Articles | Volume 15, issue 9
https://doi.org/10.5194/gmd-15-3861-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Special issue:
https://doi.org/10.5194/gmd-15-3861-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Water Ecosystems Tool (WET) 1.0 – a new generation of flexible aquatic ecosystem model
Nicolas Azaña Schnedler-Meyer
CORRESPONDING AUTHOR
National Institute of Aquatic Resources, Technical University of
Denmark (DTU), Silkeborg, Denmark
Tobias Kuhlmann Andersen
Department of Ecoscience, Aarhus University, Vejlsøvej 25, 8600
Silkeborg, Denmark
Sino-Danish Center for Education and Research, University of Chinese
Academy of Sciences, Beijing, China
Fenjuan Rose Schmidt Hu
Department of Ecoscience, Aarhus University, Vejlsøvej 25, 8600
Silkeborg, Denmark
Karsten Bolding
Department of Ecoscience, Aarhus University, Vejlsøvej 25, 8600
Silkeborg, Denmark
Sino-Danish Center for Education and Research, University of Chinese
Academy of Sciences, Beijing, China
Bolding & Bruggeman ApS, Strandgyden 25, 5466 Asperup, Denmark
Anders Nielsen
Department of Ecoscience, Aarhus University, Vejlsøvej 25, 8600
Silkeborg, Denmark
Sino-Danish Center for Education and Research, University of Chinese
Academy of Sciences, Beijing, China
Dennis Trolle
Department of Ecoscience, Aarhus University, Vejlsøvej 25, 8600
Silkeborg, Denmark
Sino-Danish Center for Education and Research, University of Chinese
Academy of Sciences, Beijing, China
Cited articles
Allan, M.: Ecological modelling of water quality management options in Lake
Waahi to support Hauanga Kai species: Technical report, Hamilton, New
Zealand, 2018.
Andersen, T. K., Nielsen, A., Jeppesen, E., Hu, F., Bolding, K., Liu, Z.,
Søndergaard, M., Johansson, L. S., and Trolle, D.: Predicting ecosystem
state changes in shallow lakes using an aquatic ecosystem model: Lake Hinge,
Denmark, an example, Ecol. Appl., 30, 1–21, https://doi.org/10.1002/eap.2160, 2020.
Arnold, J. G., Srinivasan, R., Muttiah, R. S., and Williams, J. R.: Large
area hydrologic nodeling and assessment part 1: model development, J. Am.
Water Resour. Assoc., 34, 73–89, 1998.
Bruggeman, J. and Bolding, K.: A general framework for aquatic
biogeochemical models, Environ. Model. Softw., 61, 249–265,
https://doi.org/10.1016/j.envsoft.2014.04.002, 2014.
Bruggeman, J. and Bolding, K.: parsac: parallel sensitivity analysis and
calibration, Zenodo [code], https://doi.org/10.5281/ZENODO.4280520, 2020.
Burchard, H., Bolding, K., and Villarreal, M.: GOTM, a general ocean
turbulence model: Theory, implementation and test cases, Tech Rep EUR 18745 EN European Commission,
1999.
CAEDYM team: CAEDYM (Computational Aquatic Ecosystem DYnamics Model), Model Item, OpenGMS, https://geomodeling.njnu.edu.cn/modelItem/3dcb8f17-95ed-4e5e-aa7b-3efa7ed61add (last access: 11 May 2022), 2019.
Chen, W., Nielsen, A., Andersen, T. K., Hu, F., Chou, Q., Søndergaard,
M., Jeppesen, E., and Trolle, D.: Modeling the ecological response of a
temporarily summer-stratified lake to extreme heatwaves, Water
(Switzerland), 12, 1–17, https://doi.org/10.3390/w12010094, 2020.
Dini, M. L. and Carpenter, S. R.: Fish predators, food availability and diel
vertical migration in Daphnia, J. Plankton Res., 14, 359–377,
https://doi.org/10.1093/plankt/14.3.359, 1992.
Dodson, S.: Predicting diel vertical migration of zooplankton, Limnol.
Oceanogr., 35, 1195–1200, https://doi.org/10.4319/lo.1990.35.5.1195, 1990.
