A general framework for aquatic biogeochemical models

Bruggeman, Jorn; Bolding, Karsten

doi:10.1016/j.envsoft.2014.04.002

Cited by 241 publications

(189 citation statements)

References 49 publications

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“…The model is implemented as three FABM (Bruggeman and Bolding, 2014) modules, which can be coupled at run-time (i.e., without the need for changing and re-compiling the model code): a nutrient module, a detritus module, and a plankton module that can be placed anywhere along the autotrophyheterotrophy continuum (Flynn et al, 2012) with the 'autotrophy fraction' parameter ζ, enabled by a generalized formal description of autotrophic and heterotrophic processes (Section 4.1). In the present implementation, the plankton module is coupled six times to describe interactions of three purely autotrophic, two purely heterotrophic and a mixotrophic plankton groups.…”

Section: Discussionmentioning

confidence: 99%

Modelling the plankton groups of the deep, peri-alpine Lake Bourget

Kerimoglu

Jacquet²,

Vinçon‐Leite

et al. 2017

Ecological Modelling

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Predicting phytoplankton succession and variability in natural systems remains to be a grand challenge in aquatic ecosystems research. In this study, we identi ed six major plankton groups in Lake Bourget (France), based on cell size, taxonomic properties, food-web interactions and occurrence patterns: cyanobacterium Planktothrix rubescens, small and large phytoplankton, mixotrophs, herbivorous and carnivorous zooplankton. We then developed a deterministic dynamic model that describes the dynamics of these groups in terms of carbon and phosphorus uxes, as well as of particulate organic phosphorus and dissolved inorganic provide evidence for the hypothesis that the abundance of this species before the onset of strati cation is critical for its success later in the growing season, pointing thereby to a priority e ect.

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Section: Discussionmentioning

confidence: 99%

Modelling the plankton groups of the deep, peri-alpine Lake Bourget

Kerimoglu

Jacquet²,

Vinçon‐Leite

et al. 2017

Ecological Modelling

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“…Tools for bifurcation analysis are less common. Over two-third of the models are implemented within an existing modelling framework, with the R/deSolve package ) and the Framework for Aquatic Biogeochemical Models Aquat 49:513-548 519 (FABM) (Bruggeman and Bolding 2014) being the most used of the 12 modelling frameworks that we encountered (Fig. 3d).…”

Section: Documenting Diversity In Aemsmentioning

confidence: 99%

“…One can rightfully say that the field of aquatic ecosystem modelling is quite scattered when it comes to the use of modelling frameworks. This notion was one of the incentives for developing Delft3D-Delwaq (Deltares 2014), FABM (Bruggeman and Bolding 2014) and the Database Approach to Modelling (DATM) . With 50 %, FORTRAN is the dominant programming language for coding AEMs (Fig.…”

Section: Documenting Diversity In Aemsmentioning

confidence: 99%

“…However, these frameworks are currently implemented without accounting for feedbacks between ecology and hydrodynamics. Interfaces such as OpenMI (Gregersen et al 2007) and FABM (Bruggeman and Bolding 2014) allow for such coupling and are designed to overcome the issues that emerge when integrating ecology and hydrodynamics. Examples of these issues are the different timescales and spatial schematization for ecology and hydrodynamics (e.g.…”

Section: Exploiting the Diversity In Disciplinesmentioning

confidence: 99%

“…Exploiting diversity by having a given AEM implemented in multiple frameworks Recent approaches such as DATM , FABM (Bruggeman and Bolding 2014) and the open process library in Delft3D-Delwaq (Deltares 2014) make it possible to exploit model implementations in multiple frameworks without much overhead. Therefore, a myriad of tools for model analysis (e.g.…”

Section: Exploiting the Diversity In Disciplinesmentioning

confidence: 99%

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Exploring, exploiting and evolving diversity of aquatic ecosystem models: a community perspective

et al. 2015

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Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been developed since the 1970s. We set off to explore model diversity by making an inventory among 42 aquatic ecosystem modellers, by categorizing the resulting set of models and by analysing them for diversity. We then focus on how to exploit model diversity by comparing and combining different aspects of existing models. Finally, we discuss how model diversity came about in the past and could evolve in the future. Throughout our study, we use Handling Editor: Piet Spaak.Electronic supplementary material The online version of this article (doi:10.1007/s10452-015-9544-1) contains supplementary material, which is available to authorized users. 123Aquat ) 49:513-548 DOI 10.1007 analogies from biodiversity research to analyse and interpret model diversity. We recommend to make models publicly available through open-source policies, to standardize documentation and technical implementation of models, and to compare models through ensemble modelling and interdisciplinary approaches. We end with our perspective on how the field of aquatic ecosystem modelling might develop in the next 5-10 years. To strive for clarity and to improve readability for non-modellers, we include a glossary.

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Biogeochemical control of marine productivity in the Mediterranean Sea during the last 50 years

Macías

García-Górriz

Piroddi

et al. 2014

Global Biogeochemical Cycles

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The temporal dynamics of biogeochemical variables derived from a coupled 3-D model of the Mediterranean Sea are evaluated for the last 50 years (1960–2010) against independent data on fisheries catch per unit effort (CPUE) for the same time period. Concordant patterns are found in the time series of all of the biological variables (from the model and from fisheries statistics), with low values at the beginning of the series, a later increase, with maximum levels reached at the end of the 1990s, and a posterior stabilization. Spectral analysis of the annual biological time series reveals coincident low-frequency signals in all of them. The first, more energetic signal peaks around the year 2000, while the second, less energetic signal peaks near 1982. Almost identical low-frequency signals are found in the nutrient loads of the rivers and in the integrated nutrient levels in the surface marine ecosystem. Nitrate concentration shows a maximum level in 1998, with a later stabilization to present-day values, coincident with the first low-frequency signal found in the biological series. Phosphate shows maximum concentrations around 1982 and a posterior sharp decline, in concordance with the second low-frequency signal observed in the biological series. That result seems to indicate that the control of marine productivity (plankton to fish) in the Mediterranean is principally mediated through bottom-up processes that could be traced back to the characteristics of riverine discharges. The high sensitivity of CPUE time series to environmental conditions might be another indicator of the overexploitation of this marine ecosystem.Key PointsBiogeochemical evolution of the Mediterranean over the past 50 yearsRiver nutrient loads drive primary and secondary productionsStrong link between low trophic levels and fisheries

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A general framework for aquatic biogeochemical models

Cited by 241 publications

References 49 publications

Modelling the plankton groups of the deep, peri-alpine Lake Bourget

Modelling the plankton groups of the deep, peri-alpine Lake Bourget

Exploring, exploiting and evolving diversity of aquatic ecosystem models: a community perspective

Biogeochemical control of marine productivity in the Mediterranean Sea during the last 50 years

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