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

M. E. Baird; K. A. Wild-Allen; J. Parslow; M. Mongin; B. Robson; J. Skerratt; F. Rizwi; M. Soja-Woźniak; E. Jones; M. Herzfeld; N. Margvelashvili; J. Andrewartha; C. Langlais; M. P. Adams; N. Cherukuru; M. Gustafsson; S. Hadley; P. J. Ralph; U. Rosebrock; T. Schroeder; L. Laiolo; D. Harrison; A. D. L. Steven

doi:10.5194/gmd-13-4503-2020

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

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

M. E. Baird, K. A. Wild-Allen, J. Parslow, M. Mongin, B. Robson, J. Skerratt, F. Rizwi, M. Soja-Woźniak, E. Jones, M. Herzfeld, …

Geoscientific Model Development, Vol.13(9), pp.4503-4553

25/09/2020

DOI: https://doi.org/10.5194/gmd-13-4503-2020

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Biological oceanography

Ecosystem adaptation to climate change

Since the mid-1990s, Australia's 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. 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. In EMS, the underwater light field is simulated by a spectrally resolved optical model that calculates vertical light attenuation from the scattering and absorption of 20+ optically active constituents. The BGC model itself 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 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 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. This geometric approach 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 calculated from 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 empirical biogeochemical model formulations based on populations. 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 EMS described here is implemented in the eReefs project that delivers 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.

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Title: CSIRO Environmental Modelling Suite (EMS): scientific description of the optical and biogeochemical models (vB3p0)
Creators: M. E. Baird (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
K. A. Wild-Allen (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
J. Parslow (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
M. Mongin (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
B. Robson (Author) - Australian Institute of Marine Science, Townsville, Australia
J. Skerratt (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
F. Rizwi (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
M. Soja-Woźniak (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
E. Jones (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
M. Herzfeld (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
N. Margvelashvili (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
J. Andrewartha (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
C. Langlais (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
M. P. Adams (Author) - School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
N. Cherukuru (Author) - CSIRO, Oceans and Atmosphere, Canberra, Australia
M. Gustafsson (Author) - Plant Functional Biology and Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, Australia
S. Hadley (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
P. J. Ralph (Author) - Plant Functional Biology and Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, Australia
U. Rosebrock (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
T. Schroeder (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
L. Laiolo (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
D. Harrison (Author) - Southern Cross University, Coffs Harbour, Australia
A. D. L. Steven (Author) - CSIRO, Oceans and Atmosphere, Hobart, Australia
Publication Details: Geoscientific Model Development, Vol.13(9), pp.4503-4553
Publisher: Copernicus Publications
Grant note: Funding bodies include CSIRO Wealth from Oceans Flagship, Gas Industry Social & Environmental Research Alliance (GISERA), CSIRO Coastal Carbon Cluster, Derwent Estuary Program, INFORM2, eReefs, Great Barrier Reef Foundation, Australian Climate Change Science Program, University of Technology Sydney, Department of Energy and Environment, Integrated Marine Observing System (IMOS), National Environment Science Program (NESP TWQ Hub) and the Royal Australian Navy.
Identifiers: 991012926969102368
Academic Unit: Science; Faculty of Science and Engineering
Language: English
Resource Type: Journal article

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

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