Ekau, W., Auel, H., Pörtner, H.-O., and Gilbert, D.: Impacts of hypoxia on the structure and processes in pelagic communities (zooplankton, macro-invertebrates and fish), Biogeosciences, 7, 1669–1699, https://doi.org/10.5194/bg-7-1669-2010, 2010.
Fasham, M. J. R., Ducklow, H. W., and McKelvie, S. M.: A nitrogen-based model
of plankton dynamics in the oceanic mixed layer, J. Mar. Res., 48,
591–639, https://doi.org/10.1357/002224090784984678, 1990.
González-Bergonzoni, I., Meerhoff, M., Davidson, T. A., Teixeira-de
Mello, F., Baattrup-Pedersen, A., and Jeppesen, E.: Meta-analysis Shows a
Consistent and Strong Latitudinal Pattern in Fish Omnivory Across
Ecosystems, Ecosystems, 15, 492–503, https://doi.org/10.1007/s10021-012-9524-4,
2012.
Hamilton, D. P. and Schladow, S. G.: Prediction of water quality in lakes
and reservoirs, Part I – Model description, Ecol. Modell., 96, 91–110,
1997.
Hersbach, H., Bell, B., Berrisford, P., Biavati, G., Horányi, A.,
Muñoz Sabater, J., Nicolas, J., Peubey, C., Radu, R., Rozum, I.,
Schepers, D., Simmons, A., Soci, C., Dee, D., and Thépaut, J.-N.: ERA5
hourly data on single levels from 1979 to present, Copernicus Climate Change Service (C3S) Climate Data Store (CDS) [data set],
https://doi.org/10.24381/cds.adbb2d47, 2018.
Hoyer, S. and Hamman, J. J.: xarray: N-D labeled Arrays and Datasets in
Python, J. Open Res. Softw., 5, 1–6, https://doi.org/10.5334/jors.148, 2017.
Hu, F., Bolding, K., Bruggeman, J., Jeppesen, E., Flindt, M. R., van Gerven, L., Janse, J. H., Janssen, A. B. G., Kuiper, J. J., Mooij, W. M., and Trolle, D.: FABM-PCLake – linking aquatic ecology with hydrodynamics, Geosci. Model Dev., 9, 2271–2278, https://doi.org/10.5194/gmd-9-2271-2016, 2016.
Hunter, J. D.: Matplotlib: A 2D Graphics Environment, Comput. Sci. Eng.,
9, 90–95, https://doi.org/10.1109/MCSE.2007.55, 2007.
Iglesias, C., Meerhoff, M., Johansson, L. S., González-Bergonzoni, I.,
Mazzeo, N., Pacheco, J. P., Mello, F. T. de, Goyenola, G., Lauridsen, T. L.,
Søndergaard, M., Davidson, T. A., and Jeppesen, E.: Stable isotope
analysis confirms substantial differences between subtropical and temperate
shallow lake food webs, Hydrobiologia, 784, 111–123,
https://doi.org/10.1007/s10750-016-2861-0, 2017.
Inomura, K., Deutsch, C., Masuda, T., Prášil, O. and Follows, M. J.:
Quantitative models of nitrogen-fixing organisms, Comput. Struct.
Biotechnol. J., 18, 3905–3924, https://doi.org/10.1016/j.csbj.2020.11.022, 2020.
Janse, J. H.: A model of nutrient dynamics in shallow lakes in relation to
multiple stable states, in: Shallow Lakes '95: Trophic Cascades in Shallow
Freshwater and Brackish Lakes, edited by: Kufel, L., Prejs, A., and
Rybak, J. I., Springer Netherlands, Dordrecht, 1–8, 1997.
Janse, J. H.: Model studies on the eutrophication of shallow lakes and ditches, Book, Wageningen University and Research, ISBN 90-8504-214-3, 2005.
Janse, J. H. and Aldenberg, T.: Modelling phosphorus fluxes in the
hypertrophic Loosdrecht Lakes, Hydrobiol. Bull., 24, 69–89,
https://doi.org/10.1007/BF02256750, 1990.
