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The recent widespread and recurrent coral bleaching events over the Great Barrier Reef, the largest coral reef system on Earth and a hotspot of marine biodiversity, are a reminder of the vulnerability of reef ecosystems to human activities and a warming world. Protection of the Great Barrier Reef and similar reef ecosystems across Oceania requires a better understanding of environmental and socio-economic pressures, as well as the development of integrated management strategies. The rapid expansion of Earth Observation technologies and data has greatly advanced our capability to map and monitor reef habitats, ecological processing and exposure risk, providing spatially rich data essential to support and evaluate management and conservation strategies. However, these technologies are proportionally still under-utilized, and it is important to synthesise remote-sensing-derived tools and methods currently available for mapping reef ecosystems in Oceania to facilitate their intake in coral reefs studies. Publications in this Special Issue contribute toward filling this gap and explore recent advances in remote sensing of the Great Barrier Reef and other reef ecosystems in Oceania, from novel methodological approaches (sensors, algorithm development and improved thematic classification) to applications for environmental monitoring and management. [ABSTRACT FROM AUTHOR]

Coral reefs provide important ecosystem services as well as economic and cultural benefits to society. Yet they are under significant threat from anthropogenic and natural threats, including climate change. Australia's Great Barrier Reef (GBR) is one such reef undergoing significant change. More radical interventions that go beyond traditional forms of management are being considered to help repair and restore the GBR. These are based on science and technologies that have yet to be widely tested. This paper reports on a study that seeks to identify and understand support for such interventions, and to understand the antecedents that explain support. The Norm Activation Model (NAM) was extended with a sample of 468 domestic and international tourists to Cairns, Australia. Personal norms had the largest direct influence on support for interventions, followed by attitudes. Awareness of consequences had a large positive impact on personal norms and a smaller positive impact on attitudes. A negative relationship was found between information and attitudes. Personal norms and attitudes also acted as mediators between awareness of consequences, information and support. No differences were found between domestic and international tourists. The results are discussed and theoretical and practical implications outlined. [ABSTRACT FROM AUTHOR]

Marine biodiversity and derived ecosystem services are critical to the healthy functioning of marine ecosystems, and to human economic and societal well-being. Thus, an understanding of marine biodiversity in different ecosystems is necessary for their conservation and management. Coral reefs in particular are noted for their high levels of biodiversity, and among the world's coral reefs, the subtropical Ryukyu Islands (RYS; also known as the Nansei Islands) in Japan have been shown to harbor very high levels of marine biodiversity. This study provides an overview of the state of marine biodiversity research in the RYS. First, we examined the amount of English language scientific literature in the Web of Science (WoS; 1995-2017) on six selected representative taxa spanning protists to vertebrates across six geographic sub-regions in the RYS. Our results show clear taxonomic and sub-region bias, with research on Pisces, Cnidaria, and Crustacea to be much more common than on Dinoflagellata, Echinodermata, and Mollusca. Such research was more commonly conducted in subregions with larger human populations (Okinawa, Yaeyama). Additional analyses with the Ocean Biogeographic Information System (OBIS) records show that within subregions, records are concentrated in areas directly around marine research stations and institutes (if present), further showing geographical bias within sub-regions. While not surprising, the results indicate a need to address 'understudied' taxa in 'understudied sub-regions' (Tokara, Miyako, Yakutane, Amami Oshima), particularly sub-regions away from marine research stations. Second, we compared the numbers of English language scientific papers on eight ecological topics for the RYS with numbers from selected major coral reef regions of the world; the Caribbean (CAR), Great Barrier Reef (GBR), and the Red Sea (RES). As expected, the numbers for all topics in the RYS were well below numbers from all other regions, yet within this disparity, research in the RYS on 'marine protected areas' and 'herbivory' was an order of magnitude lower than numbers in other regions. Additionally, while manuscript numbers on the RYS have increased from 1995 to 2016, the rate of increase (4.0 times) was seen to be lower than those in the CAR, RES, and GBR (4.6-8.4 times). Coral reefs in the RYS feature high levels of both endemism and anthropogenic threats, and subsequently they contain a concentration of some of the world's most critically endangered marine species. To protect these threatened species and coral reef ecosystems, more data are needed to fill the research gaps identified in this study. [ABSTRACT FROM AUTHOR]

