Ocean alkalinity enhancement (OAE) is a promising marine carbon dioxide removal (mCDR) method that aims to reduce atmospheric CO2 by increasing the ocean's storage capacity. While global ocean and Earth system models are necessary to track air-sea CO2 equilibration and far-field alkalinity transport on extended timescales, OAE efficiency is strongly influenced by local oceanography and climate. Regional ocean modeling is a powerful tool for capturing the effects of these influences on near-field plume dispersion and CO2 uptake variability. Here, we used a high-resolution, three-dimensional hydrodynamic and biogeochemical model (2 km) to evaluate the effects of deployment location and interannual climate variability on OAE efficiency in Bass Strait, southeast Australia. We simulated the addition of 113.21 Gmol of alkalinity (a theoretical uptake capacity of ~4.2 Mt CO2) over one month, via four infrastructure-constrained pathways: a desalination outfall, a shipping lane, a ferry track, and a series of coastal outfalls. These additions were repeated across three Southern Annular Mode (SAM) phase end-member winters: 2017 (positive SAM–low winds), 2021 (neutral SAM–moderate winds), and 2023 (negative SAM–strong winds). CO2 uptake efficiency variability (mol CO2/mol TA) is primarily influenced by delivery method and location (95.2%) rather than by interannual climate variability (3.9%). At the shelf-break, 70.67% ± 10.53% of added alkalinity is subducted below the mixed layer before equilibration with the atmosphere; this alkalinity is then exported from the Bass Strait region at depth. The subduction and loss of alkalinity from the region before equilibration reduces the realised CO2 uptake and contributes to efficiencies (0.11–0.27) that are lower than those simulated by a global model in the same region (0.31). This mismatch, driven by regionally specific oceanographic processes, has implications for OAE deployment and equilibration timescales in other dynamic shelf environments. To resolve these scale-dependent limitations, we recommend integrated monitoring, reporting, and verification frameworks that combine observational networks, regional models, and global models (with regional model exports as input to global models). This approach is necessary to accurately quantify net carbon removal and to constrain the long-term fate of added alkalinity.

Sigmoid growth models are often used to study population dynamics. The size of a population at equilibrium commonly depends explicitly on the availability of resources, such as an energy or nutrient source, which is not explicit in standard sigmoid growth models. A simple generalised extension of sigmoid growth models is introduced that can explicitly account for this resource-dependence, demonstrated by three examples of this family of models of increasing mathematical complexity. Each model is calibrated and compared to observed data for algae under sea-ice in Antarctic coastal waters. It was found that through careful construction, models satisfying the proposed framework can estimate key properties of a sea-ice break-out controlled tipping point for the algae, which cannot be estimated using standard sigmoid growth models. The proposed broader family of energy-dependent sigmoid growth models likely has usage in many population growth contexts where resources limit population size.

The Coral Sea houses expansive coral reefs. Reef health is inextricably linked to water temperatures, which are regulated by the hydrodynamic environment. The ocean current system in the Coral Sea is dominated by jets of the South Equatorial Current (SEC): the North Vanuatu Jet (NVJ), the North Caledonian Jet (NCJ) and the South Caledonian Jet (SCJ). We investigated the projected near-future (2050) changes in the temperature and transport structure of the Coral Sea using the three highest-resolution climate models from the high-resolution coupled modelling experiment (HighResMIP) conducted within the latest iteration of the Coupled Model Intercomparison Project Phase 6 (CMIP6). We found that the HighResMIP models successfully represented the historical temperature and transport structure of the SEC jets and their El Ni & ntilde;o-Southern Oscillation-related variability. Surface ocean warming of 0.78 and 1.12 degrees C was projected in the Coral Sea under 1.5 and 2 degrees C global air temperature warming, respectively. The maximum depth of the warming signal deepened by 30 m per decade, penetrating to 400 m by 2050. This indicated the additional thermal stress that could be experienced by Coral Sea ecosystems. Interestingly, the surface warming was associated with a sub-surface cooling between 400 and 600 m. Decreases in the transports of the NVJ and NCJ and an intensification of the SCJ were also projected in the HighResMIP models. The magnitudes of the changes were relatively small (2 % to 7 % of historical means) and of a similar order to the variability in transport associated with the El Ni & ntilde;o-Southern Oscillation. Our analysis further showed that the transport projections of the NVJ and NCJ varied with depth, where surface intensifications coincided with the areas of greatest warming. These changes could modify western boundary currents and upwelling dynamics on the Great Barrier Reef shelf.

