ORCID Profile
0000-0003-4955-2298
Current Organisations
CSIRO Marine and Atmospheric Research
,
CSIRO
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Oceanography | Biological Oceanography | Physical Oceanography | Marine And Estuarine Ecology (Incl. Marine Ichthyology) | Biological Oceanography | Ecology | Ecosystem Function | Environmental Science and Management | Ecological Applications | Natural Resource Management | Environmental Monitoring | Natural Resource Management |
ANZSRC Socio-Economic Objective (SEO)
Integrated (ecosystem) assessment and management | Oceanic processes (excl. climate related) | Marine Oceanic Processes (excl. climate related) | Estuarine and lagoon areas | Ecosystem Assessment and Management of Marine Environments | Effects of Climate Change and Variability on Australia (excl. Social Impacts) | Integrated (ecosystem) assessment and management | Fisheries—commercial | Rehabilitation of degraded coastal and estuarine areas
Related Links
Publications
Ecological Forecasting and Operational Information Systems Support Sustainable Ocean Management
Publisher: MDPI AG
Date: 16-12-2022
Abstract: In times of rapid change and rising human pressures on marine systems, information about the future state of the ocean can provide decision-makers with time to avoid adverse impacts and maximise opportunities. An ecological forecast predicts changes in ecosystems and its components due to environmental forcing such as climate variability and change, extreme weather conditions, pollution, or habitat change. Here, we summarise ex les from several sectors and a range of locations. We describe the need, approach, forecast performance, delivery system, and end user uptake. This examination shows that near-term ecological forecasts are needed by end users, decisions are being made based on forecasts, and there is an urgent need to develop operational information systems to support sustainable ocean management. An operational information system is critical for connecting to decision makers and providing an enduring approach to forecasting and proactive decision making. These operational systems require significant investment and ongoing maintenance but are key to delivering ecological forecasts for societal benefits. Iterative forecasting practices could provide continuous improvement by incorporating evaluation and feedback to overcome the limitations of the imperfect model and incomplete observations to achieve better forecast outcomes and accuracy.
Modeling What We Sample and Sampling What We Model: Challenges for Zooplankton Model Assessment
Publisher: Frontiers Media SA
Date: 22-03-2017
A numerical modeling study of the East Australian Current encircling and overwashing a warm‐core eddy
Publisher: American Geophysical Union (AGU)
Date: 2013
DOI: 10.1029/2012JC008386
Parameter optimisation of a marine ecosystem model at two contrasting stations in the Sub-Antarctic Zone
Publisher: Elsevier BV
Date: 11-2011
Day and night ichthyoplankton assemblages and zooplankton biomass size spectrum in a deep ocean island wake
Publisher: Inter-Research Science Center
Date: 20-09-2006
DOI: 10.3354/MEPS322225
Contrasting microbial assemblages in adjacent water masses associated with the East Australian Current
Publisher: Wiley
Date: 27-06-2012
DOI: 10.1111/J.1758-2229.2012.00362.X
Abstract: Different oceanographic provinces host discrete microbial assemblages that are adapted to local physicochemical conditions. We sequenced and compared the metagenomes of two microbial communities inhabiting adjacent water masses in the Tasman Sea, where the recent strengthening of the East Australian Current (EAC) has altered the ecology of coastal environments. Despite the comparable latitude of the s les, significant phylogenetic differences were apparent, including shifts in the relative frequency of matches to Cyanobacteria, Crenarchaeota and Euryarchaeota. Fine-scale variability in the structure of SAR11, Prochlorococcus and Synechococcus populations, with more matches to 'warm-water' ecotypes observed in the EAC, indicates the EAC may drive an intrusion of tropical microbes into temperate regions of the Tasman Sea. Furthermore, significant shifts in the relative importance of 17 metabolic categories indicate that the EAC prokaryotic community has different physiological properties than surrounding waters.
Water residence time controls the feedback between seagrass, sediment and light: Implications for restoration
Publisher: Elsevier BV
Date: 07-2018
Macquarie Harbour Oxygen Process model (FRDC 2016-067): CSIRO Milestone 4 Report
Publisher: CSIRO Oceans & Atmosphere
Date: 2020
DOI: 10.25919/E99S-G352
eReefs: An operational information system for managing the Great Barrier Reef
Publisher: Informa UK Limited
Date: 08-08-2019
CSIRO Environmental Modelling Suite (EMS): Scientific description of the optical and biogeochemical models (vB3p0)
Publisher: Copernicus GmbH
Date: 09-07-2019
DOI: 10.5194/GMD-2019-115
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 in iduals. For ex le, zooplankton grazing considers encounter rates of one predator on a prey field based on summing relative motion of the predator with the prey in iduals 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 ex le of the application of geometric reasoning in the formulation of aquatic ecological processes.