Introduction: Natural resource management uses expert judgement to estimate facts that inform important decisions. Unfortunately, expert judgement is often derived by informal and largely untested protocols, despite evidence that the quality of judgements can be improved with structured approaches. We attribute the lack of uptake of structured protocols to the dearth of illustrative examples that demonstrate how they can be applied within pressing time and resource constraints, while also improving judgements. Aims and methods: In this paper, we demonstrate how the IDEA protocol for structured expert elicitation may be deployed to overcome operational challenges while improving the quality of judgements. The protocol was applied to the estimation of 14 future abiotic and biotic events on the Great Barrier Reef, Australia. Seventy-six participants with varying levels of expertise related to the Great Barrier Reef were recruited and allocated randomly to eight groups. Each participant provided their judgements using the four-step question format of the IDEA protocol (‘Investigate’, ‘Discuss’, ‘Estimate’, ‘Aggregate’) through remote elicitation. When the events were realised, the participant judgements were scored in terms of accuracy, calibration and informativeness. Results and conclusions: The results demonstrate that the IDEA protocol provides a practical, cost-effective, and repeatable approach to the elicitation of quantitative estimates and uncertainty via remote elicitation. We emphasise that i) the aggregation of diverse individual judgements into pooled group judgments almost always outperformed individuals, and ii) use of a modified Delphi approach helped to remove linguistic ambiguity, and further improved individual and group judgements. Importantly, the protocol encourages review, critical appraisal and replication, each of which is required if judgements are to be used in place of data in a scientific context. The results add to the growing body of literature that demonstrates the merit of using structured elicitation protocols. We urge decision-makers and analysts to use insights and examples to improve the evidence base of expert judgement in natural resource management. [ABSTRACT FROM AUTHOR]

Adaptation, as a strategy to respond to climate change, has limits: there are conditions under which adaptation strategies fail to alleviate impacts from climate change. Research has primarily focused on identifying absolute bio-physical limits. This paper contributes empirical insight to an emerging literature on the social limits to adaptation. Such limits arise from the ways in which societies perceive, experience and respond to climate change. Using qualitative data from multi-stakeholder workshops and key-informant interviews with representatives of the fisheries and tourism sectors of the Great Barrier Reef region, we identify psycho-social and structural limits associated with key adaptation strategies, and examine how these are perceived as more or less absolute across levels of organisation. We find that actors experience social limits to adaptation when: i) the effort of pursuing a strategy exceeds the benefits of desired adaptation outcomes; ii) the particular strategy does not address the actual source of vulnerability, and; iii) the benefits derived from adaptation are undermined by external factors. We also find that social limits are not necessarily more absolute at higher levels of organisation: respondents perceived considerable opportunities to address some psycho-social limits at the national-international interface, while they considered some social limits at the local and regional levels to be effectively absolute. [ABSTRACT FROM AUTHOR]

Abstract The dynamics of nutrients, phytoplankton, zooplankton and water clarity of the iconic Great Barrier Reef World Heritage Area (GBRWHA) are influenced by seasonal variation in coastal and oceanic conditions, and anthropogenic inputs. We use the 3-dimensional coupled catchment-hydrodynamic-sediment-wave-optical-biogeochemical eReefs model to hindcast nutrient and planktonic responses to changes in seasonal and annual variability over a six-year period (2011–2016). In this paper we present a comparison of the eReefs model conducted against a range of in situ observations that included 24 water quality moorings, 2 nutrient sampling programs (with a total of 18 stations) and time-series of taxon-specific plankton abundance. At 14 near-coastal stations the simulated chlorophyll a (Chl a), when compared with chlorophyll extractions from water samples, had an average root mean square (RMS) error of 0.30 mg m−3 and a Willmott index of 0.59. For the same sites, simulated turbidity, when compared with turbidity sensors, had a Willmott index of 0.58 and simulated nitrate + nitrite had a Willmott index of 0.41 when compared with tri-annual water samples. Comparison with a spatially-resolved statistical model of zooplankton based on >900 observations in the region showed similarities in the relationship and spatial distribution of simulated and observed biomass, where both show zooplankton biomass is greatest inshore, biomass is highest around shallow reef areas and in the southern and central GBRWHA, and greater in summer than winter. Additionally, we investigate planktonic and nutrient responses to climatic variation. The first two years of the simulation coincided with La Niña events that drive greater than average winds, rainfall and river discharge. Throughout all years, simulated Chl a increases from north to south and from outer to inner coastal regions. Dissolved inorganic nitrogen, primary production and phytoplankton biomass were higher during La Niña in inshore and mid-shelf waters, while offshore regions were similar in all years from 2011 to 2016. Simulated Secchi depth was deeper offshore and decreased from offshore to inner coastal regions and from north to south. The eReefs simulation contributes to the understanding at a high spatial and temporal resolution of where and how nutrients and plankton originate and interact within the Great Barrier Reef. Highlights • Use of a 3D-catchment-hydrodynamic-sediment-wave-optical-biogeochemical model • Model encompasses the 2300 km long Great Barrier Reef from coast to Coral Sea. • Comparison of observations with simulated plankton & nutrients • Observations include remote sensing, moorings and water samples. • Simulated nutrients and plankton show realistic seasonal and interannual variation. [ABSTRACT FROM AUTHOR]