Solar radiation propagating through the water column is scattered and absorbed by optically active constituents in the ocean, in particular phytoplankton, coloured-dissolved organic matter (CDOM), suspended inorganic particulate matter (SPIM) and detritus. These wavelength-dependent processes affect the vertical distribution of heating in the water column and its stratification. The continental shelf north-east of Australia, containing the Great Barrier Reef (GBR), is characterised by highly seasonal and intermittent freshwater inputs leading to large sediment and nutrient discharges that strongly impact the water optical properties. While this complex mixture of optically active constituents is known to affect water clarity and the euphotic zone depth in the river plumes, its impact on the ocean circulation and thermal balance is still unclear at the scale of the GBR. In this study, we use a hydrodynamic-optical-biogeochemical ocean model to investigate the feedback between heat absorption by phytoplankton, CDOM and suspended sediments and ocean dynamics in the GBR region. The results show that the attenuation of the vertical heat flux due to phytoplankton, CDOM and SPIM concentrations is stronger on the continental shelf and dominated by the absorption and scattering from suspended sediments. The presence of absorbing constituents in the water column drives a temperature increase at the surface and a decrease below the mixed layer with stronger stratification and greater heat losses to the atmosphere. Inshore, the ocean heat content increases by up to 1% due to optically active constituents. Offshore, absorption by optically active constituents near the surface is compensated by less absorption underneath the mixed layer resulting in a decrease in the ocean heat content of the top 500 m. We find that considering a spatially- and temporally-variable vertical attenuation of heat due to multiple optically-active components improves hydrodynamic model skill. This study highlights the importance of the impact of water clarity and its spatial variability on hydrodynamic processes.

Marine heatwaves occurring against the backdrop of rising global sea surface temperatures have triggered mass coral bleaching and mortality. Irradiance is critical to coral growth but is also an implicating factor in photodamage, leading to the expulsion of symbiotic algae under increased temperatures. Numerical modelling is a valuable tool that can provide insight into the state of the symbiont photochemistry during coral bleaching events. However, very few numerical physiological models combine the influence of light and temperature for simulating coral bleaching. The coral bleaching model used was derived from the coral bleaching representation in the eReefs configuration of the CSIRO Environmental Modelling Suite, with the most significant change being the equation for the rate of detoxification of reactive oxygen species. Simulated physiological bleaching outcomes from the model were compared to photochemical bleaching proxies measured during an ex situ moderate degree-heating week (up to 4.4) experiment. The bleaching response of Acropora divaricata was assessed in an unshaded and 30% shade treatment. The model-simulated timing for the onset of bleaching under elevated temperatures closely corresponded with an initial photochemical decline as observed in the experiment. Increased bleaching severity under elevated temperature and unshaded light was also simulated by the model, an outcome confirmed in the experiment. This is the first experimental validation of a temperature-mediated, light-driven model of coral bleaching from the perspective of the symbiont. When forced by realistic environmental conditions, process-based mechanistic modelling could improve accuracy in predicting heterogeneous bleaching outcomes during contemporary marine heatwave events and future climate change scenarios. Mechanistic modelling will be invaluable in evaluating management interventions for deployment in coral reef environments.