Plankton dynamics due to rainfall, eutrophication, dilution, grazing and assimilation in an urbanized coastal lagoon
Publisher: Elsevier BV
Date: 08-2009
Using a phytoplankton growth model to predict the fractionation of stable carbon isotopes
Publisher: Oxford University Press (OUP)
Date: 08-2001
Simulated fate of catchment-derived sediment on the Great Barrier Reef shelf
Publisher: Elsevier BV
Date: 10-2018
DOI: 10.1016/J.MARPOLBUL.2018.08.018
Abstract: Numerical experiments using a 3D model of fine sediment transport in the Great Barrier Reef region indicate deposition of the bulk mass of catchment sediments from river plumes within a few tens of kilometres from river mouths. A very fine fraction of easily resuspended catchment sediment has a capacity to propagate over much greater distances reaching out into the mid-shelf and outer-shelf regions. The model suggests such particles, instrumental to the development of low density flocs in the marine environment, can play a critical role in altering optical properties of water masses over the shelf during wet years. The mid-term (4 year) impact of Great Barrier Reef catchments on the probability of suspended sediment concentration exceeding the ecologically significant trigger value of 2 mg/L is confined to inshore regions adjacent to river mouth locations.
Three-dimensional structure of a swarm of the salp Thalia democratica within a cold-core eddy off southeast Australia
Publisher: American Geophysical Union (AGU)
Date: 31-12-2011
DOI: 10.1029/2011JC007310
Numerical approximations of the mean absorption cross-section of a variety of randomly oriented microalgal shapes
Publisher: Springer Science and Business Media LLC
Date: 09-2003
DOI: 10.1007/S00285-003-0215-9
Abstract: The size, shape, and absorption coefficient of a microalgal cell determines, to a first order approximation, the rate at which light is absorbed by the cell. The rate of absorption determines the maximum amount of energy available for photosynthesis, and can be used to calculate the attenuation of light through the water column, including the effect of packaging pigments within discrete particles. In this paper, numerical approximations are made of the mean absorption cross-section of randomly oriented cells, aA. The shapes investigated are spheroids, rectangular prisms with a square base, cylinders, cones and double cones with aspect ratios of 0.25, 0.5, 1, 2, and 4. The results of the numerical simulations are fitted to a modified sigmoid curve, and take advantage of three analytical solutions. The results are presented in a non-dimensionalised format and are independent of size. A simple approximation using a rectangular hyperbolic curve is also given, and an approach for obtaining the upper and lower bounds of aA for more complex shapes is outlined.
A Poisson-Pareto Model of chlorophyll-A Fluorescence Signals in Marine Environments
Publisher: Cambridge University Press (CUP)
Date: 04-2015
DOI: 10.1017/S1446181115000073
Abstract: Because of its central role in the global carbon cycle, quantifying the biomass of photosynthetic microalgae in the oceans is crucial to our ability to estimate the oceans’ carbon drawdown. Many traditional methods of primary production assessment have proven to be extremely time consuming and, consequently, have handled only very small s le sizes. The recent advent of in situ bio-optical sensors, such as the water quality monitor (WQM), is now providing lower cost and higher throughput data on these crucial biological communities. These WQMs, however, only quantify the total fluorescence of all in idual cells within their optical s le windows, irrespective of size. In this paper, we further develop an established model, based on Pareto random variables, of the size structure of the microalgae community to understand the effect of the WQMs’ s ling and data pooling on their estimates of algal biomass. Unfortunately, evaluating sums of Pareto variables is a notoriously difficult problem. Here, we utilize an approximation for the right-tail of the resulting distribution to derive parameter estimates for the underlying size structure of the microalgae community.
