@article{MeyerVosMooijetal.2012, author = {Meyer, Katrin M. and Vos, Matthijs and Mooij, Wolf M. and Hol, W. H. Gera and Termorshuizen, Aad J. and van der Putten, Wim H.}, title = {Testing the paradox of enrichment along a land use gradient in a multitrophic aboveground and belowground community}, series = {PLoS one}, volume = {7}, journal = {PLoS one}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0049034}, pages = {9}, year = {2012}, abstract = {In the light of ongoing land use changes, it is important to understand how multitrophic communities perform at different land use intensities. The paradox of enrichment predicts that fertilization leads to destabilization and extinction of predator-prey systems. We tested this prediction for a land use intensity gradient from natural to highly fertilized agricultural ecosystems. We included multiple aboveground and belowground trophic levels and land use-dependent searching efficiencies of insects. To overcome logistic constraints of field experiments, we used a successfully validated simulation model to investigate plant responses to removal of herbivores and their enemies. Consistent with our predictions, instability measured by herbivore-induced plant mortality increased with increasing land use intensity. Simultaneously, the balance between herbivores and natural enemies turned increasingly towards herbivore dominance and natural enemy failure. Under natural conditions, there were more frequently significant effects of belowground herbivores and their natural enemies on plant performance, whereas there were more aboveground effects in agroecosystems. This result was partly due to the "boom-bust'' behavior of the shoot herbivore population. Plant responses to herbivore or natural enemy removal were much more abrupt than the imposed smooth land use intensity gradient. This may be due to the presence of multiple trophic levels aboveground and belowground. Our model suggests that destabilization and extinction are more likely to occur in agroecosystems than in natural communities, but the shape of the relationship is nonlinear under the influence of multiple trophic interactions. Citation: Meyer KM, Vos M, Mooij WM, Hol WHG, Termorshuizen AJ, et al. (2012) Testing the Paradox of Enrichment along a Land Use Gradient in a Multitrophic Aboveground and Belowground Community.}, language = {en} } @article{MooijBredervelddeKleinetal.2014, author = {Mooij, Wolf M. and Brederveld, Robert J. and de Klein, Jeroen J. M. and DeAngelis, Don L. and Downing, Andrea S. and Faber, Michiel and Gerla, Daan J. and Hipsey, Matthew R. and Janse, Jan H. and Janssen, Annette B. G. and Jeuken, Michel and Kooi, Bob W. and Lischke, Betty and Petzoldt, Thomas and Postma, Leo and Schep, Sebastiaan A. and Scholten, Huub and Teurlincx, Sven and Thiange, Christophe and Trolle, Dennis and van Dam, Anne A. and van Gerven, Luuk P. A. and van Nes, Egbert H. and Kuiper, Jan J.}, title = {Serving many at once: How a database approach can create unity in dynamical ecosystem modelling}, series = {Environmental modelling \& software with environment data news}, volume = {61}, journal = {Environmental modelling \& software with environment data news}, publisher = {Elsevier}, address = {Oxford}, issn = {1364-8152}, doi = {10.1016/j.envsoft.2014.04.004}, pages = {266 -- 273}, year = {2014}, abstract = {Simulation modelling in ecology is a field that is becoming increasingly compartmentalized. Here we propose a Database Approach To Modelling (DATM) to create unity in dynamical ecosystem modelling with differential equations. In this approach the storage of ecological knowledge is independent of the language and platform in which the model will be run. To create an instance of the model, the information in the database is translated and augmented with the language and platform specifics. This process is automated so that a new instance can be created each time the database is updated. We describe the approach using the simple Lotka-Volterra model and the complex ecosystem model for shallow lakes PCLake, which we automatically implement in the frameworks OSIRIS, GRIND for MATLAB, ACSL, R, DUFLOW and DELWAQ. A clear advantage of working in a database is the overview it provides. The simplicity of the approach only adds to its elegance. (C) 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-SA license (http://creativecommons.org/licenses/by-nc-sa/3.0/).}, language = {en} } @article{GrimmRevillaBergeretal.2005, author = {Grimm, Volker and Revilla, Eloy and Berger, Uta and Jeltsch, Florian and Mooij, Wolf M. and Railsback, Steven Floyd and Thulke, Hans-Hermann and Weiner, Jacob and Wiegand, Thorsten and DeAngelis, Donald L.