Gnathia antennacrassa sp. nov. from seagrass beds off Rottnest Island, Western Australia is the first record of any gnathiid from the entirety of Western Australia; the male can be distinguished from congeners by the stout peduncular articles of the antenna. Gnathia taurus sp. nov. is described from two adult specimens reared from praniza larvae found infecting elasmobranch fishes at Heron Island, southern Great Barrier Reef; the males can be distinguished from all congeners by the dorsally strongly elongate mandibles and smoothly rounded mediofrontal process on the anterior part of cephalosome. Gnathia aff. maculosa Ota & Hirose, 2009 is recorded from Australia, together with further records of G. trimaculata Coetzee, Smit, Grutter & Davies, 2009 and G. grandilaris Coetzee, Smit, Grutter & Davies, 2008, all from elasmobranch fishes. [ABSTRACT FROM AUTHOR]

Universal Adaptive Strategy Theory aims to predict how taxa and assemblages respond to disturbances on the basis of adaptive strategy group (ASG) membership. Here, we test such predictions using the adaptive strategy scheme for reef-building corals developed by Darling et al. (Ecol Lett 15:1378–1386, 2012) and a long-term dataset of coral assemblage structure from inshore reefs on the central Great Barrier Reef. Several disturbances including mass bleaching and tropical storms were recorded in this 15-year interval from 1998 to 2013. ASG membership did not predict how a given taxon responded to disturbance. In fact, all ASGs were on average equally affected by bleaching and a period of multiple disturbances. Furthermore, there were no consistent winners at these sites in response to the 1998 bleaching in contrast to previous work suggesting clear hierarchies in susceptibility to bleaching. In conclusion, while further efforts to re-evaluate the utility of ASGs for reef corals should be encouraged our results and a re-examination of the literature suggests that direct trait-based approaches might prove more useful when exploring how corals respond to disturbance. [ABSTRACT FROM AUTHOR]

Coral reef ecosystems are expected to undergo significant declines over the coming decades as oceans become warmer and more acidic. We investigate the environmental tolerances of over 650 Scleractinian coral species based on the conditions found within their present‐day ranges and in areas where they are currently absent but could potentially reach via larval dispersal. These "environmental envelopes" and connectivity constraints are then used to develop global forecasts for potential coral species richness under two emission scenarios, representing the Paris Agreement target ("SSP1‐2.6") and high levels of emissions ("SSP5‐8.5"). Although we do not directly predict coral mortality or adaptation, the projected changes to environmental suitability suggest considerable declines in coral species richness for the majority of the world's tropical coral reefs, with a net loss in average local richness of 73% (Paris Agreement) to 91% (High Emissions) by 2080–2090 and particularly large declines across sites in the Great Barrier Reef, Coral Sea, Western Indian Ocean, and Caribbean. However, at the regional scale, we find that environmental suitability for the majority of coral species can be largely maintained under the Paris Agreement target, with 0%–30% potential net species lost in most regions (increasing to 50% for the Great Barrier Reef) as opposed to 80%–90% losses under High Emissions. Projections for subtropical areas suggest that range expansion will give rise to coral reefs with low species richness (typically 10–20 coral species per region) and will not meaningfully offset declines in the tropics. This work represents the first global projection of coral species richness under oceanic warming and acidification. Our results highlight the critical importance of mitigating climate change to avoid potentially massive extinctions of coral species. [ABSTRACT FROM AUTHOR]

Natural bleaching events provide an opportunity to examine how local‐scale environmental variation influences bleaching severity and recovery. During the 2020 marine heat wave, we documented widespread and severe coral bleaching affecting 75%–98% of coral cover throughout the Keppel Islands in the southern inshore Great Barrier Reef. Acropora, Pocillopora, and Porites were the most severely affected genera, while Montipora was comparatively less susceptible. Site‐specific heat‐exposure metrics were not correlated with Acropora bleaching severity, but recovery was faster at sites that experienced lower heat exposure. Despite severe bleaching and exposure to accumulated heat that often results in coral mortality (degree heating weeks ~4–8), cover remained stable. Approximately 94% of fate‐tracked Acropora millepora colonies survived, perhaps due to reduced irradiance stress from high turbidity, heterotrophic feeding, and large tidal flows that can increase mass transfer. Severe bleaching followed by rapid recovery and the continuing dominance of Acropora populations in the Keppel Islands is indicative of high resilience. These coral communities have survived a 0.8°C increase in average temperatures over the last 150 years. However, recovery following the 2020 bleaching was driven by the easing of thermal stress, which may challenge their recovery potential under further warming. [ABSTRACT FROM AUTHOR]