Impact of catchment loads of nutrients and sediments on marine water quality on the Great Barrier Reef: An application of the eReefs marine modelling system
Publisher: Elsevier BV
Date: 06-2021
Towards a mechanistic model of plankton population dynamics
Publisher: Oxford University Press (OUP)
Date: 1999
The exposure of the Great Barrier Reef to ocean acidification
Publisher: Springer Science and Business Media LLC
Date: 23-02-2016
DOI: 10.1038/NCOMMS10732
Abstract: 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 (Ω a ). The downscaling of ocean acidification projections from global to GBR scales requires the set of regional drivers controlling Ω a to be resolved. Here we use a regional coupled circulation–biogeochemical model and observations to estimate the Ω a experienced by the 3,581 reefs of the GBR, and to apportion the contributions of the hydrological cycle, regional hydrodynamics and metabolism on Ω a variability. We find more detail, and a greater range (1.43), than previously compiled coarse maps of Ω a of the region (0.4), or in observations (1.0). Most of the variability in Ω a is due to processes upstream of the reef in question. As a result, future decline in Ω a is likely to be steeper on the GBR than currently projected by the IPCC assessment report.
A biophysical representation of seagrass growth for application in a complex shallow-water biogeochemical model
Publisher: Elsevier BV
Date: 04-2016
The strengthening East Australian Current, its eddies and biological effects - an introduction and overview
Publisher: Elsevier BV
Date: 03-2011
Large-scale interventions may delay decline of the Great Barrier Reef
Publisher: The Royal Society
Date: 04-2021
DOI: 10.1098/RSOS.201296
Abstract: On the iconic Great Barrier Reef (GBR), the cumulative impacts of tropical cyclones, marine heatwaves and regular outbreaks of coral-eating crown-of-thorns starfish (CoTS) have severely depleted coral cover. Climate change will further exacerbate this situation over the coming decades unless effective interventions are implemented. Evaluating the efficacy of alternative interventions in a complex system experiencing major cumulative impacts can only be achieved through a systems modelling approach. We have evaluated combinations of interventions using a coral reef meta-community model. The model consisted of a dynamic network of 3753 reefs supporting communities of corals and CoTS connected through ocean larval dispersal, and exposed to changing regimes of tropical cyclones, flood plumes, marine heatwaves and ocean acidification. Interventions included reducing flood plume impacts, expanding control of CoTS populations, stabilizing coral rubble, managing solar radiation and introducing heat-tolerant coral strains. Without intervention, all climate scenarios resulted in precipitous declines in GBR coral cover over the next 50 years. The most effective strategies in delaying decline were combinations that protected coral from both predation (CoTS control) and thermal stress (solar radiation management) deployed at large scale. Successful implementation could expand opportunities for climate action, natural adaptation and socioeconomic adjustment by at least one to two decades.
Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef
Publisher: Copernicus GmbH
Date: 09-05-2016
DOI: 10.5194/BG-2016-168
Abstract: Abstract. Skilful 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 Color 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 the additional signal from bottom reflectance. Rather than assimilate quantities calculated using error-prone IOP algorithms, this study demonstrates the advantages of assimilating quantities calculated directly from the less error-prone satellite remote-sensing reflectance. The assimilation of a directly-observed quantity, in this case remote-sensing reflectance, is analogous to the assimilation of temperature brightness in Numerical Weather Prediction (NWP), or along-track sea-surface height in hydrodynamic models. To assimilate the observed reflectance, we use an in-water optical model to produce an equivalent simulated remote-sensing reflectance, and calculate the mis-match between the observed and simulated quantities to constrain the BGC model with a Deterministic Ensemble Kalman Filter (DEnKF). Using the assumption that simulated surface Chl-a is equivalent to remotely-sensed OC3M estimate of Chl-a resulted in a forecast error of approximately 75 %. Alternatively, assimilation of remote-sensing reflectance resulted in a forecast error of less than 40 %. Thus, in the coastal waters of the GBR, assimilating remote-sensing reflectance halved the forecast errors. When the analysis and forecast fields from the assimilation system are compared with the non-assimilating model, an independent comparison to in-situ observations of Chl-a, TSS, and dissolved inorganic nutrients (NO3, NH4 and DIP) show that errors are reduced by up to 90 %. In all cases, the assimilation system improves the result compared to the non-assimilating model. This 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.
Effect of phytoplankton community size structure on remote-sensing reflectance and chlorophyll a products
Publisher: Elsevier BV
Date: 11-2020
Emulator-assisted data assimilation in complex models Ocean Dynamics.
