A Dynamic Energy Budget (DEB) model for the keystone predator Pisaster ochraceus.

Antarctic marine organisms are adapted to an extreme environment, characterized by a very low but stable temperature and a strong seasonality in food availability arousing from variations in day length. Ocean organisms are particularly vulnerable to global climate change with some regions being impacted by temperature increase and changes in primary production. Climate change also affects the biotic components of marine ecosystems and has an impact on the distribution and seasonal physiology of Antarctic marine organisms. Knowledge on the impact of climate change in key species is highly important because their performance affects ecosystem functioning. To predict the effects of climate change on marine ecosystems, a holistic understanding of the life history and physiology of Antarctic key species is urgently needed. DEB (Dynamic Energy Budget) theory captures the metabolic processes of an organism through its entire life cycle as a function of temperature and food availability. The DEB model is a tool that can be used to model lifetime feeding, growth, reproduction, and their responses to changes in biotic and abiotic conditions. In this study, we estimate the DEB model parameters for the bivalve Laternula elliptica using literature-extracted and field data. The DEB model we present here aims at better understanding the biology of L. elliptica and its levels of adaptation to its habitat with a special focus on food seasonality. The model parameters describe a metabolism specifically adapted to low temperatures, with a low maintenance cost and a high capacity to uptake and mobilise energy, providing this organism with a level of energetic performance matching that of related species from temperate regions. It was also found that L. elliptica has a large energy reserve that allows enduring long periods of starvation. Additionally, we applied DEB parameters to time-series data on biological traits (organism condition, gonad growth) to describe the effect of a varying environment in food and temperature on the organism condition and energy use. The DEB model developed here for L. elliptica allowed us to improve benchmark knowledge on the ecophysiology of this key species, providing new insights in the role of food availability and temperature on its life cycle and reproduction strategy.

A working group at the National Institute for Mathematical and Biological Synthesis (NIMBioS) explored the feasibility of integrating 2 complementary approaches relevant to ecological risk assessment. Adverse outcome pathway (AOP) models provide "bottom-up" mechanisms to predict specific toxicological effects that could affect an individual's ability to grow, reproduce, and/or survive from a molecular initiating event. Dynamic energy budget (DEB) models offer a "top-down" approach that reverse engineers stressor effects on growth, reproduction, and/or survival into modular characterizations related to the acquisition and processing of energy resources. Thus, AOP models quantify linkages between measurable molecular, cellular, or organ-level events, but they do not offer an explicit route to integratively characterize stressor effects at higher levels of organization. While DEB models provide the inherent basis to link effects on individuals to those at the population and ecosystem levels, their use of abstract variables obscures mechanistic connections to suborganismal biology. To take advantage of both approaches, we developed a conceptual model to link DEB and AOP models by interpreting AOP key events as measures of damage-inducing processes affecting DEB variables and rates. We report on the type and structure of data that are generated for AOP models that may also be useful for DEB models. We also report on case studies under development that merge information collected for AOPs with DEB models and highlight some of the challenges. Finally, we discuss how the linkage of these 2 approaches can improve ecological risk assessment, with possibilities for progress in predicting population responses to toxicant exposures within realistic environments. Integr Environ Assess Manag 2018;14:615-624. © 2018 SETAC.

Marine organisms in Antarctica are adapted to an extreme ecosystem including extremely stable temperatures and strong seasonality due to changes in day length. It is now largely accepted that Southern Ocean organisms are particularly vulnerable to global warming with some regions already being challenged by a rapid increase of temperature. Climate change affects both the physical and biotic components of marine ecosystems and will have an impact on the distribution and population dynamics of Antarctic marine organisms. To predict and assess the effect of climate change on marine ecosystems a more comprehensive knowledge of the life history and physiology of key species is urgently needed. In this study we estimate the Dynamic Energy Budget (DEB) model parameters for key benthic Antarctic species the sea star Odontaster validus using available information from literature and experiments. The DEB theory is unique in capturing the metabolic processes of an organism through its entire life cycle as a function of temperature and food availability. The DEB model allows for the inclusion of the different life history stages, and thus, becomes a tool that can be used to model lifetime feeding, growth, reproduction, and their responses to changes in biotic and abiotic conditions. The DEB model presented here includes the estimation of reproduction handling rules for the development of simultaneous oocyte cohorts within the gonad. Additionally it links the DEB model reserves to the pyloric caeca an organ whose function has long been ascribed to energy storage. Model parameters described a slowed down metabolism of long living animals that mature slowly. O. validus has a large reserve that—matching low maintenance costs- allow withstanding long periods of starvation. Gonad development is continuous and individual cohorts developed within the gonads grow in biomass following a power function of the age of the cohort. The DEB model developed here for O. validus allowed us to increase our knowledge on the ecophysiology of this species, providing new insights on the role of food availability and temperature on its life cycle and reproduction strategy.