A prevailing hypothesis of microbial biogeography holds that all species are ubiquitous, but this may lead to fitting Pacific specimens into European taxa on the basis of light microscopy. There is now evidence of regional endemicity in freshwater diatoms in Australia and recent studies have shown large diversity in the Guam marine Licmophora flora. The aim was to compare Australian samples with Guam Licmophora spp., especially their girdle bands. Valves and girdle bands from samples collected from Australia and Micronesia were described from observations made via light and scanning-electron microscopy. Of the nine species present in Australian samples, six were previously undescribed. Species with unusual characters included Licmophora insolita Lobban & Emm.S.Santos sp. nov. with a novel location for the apical rimoportula and a Tharngan strip on the valvocopula; Licmophora ballerina Lobban & S.Blanco sp. nov., with distinctive 3rd and 4th pleurae; and the licmosphenioid Licmophora johnwestii Lobban & Emm.S.Santos sp. nov. Specimens resembling Licmophora debilis (Kütz.) Grunow and L. abbreviata C.Agardh, described from Europe, occurred in Great Barrier Reef samples. The study brings the Guam flora to 20 novel v. 2 matching Atlantic–European taxa. The proportion of new to known species in Australian and Guam samples suggests regional endemicity, at least being broadly different from European Licmophora floras. Whereas one expects to see different land plants and animals in different places, the 'everything-is-everywhere' hypothesis of microbial biogeography, e.g. unicellular algae, tends to become a self-fulfilling prophesy. We found a high proportion of new species in our samples. This is evidence for regional endemicity in marine diatoms, i.e. that the Licmophora flora(s) in eastern Australia and Guam are different from the European floras on which identification is often based. [ABSTRACT FROM AUTHOR]

Tropical cyclones generate large waves that physically damage coral communities and are commonly cited as a worsening threat to coral reefs under climate change. However, beyond projections of ocean basin‐scale changes in cyclone intensity, the other determinants of future coral reef damage such as cyclone size and duration remain uncertain. Here, we determine the extent to which downscaled cyclones represent observed cyclone characteristics that influence wave damage to Australian coral reef regions. We then investigate mid‐century (2040–2060) and end of century (2080–2100) downscaled tracks to assess whether cyclone characteristics will change with future warming under a high‐emissions scenario. We find that spatial uncertainties in downscaled cyclogenesis and track positions limit estimates of reef damage for individual coral reefs and regions. Further, the models are unable to reproduce the most reef damaging cyclones for any of the regions. The downscaled tracks capture observed cyclone characteristics, such as size, impacting the Great Barrier Reef well, but perform poorly for the Northern Territory, with mixed performance for the Coral Sea and Western Australia. We find no clear evidence that cyclones will cause more damage to Australian coral reef regions in the future, at least based on the climate models and downscaling approach examined here. There is increasing interest in using tropical cyclone projections to assess future coral reef exposure to damaging waves. We recommend caution when interpreting such projections due to large uncertainty in the mechanisms that influence reef damaging tropical cyclone characteristics and how these will change with future warming. Plain Language Summary: Tropical cyclone intensity, size and duration together determine the extent to which their waves damage coral reefs. Increased tropical cyclone intensity with climate change is often cited as evidence that tropical cyclones will cause more damage to coral reefs in the future but changes to size and duration remain uncertain. Here, we determine whether tropical cyclones simulated from climate models can represent the observed tropical cyclone characteristics that are important for estimating wave damage to coral reefs and assess how these characteristics might change in the future. We find that the tropical cyclones simulated from climate models capture the observed cyclone characteristics well for those impacting the Great Barrier Reef (with the exception of the most damaging cyclones) with mixed to poor performance for other regions. The projections of future reef damage are uncertain with some models projecting increases and others decreases. Tropical cyclone projections are used in conservation planning to identify and protect the coral reefs least exposed to future tropical cyclones. However, we find that the simulated tropical cyclone tracks explored here are unlikely to represent future reef damaging tropical cyclone characteristics well if used in conservation decision making. Key Points: Wave damage to coral communities from tropical cyclones depends on their intensity, size and duration while tracking near coral reefsDownscaled tracks capture observed cyclone characteristics impacting the Great Barrier Reef with mixed to poor performance in other regionsProjections vary by region and cyclone characteristic with some models projecting increases and others decreases in future reef damage [ABSTRACT FROM AUTHOR]