Publisher: Springer Science and Business Media LLC
Date: 04-08-2016
South East Queensland Modelling report published as SEQ RWQM V3 Phase II Final Report with Biogeochemical Modelling (Ch 4) update
Publisher: CSIRO
Date: 2014
Self-organisation of zooplankton communities produces similar food chain lengths throughout the ocean
Publisher: Research Square Platform LLC
Date: 25-04-2022
DOI: 10.21203/RS.3.RS-1186379/V1
Abstract: For over 50 years, the conceptualisation of low-nutrient oligotrophic systems having longer food chains and thus lower energy transfer to fish than their high-nutrient eutrophic counterparts 1 has achieved the status of an ecological paradigm. However, recent global assessments indicate global fish biomass could be much higher than previously thought 2–4 , suggesting that our traditional understanding of food webs may need to be revisited. Here, we challenge the classical paradigm by exploring the role of zooplankton in food webs across the world’s oceans. Using observed zooplankton size spectra, and output from a size-spectrum model that resolves nine zooplankton groups, we conclude that food chains in oligotrophic (low-nutrient) and eutrophic (high-nutrient) systems have similar lengths. We offer a compelling hypothesis to explain this emergent pattern: self-organisation of zooplankton groups across the global productivity gradient regulates food chain length. We find that in oligotrophic systems the increased carnivory and longer food chains are offset by relatively large gelatinous filter feeders eating the dominant small phytoplankton, resulting in shorter-than-expected food chains, but decreasing food quality for fish. Our findings highlight the pivotal role zooplankton play in regulating energy transfer. Better resolution of zooplankton groups, their feeding relationships and carbon content in models will increase our ability to estimate current global fish biomass 5 , project future fish biomass under climate change 6–8 , and provide more-robust forecasts of nutrient 9 and carbon cycling 10 .
Nutrient and plankton dynamics in an intermittently closed/open lagoon, Smiths Lake, south-eastern Australia: An ecological model
Publisher: Elsevier BV
Date: 05-2007
Modeling photoinhibition-driven bleaching in Scleractinian coral as a function of light, temperature, and heterotrophy
Publisher: Wiley
Date: 03-2014
A dynamic model of the cellular carbon to chlorophyll ratio applied to a batch culture and a continental shelf ecosystem
Publisher: Wiley
Date: 14-06-2013
The effect of surface flooding on the physical-biogeochemical dynamics of a warm-core eddy off southeast Australia
Publisher: Elsevier BV
Date: 03-2011
A size-resolved pelagic ecosystem model
Publisher: Elsevier BV
Date: 05-2007
The effect of packaging of chlorophyll within phytoplankton and light scattering in a coupled physical - biological ocean model
Publisher: CSIRO Publishing
Date: 2007
DOI: 10.1071/MF07055
Abstract: A coupled physical–biological model forced with spectrally resolved solar radiation is used to investigate the effect of packaging of pigment and light scattering on physical and biological properties in the open ocean. Simulations are undertaken with three alternate formulations of vertical attenuation, which consider: (1) chlorophyll as dissolved in the water column (2) chlorophyll packaged into phytoplankton cells with no scattering and (3) packaged chlorophyll with scattering. In the coupled model, depth-resolved solar heating depends on the vertical profile of phytoplankton concentration, creating a feedback mechanism between the physical and biological states. The particular scenario investigated is a northerly wind off the coast of south-east Australia. The packaging of chlorophyll approximately halves the attenuation rate of 340–500 nm light and a phytoplankton maximum forms ~10 m deeper than in the dissolved chlorophyll case, with a corresponding adjustment of the dissolved inorganic nitrogen and zooplankton fields. Scattering approximately doubles the vertical attenuation of 340–600 nm light, lifting the phytoplankton maximum by ~10 m when compared with the packaged chlorophyll case. Additionally, strong horizontal gradients in chlorophyll distribution associated with filaments of upwelled water inshore of the East Australian Current, when modelled with alternate formulations of vertical light attenuation, result in circulation changes. The explicit representation of the packaging of pigment and light scattering is worth considering in coupled physical–biological modelling studies.
A database of chlorophyll a in Australian waters
Publisher: Springer Science and Business Media LLC
Date: 20-02-2018
Abstract: Chlorophyll a is the most commonly used indicator of phytoplankton biomass in the marine environment. It is relatively simple and cost effective to measure when compared to phytoplankton abundance and is thus routinely included in many surveys. Here we collate 173, 333 records of chlorophyll a collected since 1965 from Australian waters gathered from researchers on regular coastal monitoring surveys and ocean voyages into a single repository. This dataset includes the chlorophyll a values as measured from s les analysed using spectrophotometry, fluorometry and high performance liquid chromatography (HPLC). The Australian Chlorophyll a database is freely available through the Australian Ocean Data Network portal ( portal.aodn.org.au/ ). These data can be used in isolation as an index of phytoplankton biomass or in combination with other data to provide insight into water quality, ecosystem state, and relationships with other trophic levels such as zooplankton or fish.