Janse, J. H. and van Liere, L.: PCLake: A modelling tool for the evaluation
of lakes restoration scenarios, Water Sci. Technol., 31, 371–374,
1995.
Janse, J. H., Aldenberg, T., and Kramer, P. R. G.: A mathematical model of
the phosphorus cycle in Lake Loosdrecht and simulation of additional
measures, Hydrobiologia, 233, 119–136, https://doi.org/10.1007/BF00016101, 1992.
Janssen, A. B. G., Arhonditsis, G. B., Beusen, A., Bolding, K., Bruce, L.,
Bruggeman, J., Couture, R.-M., Downing, A. S., Elliott, J. A., Frassl, M.
A., Gal, G., Gerla, D. J., Hipsey, M. R., Hu, F., Ives, S. C., Janse, J. H.,
Jeppesen, E., Jöhnk, K. D., Kneis, D., Kong, X., Kuiper, J. J., Lehmann,
M. K., Lemmen, C., Özkundakci, D., Petzoldt, T., Rinke, K., Robson, B.
J., Sachse, R., Schep, S. A., Schmid, M., Scholten, H., Teurlincx, S.,
Trolle, D., Troost, T. A., Dam, A. A. Van, Van Gerven, L. P. A., Weijerman,
M., Wells, S. A., and Mooij, W. M.: Exploring, exploiting and evolving
diversity of aquatic ecosystem models: a community perspective, Aquat.
Ecol., 49, 513–548, https://doi.org/10.1007/s10452-015-9544-1, 2015.
Janssen, A. B. G., Teurlincx, S., Beusen, A. H. W., Huijbregts, M. A. J.,
Rost, J., Schipper, A. M., Seelen, L. M. S., Mooij, W. M., and Janse, J. H.:
PCLake+: A process-based ecological model to assess the trophic state of
stratified and non-stratified freshwater lakes worldwide, Ecol. Modell.,
396, 23–32, https://doi.org/10.1016/j.ecolmodel.2019.01.006, 2019.
Jeppesen, E., Meerhoff, M., Holmgren, K., González-Bergonzoni, I.,
Teixeira-de Mello, F., Declerck, S. A. J., De Meester, L., Søndergaard,
M., Lauridsen, T. L., Bjerring, R., Conde-Porcuna, J. M., Mazzeo, N.,
Iglesias, C., Reizenstein, M., Malmquist, H. J., Liu, Z., Balayla, D., and
Lazzaro, X.: Impacts of climate warming on lake fish community structure and
potential effects on ecosystem function, Hydrobiologia, 646, 73–90,
https://doi.org/10.1007/s10750-010-0171-5, 2010.
Johansson, L. S., Søndergaard, M., Sørensen, P. B., Nielsen, A.,
Jeppesen, E., Wiberg-Larsen, P., and Landkildehus, F.: Søer 2018, Novana,
http://dce2.au.dk/pub/SR354.pdf (last access: 11 May 2022), 2019.
Jørgensen, T. B., Bjerring, R., Johansson, L. S., Søndergaard, M., Sortkjær, L., and Landkildehus,
F.: Søer 2006, NOVANA, Danmarks Miljøundersøgelser, Aarhus Universitet,
66 pp., Faglig rapport fra DMU nr. 641, ISBN: 978-87-7073-013-6, http://www.dmu.dk/Pub/FR641.pdf (last access: 11 May 2022), 2007.
Lambert, W.: The Adaptive Significance of Diel Vertical Migration of
Zooplankton, Funct. Ecol., 3, 21–27, 1989.
Leach, T. H., Beisner, B. E., Carey, C. C., Pernica, P., Rose, K. C., Huot,
Y., Brentrup, J. A., Domaizon, I., Grossart, H. P., Ibelings, B. W.,
Jacquet, S., Kelly, P. T., Rusak, J. A., Stockwell, J. D., Straile, D., and
Verburg, P.: Patterns and drivers of deep chlorophyll maxima structure in
100 lakes: The relative importance of light and thermal stratification,
Limnol. Oceanogr., 63, 628–646, https://doi.org/10.1002/lno.10656, 2018.
