high spatial and temporal resolution to investigate these processes in conjunction with further model studies.

Key Questions and Recent Research Advances on Harmful Algal Blooms in Relation to Nutrients and Eutrophication

The Core Research Project on HABs in Eutrophic Systems was one of the projects implemented under the Global Ecology and Oceanography of Harmful Algal Blooms (GEOHAB) program. Building on several Open Science Meetings and associated international efforts, this project focused on a number of key questions that related to the types of harmful algal species found in eutrophic systems, the drivers of nutrient changes and their effects, as well as interactions with community composition of all members of the food web. Substantial progress was made on all of the identified key questions and that progress is reviewed in this chapter. In all, the evidence is unequivocal that harmful algae can be directly and/or indirectly stimulated by nutrient over-enrichment and that chronic, subtle effects, such as changes in nutrient proportion or form, can be equally important or even more important than the obvious, acute effects. Furthermore, nutrient enrichment interacts with other major drivers, such as hydrology, food web interactions, and climate change, in both direct and indirect ways. Many questions remain, however. Much needs to be done in parameterizing rates, characterizing traits, and how they are both externally driven and internally dynamically regulated. Many species are understudied. Work needs to advance in understanding the physiological responses to excess nutrient availability and relationships with toxicity, among other physiological processes. A new emphasis on improved model formulations is needed, linking land-use models with regional ocean models and that incorporate dynamic physiological behavior. Given the pace at which nutrient loads continue to pollute the global landscape and the global expansion of HABs, continued international collaborative efforts in understanding changing nutrients and their relationships with HABs are not only necessary, but urgently needed.

Biological or microbial carbon pump? The role of phytoplankton stoichiometry in ocean carbon sequestration

Once fixed by photosynthesis carbon becomes part of the marine food web. The fate of this carbon has two possible outcomes: it may be respired and released back to the ocean and potentially to the atmosphere as CO2 or retained in the ocean interior and/or marine sediments for extended time scales. The most important biologically mediated processes responsible for long term carbon storage in the ocean are the biological carbon pump (BCP) and the microbial carbon pump (MCP). While acting simultaneously in the ocean, the balance between these two mechanisms is thought to vary depending on the trophic state of the environment. Using previously published formulations, we propose a modelling framework to simulate variability in the MCP: BCP ratio as a function of external nutrients. Our results suggest that the role of the MCP might become more significant under future climate change conditions where increased stratification enhances the oligotrophic nature of the surface ocean. Based on these model results, we propose a conceptual framework in which the internal stoichiometry of phytoplankton, modulating both grazing pressure and DOM production (via phytoplankton exudation), plays a crucial role in regulating the MCP: BCP ratio.