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FABM-Pclake – Linking Aquatic Ecology with Hydrodynamics University of Southern Denmark FABM-PCLake Linking aquatic ecology with hydrodynamics Hu, F.; Bolding, Karsten; Bruggeman, Jorn; Jeppesen, Erik; Flindt, Mogens; Van Gerven, Luuk P A; Janse, Jan H.; Janssen, Annette B G; Kuiper, Jan J; Mooij, Wolf M.; Trolle, Dennis Published in: Geoscientific Model Development DOI: 10.5194/gmd-9-2271-2016 Publication date: 2016 Document version: Final published version Document license: CC BY Citation for pulished version (APA): Hu, F., Bolding, K., Bruggeman, J., Jeppesen, E., Flindt, M., Van Gerven, L. P. A., Janse, J. H., Janssen, A. B. G., Kuiper, J. J., Mooij, W. M., & Trolle, D. (2016). FABM-PCLake: Linking aquatic ecology with hydrodynamics. Geoscientific Model Development, 9, 2271-2278. https://doi.org/10.5194/gmd-9-2271-2016 Go to publication entry in University of Southern Denmark's Research Portal Terms of use This work is brought to you by the University of Southern Denmark. Unless otherwise specified it has been shared according to the terms for self-archiving. If no other license is stated, these terms apply: • You may download this work for personal use only. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying this open access version If you believe that this document breaches copyright please contact us providing details and we will investigate your claim. Please direct all enquiries to [email protected] Download date: 26. Sep. 2021 Geosci. Model Dev., 9, 2271–2278, 2016 www.geosci-model-dev.net/9/2271/2016/ doi:10.5194/gmd-9-2271-2016 © Author(s) 2016. CC Attribution 3.0 License. FABM-PCLake – linking aquatic ecology with hydrodynamics Fenjuan Hu1,2, Karsten Bolding1,3, Jorn Bruggeman3,4, Erik Jeppesen1,5, Morgens R. Flindt2, Luuk van Gerven6,7, Jan H. Janse6,8, Annette B. G. Janssen6,7, Jan J. Kuiper6,7, Wolf M. Mooij6,7, and Dennis Trolle1,5 1Aarhus University, Department of Bioscience, Vejlsøvej 25, 8600 Silkeborg, Denmark 2University of Southern Denmark, Department of Biology, Campusvej 55, 5230 Odense M, Denmark 3Bolding & Bruggeman ApS, Strandgyden 25, 5466 Asperup, Denmark 4Plymouth Marine Laboratory, Prospect Place, the Hoe, Plymouth PL1 3DH, UK 5Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China 6Netherlands Institute of Ecology, Department of Aquatic Ecology, 6700 AB Wageningen, the Netherlands 7Wageningen University, Department of Aquatic Ecology and Water Quality Management, 6700 AA, the Netherlands 8PBL Netherlands Environmental Assessment Agency, Dept. of Nature and Rural Areas, 3720 AH Bilthoven, the Netherlands Correspondence to: Fenjuan Hu ([email protected]) Received: 1 December 2015 – Published in Geosci. Model Dev. Discuss.: 3 February 2016 Revised: 15 June 2016 – Accepted: 16 June 2016 – Published: 1 July 2016 Abstract. This study presents FABM-PCLake, a redesigned ilation and multi-model ensemble simulations. Examples of structure of the PCLake aquatic ecosystem model, which we potential new model applications include climate change im- implemented in the Framework for Aquatic Biogeochemi- pact studies and environmental impact assessment scenarios cal Models (FABM). In contrast to the original model, which for temperate, sub-tropical and tropical lakes and reservoirs. was designed for temperate, fully mixed freshwater lakes, the new FABM-PCLake represents an integrated aquatic ecosys- tem model that can be linked with different hydrodynamic models and allows simulations of hydrodynamic and biogeo- 1 Introduction chemical processes for zero-dimensional, one-dimensional as well as three-dimensional environments. FABM-PCLake The field of aquatic ecosystem modeling has undergone describes interactions between multiple trophic levels, in- waves of development during the past decades, and mod- cluding piscivorous, zooplanktivorous and benthivorous fish, els have grown in complexity in terms of ecosystem com- zooplankton, zoobenthos, three groups of phytoplankton and ponents and processes included (Robson, 2014). However, rooted macrophytes. The model also accounts for oxygen dy- even though hundreds of models have been formulated for namics and nutrient cycling for nitrogen, phosphorus and sil- research or management purposes, only a handful has found icon, both within the pelagic and benthic domains. FABM- frequent use and ongoing development (Trolle et al., 2012). PCLake includes a two-way communication between the bio- This reflects the fact that many models are being built with geochemical processes and the physics, where some biogeo- the same or similar properties, and thus that model develop- chemical state variables (e.g., phytoplankton) influence light ment for the past decades has been subject to some degree of attenuation and