Simulated nutrient and plankton dynamics in the Great Barrier Reef (2011–2016)

Skerratt, Jennifer; Mongin, Mathieu; Baird, Mark E.; Wild-Allen, Karen; Robson, Barbara; Schaffelke, Britta; Davies, Claire; Richardson, Anthony J.; Margvelashvili, Nugzar; Soja‐Woźniak, Monika; Steven, Andrew D. L.

doi:10.1016/j.jmarsys.2018.12.006

Cited by 37 publications

(26 citation statements)

References 48 publications

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“…The biogeochemical model outputs have been compared to a range of in situ observations including 24 water quality moorings, 2 nutrient sampling programmes (with a total of 18 stations) and time-series of taxon-specific plankton abundance (Skerratt et al 2019). As would be expected, the skill of the biogeochemical components was less than that of the physical properties.…”

Section: Calibration Assimilation and Validationmentioning

confidence: 99%

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

Steven

Baird

Brinkman

et al. 2019

Journal of Operational Oceanography

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eReefs is a comprehensive interoperable information platform that has been developed for the Great Barrier Reef (GBR) region to provide users with access to improved environmental intelligence allowing them to assess past, present, and future conditions, as well as management options to mitigate the risks associated with multiple and sometimes competing uses of the GBR. eReefs is built upon an integrated system of data, catchment and marine models, visualisation, reporting and decision support tools that span the entire GBR area. This communication briefly describes eReefs architecture and components and provides examples of applications that have been used to inform policy and management decisions, and finally discusses challenges and key learnings and considers future developments and applications.

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Section: Calibration Assimilation and Validationmentioning

confidence: 99%

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

Steven

Baird

Brinkman

et al. 2019

Journal of Operational Oceanography

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“…The capacity to identify taxa to species is especially important for resolving biological diversity around Australia's, see for example phytoplankton provinces (Figure 1). We have recently completed a major revision of the dinoflagellate genus Tripos in Australian waters using data from the NRS, under the guidance of Professor Gustaaf (Skerratt et al, 2019). (B) Zooplankton total grazing (mg C/m3/day) output from the eReefs model (Skerratt et al, 2019).…”

Section: Partnering With Taxonomic Expertsmentioning

confidence: 99%

“…In the relatively rare instances where zooplankton were assessed in biogeochemical models, they were more poorly simulated than almost any other state variable. Gridded products are commonly used in model assessment, from SST to chlorophyll a; we have developed the first gridded products for zooplankton biomass such as that used for assessment of the eReefs biogeochemical model on the Great Barrier Reef (Skerratt et al, 2019) (Figure 8). Given that many significant management issues are tackled by biogeochemical and ecosystem models -including impacts of sediment dumping from dredging, potential management strategies for managing crown-of-thorns, assessing trade-offs of multiple-use of common fisheries resources and coastal aquaculture, and socio-economic impacts of different management decisions -products for model assessment based on plankton data can directly improve our marine management.…”

Section: Product Development To Extend Uptake and Improve Impactmentioning

confidence: 99%

Australia’s Long-Term Plankton Observations: The Integrated Marine Observing System National Reference Station Network

et al. 2019

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The Integrated Marine Observing System National Reference Station network provides unprecedented open access to species-level phytoplankton and zooplankton data for researchers, managers and policy makers interested in resource condition, and detecting and understanding the magnitude and time-scales of change in our marine environment. We describe how to access spatial and temporal plankton data collected from the seven reference stations located around the Australian coastline, and a summary of the associated physical and chemical parameters measured that help in the interpretation of plankton data. Details on the rationale for site locations, sampling methodologies and laboratory analysis protocols are provided to assist with use of the data, and design of complimentary investigations. Information on taxonomic entities reported in the plankton database, and changes in taxonomic nomenclature and other issues that may affect data interpretation, are included. Data from more than 1250 plankton samples are freely available via the Australian Ocean Data Network portal and we encourage uptake and use of this continental-scale dataset, giving summaries of data currently available and some practical applications. The full methods manual that includes sampling and analysis protocols for the Integrated Marine Observing System Biogeochemical Operations can be found on-line.

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“…A more recent assessment of the biogeochemical model (vB2p0) compared simulations against a range of in situ observations that included 24 water quality moorings, 2 nutrient sampling programs (with a total of 18 stations) and time-series of taxonspecific plankton abundance. In addition to providing a range of skill metrics, the assessment included analysis of seasonal plankton dynamics (Skerratt et al, 2019).…”

Section: Model Evaluationmentioning

confidence: 99%

“…The techniques and observations used in Skerratt et al (2019) have been compared to the version described in this paper (vB3p0) (see Supplementary Material). This includes observations of Chl a, dissolved inorganic carbon, nitrogen, phosphorus and ammonia, dissolved organic nitrogen and phosphorus, alkalinity, pH, aragonite saturation, mass of suspended sediments and turbidity and Secchi depth.…”

Section: Model Evaluationmentioning

confidence: 99%

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

Baird¹,

Wild-Allen²,

Parslow³

et al. 2019

Preprint

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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.

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Simulated nutrient and plankton dynamics in the Great Barrier Reef (2011–2016)

Cited by 37 publications

References 48 publications

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

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

Australia’s Long-Term Plankton Observations: The Integrated Marine Observing System National Reference Station Network

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

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