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Coastal generalized ecosystem model (CGEM) 1.0: Flexible model formulations for simulating complex biogeochemical processes in aquatic ecosystems

Author

Listed:
  • Jarvis, Brandon M.
  • Lehrter, John C.
  • Lowe, Lisa
  • Penta, Bradley
  • Wan, Yongshan
  • Duvall, Melissa
  • Simmons, Cody
  • Melendez, Wilson
  • Ko, Dong S.

Abstract

The Coastal Generalized Ecosystem Model (CGEM) is a biogeochemical model developed to study regulating processes of water-column optical properties, water-column and benthic carbon, oxygen, and nutrient cycles, and phytoplankton and zooplankton dynamics. CGEM offers numerous formulations for important rate processes, providing users flexibility in altering model structure. This flexibility also provides a means for evaluating model structural uncertainty and impacts on simulations, which are rarely evaluated with numerical ecosystem models. As an open-source model, CGEM also offers users the option to implement new formulations or modify existing routines. We also provide a full description of the model formulations, state variables, and model parameters in CGEM. Using two published case studies, we explore how different formulations for light attenuation, phytoplankton temperature growth response, and sediment processes impact simulations. We discuss CGEM's role as a new ecosystem model within the modeling community and opportunities to address current and future water quality issues.

Suggested Citation

  • Jarvis, Brandon M. & Lehrter, John C. & Lowe, Lisa & Penta, Bradley & Wan, Yongshan & Duvall, Melissa & Simmons, Cody & Melendez, Wilson & Ko, Dong S., 2024. "Coastal generalized ecosystem model (CGEM) 1.0: Flexible model formulations for simulating complex biogeochemical processes in aquatic ecosystems," Ecological Modelling, Elsevier, vol. 496(C).
    • Handle: RePEc:eee:ecomod:v:496:y:2024:i:c:s0304380024002199
    DOI: 10.1016/j.ecolmodel.2024.110831
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    References listed on IDEAS

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    1. Beck, Marcus W. & Lehrter, John C. & Lowe, Lisa L. & Jarvis, Brandon M., 2017. "Parameter sensitivity and identifiability for a biogeochemical model of hypoxia in the northern Gulf of Mexico," Ecological Modelling, Elsevier, vol. 363(C), pages 17-30.
    2. Zhang, Zhonglong & Sun, Bowen & Johnson, Billy E., 2015. "Integration of a benthic sediment diagenesis module into the two dimensional hydrodynamic and water quality model – CE-QUAL-W2," Ecological Modelling, Elsevier, vol. 297(C), pages 213-231.
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    4. Stephanie A. Henson & B. B. Cael & Stephanie R. Allen & Stephanie Dutkiewicz, 2021. "Future phytoplankton diversity in a changing climate," Nature Communications, Nature, vol. 12(1), pages 1-8, December.
    5. Eldridge, Peter M. & Roelke, Daniel L., 2010. "Origins and scales of hypoxia on the Louisiana shelf: Importance of seasonal plankton dynamics and river nutrients and discharge," Ecological Modelling, Elsevier, vol. 221(7), pages 1028-1042.
    6. Priyadarshi, Anupam & Chandra, Ram & Kishi, Michio J. & Smith, S.Lan & Yamazaki, Hidekatsu, 2022. "Understanding plankton ecosystem dynamics under realistic micro-scale variability requires modeling at least three trophic levels," Ecological Modelling, Elsevier, vol. 467(C).
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