Hierarchical Emulation & Data Assimilation into the Sediment Transport Model

AbstractSynthetic observations of the suspended sediment concentration in an idealised macro-tidal estuary are assimilated into the 3d sediment transport model. The assimilation scheme relies on fast and cheap surrogates of the complex model (called emulators) to update the model's state variables and its 2 parameters. A scenario with a hierarchically structured emulator is contrasted to the scenario with a more conventional non-hierarchical emulator. Numerical experiments indicate that for a given size of the ensemble an emulator which replicates a hierarchical structure of the model tends to provide a better approximation of that model. Improving the quality of the emulator translates into the improved quality of the assimilation products

Impact of catchment-derived nutrients and sediments on marine water quality on the Great Barrier Reef: an application of the eReefs marine modelling system

Water quality of the Great Barrier Reef (GBR) is determined by a range of natural and anthropogenic drivers that are resolved in the eReefs coupled hydrodynamic - biogeochemical marine model forced by a process-based catchment model, GBR Dynamic SedNet. Model simulations presented here quantify the impact of anthropogenic catchment loads of sediments and nutrients on a range of marine water quality variables. Simulations of 2011–2018 show that reduction of anthropogenic catchment loads results in improved water quality, especially within river plumes. Within the 16 resolved river plumes, anthropogenic loads increased chlorophyll concentration by 0.10 (0.02–0.25) mg Chl m−3. Reductions of anthropogenic loads following proposed Reef 2050 Water Quality Improvement Plan targets reduced chlorophyll concentration in the plumes by 0.04 (0.01–0.10) mg Chl m−3. Our simulations demonstrate the impact of anthropogenic loads on GBR water quality and quantify the benefits of improved catchment management

Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef

Skillful marine biogeochemical (BGC) models are required to understand a range of coastal and global phenomena such as changes in nitrogen and carbon cycles. The refinement of BGC models through the assimilation of variables calculated from observed in-water inherent optical properties (IOPs), such as phytoplankton absorption, is problematic. Empirically derived relationships between IOPs and variables such as chlorophyll-a concentration (Chl a), total suspended solids (TSS) and coloured dissolved organic matter (CDOM) have been shown to have errors that can exceed 100% of the observed quantity. These errors are greatest in shallow coastal regions, such as the Great Barrier Reef (GBR), due to the additional signal from bottom reflectance. Rather than assimilate quantities calculated using IOP algorithms, this study demonstrates the advantages of assimilating quantities calculated directly from the less error-prone satellite remote-sensing reflectance (RSR). To assimilate the observed RSR, we use an in-water optical model to produce an equivalent simulated RSR and calculate the mismatch between the observed and simulated quantities to constrain the BGC model with a deterministic ensemble Kalman filter (DEnKF). The traditional assumption that simulated surface Chl a is equivalent to the remotely sensed OC3M estimate of Chl a resulted in a forecast error of approximately 75 %. We show this error can be halved by instead using simulated RSR to constrain the model via the assimilation system. When the analysis and forecast fields from the RSR-based assimilation system are compared with the non-assimilating model, a comparison against independent in situ observations of Chl a, TSS and dissolved inorganic nutrients (NO3, NH4 and DIP) showed that errors are reduced by up to 90 %. In all cases, the assimilation system improves the simulation compared to the non-assimilating model. Our approach allows for the incorporation of vast quantities of remote-sensing observations that have in the past been discarded due to shallow water and/or artefacts introduced by terrestrially derived TSS and CDOM or the lack of a calibrated regional IOP algorithm

The exposure of the Great Barrier Reef to ocean acidification

The Great Barrier Reef (GBR) is founded on reef-building corals. Corals build their exoskeleton with aragonite, but ocean acidification is lowering the aragonite saturation state of seawater (Omega(a)). The downscaling of ocean acidification projections from global to GBR scales requires the set of regional drivers controlling Omega(a) to be resolved. Here we use a regional coupled circulation-biogeochemical model and observations to estimate the Omega(a) experienced by the 3,581 reefs of the GBR, and to apportion the contributions of the hydrological cycle, regional hydrodynamics and metabolism on Omega(a) variability. We find more detail, and a greater range (1.43), than previously compiled coarse maps of Omega(a) of the region (0.4), or in observations (1.0). Most of the variability in Omega(a) is due to processes upstream of the reef in question. As a result, future decline in Omega(a) is likely to be steeper on the GBR than currently projected by the IPCC assessment report

