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

Abstract

Abstract. 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.

Shifts in coralline algae, macroalgae, and coral juveniles in the Great Barrier Reef associated with present‐day ocean acidification

“…Environmental predictor values were estimated for all survey sites (Figure ) using the 4 km resolution e Reefs coupled biogeochemical, hydrodynamic, optical, and sediment model (Baird et al, ; version GBR4 BGC 2.0). They were calculated for the nearest model grid cell to each of the ecological survey sites, for 2 m below mean astronomic sea level.…”

“…Aragonite saturation state (Ω ar ) was chosen as the seawater carbon chemistry variable. Ω ar in the eReefs model is calculated from changes in dissolved inorganic carbon and total alkalinity in the seawater, and model estimates are not significantly affected by the model estimates of reef benthos (see Baird et al, for details on eReefs model calculations). The other environmental variables were: suspended fine inorganic sediment (sum of “fine mud” and “carbonate sand” sediment fractions <30 µm; g/m 3 ), chlorophyll a (mg/m 3 ), temperature (°C), and benthic light at the depth of each survey (24 hr mean photosynthetically active irradiance, PAR; mol photons m −2 s −1 , calculated specifically for the depth at which each survey was conducted; Figure ).…”

“…GBR seawater nutrients and phytoplankton have significantly increased over the past 50–60 years (Bell, ), and in situ water samples suggest that p CO 2 concentrations on selected inshore reefs of the GBR may have increased 2.5–3 times faster than offshore and atmospheric values within the last 30 years (Uthicke et al, ). A GBR‐wide coupled hydrodynamic and biogeochemical ecosystem model ( e Reefs) shows that present‐day aragonite saturation state (Ω ar ) is lower inshore and in the southern GBR than in the adjacent open ocean (Baird et al, ; Mongin et al, ; Skerratt et al, ).…”

Variations in Mid‐ to Late Holocene Nitrogen Supply to Northern Great Barrier Reef Halimeda Macroalgal Bioherms

“…The distribution of Halimeda bioherms north of 16°S latitude where bioherms are present at Cape York and the Ribbon Reefs but absent from Princess Charlotte Bay (Figures 1, 4b, and 4c), is entirely consistent with seasonal GBR shelf-edge temperature and NO 3 concentrations. The CSIRO eReefs hydrodynamic and biogeochemical models (Baird et al, 2020;Steven et al, 2019) suggest that episodic upwelling (characterized by pulses of cooler water with increased NO 3 concentration) is most intense in the Cooktown/Ribbon MCNEIL ET AL.…”

“…The GBR temperature and nitrate visualization presented in Figure 4 represents a snapshot derived from the CSIRO eReefs hydrodynamic and biogeochemical 4 km models (Baird et al, 2020;Steven et al, 2019). The eReefs modeling system uses the CSIRO Environmental Modeling Suite (Baird et al, 2020)…”