thereby the spatial and temporal distributions “re-inventing the wheel” as discussed by Mooij et al. (2010). of light and heat. At the same time, the physical environment, Another drawback of many aquatic ecosystem models is including water currents, light and temperature influence a the typical discrepancy in complexity between the ecosys- wide range of biogeochemical processes. The model enables tem representation and the physical environment. High com- studies on ecosystem dynamics in physically heterogeneous plexity in ecosystem conceptualizations therefore generally environments (e.g., stratifying water bodies, and water bod- comes at the expense of simple or no hydrodynamic repre- ies with horizontal gradients in physical and biogeochemi- sentation (e.g., PCLake; Janse and van Liere, 1995; Janse, cal properties), and through FABM also enables data assim- 2005; Janse et al., 2008, and EcoPath; Christensen and Pauly, 1992). By contrast, physically resolved hydrodynamic mod- Published by Copernicus Publications on behalf of the European Geosciences Union. 2272 F. Hu et al.: FABM-PCLake els often include no or only simple ecosystem representa- as a result of self-enhancing feedback mechanisms within the tions and disregard higher trophic levels. Few studies have ecosystem. attempted to couple aquatic ecosystem dynamics with hy- FABM, in which we have now implemented PCLake, is a drodynamics (e.g., Hamilton and Schladow, 1997; Pereira framework for biogeochemical models of marine and fresh- et al., 2006; Fragoso et al., 2009), sometimes also includ- water systems (Bruggeman and Bolding, 2014). FABM en- ing higher trophic levels (Makler-Pick et al., 2011). How- ables complex biogeochemical models to be developed as ever, none of these models are validated for higher trophic sets of stand-alone, process-specific modules. These can be levels (i.e., fish) and the source codes are also not readily combined at runtime to create custom-made models. As out- available for further development. To avoid “re-inventing the lined in detail by Bruggeman and Bolding (2014), FABM di- wheel”, and to overcome this discrepancy in complexity be- vides the coupled advection–diffusion reaction equation that tween the ecological and physical representations, a way for- governs the dynamics of biogeochemical variables into two ward is to enable an easy coupling between existing ecosys- parts: a reaction part (i.e., sink and source terms) provided tem models and hydrodynamic models. Thus, the complex- by the biogeochemical models, and a transport part han- ity of the conceptual biogeochemical model and the physical dled by the hydrodynamic (i.e., physical) models. The trans- representation may ideally easily be adapted to best suit the port part includes advection, diffusion and potential vertical needs and purposes of a given study. Meanwhile, utilizing movements (sinking, floating and potentially active move- an open-source platform would help promote model avail- ment), and also dilution and concentration processes. There- ability and also further development (Trolle et al., 2012). To fore, based on local variables (including, for example, local this end, we implemented and modified a well-developed and light conditions, temperature and concentrations of state vari- widely applied ecosystem model, PCLake, within FABM, the ables) provided by a hydrodynamic model, the biogeochem- Framework for Aquatic Biogeochemical Models by Brugge- ical model calculates rates of sink and source terms at cur- man and Bolding (2014). FABM enables a flexible coupling rent time and space and passes the rates to the hydrodynamic of ecosystem processes in PCLake with a selection of hy- model via FABM. The hydrodynamic model will then handle drodynamic models representing zero- to three-dimensional numerical integration of the biogeochemical processes and hydrodynamics. transport, and then pass updated states via FABM back to the biogeochemical model – and this process will continue un- til the user-defined end-time of a simulation. FABM thereby enables model applications of different physical representa- 2 Implementation of PCLake in FABM tions (ranging from zero-dimensional to three-dimensional) without the need to change the biogeochemical source code. PCLake was originally a zero-dimensional ecological model Most of the pelagic state variables in a biogeochemical model for shallow lakes developed by Janse and van Liere (1995), implemented in FABM will typically be transported by the and it has been widely applied (for example, Stoneviciusˇ hydrodynamics. However, some pelagic variables, particu- and Taminskas, 2007; Mooij et al., 2009; Nielsen et al., larly relevant for higher trophic levels such as fish (that may
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