Inshore marine seascapes support a diversity of interconnected habitats and are an important focus for biodiversity conservation. This study examines the importance of habitat attributes to fish assemblages across a mosaic of inshore habitats: coral reefs, rocky reefs, macroalgae beds and sand/rubble beds. Fishes and benthic habitats were surveyed at 34 sites around continental islands of the central Great Barrier Reef using baited remote underwater video stations (BRUVS). Species richness was influenced foremost by habitat type and also by structural complexity within habitat types. The most speciose assemblages occurred in coral and rocky reef habitats with high structural complexity, provided by the presence of coral bommies/overhangs, boulders and rock crevices. Nonetheless, macroalgae and sand/rubble beds also supported unique species, and therefore contributed to the overall richness of fish assemblages in the seascape. Most trophic groups had positive associations with complexity, which was the most important predictor for abundance of piscivorous fishes and mobile planktivores. There was significant differentiation of fish assemblages among habitats, with the notable exception of coral and rocky reefs. Species assemblages overlapped substantially between coral and rocky reefs, which had 60% common species, despite coral cover being lower on rocky reefs. This suggests that, for many species, rocky and coral substrates can provide equivalent habitat structure, emphasizing the importance of complexity in providing habitat refuges, and highlighting the contribution of rocky reefs to habitat provision within tropical seascapes. The results of this study support an emerging recognition of the collective value of habitat mosaics in inshore marine ecosystems. [ABSTRACT FROM AUTHOR]

Estimating the impact of environmental processes on vertical reef development in geological time is a very challenging task. pyReef-Core is a deterministic carbonate stratigraphic forward model designed to simulate the key biological and environmental processes that determine vertical reef accretion and assemblage changes in fossil reef drill cores. We present a Bayesian framework called Bayesreef for the estimation and uncertainty quantification of parameters in pyReef-Core that represent environmental conditions affecting the growth of coral assemblages in geological timescales. Weencounter multimodal posterior distributions and investigate the challenges of sampling using Markov chain Monte-Carlo (MCMC) methods, which includes parallel tempering MCMC. We use a synthetic reef-core to investigate fundamental issues and then apply the methodology to a selected reef-core from the Great Barrier Reef in Australia. The results show that Bayesreef accurately estimates and provides uncertainty quantification of the selected parameters that represent environment and ecological conditions in pyReef-Core. Bayesreef provides insights into the complex posterior distributions of the parameters in pyReef-Core , which provides the groundwork for future research in this area. • Estimating the impact of environmental processes on vertical reef development in geological time is a very challenging task. • pyReef-Core is a deterministic carbonate stratigraphic forward model designed to simulate the key biological and environmental processes. • This paper presents Bayesreef for the estimation and uncertainty quantification of parameters in pyReef-Core. • The results show that Bayesreef accurately estimates and provides uncertainty quantification for parameters in pyReef-Core. • Bayesreef provides insights in of pyReef-Core and establishes the groundwork for future research. [ABSTRACT FROM AUTHOR]

We review the evidence for bio-regulation by coral reefs of local climate through stress-induced emissions of aerosol precursors, such as dimethylsulfide. This is an issue that goes to the core of the coral ecosystem's ability to maintain homeostasis in the face of increasing climate change impacts and other anthropogenic pressures. We examine this through an analysis of data on aerosol emissions by corals of the Great Barrier Reef, Australia. We focus on the relationship with local stressors, such as surface irradiance levels and sea surface temperature, both before and after notable coral bleaching events. We conclude that coral reefs may be able to regulate their exposure to environmental stressors through modification of the optical properties of the atmosphere, however this ability may be impaired as climate change intensifies. [ABSTRACT FROM AUTHOR]

Ocean warming threatens the functioning of coral reef ecosystems by inducing mass coral bleaching and mortality events. The link between temperature and coral bleaching is now well-established based on observations that mass bleaching events usually occur when seawater temperatures are anomalously high. However, times of high heat stress but without coral bleaching are equally important because they can inform an understanding of factors that regulate temperature-induced bleaching. Here, we investigate the absence of mass coral bleaching on the Great Barrier Reef (GBR) during austral summer 2004. Using four gridded sea surface temperature data products, validated with in situ temperature loggers, we demonstrate that the summer of 2004 was among the warmest summers of the satellite era (1982-2017) on the GBR. At least half of the GBR experienced temperatures that were high enough to initiate bleaching in other years, yet mass bleaching was not reported during 2004. The absence of bleaching is not fully explained by wind speed or cloud cover. Rather, 2004 is clearly differentiated from bleaching years by the slow speed of the East Australian Current (EAC) offshore of the GBR. An anomalously slow EAC during summer 2004 may have dampened the upwelling of nutrient-rich waters onto the GBR shelf, potentially mitigating bleaching due to the lower susceptibility of corals to heat stress in low-nutrient conditions. Although other factors such as irradiance or acclimatization may have played a role in the absence of mass bleaching, 2004 remains a key case study for demonstrating the dynamic nature of coral responses to marine heatwaves. [ABSTRACT FROM AUTHOR]