Meerhoff, M., Teixeira-de Mello, F., Kruk, C., Alonso, C.,
González-Bergonzoni, I., Pacheco, J. P., Lacerot, G., Arim, M.,
Beklioglu, M., Brucet, S., Goyenola, G., Iglesias, C., Mazzeo, N., Kosten,
S., and Jeppesen, E.: Environmental Warming in Shallow Lakes. A Review of
Potential Changes in Community Structure as Evidenced from Space-for-Time
Substitution Approaches, Adv. Ecol. Res., 46, 259–349, https://doi.org/10.1016/B978-0-12-396992-7.00004-6, 2012.
Mehner, T.: Diel vertical migration of freshwater fishes – proximate
triggers, ultimate causes and research perspectives, Freshw. Biol., 57,
1342–1359, https://doi.org/10.1111/j.1365-2427.2012.02811.x, 2012.
Mooij, W. M., Trolle, D., Jeppesen, E., Arhonditsis, G., Belolipetsky, P.
V., Chitamwebwa, D. B. R., Degermendzhy, A. G., DeAngelis, D. L., De
Senerpont Domis, L. N., Downing, A. S., Elliott, J. A., Fragoso, C. R.,
Gaedke, U., Genova, S. N., Gulati, R. D., Håkanson, L., Hamilton, D. P.,
Hipsey, M. R., 't Hoen, J., Hülsmann, S., Los, F. H., Makler-Pick, V.,
Petzoldt, T., Prokopkin, I. G., Rinke, K., Schep, S. A., Tominaga, K., van
Dam, A. A., van Nes, E. H., Wells, S. A., and Janse, J. H.: Challenges and
opportunities for integrating lake ecosystem modelling approaches, Aquat.
Ecol., 44, 633–667, https://doi.org/10.1007/s10452-010-9339-3, 2010.
Nielsen, A., Bolding, K., Hu, F., and Trolle, D.: An open source QGIS-based
work flow for model application and experimentation with aquatic ecosystems,
Environ. Model. Softw., 95, 358–364, https://doi.org/10.1016/j.envsoft.2017.06.032,
2017.
Nielsen, A., Schmidt Hu, F. R., Schnedler-Meyer, N. A., Bolding, K.,
Andersen, T. K., and Trolle, D.: Introducing QWET – A QGIS-plugin for
application, evaluation and experimentation with the WET model:
Environmental Modelling and Software, Environ. Model. Softw., 135, 104886,
https://doi.org/10.1016/j.envsoft.2020.104886, 2021.
Olli, K.: Diel vertical migration of phytoplankton and heterotrophic
flagellates in the Gulf of Riga, J. Mar. Syst., 23, 145–163,
https://doi.org/10.1016/S0924-7963(99)00055-X, 1999.
Paerl, H. W., Scott, J. . T., McCarthy, M. J., Newell, S. E., Gardner, W.
S., Havens, K. E., Hoffman, D. K., Wilhelm, S. W., and Wurtsbaugh, W. A.: It
Takes Two to Tango: When and Where Dual Nutrient (N & P) Reductions Are
Needed to Protect Lakes and Downstream Ecosystems, Environ. Sci. Technol.,
50, 10805–10813, https://doi.org/10.1021/acs.est.6b02575, 2016.
Reinl, K. L., Brookes, J. D., Carey, C. C., Harris, T. D., Ibelings, B. W.,
Morales-Williams, A. M., De Senerpont Domis, L. N., Atkins, K. S., Isles, P.
D. F., Mesman, J. P., North, R. L., Rudstam, L. G., Stelzer, J. A. A.,
Venkiteswaran, J. J., Yokota, K., and Zhan, Q.: Cyanobacterial blooms in
oligotrophic lakes: Shifting the high-nutrient paradigm, Freshw. Biol.,
66, 1846–1859, https://doi.org/10.1111/fwb.13791, 2021.
Rolighed, J., Jeppesen, E., Søndergaard, M., Bjerring, R., Janse, J. H.,
Mooij, W. M., and Trolle, D.: Climate Change Will Make Recovery from
Eutrophication More Difficult in Shallow Danish Lake Søbygaard, Water,
8, 1–20, https://doi.org/10.3390/w8100459, 2016.