Quantifying and modelling the carbon sequestration capacity of seagrass meadows - A critical assessment
Publisher: Elsevier BV
Date: 06-2014
DOI: 10.1016/J.MARPOLBUL.2013.07.038
Abstract: Seagrasses are among the planet's most effective natural ecosystems for sequestering (capturing and storing) carbon (C) but if degraded, they could leak stored C into the atmosphere and accelerate global warming. Quantifying and modelling the C sequestration capacity is therefore critical for successfully managing seagrass ecosystems to maintain their substantial abatement potential. At present, there is no mechanism to support carbon financing linked to seagrass. For seagrasses to be recognised by the IPCC and the voluntary C market, standard stock assessment methodologies and inventories of seagrass C stocks are required. Developing accurate C budgets for seagrass meadows is indeed complex we discuss these complexities, and, in addition, we review techniques and methodologies that will aid development of C budgets. We also consider a simple process-based data assimilation model for predicting how seagrasses will respond to future change, accompanied by a practical list of research priorities.
Relative impact of seasonal and oceanographic drivers on surface chlorophyll a along a Western Boundary Current
Publisher: Elsevier BV
Date: 2014
Erratum: Changes in pH at the exterior surface of plankton with ocean acidification
Publisher: Springer Science and Business Media LLC
Date: 27-09-2012
DOI: 10.1038/NCLIMATE1696
Biological response to circulation driven by mean summertime winds off central Chile: A numerical model study
Publisher: American Geophysical Union (AGU)
Date: 07-2007
DOI: 10.1029/2006JC003655
Biological properties across the Tasman Front off southeast Australia
Publisher: Elsevier BV
Date: 11-2008
A plankton population model with biomechanical descriptions of biological processes in an idealised 2D ocean basin
Publisher: Elsevier BV
Date: 10-2004
Reply to 'In defence of the Cell Quota model of micro-algal growth' by M. R. Droop
Publisher: Oxford University Press (OUP)
Date: 2003
Over 75 years of zooplankton data from Australia
Publisher: Wiley
Date: 11-2014
DOI: 10.1890/14-0697.1
Ocean acidification: Linking science to management solutions using the Great Barrier Reef as a case study
Publisher: Elsevier BV
Date: 11-2016
DOI: 10.1016/J.JENVMAN.2016.07.038
Abstract: Coral reefs are one of the most vulnerable ecosystems to ocean acidification. While our understanding of the potential impacts of ocean acidification on coral reef ecosystems is growing, gaps remain that limit our ability to translate scientific knowledge into management action. To guide solution-based research, we review the current knowledge of ocean acidification impacts on coral reefs alongside management needs and priorities. We use the world's largest continuous reef system, Australia's Great Barrier Reef (GBR), as a case study. We integrate scientific knowledge gained from a variety of approaches (e.g., laboratory studies, field observations, and ecosystem modelling) and scales (e.g., cell, organism, ecosystem) that underpin a systems-level understanding of how ocean acidification is likely to impact the GBR and associated goods and services. We then discuss local and regional management options that may be effective to help mitigate the effects of ocean acidification on the GBR, with likely application to other coral reef systems. We develop a research framework for linking solution-based ocean acidification research to practical management options. The framework assists in identifying effective and cost-efficient options for supporting ecosystem resilience. The framework enables on-the-ground OA management to be the focus, while not losing sight of CO2 mitigation as the ultimate solution.
