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 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.

Model fit versus biological relevance: Evaluating photosynthesis-temperature models for three tropical seagrass species

“…P max estimates maximum productivity, which can be used to compare seagrass growth traits between different species29. Our obtained Q 10 values for photosynthesis experimentally verify the hypothesis that Q 10 values generally range between 2 and 330, an assumption which is applied in coastal ecological models31. Several empirical photosynthesis-temperature models include P max , T opt and T max as parameters (Table 1), so these parameters are transferable to empirical photosynthesis-temperature models other than the Yan and Hunt model, and could also be implemented in plant growth models that are based on carbon balance32.…”

eReefs: An operational information system for managing the Great Barrier Reef

“…Supporting these components are a spectrally-resolved optical model (Baird et al 2016a) that estimates scalar irradiance for both pelagic and benthic production rates and calculates normalised water leaving radiance for comparison with satellite observations; a data assimilation system that uses the mismatch between observed and simulated normalised water leaving radiance (Jones et al 2016), wave models and an offline transport model that is used by the sediment and biogeochemical models (Gillibrand and Herzfeld 2015). All these components are part of the Environmental Modelling Suite (EMS) and are publicly and freely available (https://research.csiro.au/cem/software/ems/) and discussed in detail in Baird et al (2019).…”

“…The sediment and biogeochemical models (GBR-BGC), discussed extensively in Baird et al (2019), operate in both the water column and sediment layers, with exchange of mass across the interface via settling, resuspension and mixing ( Figure 3). Ecological processes represented include: the photosynthetic growth of 4 categories of phytoplankton, three classes of seagrass, macroalgae, and coral zooxanthellae; secondary production by zooplankton and corals; gas exchanges of oxygen and carbon dioxide, and transformations of nitrogen, phosphorus and carbon in dissolved and particulate forms (Figure 3).…”

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.…”