}, title = {Pattern-oriented modeling of agend-based complex systems : lessons from ecology}, year = {2005}, abstract = {Agent-based complex systems are dynamic networks of many interacting agents; examples include ecosystems, financial markets, and cities. The search for general principles underlying the internal organization of such systems often uses bottom-up simulation models such as cellular automata and agent-based models. No general framework for designing, testing, and analyzing bottom-up models has yet been established, but recent advances in ecological modeling have come together in a general strategy we call pattern-oriented modeling. This strategy provides a unifying framework for decoding the internal organization of agent-based complex systems and may lead toward unifying algorithmic theories of the relation between adaptive behavior and system complexity}, language = {en} } @article{SachsePetzoldtBlumstocketal.2014, author = {Sachse, Rene and Petzoldt, Thomas and Blumstock, Maria and Moreira, Santiago and Paetzig, Marlene and Ruecker, Jacqueline and Janse, Jan H. and Mooij, Wolf M. and Hilt, Sabine}, title = {Extending one-dimensional models for deep lakes to simulate the impact of submerged macrophytes on water quality}, series = {Environmental modelling \& software with environment data news}, volume = {61}, journal = {Environmental modelling \& software with environment data news}, publisher = {Elsevier}, address = {Oxford}, issn = {1364-8152}, doi = {10.1016/j.envsoft.2014.05.023}, pages = {410 -- 423}, year = {2014}, abstract = {Submerged macrophytes can stabilise clear water conditions in shallow lakes. However, many existing models for deep lakes neglect their impact. Here, we tested the hypothesis that submerged macrophytes can affect the water clarity in deep lakes. A one-dimensional, vertically resolved macrophyte model was developed based on PCLake and coupled to SALMO-1D and GOTM hydrophysics and validated against field data. Validation showed good coherence in dynamic growth patterns and colonisation depths. In our simulations the presence of submerged macrophytes resulted in up to 50\% less phytoplankton biomass in the shallowest simulated lake (11 m) and still 15\% less phytoplankton was predicted in 100 m deep oligotrophic lakes. Nutrient loading, lake depth, and lake shape had a strong influence on macrophyte effects. Nutrient competition was found to be the strongest biological interaction. Despite a number of limitations, the derived dynamic lake model suggests significant effects of submerged macrophytes on deep lake water quality. (C) 2014 Elsevier Ltd. All rights reserved.}, language = {en} } @article{JanssenArhonditsisBeusenetal.2015, author = {Janssen, Annette B. G. and Arhonditsis, George B. and Beusen, Arthur and Bolding, Karsten and Bruce, Louise and Bruggeman, Jorn and Couture, Raoul-Marie and Downing, Andrea S. and Elliott, J. Alex and Frassl, Marieke A. and Gal, Gideon and Gerla, Daan J. and Hipsey, Matthew R. and Hu, Fenjuan and Ives, Stephen C. and Janse, Jan H. and Jeppesen, Erik and Joehnk, Klaus D. and Kneis, David and Kong, Xiangzhen and Kuiper, Jan J. and Lehmann, Moritz K. and Lemmen, Carsten and Oezkundakci, Deniz and Petzoldt, Thomas and Rinke, Karsten and Robson, Barbara J. and Sachse, Rene and Schep, Sebastiaan A. and Schmid, Martin and Scholten, Huub and Teurlincx, Sven and Trolle, Dennis and Troost, Tineke A. and Van Dam, Anne A. and Van Gerven, Luuk P. A. and Weijerman, Mariska and Wells, Scott A. and Mooij, Wolf M.}, title = {Exploring, exploiting and evolving diversity of aquatic ecosystem models: a community perspective}, series = {Aquatic ecology : the international forum covering research in freshwater and marine environments}, volume = {49}, journal = {Aquatic ecology : the international forum covering research in freshwater and marine environments}, number = {4}, publisher = {Springer}, address = {Dordrecht}, issn = {1386-2588}, doi = {10.1007/s10452-015-9544-1}, pages = {513 -- 548}, year = {2015}, abstract = {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 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.