Entrainment of larval fish assemblages from the inner shelf into the East Australian Current and into the western Tasman Front
Publisher: Wiley
Date: 26-07-2011
Mass-transfer-limited nitrate uptake on a coral reef flat, Warraber Island, Torres Strait, Australia
Publisher: Springer Science and Business Media LLC
Date: 28-07-2004
Seagrass resistance to light deprivation: Implications for resilience
Publisher: Springer International Publishing
Date: 2018
The interchangeability of autotrophic and heterotrophic nitrogen sources in Scleractinian coral symbiotic relationships: A numerical study
Publisher: Elsevier BV
Date: 02-2013
The effect of natural and anthropogenic nutrient and sediment loads on reactive oxygen stress in zooxanthellae on runoff-exposed reefs
Publisher: Elsevier BV
Date: 07-2021
Optimising cool-water injections to reduce thermal stress on coral reefs of the Great Barrier Reef
Publisher: Public Library of Science (PLoS)
Date: 20-10-2020
Increasing model structural complexity inhibits the growth of initial condition errors
Publisher: Elsevier BV
Date: 12-2010
Reversing ocean acidification along the Great Barrier Reef using alkalinity injection
Publisher: IOP Publishing
Date: 06-2021
Abstract: The Great Barrier Reef (GBR) is a globally significant coral reef system supporting productive and erse ecosystems. The GBR is under increasing threat from climate change and local anthropogenic stressors, with its general condition degrading over recent decades. In response to this, a number of techniques have been proposed to offset or ameliorate environmental changes. In this study, we use a coupled hydrodynamic-biogeochemical model of the GBR and surrounding ocean to simulate artificial ocean alkalinisation (AOA) as a means to reverse the impact of global ocean acidification on GBR reefs. Our results demonstrate that a continuous release of 90 000 t of alkalinity every 3 d over one year along the entire length of the GBR, following the Gladstone-Weipa bulk carrier route, increases the mean aragonite saturation state ( Ω a r ) across the GBR’s 3860 reefs by 0.05. This change offsets just over 4 years (∼4.2) of ocean acidification under the present rate of anthropogenic carbon emissions. The injection raises Ω a r in the 250 reefs closest to the route by ⩾ 0.15 , reversing further projected Ocean Acidification. Following cessation of alkalinity injection Ω a r returns to the value of the waters in the absence of AOA over a 6 month period, primarily due to transport of additional alkalinity into the Coral Sea. Significantly, our study provides for the first time a model of AOA applied along existing shipping infrastructure that has been used to investigate shelf scale impacts. Thus, amelioration of decades of OA on the GBR is feasible using existing infrastructure, but is likely to be extremely expensive, include as yet unquantified risks, and would need to be undertaken continuously until such time, probably centuries in the future, when atmospheric CO 2 concentrations have returned to today’s values.
CSIRO Environmental Modelling Suite (EMS): scientific description of the optical and biogeochemical models (vB3p0)
Publisher: Copernicus GmbH
Date: 25-09-2020
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 in iduals. For ex le, zooplankton grazing considers encounter rates of one predator on a prey field based on summing relative motion of the predator with the prey in iduals 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 ex le of the application of geometric reasoning in the formulation of aquatic ecological processes.
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.
Publisher: Elsevier BV
Date: 04-2016
Relative effects of physical and biological processes on nutrient and phytoplankton dynamics in a shallow estuary after a storm event
Publisher: Springer Science and Business Media LLC
Date: 02-2006
DOI: 10.1007/BF02784701
Optimising reef-scale CO2 removal by seaweed to buffer ocean acidification
Publisher: IOP Publishing
Date: 03-2016
Skill Assessment and Analysis of a Coupled Hydrodynamic Biogeochemical Model of the Great Barrier Reef
Publisher: Elsevier BV
Date: 10-2018
Particulate Backscattering Ratio as an Indicator of Changing Particle Composition in Coastal Waters: Observations From Great Barrier Reef Waters
Publisher: American Geophysical Union (AGU)
Date: 08-2019
DOI: 10.1029/2019JC014998
Limits to prediction in a size-resolved pelagic ecosystem model
Publisher: Oxford University Press (OUP)
Date: 18-03-2010
Long-term changes in temperate Australian coastal waters: Implications for phytoplankton
Publisher: Inter-Research Science Center
Date: 18-11-2009
DOI: 10.3354/MEPS08297
On relating physical limits to the carbon: nitrogen ratio of unicellular algae and benthic plants
Publisher: Elsevier BV
Date: 08-2004
Changes in pH at the exterior surface of plankton with ocean acidification
Publisher: Springer Science and Business Media LLC
Date: 15-04-2012
DOI: 10.1038/NCLIMATE1489
Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef.
Publisher: Copernicus GmbH
Date: 07-12-2016
Abstract: Abstract. 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.