Mass coral bleaching events have become increasingly frequent since the 1980s as sea surface temperatures have risen. Extremes of light and temperature stress leading to coral bleaching can develop when doldrum meteorological conditions occur during a marine heatwave event. The coral bleaching model simulates bleaching by tracking the build-up of reactive oxygen species driven by temperature-mediated, light-driven oxidative stress, triggering symbiont cell expulsion. This study is the first to evaluate the coral bleaching model for its ability to simulate heat and light stress dynamics in the coral Acropora kenti over multiple doldrum events and an intermediate recovery period. We tested model fidelity by comparing model predictions against laboratory measurements of coral bleaching stress taken during an emulated multi-doldrum marine heatwave event, incorporating artificial shade treatments. The model consistently predicted greater bleaching at increased temperatures and reduced shade levels, with an intermediate recovery period simulated between the doldrum events. Simulated bleaching stress captured up to fifty per cent of the variation in observed antioxidant enzyme activity. This study confirms that the significant emergent features of the model are present, as overall, the model adequately represented bleaching outcomes concerning the interactions between temperature and light. Thus, process-based modelling could be a valuable tool for predicting bleaching outcomes and optimising shading techniques, providing scientific managers with actionable strategies for mitigating coral bleaching.

MotivationHere, we make available a second version of the BioTIME database, which compiles records of abundance estimates for species in sample events of ecological assemblages through time. The updated version expands version 1.0 of the database by doubling the number of studies and includes substantial additional curation to the taxonomic accuracy of the records, as well as the metadata. Moreover, we now provide an R package (BioTIMEr) to facilitate use of the database.Main Types of Variables IncludedThe database is composed of one main data table containing the abundance records and 11 metadata tables. The data are organised in a hierarchy of scales where 11,989,233 records are nested in 1,603,067 sample events, from 553,253 sampling locations, which are nested in 708 studies. A study is defined as a sampling methodology applied to an assemblage for a minimum of 2 years.Spatial Location and GrainSampling locations in BioTIME are distributed across the planet, including marine, terrestrial and freshwater realms. Spatial grain size and extent vary across studies depending on sampling methodology. We recommend gridding of sampling locations into areas of consistent size.Time Period and GrainThe earliest time series in BioTIME start in 1874, and the most recent records are from 2023. Temporal grain and duration vary across studies. We recommend doing sample-level rarefaction to ensure consistent sampling effort through time before calculating any diversity metric.Major Taxa and Level of MeasurementThe database includes any eukaryotic taxa, with a combined total of 56,400 taxa.Software Formatcsv and. SQL.

Although global warming is leading to more frequent mass coral bleaching events worldwide, parts of the Great Barrier Reef (GBR) have consistently escaped severe coral bleaching. Modeling and satellite observations show that climate refugia are created by the upwelling of cooler water to the surface through the interactions of tides and currents with dense reef structures. Here, we use a high-resolution nested regional ocean model to investigate the future status of two relatively large refugia. On the basis of model projections under a high-emission scenario, we find that the upwelling mechanisms will stay active in a warming climate, and these regions are likely to remain approximately more than 1°C cooler than surrounding waters until at least into the 2080s, providing thermal relief to corals. Identification and protection of these refugia may help facilitate reef survival and related biodiversity preservation by allowing their corals time to acclimatize and adapt and ultimately provide source populations to replenish the rest of the reef.

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Coral bleaching is occurring more frequently as the climate changes, with multiple mass mortality events recently recorded on the Great Barrier Reef. Thermal stress coupled with high irradiance have previously been shown to be primary causes for coral bleaching. Therefore, a reduction in either of these pressures could reduce coral stress and eventual bleaching. Herein, we report the early development of a novel technology capable of reducing the amount of light entering a water body by ~20% in open ocean conditions. This mono-particle “sun shield” consists of an ultra-thin monolayer material and reflective calcium carbonate particles. The monolayer enables spreading of the particles into a thin film across the water surface, with only small amounts of material needed: 7.1 g/m2. A numerical modelling case study of residence times and the build-up of reactive oxygen stress in corals showed that the successful application of a stable film over the Lizard Island reef flat could reduce the reactive oxygen stress to below bleaching levels across approximately 1.5 km2 of reef area. With further development, mono-particle films such as this have the potential to be deployed over at-risk coral reefs at relatively small scales during predicted heatwave conditions, potentially reducing the severity of bleaching on coral reefs.