Ecological risk assessment quantifies the likelihood of undesirable impacts of stressors, primarily at high levels of biological organization. Data used to inform ecological risk assessments come primarily from tests on individual organisms or from suborganismal studies, indicating a disconnect between primary data and protection goals. We know how to relate individual responses to population dynamics using individual-based models, and there are emerging ideas on how to make connections to ecosystem services. However, there is no established methodology to connect effects seen at higher levels of biological organization with suborganismal dynamics, despite progress made in identifying Adverse Outcome Pathways (AOPs) that link molecular initiating events to ecologically relevant key events. This chapter is a product of a working group at the National Center for Mathematical and Biological Synthesis (NIMBioS) that assessed the feasibility of using dynamic energy budget (DEB) models of individual organisms as a “pivot” connecting suborganismal processes to higher level ecological processes. AOP models quantify explicit molecular, cellular or organ-level processes, but do not offer a route to linking sub-organismal damage to adverse effects on individual growth, reproduction, and survival, which can be propagated to the population level through individual-based models. DEB models describe these processes, but use abstract variables with undetermined connections to suborganismal biology. We propose linking DEB and quantitative AOP models by interpreting AOP key events as measures of damage-inducing processes in a DEB model. Here, we present a conceptual model for linking AOPs to DEB models and review existing modeling tools available for both AOP and DEB.

A dynamic energy budget (DEB) model for the energy usage and reproduction of the Icelandic capelin ( Mallotus villosus)

The simulations and predictions obtained from mathematical models of bioprocesses conducted by microorganisms are not overvalued. Mechanistic models are bringing a better process understanding and the possibility of simulating unmeasurable variables. The Dynamic Energy Budget (DEB) model is an energy balance that can be formulated for any living organism and can be classified as a structured model. In this study, the DEB model was used to describe E. coli growth in a batch reactor in carbon and nitrogen substrate limitation conditions. The DEB model provides a possibility to follow the changes in the microbes’ cells including their elemental composition and content of some important cell ingredients in different growth phases in substrate limitation conditions which makes it more informative compared to Monod’s model. The model can be used as an optimal choice between Monod-like models and flux-based approaches.Key points• The DEB model can be used to catch changes in elemental composition of E. coli• Bacteria batch culture growth phases can be explained by the DEB model• The DEB model is more informative compared to Monod’s based models

Dynamic energy budget model for the complete life cycle of chub mackerel in the Northwest Pacific

In this study, the food conditions for mussels are estimated at different locations within the Oosterschelde. In 2014, 2015 and 2016, mussels with a uniform size were placed in baskets at the borders of commercial culture plots distributed over the Oosterschelde. Each month, a subsample was taken from each basket to measure growth (shell length and individual weight) of the mussels. The results show a variation in growth performance, both in shell length as in flesh weight, between the different locations. A model approach was used to translate the spatial differences in growth to spatial differences in food conditions. A Dynamic Energy Budget (DEB) model was fitted to the data in order to trace-back the food conditions. During this fitting, the food correction factor (ψψ) was optimized. ψψ can be interpreted as an indication of the food conditions (algae concentration, quality, current velocity) at that specific location in comparison to the average food conditions in the whole Oosterschelde. The results show that there is a spatial, but also year-to-year variation in food conditions within the Oosterschelde. Locations with the best food conditions were Neeltje Jans N in 2015 and Hammen 9, Dortsman and Krabbenkreek in 2016. Growth of the mussels in the baskets in 2014 was lower than in 2015 and 2016. This is probably caused by the larger size of the mussels that were used in 2014 and the fact that the growth of mussels reduces with size. In contravention to the expectations, there was no clear pattern in growth conditions from the western part of the Oosterschelde to the eastern and northern part. For example, the growth of the mussels at the two locations in the northern part of the Oosterschelde (Krabbenkreek and Viane) where ralatively good compared to the other locations. In practice, however, mussel farmers use the culture plots in the northern part mainly for storage of seed and halfgrown mussels. Possibly the mussels in the baskets perform better in this area than on the bottom culture plots. The DEB model is a good tool to trace-back the food conditions from the measured growth data. The parameters for blue mussel, that is used for the DEB model should be updated. The parameters are presently based on historical data, whereas new data are available.

Sublethal effects of binary mixtures of Cu2+ and Cd2+ on Daphnia magna: Standard Dynamic Energy Budget (DEB) model analysis

Climate change is having dramatic effects on the diversity and distribution of species. Many of these effects are mediated by how an organism’s physiological patterns of resource allocation translate into fitness through effects on growth, survival and reproduction. Empirically, resource allocation is challenging to measure directly and so has often been approached using mathematical models, such as Dynamic Energy Budget (DEB) models. The fact that all plants require a very similar set of exogenous resources, namely light, water and nutrients, integrates well with the DEB framework in which a small number of variables and processes linked through pathways represent an organism’s state as it changes through time. Most DEB theory has been developed in reference to animals and microorganisms. However, terrestrial vascular plants differ from these organisms in fundamental ways that make resource allocation, and the trade-offs and feedbacks arising from it, particularly fundamental to their life histories, but also challenging to represent using existing DEB theory. Here, we describe key features of the anatomy, morphology, physiology, biochemistry, and ecology of terrestrial vascular plants that should be considered in the development of a generic DEB model for plants. We then describe possible approaches to doing so using existing DEB theory and point out features that may require significant development for DEB theory to accommodate them. We end by presenting a generic DEB model for plants that accounts for many of these key features and describing gaps that would need to be addressed for DEB theory to predict the responses of plants to climate change. DEB models offer a powerful and generalizable framework for modelling resource allocation in terrestrial vascular plants, and our review contributes a framework for expansion and development of DEB theory to address how plants respond to anthropogenic change.