Simulated plankton and nutrient dynamics in the Great Barrier Reef (2011-2016)
Publisher: Elsevier BV
Date: 04-2019
The interacting effects of photosynthesis, calcification and water circulation on carbon chemistry variability on a coral reef flat: A modelling study
Publisher: Elsevier BV
Date: 07-2014
Modelling coastal connectivity in a Western Boundary Current: Seasonal and inter-annual variability
Publisher: Elsevier BV
Date: 03-2011
Analysis of southeast Australian zooplankton observations of 1938-42 using synoptic oceanographic conditions
Publisher: Elsevier BV
Date: 03-2011
Modelling the impact of phytoplankton cell size and abundance on inherent optical properties (IOPs) and a remotely sensed chlorophyll-a product
Publisher: Elsevier BV
Date: 2021
Information content of in situ and remotely sensed chlorophyll-a: Learning from size-structured phytoplankton model
Publisher: Elsevier BV
Date: 07-2018
Effect of wind on continental shelf carbon fluxes off southeast Australia: A numerical model
Publisher: American Geophysical Union (AGU)
Date: 05-2009
DOI: 10.1029/2008JC004946
Modelling the interacting effects of nutrient uptake, light capture and temperature on phytoplankton growth
Publisher: Oxford University Press (OUP)
Date: 08-2001
Synergy between Ocean Colour and Biogeochemical/ Ecosystem Models.
Publisher: International Ocean Colour Coordinating Group (IOCCG)
Date: 2020
DOI: 10.25607/OBP-711
Physical oceanographic processes influence bio-optical properties in the Tasman Sea
Publisher: Elsevier BV
Date: 04-2016
Towards evidence-based parameter values and priors for aquatic ecosystem modelling
Publisher: Elsevier BV
Date: 02-2018
Measurement and prediction of mass transfer to experimental coral reef communities
Publisher: Wiley
Date: 12-1997
Distribution of life-history stages of the salp Thalia democratica in shelf waters during a spring bloom
Publisher: Inter-Research Science Center
Date: 26-05-2011
DOI: 10.3354/MEPS09090
Cyclonic entrainment of preconditioned shelf waters into a frontal eddy
Publisher: American Geophysical Union (AGU)
Date: 02-2015
DOI: 10.1002/2014JC010301
The formation of a cold-core eddy in the East Australian Current
Publisher: Elsevier BV
Date: 02-2016
Enhanced assessment of the eReefs biogeochemical model for the Great Barrier Reef using the Concept/State/Process/System model evaluation framework
Publisher: Elsevier BV
Date: 07-2020
Estimation of the Global Distribution of Phytoplankton Light Absorption from Pigment Concentrations
Publisher: American Geophysical Union (AGU)
Date: 08-2022
DOI: 10.1029/2022JC018494
Abstract: Light absorption by phytoplankton drives marine primary production and determines ocean color. Phytoplankton absorption is a function of the pigment composition, wavelength, intracellular pigment concentration, and the cells' type. This paper presents phytoplankton absorption spectra reconstructed from in situ pigment concentration and a library of pigment‐specific absorption coefficients from 32 in idual pigment standards, including chlorophylls, caretonoids and phycobilins. The s les dominated by small phytoplankton show no significant difference between calculated absorption and that measured by a spectrophotometer. The component of absorption due to large cells, determined by diagnostic pigments analysis, required correction for the package effect. For the global ocean, the reconstructed phytoplankton absorption was overestimated by 16% at 443 nm and underestimated by 13% over the range between 400 and 700 nm. Following our reconstruction protocol, this approach allows the estimation of phytoplankton absorption spectra from many locations where pigment concentration has been measured, but no directly observed phytoplankton absorption measurements are available.
Microbial tropicalization driven by a strengthening western ocean boundary current
Publisher: Wiley
Date: 27-07-2020
DOI: 10.1111/GCB.15257
Supplementary material to "CSIRO Environmental Modelling Suite (EMS): Scientific description of the optical and biogeochemical models (vB3p0)"
Publisher: Copernicus GmbH
Date: 09-07-2019
Phytoplankton growth in the Australian sector of the Southern Ocean, examined by optimising ecosystem model parameters
Publisher: Elsevier BV
Date: 12-2013
An integrated study of the Gladstone marine system
Publisher: CSIRO
Date: 2015
Cumulative impacts across Australia’s Great Barrier Reef: a mechanistic evaluation
Publisher: Wiley
Date: 28-12-2021
DOI: 10.1002/ECM.1494