Ross, O. N. and Sharples, J.: Phytoplankton motility and the competition for
nutrients in the thermocline, Mar. Ecol. Prog. Ser., 347, 21–38,
https://doi.org/10.3354/meps06999, 2007.
Sainmont, J., Thygesen, U. H., and Visser, A. W.: Diel vertical migration
arising in a habitat selection game, Theor. Ecol., 6, 241–251,
https://doi.org/10.1007/s12080-012-0174-0, 2013.
Saloranta, T. M. and Andersen, T.: MyLake-A multi-year lake simulation model
code suitable for uncertainty and sensitivity analysis simulations, Ecol.
Modell., 207, 45–60, https://doi.org/10.1016/j.ecolmodel.2007.03.018, 2007.
Schnedler-Meyer, N. A., Andersen, T. K., Hu, F. R. S., Bolding, K., Anders, N., and Trolle, D.: WET: Water Ecosystems Tool v1.0 (v1.0), Zenodo [code], https://doi.org/10.5281/zenodo.6482852, 2022.
Shatwell, T. and Köhler, J.: Decreased nitrogen loading controls summer
cyanobacterial blooms without promoting nitrogen-fixing taxa: Long-term
response of a shallow lake, Limnol. Oceanogr., 64, S166–S178,
https://doi.org/10.1002/lno.11002, 2019.
Soares, L. M. V. and Calijuri, M. do C.: Deterministic modelling of
freshwater lakes and reservoirs: Current trends and recent progress,
Environ. Model. Softw., 144, 105143,
https://doi.org/10.1016/j.envsoft.2021.105143, 2021.
Stips, A., Bolding, K., Pohlmann, T., and Burchard, H.: Simulating the temporal and spatial dynamics of the North Sea using the new model GETM (general estuarine transport model), Ocean Dynam., 54, 266–283, https://doi.org/10.1007/s10236-003-0077-0, 2004.
Trolle, D., Hamilton, D. P., Hipsey, M. R., Bolding, K., Bruggemann, J.,
Mooij, W. M., Janse, J. H., Nielsen, A., Jeppesen, E., Elliott, J. A.,
Makler-Pick, V., Petzoldt, T., Rinke, K., Flindt, M. R., Arhonditsis, G. B.,
Gal, G., Bjerring, R., Tominaga, K., Hoen, J., Downing, A. S., Marques, D.
M., Fragoso, C. R., Søndergaard, M., and Hanson, P. C.: A community-based
framework for aquatic ecosystem models, Hydrobiologia, 683, 25–34,
https://doi.org/10.1007/s10750-011-0957-0, 2012.
Vanderploeg, H. A., Ludsin, S. A., Ruberg, S. A., Höök, T. O.,
Pothoven, S. A., Brandt, S. B., Lang, G. A., Liebig, J. R., and Cavaletto, J.
F.: Hypoxia affects spatial distributions and overlap of pelagic fish,
zooplankton, and phytoplankton in Lake Erie, J. Exp. Mar. Bio. Ecol.,
381, S92–S107, https://doi.org/10.1016/j.jembe.2009.07.027, 2009.
Waskom, M. L.: seaborn: statistical data visualization, J. Open Source
Softw., 6, 3021, https://doi.org/10.21105/joss.03021, 2021.
Wentzky, V. C., Tittel, J., Jäger, C. G., Bruggeman, J., and Rinke, K.:
Seasonal succession of functional traits in phytoplankton communities and
their interaction with trophic state, J. Ecol., 108, 1649–1663,
https://doi.org/10.1111/1365-2745.13395, 2020.
Short summary
We present the Water Ecosystems Tool (WET) – a new modular aquatic ecosystem model configurable to a wide array of physical setups, ecosystems and research questions based on the popular FABM–PCLake model. We aim for the model to become a community staple, thus helping to consolidate the state of the art under a few flexible models, with the aim of improving comparability across studies and preventing the
re-inventions of the wheelthat are common to our scientific modeling community.
We present the Water Ecosystems Tool (WET) – a new modular aquatic ecosystem model configurable...
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