Bedload sediment transport dynamics in a macrotidal embayment, and implications for export to the southern Great Barrier Reef shelf

Keppel Bay is a macrotidal ernbayment on a tectonically stable, tropical coast, which links the Fitzroy River with the Great Barrier Reef continental shelf Estuaries and deltas act as conduits between catchments and inner shelf environments. Therefore, understanding sediment transport pathways in these complex systems is essential for the management of ecosystems such as coral-reefs that are potentially vulnerable to enhanced river sediment loads. Furthermore, the morphology and sediment dynamics of subtidal sand ridges and dunes are relatively poorly characterised in macrotidal estuaries, particularly in turbid, episodic systems such as the Fitzroy River and Keppel Bay. Our sedimentological analysis of seabed samples, shear-stress modelling and three-dimensional acoustic imaging reveals that Keppel Bay is a mixed wave- and tide-dominated estuarine system. Areas of sediment starvation and shoreward transport characterise the offshore zone, whereas a complex of both active and relict tidal sand ridges, and associated subaqueous dunes, dominate the relatively protected southern Keppel Bay. Transport within this region is highly dynamic and variable, with ebb-dominated sediment transport through tidal channels into the outer bay where there is a switch to wave-dominated shoreward transport. Ultimately, bedload sediments appear to be reworked back inshore and to the north, and are gradually infilling the bedrock-defined embayment. Our characterisation of the Keppel Bay system provides a detailed example of the physiography of the seaward portion of a tide-dominated system, and shows that sediment transport in these areas is influenced by a variable hydrodynamic regime as well as relict channels and bedrock topography. (c) 2007 Elsevier B.V. All rights reserved

Remote-sensing reflectance and true colour produced by a coupled hydrodynamic, optical, sediment, biogeochemical model of the Great Barrier Reef, Australia: comparison with satellite data

Aquatic biogeochemical models are vital tools in understanding and predicting human impacts on water clarity. In this paper, we develop a spectrally-resolved optical model that produces remote-sensing reflectance as a function of depth-resolved biogeochemical model properties such as phytoplankton biomass, suspended sediment concentrations and benthic reflectance. We compare simulated remote sensing reflectance from a 4 km resolution coupled hydrodynamic, optical, sediment and biogeochemical model configured for the Great Barrier Reef with observed remote-sensing reflectance from the MODIS sensor at the 8 ocean colour bands. The optical model is sufficiently accurate to capture the remote-sensing reflectance that would arise from a specific biogeochemical state. Thus the mismatch between simulated and observed remote-sensing reflectance provides an excellent metric for model assessment of the coupled biogeochemical model. Finally, we combine simulated remote-sensing reflectance in a red/green/blue colour model to produce simulated true colour images during the passage of Tropical Cyclone Yasi in February 2011

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

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

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

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. </p

The Fitzroy contaminants project a study of the nutrient and fine-sediment dynamics of the Fitzroy Estuary and Keppel Bay /

The Fitzroy catchment is the largest Queensland catchment discharging to the Great Barrier Reef (GBR) lagoon. Sediments and nutrients together with anthropogenic pollutants originating upstream in the catchment are discharged from the Fitzroy River via the Fitzroy Estuary (FE) and ultimately into Keppel Bay (KB). The estuary and the bay act as natural chemical reactors where the materials delivered undergo chemical and physical transformations before some are deposited and stored in the growing deltaic and beach areas, with the remainder transported eastward to the southern zone of the GBR lagoon. The Reef Water Quality Protection Plan is a recent State–Commonwealth initiative which aims to improve land-use management practices within many Queensland catchments with the intent of reducing the loads of sediments, nutrients and other potentially deleterious substances entering the GBR lagoon. The background knowledge to make realistic predictions of the response of the FE and KB ecosystems to changed sediment and nutrient deliveries did not exist when this project started. The Agricultural Contaminants Project (Project AC) was developed to address these knowledge gaps and to produce a predictive framework to aid managers in the evaluation of various load reduction strategies