Trichodesmium cells aggregate and form single trichomes or larger colonies and possess strong intracellular gas vesicles that generate strong positive buoyancy and facilitate the vertical migration of colonies. Trichodesmium is proposed to be an important source of nitrogen in the Great Barrier Reef (GBR) with implications for nutrient cycling and eutrophication. To understand the dynamics of Trichodesmium in the GBR ecosystem, reliable model predictions of Trichodesmium growth, nitrogen fixation and distribution are required. The sinking rates of Trichodesmium colonies have been reported to be dependent on the shape and size of colonies, and the orientation of colonies in seawater. Therefore, to better simulate the vertical movement of Trichodesmium in the GBR, and subsequent biogeochemical dynamics, the Trichodesmium processes in the eReefs biogeochemical model was modified by applying the form resistance factor to the sinking velocities of tuft-shaped Trichodesmium colonies. Our model results compare well with observations from the Australian Institute of Marine Science Marine Monitoring Program sensor network sites and capture the emergent patterns of phytoplankton size spectrum observed in nature. The modified model formulations improve the physiological realism of the Trichodesmium growth submodel of the eReefs marine biogeochemical models, and can help to improve the understanding of Trichodesmium dynamics for effective GBR water quality management.

Combining ecological field observations and mapping with model outputs is a powerful approach for understanding complex marine and coastal systems.In our study over three wet seasons, we used the eReefs 1 km resolution marine model to simulate the dispersal of diuron, a pesticide commonly found in river catchments that flow into the Great Barrier Reef (GBR) marine environment.By mapping the model outputs together with observed coastal coral reef and seagrass beds, we were able to determine the areas of the GBR, seagrass and coral where diuron plumes exceeded ecologically toxic concentrations (1400, 175 and 60 km2 respectively).This information can guide decision-making processes by producing a more comprehensive understanding of the catchment and ocean dynamics within the region.Moreover, marine model outputs using scenarios of agricultural runoff can be used to make predictions about potential changes such as increased pesticide use and its impact on ecologically sensitive areas.By providing a more complete understanding of complex ecological systems, this approach can help decision-makers make more informed decisions and better manage sediment, nutrient, and pesticide runoff from catchments.In addition, once ecologically vulnerable marine areas have been identified, models such as the eReefs marine model can be used to determine the best field site locations for monitoring and collecting ecological data.For example, models can predict where certain species are likely to occur and where river plumes converge, guiding the selection of field sites.By using models to guide field site selection, researchers can maximize the efficiency and location of their data collection efforts and obtain a more comprehensive understanding of the marine ecosystem.

Pesticides from urban and agricultural runoff have been detected at concentrations above current water quality guidelines in the Great Barrier Reef (GBR) marine environment. We quantify the load of the pesticide diuron entering GBR waters using the GBR-Dynamic SedNet catchment model. After comparison of simulated distributions with observations at 11 monitoring sites we determined a half-life of diuron in GBR marine waters of 40 days. We followed diuron dispersal in the GBR (2016-2018) using the 1 km resolution eReefs marine model. The highest diuron concentrations in GBR waters occurred in the Mackay-Whitsunday region with a spike in January and March 2017, associated with 126 and 118 kg d-1 diuron loads from Plane Creek and the O'Connell River respectively. We quantify areas of GBR waters exposed to potentially ecotoxic concentrations of diuron. Between 2016 and 2018, 400 km2 and 1400 km2 of the GBR were exposed to concentrations exceeding ecosystem threshold values of 0.43 and 0.075 μg L-1 respectively. Using observed mapped coral and seagrass habitat, 175 km2 of seagrass beds and 50 km2 of coral habitats had peak diuron concentrations above 0.075 μg L-1 during this period. While the highest concentrations are localised to river plumes and inshore environments, non-zero diuron concentrations extend along the Queensland coast. These simulations provide new knowledge for the understanding of pesticide dispersal and management-use in GBR catchments and the design of in-water monitoring systems.