Abstract: Cumulative impacts assessments on marine ecosystems have been hindered by the difficulty of collecting environmental data and identifying drivers of community dynamics beyond local scales. On coral reefs, an additional challenge is to disentangle the relative influence of multiple drivers that operate at different stages of coral ontogeny. We integrated coral life history, population dynamics, and spatially explicit environmental drivers to assess the relative and cumulative impacts of multiple stressors across 2,300 km of the world’s largest coral reef ecosystem, Australia’s Great Barrier Reef (GBR). Using literature data, we characterized relationships between coral life history processes (reproduction, larval dispersal, recruitment, growth, and mortality) and environmental variables. We then simulated coral demographics and stressor impacts at the organism (coral colony) level on ,800 in idual reefs linked by larval connectivity and exposed to temporally and spatially realistic regimes of acute (crown‐of‐thorns starfish outbreaks, cyclones, and mass coral bleaching) and chronic (water‐quality) stressors. Model simulations produced a credible reconstruction of recent (2008–2020) coral trajectories consistent with monitoring observations, while estimating the impacts of each stressor at reef and regional scales. Overall, simulated coral populations declined by one‐third across the GBR, from an average of ~29% to ~19% hard coral cover. By 2020, % of the GBR had coral cover higher than 30%, a status of reef health corroborated by scarce and sparsely distributed monitoring data. Reef‐wide annual rates of coral mortality were driven by bleaching (48%) ahead of cyclones (41%) and starfish predation (11%). Beyond the reconstructed status and trends, the model enabled the emergence of complex interactions that compound the effects of multiple stressors while promoting a mechanistic understanding of coral cover dynamics. Drivers of coral cover growth were identified notably, water quality (suspended sediments) was estimated to delay recovery for at least 25% of inshore reefs. Standardized rates of coral loss and recovery allowed the integration of all cumulative impacts to determine the equilibrium cover for each reef. This metric, combined with maps of impacts, recovery potential, water‐quality thresholds, and reef state metrics, facilitates strategic spatial planning and resilience‐based management across the GBR.
Coupled physical-biological modelling study of the East Australian Current with idealised wind forcing. Part I: Biological model intercomparison
Publisher: Elsevier BV
Date: 02-2006
eReefs Infrastructure 2019: Capacity to facilitate user access and scale-up of services
Publisher: CSIRO
Date: 2019
Coupled physical-biological modelling study of the East Australian Current with idealised wind forcing: Part II. Biological dynamical analysis
Publisher: Elsevier BV
Date: 02-2006
The southward transport of sub‐mesoscale lenses of Bass Strait Water in the centre of anti‐cyclonic mesoscale eddies
Publisher: American Geophysical Union (AGU)
Date: 2012
DOI: 10.1029/2011GL050643
The use of mechanistic descriptions of algal growth and zooplankton grazing in an estuarine eutrophication model
Publisher: Elsevier BV
Date: 03-2003
An avenue of eddies: Quantifying the biophysical properties of mesoscale eddies in the Tasman Sea
Publisher: American Geophysical Union (AGU)
Date: 28-08-2012
DOI: 10.1029/2012GL053091
Past the Precipice? Projected Coral Habitability Under Global Heating
Publisher: American Geophysical Union (AGU)
Date: 05-2022
DOI: 10.1029/2021EF002608
Abstract: Coral reefs are rapidly declining due to local environmental degradation and global climate change. In particular, corals are vulnerable to ocean heating. Anomalously hot sea surface temperatures (SSTs) create conditions for severe bleaching or direct thermal death. We use SST observations and CMIP6 model SST to project thermal conditions at reef locations at a resolution of 1 km, a 16‐fold improvement over prior studies, under four climate emissions scenarios. We use a novel statistical downscaling method which is significantly more skillful than the standard method, especially at near‐coastal pixels where many reefs are found. For each location we present projections of thermal departure (TD, the date after which a location with steadily increasing heat exceeds a given thermal metric) for severe bleaching recurs every 5 years (TD5Y) and every 10 years (TD10Y), accounting for a range of post‐bleaching reef recovery/degradation. As of 2021, we find that over 91% and 79% of 1 km 2 reefs have exceeded TD10Y and TD5Y, respectively, suggesting that widespread long‐term coral degradation is no longer avoidable. We project 99% of 1 km 2 reefs to exceed TD5Y by 2034, 2036, and 2040 under SSP5‐8.5, SSP3‐7.0, and SSP2‐4.5 respectively. We project that 2%–5% of reef locations remain below TD5Y at 1.5°C of mean global heating, but 0% remain at 2.0°C. These results demonstrate the importance of further improving ecological projection capacity for climate‐vulnerable marine and terrestrial species and ecosystems, including identifying refugia and guiding conservation efforts. Ultimately, saving coral reefs will require rapidly reducing and eliminating greenhouse gas emissions.
Related Organisations
Commonwealth Scientific And Industrial Research Organisation
Location: Australia
University Of Warwick
Location: United Kingdom of Great Britain and Northern Ireland
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