}, language = {en} } @article{LischkeHiltJanseetal.2014, author = {Lischke, Betty and Hilt, Sabine and Janse, Jan H. and Kuiper, Jan J. and Mehner, Thomas and Mooij, Wolf M. and Gaedke, Ursula}, title = {Enhanced input of terrestrial particulate organic matter reduces the resilience of the clear-water state of shallow lakes: A model study}, series = {Ecosystems}, volume = {17}, journal = {Ecosystems}, number = {4}, publisher = {Springer}, address = {New York}, issn = {1432-9840}, doi = {10.1007/s10021-014-9747-7}, pages = {616 -- 626}, year = {2014}, abstract = {The amount of terrestrial particulate organic matter (t-POM) entering lakes is predicted to increase as a result of climate change. This may especially alter the structure and functioning of ecosystems in small, shallow lakes which can rapidly shift from a clear-water, macrophyte-dominated into a turbid, phytoplankton-dominated state. We used the integrative ecosystem model PCLake to predict how rising t-POM inputs affect the resilience of the clear-water state. PCLake links a pelagic and benthic food chain with abiotic components by a number of direct and indirect effects. We focused on three pathways (zoobenthos, zooplankton, light availability) by which elevated t-POM inputs (with and without additional nutrients) may modify the critical nutrient loading thresholds at which a clear-water lake becomes turbid and vice versa. Our model results show that (1) increased zoobenthos biomass due to the enhanced food availability results in more benthivorous fish which reduce light availability due to bioturbation, (2) zooplankton biomass does not change, but suspended t-POM reduces the consumption of autochthonous particulate organic matter which increases the turbidity, and (3) the suspended t-POM reduces the light availability for submerged macrophytes. Therefore, light availability is the key process that is indirectly or directly changed by t-POM input. This strikingly resembles the deteriorating effect of terrestrial dissolved organic matter on the light climate of lakes. In all scenarios, the resilience of the clear-water state is reduced thus making the turbid state more likely at a given nutrient loading. Therefore, our study suggests that rising t-POM input can add to the effects of climate warming making reductions in nutrient loadings even more urgent.}, language = {en} } @article{MooijTrolleJeppesenetal.2010, author = {Mooij, Wolf M. and Trolle, Dennis and Jeppesen, Erik and Arhonditsis, George B. and Belolipetsky, Pavel V. and Chitamwebwa, Deonatus B. R. and Degermendzhy, Andrey G. and DeAngelis, Donald L. and Domis, Lisette Nicole de Senerpont and Downing, Andrea S. and Elliott, J. Alex and Fragoso Jr, Carlos Ruberto and Gaedke, Ursula and Genova, Svetlana N. and Gulati, Ramesh D. and H{\aa}kanson, Lars and Hamilton, David P. and Hipsey, Matthew R. and 't Hoen, Jochem and H{\"u}lsmann, Stephan and Los, F. Hans and Makler-Pick, Vardit and Petzoldt, Thomas and Prokopkin, Igor G. and Rinke, Karsten and Schep, Sebastiaan A. and Tominaga, Koji and Van Dam, Anne A. and Van Nes, Egbert H. and Wells, Scott A. and Janse, Jan H.}, title = {Challenges and opportunities for integrating lake ecosystem modelling approaches}, series = {Aquatic ecology}, volume = {44}, journal = {Aquatic ecology}, publisher = {Springer Science + Business Media B.V.}, address = {Dordrecht}, issn = {1573-5125}, doi = {10.1007/s10452-010-9339-3}, pages = {633 -- 667}, year = {2010}, abstract = {A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and traitbased models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem models.}, language = {en} } @misc{SommerAdrianDomisetal.2012, author = {Sommer, Ulrich and Adrian, Rita and Domis, Lisette Nicole de Senerpont and Elser, James J. and Gaedke, Ursula and Ibelings, Bas and Jeppesen, Erik and Lurling, Miquel and Molinero, Juan Carlos and Mooij, Wolf M. and van Donk, Ellen and Winder, Monika}, title = {Beyond the Plankton Ecology Group (PEG) Model mechanisms driving plankton succession}, series = {Annual review of ecology, evolution, and systematics}, volume = {43}, journal = {Annual review of ecology, evolution, and systematics}, number = {2-4}, editor = {Futuyma, DJ}, publisher = {Annual Reviews}, address = {Palo Alto}, isbn = {978-0-8243-1443-9}, issn = {1543-592X}, doi = {10.1146/annurev-ecolsys-110411-160251}, pages = {429 -- 448}, year = {2012}, abstract = {The seasonal succession of plankton is an annually repeated process of community assembly during which all major external factors and internal interactions shaping communities can be studied. A quarter of a century ago, the state of this understanding was described by the verbal plankton ecology group (PEG) model. It emphasized the role of physical factors, grazing and nutrient limitation for phytoplankton, and the role of food limitation and fish predation for zooplankton. Although originally targeted at lake ecosystems, it was also adopted by marine plankton ecologists. Since then, a suite of ecological interactions previously underestimated in importance have become research foci: overwintering of key organisms, the microbial food web, parasitism, and food quality as a limiting factor and an extended role of higher order predators. A review of the impact of these novel interactions on plankton seasonal succession reveals limited effects on gross seasonal biomass patterns, but strong effects on species replacements.