Predation on parasites is an important ecological process, but few experimental studies have examined the long-term impacts on the prey. Cleaner fish prey upon large numbers and selectively feed on the larger individuals of the ectoparasitic stage of gnathiid isopods. Removal of cleaner fish Labroides dimidiatus for 1.5–12.5 years negatively affects coral reef fishes, but the mechanism is unclear. A reduction in local parasite populations or the size of individual parasites would benefit all susceptible fishes. We tested whether cleaner presence reduces local gnathiid populations using 18 patch-reefs distributed between two sites (both at Lizard Island, Great Barrier Reef) which were maintained cleaner-free or undisturbed for 12 years. Using emergence traps (1 m2), free-living gnathiid stages were sampled before and after cleaner fish were removed during the day and night, up to 11 times over the course of the experiment. There were effects of the removal in the predicted direction, driven largely by the response at one site over the other involving 200% more gnathiids, but manifested only in the daytime sampling after 4 months. There was also a main effect (36%) for the shared sample dates at both sites after 12 years. Gnathiid size occasionally differed with cleaner presence, but in no consistent way over time. Contrary to our predictions, changes in free-living gnathiid population numbers and their size structure rarely reflected the changes in fish populations and individuals observed on cleaner-free reefs. Therefore, evidence that this predator alone regulates gnathiids remains limited, suggesting other contributing processes are involved. [ABSTRACT FROM AUTHOR]

Trichodesmium, a filamentous bloom-forming marine cyanobacterium, plays a key role in the biogeochemistry of oligotrophic ocean regions because of the ability to fix nitrogen. Naturally occurring in the Great Barrier Reef (GBR), the contribution of Trichodesmium to the nutrient budget may be of the same order as that entering the system via catchment runoff. However, the cyclicity of Trichodesmium in the GBR is poorly understood and sparsely documented because of the lack of sufficient observations. This study provides the first systematic analysis of Trichodesmium spatial and temporal occurrences in the GBR over the decade-long MERIS ocean color mission (2002–2012). Trichodesmium surface expressions were detected using the Maximum Chlorophyll Index (MCI) applied to MERIS satellite imagery of the GBR lagoonal waters. The MCI performed well (76%), albeit tested on a limited set of images (N = 25) coincident with field measurements. A north (Cape York) to south (Fitzroy) increase in the extent, frequency and timing of the surface expressions characterized the GBR, with surface expressions extending over several hundreds of kilometers. The two southernmost subregions Mackay and Fitzroy accounted for the most (70%) bloom events. The bloom timing of Trichodesmium varied from May in the north to November in the south, with wet season conditions less favorable to Trichodesmium aggregations. MODIS-Aqua Sea Surface Temperature (SST) datasets, wind speed and field measurements of nutrient concentrations were used in combination with MCI positive instances to assess the blooms’ driving factors. Low wind speed (<6 m.s-1) and SST > 24°C were associated with the largest surface aggregations. Generalized additive models (GAM) indicated an increase in bloom occurrences over the 10-year period with seasonal bloom patterns regionally distinct. Interannual variability in SST partially (14%) explained bloom occurrences, and other drivers, such as the subregion and the nutrient budget, likely regulate Trichodesmium surface aggregations in the GBR. [ABSTRACT FROM AUTHOR]

Synchronised multispecies mass spawning events are striking features of reproduction in corals. This synchronous gamete release of thousands of animals over vast stretches of reef is thought to be cued by rhythms of the Moon. However, the mechanisms are not fully understood. We propose an explanation that may contribute to understanding this mechanism, that spawning is triggered by the coincidence of two factors, each in different lunar rhythms. We investigate this proposal in case studies using seven years of coral spawning data from two locations: Kochi, Japan and Lizard Island, Australia. Our calculations show that a feature in a lunar synodic rhythm (the third quarter) will synchronise with a feature in a lunar non-synodic rhythm (the zero declination) usually once, although occasionally twice in a year. Supported by data on the date of spawning from the two locations, we suggest that this coincidence of lunar factors exerts an important influence on the timing of annual mass spawning in corals. This coincidence may be associated with low atmospheric pressure. Spawning at the time of the third lunar quarter may favour fertilisation success due to the reduced currents during neap tides associated with the lower gravitational pressure of the lunar quarters. [ABSTRACT FROM AUTHOR]

