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Geoscientific Model Development An interactive open-access journal of the European Geosciences Union
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Discussion papers
https://doi.org/10.5194/gmd-2019-115
© Author(s) 2019. This work is distributed under
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/gmd-2019-115
© Author(s) 2019. This work is distributed under
the Creative Commons Attribution 4.0 License.

Submitted as: model description paper 09 Jul 2019

Submitted as: model description paper | 09 Jul 2019

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This discussion paper is a preprint. It is a manuscript under review for the journal Geoscientific Model Development (GMD).

CSIRO Environmental Modelling Suite (EMS): Scientific description of the optical and biogeochemical models (vB3p0)

Mark E. Baird1, Karen A. Wild-Allen1, John Parslow1, Mathieu Mongin1, Barbara Robson2, Jennifer Skerratt1, Farhan Rizwi1, Monika Soja-Woznaik1, Emlyn Jones1, Mike Herzfeld1, Nugzar Margvelashvili1, John Andrewartha1, Clothilde Langlais1, Matthew P. Adams3, Nagur Cherukuru4, Malin Gustafsson5, Scott Hadley1, Peter J. Ralph5, Uwe Rosebrock1, Thomas Schroeder1, Leonardo Laiolo1, Daniel Harrison6, and Andrew D. L. Steven1 Mark E. Baird et al.
  • 1CSIRO, Oceans and Atmosphere, Hobart, Australia
  • 2Australian Institute of Marine Science, Townsville, Australia
  • 3School of Chemical Engineering, The University of Queensland, Brisbane, Australia
  • 4CSIRO, Land and Water, Canberra, Australia
  • 5Plant Functional Biology and Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, Australia
  • 6Southern Cross University, Coffs Harbour, Australia

Abstract. Since the mid 1990s, Australia's Commonwealth Science Industry and Research Organisation (CSIRO) has developed a biogeochemical (BGC) model for coupling with a hydrodynamic and sediment model for application in estuaries, coastal waters and shelf seas. The suite of coupled models is referred to as the CSIRO Environmental Modelling Suite (EMS) and has been applied at tens of locations around the Australian continent. At a mature point in the BGC model's development, this paper presents a full mathematical description, as well as links to the freely available code and User Guide. The mathematical description is structured into processes so that the details of new parameterisations can be easily identified, along with their derivation. The EMS BGC model cycles carbon, nitrogen, phosphorous and oxygen through multiple phytoplankton, zooplankton, detritus and dissolved organic and inorganic forms in multiple water column and sediment layers. The underwater light field is simulated by a spectrally-resolved optical model that includes the calculation of water-leaving reflectance for validation with remote sensing. The water column is dynamically coupled to the sediment to resolve deposition, resuspension and benthic-pelagic biogeochemical fluxes. With a focus on shallow waters, the model also includes particularly-detailed representations of benthic plants such as seagrass, macroalgae and coral polyps. A second focus has been on, where possible, the use of geometric derivations of physical limits to constrain ecological rates, which generally requires population-based rates to be derived from initially considering the size and shape of individuals. For example, zooplankton grazing considers encounter rates of one predator on a prey field based on summing relative motion of the predator with the prey individuals and the search area, chlorophyll synthesis includes a geometrically-derived self-shading term, and the bottom coverage of benthic plants is generically-related to their biomass using an exponential form derived from geometric arguments. This geometric approach has led to a more algebraically-complicated set of equations when compared to more empirical biogeochemical model formulations. But while being algebraically-complicated, the model has fewer unconstrained parameters and is therefore simpler to move between applications than it would otherwise be. The version of the biogeochemistry described here is implemented in the eReefs project that is delivering a near real time coupled hydrodynamic, sediment and biogeochemical simulation of the Great Barrier Reef, northeast Australia, and its formulation provides an example of the application of geometric reasoning in the formulation of aquatic ecological processes.

Mark E. Baird et al.
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Short summary
For 20+ years the Commonwealth Science Industry and Research Organisation (CSIRO) has been developing a biogeochemical (BGC) model for coupling with a hydrodynamic and sediment model for application in estuaries, coastal waters and shelf seas. This paper provides a full mathematical description (equations, parameters), model evaluation and access to the numerical code. The model is particularly suited to applications in shallow waters where benthic processes are critical to ecosystem function.
For 20+ years the Commonwealth Science Industry and Research Organisation (CSIRO) has been...
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