}, language = {en} } @article{vanGervenBredervelddeKleinetal.2015, author = {van Gerven, Luuk P. A. and Brederveld, Robert J. and de Klein, Jeroen J. M. and DeAngelis, Don L. and Downing, Andrea S. and Faber, Michiel and Gerla, Daan J. and Janse, Jan H. and Janssen, Annette B. G. and Jeuken, Michel and Kooi, Bob W. and Kuiper, Jan J. and Lischke, Betty and Liu, Sien and Petzoldt, Thomas and Schep, Sebastiaan A. and Teurlincx, Sven and Thiange, Christophe and Trolle, Dennis and van Nes, Egbert H. and Mooij, Wolf M.}, title = {Advantages of concurrent use of multiple software frameworks in water quality modelling using a database approach}, series = {Fundamental and applied limnology : official journal of the International Association of Theoretical and Applied Limnology}, volume = {186}, journal = {Fundamental and applied limnology : official journal of the International Association of Theoretical and Applied Limnology}, number = {1-2}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {1863-9135}, doi = {10.1127/fal/2015/0631}, pages = {5 -- 20}, year = {2015}, abstract = {Water quality modelling deals with multidisciplinary questions ranging from fundamental to applied. Addressing this broad range of questions requires multiple analysis techniques and therefore multiple frameworks. Through the recently developed database approach to modelling (DATM), it has become possible to run a model in multiple software frameworks without much overhead. Here we apply DATM to the ecosystem model for ditches PCDitch and its twin model for shallow lakes PCLake. Using DATM, we run these models in six frameworks (ACSL, DELWAQ, DUFLOW, GRIND for MATLAB, OSIRIS and R), and report on the possible model analyses with tools provided by each framework. We conclude that the dynamic link between frameworks and models resulting from DATM has the following main advantages: it allows one to use the framework one is familiar with for most model analyses and eases switching between frameworks for complementary model analyses, including the switch between a 0-D and 1-D to 3-D setting. Moreover, the strength of each framework - including runtime performance - can now be easily exploited. We envision that a community-based further development of the concept can contribute to the future development of water quality modelling, not only by addressing multidisciplinary questions but also by facilitating the exchange of models and process formulations within the community of water quality modellers.}, language = {en} } @article{GrimmBergerBastiansenetal.2006, author = {Grimm, Volker and Berger, Uta and Bastiansen, Finn and Eliassen, Sigrunn and Ginot, Vincent and Giske, Jarl and Goss-Custard, John and Grand, Tamara and Heinz, Simone K. and Huse, Geir and Huth, Andreas and Jepsen, Jane U. and Jorgensen, Christian and Mooij, Wolf M. and Mueller, Birgit and Piou, Cyril and Railsback, Steven Floyd and Robbins, Andrew M. and Robbins, Martha M. and Rossmanith, Eva and Rueger, Nadja and Strand, Espen and Souissi, Sami and Stillman, Richard A. and Vabo, Rune and Visser, Ute and DeAngelis, Donald L.}, title = {A standard protocol for describing individual-based and agent-based models}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {198}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2006.04.023}, pages = {115 -- 126}, year = {2006}, abstract = {Simulation models that describe autonomous individual organisms (individual based models, IBM) or agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in many other disciplines dealing with complex systems made up of autonomous entities. However, there is no standard protocol for describing such simulation models, which can make them difficult to understand and to duplicate. This paper presents a proposed standard protocol, ODD, for describing IBMs and ABMs, developed and tested by 28 modellers who cover a wide range of fields within ecology. This protocol consists of three blocks (Overview, Design concepts, and Details), which are subdivided into seven elements: Purpose, State variables and scales, Process overview and scheduling, Design concepts, Initialization, Input, and Submodels. We explain which aspects of a model should be described in each element, and we present an example to illustrate the protocol in use. In addition, 19 examples are available in an Online Appendix. We consider ODD as a first step for establishing a more detailed common format of the description of IBMs and ABMs. Once initiated, the protocol will hopefully evolve as it becomes used by a sufficiently large proportion of modellers. (c) 2006 Elsevier B.V. All rights reserved.}, language = {en} }