From food‐dependent statistics to metabolic parameters, a practical guide to the use of dynamic energy budget theory

Kooijman, S.A.L.M.; Sousa, Tânia; Pecquerie, Laure; Meer, Jaap van der; Jager, Tjalling

doi:10.1111/j.1469-185x.2008.00053.x

Cited by 129 publications

(138 citation statements)

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“…Moreover, studies report non-destructive methods that follow stable isotope ratios in time for a given individual in particular tissues such as blood cells or protein plasma, and also in hairs and feathers ). Measurements in time are of particular importance for the application of DEB theory (Kooijman et al 2008). Application of the theory to such datasets could be a fruitful strategy for better understanding the impact of dynamic environments.…”

Section: Discussionmentioning

confidence: 99%

The impact of metabolism on stable isotope dynamics: a theoretical framework

Pecquerie

Nisbet

Fablet

et al. 2010

Phil. Trans. R. Soc. B

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Stable isotope analysis is a powerful tool used for reconstructing individual life histories, identifying food-web structures and tracking flow of elemental matter through ecosystems. The mechanisms determining isotopic incorporation rates and discrimination factors are, however, poorly understood which hinders a reliable interpretation of field data when no experimental data are available. Here, we extend dynamic energy budget (DEB) theory with a limited set of new assumptions and rules in order to study the impact of metabolism on stable isotope dynamics in a mechanistic way. We calculate fluxes of stable isotopes within an organism by following fluxes of molecules involved in a limited number of macrochemical reactions: assimilation, growth but also structure turnover that is here explicitly treated. Two mechanisms are involved in the discrimination of isotopes: (i) selection of molecules occurs at the partitioning of assimilation, growth and turnover into anabolic and catabolic sub-fluxes and (ii) reshuffling of atoms occurs during transformations. Such a framework allows for isotopic routing which is known as a key, but poorly studied, mechanism. As DEB theory specifies the impact of environmental conditions and individual state on molecule fluxes, we discuss how scenario analysis within this framework could help reveal common mechanisms across taxa.

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Section: Discussionmentioning

confidence: 99%

The impact of metabolism on stable isotope dynamics: a theoretical framework

Pecquerie

Nisbet

Fablet

et al. 2010

Phil. Trans. R. Soc. B

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“…Here [E m ] (J cm −3 ) is the maximum energy density and L m (cm) is the maximum volumetric length, the volumetric length being denoted with L = L m l. The dynamics of the non-dimensionalized state variables are readily deduced from Kooijman et al (2008) and are the following:…”

Section: Equations Of the Standard Deb Modelmentioning

confidence: 99%

“…The capelin and anchovies are similar fish in size and energetics, and both store energy mostly as lipids in their muscle. We fit the DEB parameters to the data on capelin and compare the resulting parameter values to those of the anchovies, obtaining similar results.In Section 2.2 we give a brief account of the state variables of the standard DEB model which can be found in Kooijman et al (2008). Furthermore, we introduce a new variable to account for the roe production of individuals in Section 2.4.…”

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

Einarsson

Birnir

Sigurðsson

2011

Journal of Theoretical Biology

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is closely related to bioenergetics that focuses on molecular aspects and metabolic pathways in a thermodynamic setting. DEB theory treats individuals as nonlinear dynamics systems that follow predictable patterns during their life cycle. This approach has firm physiological roots and provides a sound basis for population dynamic theories (Nisbet et al., 2000;Kooijman, 2010). We refer to Kooijman (2010) for a full description of the DEB theory. A conceptual introduction is given in Kooijman (2001), and further guides and discussion can be found in van der Meer (2006) and Sousa et al. (2008) DEB theory is ultimately the theory of life. Its aim is to describe all life forms within the same framework. The complexity of the DEB model will depend on the complexity of the species at hand. For the Icelandic capelin, we use a basic form of the DEB model with one food substrate and one type of reserve. These assumptions can be generalized (Kooijman, 2010).DEB theory has been successfully applied to anchovy (Engraulis engrasicolus) in the Bay of Biscay (Pecquerie et al., 2009) where their whole life cycle was modeled. The capelin and anchovies are similar fish in size and energetics, and both store energy mostly as lipids in their muscle. We fit the DEB parameters to the data on capelin and compare the resulting parameter values to those of the anchovies, obtaining similar results.In Section 2.2 we give a brief account of the state variables of the standard DEB model which can be found in Kooijman et al. (2008). Furthermore, we introduce a new variable to account for the roe production of individuals in Section 2.4.

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“…the head -body length excluding a tail) is proportional to the volumetric structural length L, i.e. the cubic root for structural volume: L ¼ d M L f , where d M is the constant shape coefficient, see Kooijman et al (2008). Figure 1 presents an overview of the various processes that are delineated by the standard DEB model.…”

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confidence: 99%

Dynamic energy budget theory restores coherence in biology

Sousa¹,

Domingos²,

Poggiale

et al. 2010

Phil. Trans. R. Soc. B

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We present the state of the art of the development of dynamic energy budget theory, and its expected developments in the near future within the molecular, physiological and ecological domains. The degree of formalization in the set-up of the theory, with its roots in chemistry, physics, thermodynamics, evolution and the consistent application of Occam's razor, is discussed. We place the various contributions in the theme issue within this theoretical setting, and sketch the scope of actual and potential applications.Keywords: dynamic energy budget theory; biology; metabolism; ecology; evolution; energetics REACHING OUT FOR GENERALITYIn physics, there is a quest for a unified theory. Physical theories have a broad spectrum of application, a strong mathematical background and are subject to numerous empirical tests. By contrast, in biology, mathematical theory has played a secondary role because biology is frequently seen as a science of exceptions and particular cases, with little interest in abstraction and generalization. Exceptions are the research being done in the fields of theoretical biology and mathematical biology. However, theoretical and mathematical biology have frequently been carried out without a concern for empirical testing. When this concern appears, models are of narrow application, reducing their theoretical breadth. The dynamic energy budget (DEB) theory starts from the Dutch tradition of theoretical and mathematical biology, but couples it with a fundamental concern in producing general theory that is subjected to careful empirical testing.DEB theory aims to capture the quantitative aspects of metabolism at the individual level for organisms of all species. It builds on the premise that the mechanisms that are responsible for the organization of metabolism are not species-specific (Kooijman 2001(Kooijman , 2010. This hope for generality is supported by (i) the universality of physics and evolution and (ii) the existence of widespread biological empirical patterns among organisms . Table 1 synthesizes the essential criteria for any general model for the metabolism of individuals. We explore the links between DEB theory and each of the proposed criteria in the following paragraphs. DEB theory is explicitly based on the conservation of mass, isotopes, energy and time, including the inherent degradation of energy associated with all processes. So it complies to criteria 1, table 1.The DEB theory is biologically implicit, so it applies to all species. Species-specific restrictions of DEB models are explained and predicted by the theory (criterion 5, table 1). For example, consider the most important difference between DEB models, the number of reserves (biomass components that fuel metabolism) and structures (biomass components that have maintenance needs) that are delineated. This depends on the degree of coupling of the various substrates an organism needs. Animals feed on other organisms, which couples uptake of the various substrates (proteins, carbohydrates, lipids, nutrients) tightly and ex...

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From food‐dependent statistics to metabolic parameters, a practical guide to the use of dynamic energy budget theory

Cited by 129 publications

References 26 publications

The impact of metabolism on stable isotope dynamics: a theoretical framework

The impact of metabolism on stable isotope dynamics: a theoretical framework

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

Dynamic energy budget theory restores coherence in biology

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