Coral reefs are increasingly degraded by climate-induced bleaching and storm damage. Reef recovery relies on recruitment of young fishes for the replenishment of functionally important taxa. Acoustic cues guide the orientation, habitat selection, and settlement of many fishes, but these processes may be impaired if degradation alters reef soundscapes. Here, we report spatiotemporally matched evidence of soundscapes altered by degradation from recordings taken before and after recent severe damage on Australia's Great Barrier Reef. Postdegradation soundscapes were an average of 15 dB re 1 μPa quieter and had significantly reduced acoustic complexity, richness, and rates of invertebrate snaps compared with their predegradation equivalents. We then used these matched recordings in complementary light-trap and patch-reef experiments to assess responses of wild fish larvae under natural conditions. We show that postdegradation soundscapes were 8% less attractive to presettlement larvae and resulted in 40%less settlement of juvenile fishes than predegradation soundscapes; postdegradation soundscapes were no more attractive than open-ocean sound. However, our experimental design does not allow an estimate of how much attraction and settlement to isolated postdegradation soundscapes might change compared with isolated predegradation soundscapes. Reductions in attraction and settlement were qualitatively similar across and within all trophic guilds and taxonomic groups analyzed. These patterns may lead to declines in fish populations, exacerbating degradation. Acoustic changes might therefore trigger a feedback loop that could impair reef resilience. To understand fully the recovery potential of coral reefs, we must learn to listen. [ABSTRACT FROM AUTHOR]

Australia’s iconic Great Barrier Reef (GBR) continues to suffer from repeated impacts of cyclones, coral bleaching, and outbreaks of the coral-eating crown-of-thorns starfish (COTS), losing much of its coral cover in the process. This raises the question of the ecosystem’s systemic resilience and its ability to rebound after large-scale population loss. Here, we reveal that around 100 reefs of the GBR, or around 3%, have the ideal properties to facilitate recovery of disturbed areas, thereby imparting a level of systemic resilience and aiding its continued recovery. These reefs (1) are highly connected by ocean currents to the wider reef network, (2) have a relatively low risk of exposure to disturbances so that they are likely to provide replenishment when other reefs are depleted, and (3) have an ability to promote recovery of desirable species but are unlikely to either experience or spread COTS outbreaks. The great replenishment potential of these ‘robust source reefs’, which may supply 47% of the ecosystem in a single dispersal event, emerges from the interaction between oceanographic conditions and geographic location, a process that is likely to be repeated in other reef systems. Such natural resilience of reef systems will become increasingly important as the frequency of disturbances accelerates under climate change. [ABSTRACT FROM AUTHOR]

The presence of banding in the skeleton of coralline algae has been reported in many species, primarily from temperate and polar regions. Similar to tree rings, skeletal banding can provide information on growth rate, age, and longevity; as well as records of past environmental conditions and the coralline alga’s growth responses to such changes. The aim of this study was to explore the presence and characterise the nature of banding in the tropical coralline alga Porolithon onkodes, an abundant and key reef-building species on the Great Barrier Reef (GBR) Australia, and the Indo-Pacific in general. To achieve this we employed various methods including X-ray diffraction (XRD) to determine seasonal mol% magnesium (Mg), mineralogy mapping to investigate changes in dominant mineral phases, scanning electron microscopy–electron dispersive spectroscopy (SEM-EDS), and micro-computed tomography (micro-CT) scanning to examine changes in cell size and density banding, and UV light to examine reproductive (conceptacle) banding. Seasonal variation in the Mg content of the skeleton did occur and followed previously recorded variations with the highest mol% MgCO3 in summer and lowest in winter, confirming the positive relationship between seawater temperature and mol% MgCO3. Rows of conceptacles viewed under UV light provided easily distinguishable bands that could be used to measure vertical growth rate (1.4 mm year-1) and age of the organism. Micro-CT scanning showed obvious banding patterns in relation to skeletal density, and mineralogical mapping revealed patterns of banding created by changes in Mg content. Thus, we present new evidence for seasonal banding patterns in the tropical coralline alga P. onkodes. This banding in the P. onkodes skeleton can provide valuable information into the present and past life history of this important reef-building species, and is essential to assess and predict the response of these organisms to future climate and environmental changes. [ABSTRACT FROM AUTHOR]

The broad range in physiological variation displayed by Symbiodinium spp. has proven imperative during periods of environmental change and contribute to the survival of their coral host. Characterizing how host and Symbiodinium community assemblages differ across environmentally distinct habitats provides useful information to predict how corals will respond to major environmental change. Despite the extensive characterizations of Symbiodinium diversity found amongst reef cnidarians on the Great Barrier Reef (GBR) substantial biogeographic gaps exist, especially across inshore habitats. Here, we investigate Symbiodinium community patterns in invertebrates from inshore and mid-shelf reefs on the southern GBR, Australia. Dominant Symbiodinium types were characterized using denaturing gradient gel electrophoresis fingerprinting and sequencing of the ITS2 region of the ribosomal DNA. Twenty one genetically distinct Symbiodinium types including four novel types were identified from 321 reef-invertebrate samples comprising three sub-generic clades (A, C, and D). A range of host genera harbored C22a, which is normally rare or absent from inshore or low latitude reefs in the GBR. Multivariate analysis showed that host identity and sea surface temperature best explained the variation in symbiont communities across sites. Patterns of changes in Symbiodinium community assemblage over small geographic distances (100s of kilometers or less) indicate the likelihood that shifts in Symbiodinium distributions and associated host populations, may occur in response to future climate change impacting the GBR. [ABSTRACT FROM AUTHOR]

