C and N gross growth efficiencies of copepod egg production studied using a Dynamic Energy Budget model

Kuijper, Lothar D. J.

doi:10.1093/plankt/fbh020

Cited by 50 publications

(52 citation statements)

References 41 publications

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“…This mechanism is particularly relevant when several food items are considered or when reserve and structure of the food items are considered (e.g. Kuijper et al 2004;Kooijman et al 2007).…”

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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“…The rate of biomass production is governed by the synthesizing unit (SU) expression for colimitation, which offers a flux-based description of classic multisubstrate enzyme kinetics under the assumption of negligible substrate dissociation (Kooijman 1998(Kooijman , 2000Kuijper et al 2004). The SU-governed rate at which new biomass is produced equals…”

Section: Methodsmentioning

confidence: 99%

A biodiversity‐inspired approach to aquatic ecosystem modeling

Bruggeman

Kooijman

2007

Limnology & Oceanography

121

108

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Current aquatic ecosystem models accommodate increasing amounts of physiological detail, but marginalize the role of biodiversity by aggregating multitudes of different species. We propose that at present, understanding of aquatic ecosystems is likely to benefit more from improved descriptions of biodiversity and succession than from incorporation of more realistic physiology. To illustrate how biodiversity can be accounted for, we define the system of infinite diversity (SID), which characterizes ecosystems in the spirit of complex adaptive systems theory as single units adapting to environmental pressure. The SID describes an ecosystem with one generic population model and continuity in species-characterizing parameters, and acquires rich dynamics by modeling succession as evolution of the parameter value distribution. This is illustrated by a four-parameter phytoplankton model that minimizes physiological detail, but includes a sophisticated representation of community diversity and interspecific differences. This model captures several well-known aquatic ecosystem features, including formation of a deep chlorophyll maximum and nutrient-driven seasonal succession. As such, it integrates theories on changes in species composition in both time and space. We argue that despite a lack of physiological detail, SIDs may ultimately prove a valuable tool for further qualitative and quantitative understanding of ecosystems.Biodiversity poses a perennial problem for ecosystem modelers. Confronted with a reality fraught with species, dependencies, and physiological detail, one cannot help but think that simple models cannot do it justice (Anderson 2005). Simple models aggregate large numbers of species into single state variables, and by doing so they lose the ability to reproduce ranges of behavior shown by detailed species-explicit models (Raick et al. 2006). Also, the use of aggregation puts models at a greater distance from empirical results, first because assimilation of empirically determined, species-specific parameter values to parameters of virtual aggregates of species is a difficult and largely subjective process; second because aggregate models provide only indirect information about individual species observed in the field. Not surprisingly, large ecosystem models that describe many classes of species explicitly have recently gained in popularity (Baretta et al. 1995; Quéré et al. 2005). However, continued diversification of functional groups may create more problems than it solves. Increasing the number of groups within ecosystem models dilutes the available empirical information per model unit, and therefore increases the uncertainty per parameter. Considering the substantial uncertainty already associated with parameters of moderate-size ecosystem models, this route seems unappealing. Also, it is easy to overlook that as the number of variables within an ecosystem model increases, so does the amount of information needed to initialize the model. A utopian species-complete model would require ini...

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“…These rules can include a parameter dictating the return flux to the reserve pools of materials rejected by the SUs, controlling the extent to which nutrients ingested in excess are stored. Such a DEB model was first developed by Kuijper et al (2004a) Raubenheimer & Simpson (1994) and Simpson et al (2004) for a discussion of this matter in relation to GF). The dynamics of the SU for growth dictate that growth rate is fast for the right mix of protein and carbohydrate, slow if one of them dominates and zero if protein is absent.…”

Section: Connecting the Three Modelling Approachesmentioning

confidence: 99%

“…We have applied the simpler scenario used by Kuijper et al (2004a) to illustrate how DEB and GF can be integrated to model nutritional targets (see electronic supplementary material for detailed methods and parameters). We applied the DEB model to calculate egg production in a copepod as a function of ingested carbohydrate and protein, but extend Kuijper's approach by using the GF to integrate cost functions relating to longevity and stored nutrient excesses.…”

Section: Connecting the Three Modelling Approachesmentioning

confidence: 99%

Modelling the ecological niche from functional traits

Kearney

Simpson

Raubenheimer

et al. 2010

Phil. Trans. R. Soc. B

286

308

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The niche concept is central to ecology but is often depicted descriptively through observing associations between organisms and habitats. Here, we argue for the importance of mechanistically modelling niches based on functional traits of organisms and explore the possibilities for achieving this through the integration of three theoretical frameworks: biophysical ecology (BE), the geometric framework for nutrition (GF) and dynamic energy budget (DEB) models. These three frameworks are fundamentally based on the conservation laws of thermodynamics, describing energy and mass balance at the level of the individual and capturing the prodigious predictive power of the concepts of 'homeostasis' and 'evolutionary fitness'. BE and the GF provide mechanistic multi-dimensional depictions of climatic and nutritional niches, respectively, providing a foundation for linking organismal traits (morphology, physiology, behaviour) with habitat characteristics. In turn, they provide driving inputs and cost functions for mass/energy allocation within the individual as determined by DEB models. We show how integration of the three frameworks permits calculation of activity constraints, vital rates (survival, development, growth, reproduction) and ultimately population growth rates and species distributions. When integrated with contemporary niche theory, functional trait niche models hold great promise for tackling major questions in ecology and evolutionary biology.

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C and N gross growth efficiencies of copepod egg production studied using a Dynamic Energy Budget model

Cited by 50 publications

References 41 publications

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

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

A biodiversity‐inspired approach to aquatic ecosystem modeling

Modelling the ecological niche from functional traits

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