Continental shelves are key to societal interactions with the oceans, supporting >90% of the world's fisheries through highly productive ecosystems. Previous research has shown that phytoplankton biomass is generally higher on the inner continental shelves, often due to increased nutrient inputs from upwelling or coastal run-off. However, consistency in observed vertical and horizontal gradients (in abundance, biomass or size) of larger particulates, including zooplankton, on continental shelves has not been established. Using an optical plankton counter and CTD mounted on an undulating towed body, we present high-resolution vertically resolved profiles of pelagic particle size structure across a continental shelf. Biomass was highest inshore, declining with distance from shore and with depth in the top 100 m of the water column, although the presence of frontal zones can alter this pattern. In the region adjacent to the East Australian Current (EAC), uplift generated by either the EAC interacting with the continental slope or upwelling-favorable winds, correlated with smaller geometric mean sizes and steeper size spectrum slopes, particularly in the presence of frontal features. South of the EAC separation, the continental shelf water mass was more homogenous but still displayed the same horizontal and vertical patterns in particulate biomass and mean size. By combining our observations in a global comparison, we demonstrate consistent particulate distributions on continental shelves where the inner shelf has higher biomass with a steeper size spectrum slope compared to offshore. The highly productive inner shelf supports zooplankton communities vital to temperate ecosystems and coastal fisheries, through their consistently high biomass. Plain Language Summary It is commonly accepted that chlorophyll a and phytoplankton are more abundant on continental shelves compared to the open ocean due to nutrient enrichment from either upwelling or terrestrial inputs. Little is known about the consistency in larger particulates, including zooplankton. We present the first depth resolved cross-shelf transects of zooplankton sized particulates. We show globally consistent patterns where close to the coast there is higher abundance and biomass, smaller geometric mean size and a steeper size spectrum slope representing a more productive community.

Trichodesmium can fix nitrogen that is later released into the water column. This process may be a major source of ‘new’ nitrogen in the Great Barrier Reef (GBR), but to date this contribution is poorly resolved. We have estimated the seasonal, spatial and annual contributions of Trichodesmium to the annual nitrogen budget of the GBR using the eReefs marine models. Models were run for the interval December 2010 to November 2012. During this period La Niña conditions produced record rainfalls and widespread flooding of GBR catchments. Model outputs suggest nitrogen fixation by Trichodesmium in the GBR (which covers about 348,000 km2) contributes approximately 0.5 MT/yr, exceeding the total average annual riverine nitrogen loads (0.05–0.08 MT/yr). Nitrogen fixation loads are exceeded by riverine loads only if the comparison is restricted to inshore waters and during the wet season. The river pollution is likely to have impacts in freshwater wetlands, mangroves, seagrasses and in-shore coral reefs; while Trichodesmium blooms are likely to be less intense but more widespread and affect offshore coral reefs and other oceanic ecosystems. Phosphorus and iron are suggested to be potential drivers of Trichodesmium growth and nitrogen fixation. This result is provisional but reinforces the need for more detailed assessment and reliable quantification of the annual nitrogen contribution from nitrogen fixation in the GBR and other coastal waters. Such advances will improve understandings of the role of terrestrial nitrogen loads in the GBR and of terrestrial phosphorus and iron loads which can modulate Trichodesmium abundance. These findings will help to broaden the focus of water quality management programmes and support management to improve GBR water quality.

ABSTRACTCumulative 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 >3,800 individual 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, corals declined by one third across the GBR, from an average ∼29% to ∼19% hard coral cover. By 2020, less than 20% of the GBR had coral cover higher than 30%. Global 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.

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 examples 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.

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 counterparts1 has achieved the status of an ecological paradigm. However, recent global assessments indicate global fish biomass could be much higher than previously thought2–4, 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 change6–8, and provide more-robust forecasts of nutrient9 and carbon cycling10.

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 individual pigment standards, including chlorophylls, caretonoids and phycobilins. The samples 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.

Improvements in physiological understanding, observational capabilities, and computational power have led modelers of phytoplankton in natural systems to represent more phytoplankton classes with better differentiated characteristics. In this chapter, we describe the key phytoplankton processes that are used to differentiate plankton, including phytoplankton absorption, photoadaptation, and elemental stoichiometry ratios. We then briefly survey model applications, in which resolving phytoplankton diversity matter are important: ocean-color, harmful algal blooms, carbon export to the deep ocean, as well as climate change-induced shifts in planktonic communities. Researchers are finding significant benefits from improved representation of phytoplankton types, so it is likely this work will continue to develop in the future.