Physiological performance of plaice Pleuronectes platessa (L.): A comparison of static and dynamic energy budgets

Losses due to predation are recognized as an important factor affecting shellfish stocks, restoration efforts and aquaculture production. Managing and mitigating the impact of predators require information on the population dynamics and functional responses to prey availability under varying environmental conditions. Asterias spp. are well-known keystone predators with the capacity to exert a top down control on shellfish populations. Asterias spp. populations are extremely plastic, booming fast when prey is abundant and exhibiting a remarkable individual resilience to starvation and adverse environmental conditions. These aspects have led Asterias spp. to be considered pests by shellfish producers and fishers and to be catalogued among the most devastating invasive species. Assessment and mitigation of the impact of Asterias rubens in northern Europe have been the objective of several projects. However, there is still a limited understanding of the processes behind A. rubens population plasticity and how environmental conditions affect individual growth and predation. Under these circumstances a comprehensive eco-physiological model becomes necessary. These models can integrate available information on biology and eco-physiology to gain understanding of the effect of the environmental conditions on the impact of A. rubens.In this work, we performed a number of eco-physiological experiments and combined them with field data from a Danish estuary to estimate and validate the parameters of a dynamic energy budget (DEB) model for the whole life cycle of A. rubens. DEB models can be used to assess the effects of environmental variability on the life cycle and key population traits allowing the prediction of the performance, abundance, resource requirements and potential distribution of individuals and populations under dynamic environments. As such the DEB model presented in this study aims to become a tool to be used to assess and manage the impact of A. rubens in cultured and natural shellfish populations. The successfully parameterised DEB model describes A. rubens as a plastic species, an efficient predator with low maintenance costs and, at least while feeding on mussels, a high energy yield from its prey. The model validation against independent data resulted in the model being capable to assess growth, food demand, reproductive output and reserves dynamics of A. rubens under experimental and natural conditions. Moreover, application of the model to the Limfjorden seastar fishery is used to further discuss the use of the model to understand biology and ecology of this pest species in the context with the management of shellfish stocks and impact mitigation.

A dynamic energy budget (DEB) model to assess the sublethal effects of imidacloprid toward Gammarus pulex at different temperatures

Summary 1. Dynamic energy budget (DEB) models describe how individuals acquire and utilize energy, and can serve as a link between different levels of biological organization. 2. We describe the formulation and testing of DEB models, and show how the dynamics of individual organisms link to molecular processes, to population dynamics, and (more tenuously) to ecosystem dynamics. 3. DEB models offer mechanistic explanations of body‐size scaling relationships. 4. DEB models constitute powerful tools for applications in toxicology and biotechnology. 5. Challenging questions arise when linking DEB models with evolutionary theory.

Ecological effects of environmental stressors are commonly evaluated using organismal or suborganismal data, such as standardized toxicity tests that characterize responses of individuals (e.g., mortality and reproduction) and a rapidly growing body of "omics" data. A key challenge for environmental risk assessment is relating such information to population dynamics. One approach uses dynamic energy budget (DEB) models that relate growth and reproduction of individuals to underlying flows of energy and elemental matter. We hypothesize that suborganismal information identifies DEB parameters that are most likely impacted by a particular stressor and that the DEB model can then project suborganismal effects on life history and population endpoints. We formulate and parameterize a model of growth and reproduction for the water flea Daphnia magna. Our model resembles previous generic bioenergetic models, but has explicit representation of discrete molts, an important feature of Daphnia life history. We test its ability to predict six endpoints commonly used in chronic toxicity studies in specified food environments. With just one adjustable parameter, the model successfully predicts growth and reproduction of individuals from a wide array of experiments performed in multiple laboratories using different clones of D. magna raised on different food sources. Fecundity is the most sensitive endpoint, and there is broad correlation between the sensitivities of fecundity and long-run growth rate, as is desirable for the default metric used in chronic toxicity tests. Under some assumptions, we can combine our DEB model with the Euler-Lotka equation to estimate longrun population growth rates at different food levels. A review of Daphnia gene-expression experiments on the effects of contaminant exposure reveals several connections to model parameters, in particular a general trend of increased transcript expression of genes involved in energy assimilation and utilization at concentrations affecting growth and reproduction. The sensitivity of fecundity to many model parameters was consistent with frequent generalized observations of decreased expression of genes involved in reproductive physiology, but interpretation of these observations requires further mechanistic modeling. We thus propose an approach based on generic DEB models incorporating few essential species-specific features for rapid extrapolation of ecotoxicogenomic assays for Daphnia-based population risk assessment.