Sedimentation is considered the most widespread contemporary, human-induced perturbation on reefs, and yet if the problems associated with its estimation using sediment traps are recognized, there have been few reliable measurements made over time frames relevant to the local organisms. This study describes the design, calibration and testing of an in situ optical backscatter sediment deposition sensor capable of measuring sedimentation over intervals of a few hours. The instrument has been reconfigured from an earlier version to include 15 measurement points instead of one, and to have a more rugose measuring surface with a microtopography similar to a coral. Laboratory tests of the instrument with different sediment types, colours, particle sizes and under different flow regimes gave similar accumulation estimates to SedPods, but lower estimates than sediment traps. At higher flow rates (9-17 cm s), the deposition sensor and SedPods gave estimates >10× lower than trap accumulation rates. The instrument was deployed for 39 d in a highly turbid inshore area in the Great Barrier Reef. Sediment deposition varied by several orders of magnitude, occurring in either a relatively uniform (constant) pattern or a pulsed pattern characterized by short-term (4-6 h) periods of 'enhanced' deposition, occurring daily or twice daily and modulated by the tidal phase. For the whole deployment, which included several very high wind events and suspended sediment concentrations (SSCs) >100 mg L, deposition rates averaged 19 ± 16 mg cm d. For the first half of the deployment, where SSCs varied from <1 to 28 mg L which is more typical for the study area, the deposition rate averaged only 8 ± 5 mg cm d. The capacity to measure sedimentation rates over a few hours is discussed in terms of examining the risk from sediment deposition associated with catchment run-off, natural wind/wave events and dredging activities. [ABSTRACT FROM AUTHOR]

Ocean warming under climate change threatens coral reefs directly, through fatal heat stress to corals and indirectly, by boosting the energy of cyclones that cause coral destruction and loss of associated organisms. Although cyclone frequency is unlikely to rise, cyclone intensity is predicted to increase globally, causing more frequent occurrences of the most destructive cyclones with potentially severe consequences for coral reef ecosystems. While increasing heat stress is considered a pervasive risk to coral reefs, quantitative estimates of threats from cyclone intensification are lacking due to limited data on cyclone impacts to inform projections. Here, using extensive data from Australia's Great Barrier Reef ( GBR), we show that increases in cyclone intensity predicted for this century are sufficient to greatly accelerate coral reef degradation. Coral losses on the outer GBR were small, localized and offset by gains on undisturbed reefs for more than a decade, despite numerous cyclones and periods of record heat stress, until three unusually intense cyclones over 5 years drove coral cover to record lows over >1500 km. Ecological damage was particularly severe in the central-southern region where 68% of coral cover was destroyed over >1000 km, forcing record declines in the species richness and abundance of associated fish communities, with many local extirpations. Four years later, recovery of average coral cover was relatively slow and there were further declines in fish species richness and abundance. Slow recovery of community diversity appears likely from such a degraded starting point. Highly unusual characteristics of two of the cyclones, aside from high intensity, inflated the extent of severe ecological damage that would more typically have occurred over 100s of km. Modelling published predictions of future cyclone activity, the likelihood of more intense cyclones within time frames of coral recovery by mid-century poses a global threat to coral reefs and dependent societies. [ABSTRACT FROM AUTHOR]

The crown-of-thorns starfish Acanthaster planci (COTS) has contributed greatly to declines in coral cover on Australia’s Great Barrier Reef, and remains one of the major acute disturbances on Indo-Pacific coral reefs. Despite uncertainty about the underlying causes of outbreaks and the management responses that might address them, few studies have critically and directly compared competing hypotheses. This study uses qualitative modelling to compare hypotheses relating to outbreak initiation, explicitly considering the potential role of positive feedbacks, elevated nutrients, and removal of starfish predators by fishing. When nutrients and fishing are considered in isolation, the models indicate that a range of alternative hypotheses are capable of explaining outbreak initiation with similar levels of certainty. The models also suggest that outbreaks may be caused by multiple factors operating simultaneously, rather than by single proximal causes. As the complexity and realism of the models increased, the certainty of outcomes decreased, but key areas that require further research to improve the structure of the models were identified. Nutrient additions were likely to result in outbreaks only when COTS larvae alone benefitted from nutrients. Similarly, the effects of fishing on the decline of corals depended on the complexity of interactions among several categories of fishes. Our work suggests that management approaches which seek to be robust to model structure uncertainty should allow for multiple potential causes of outbreaks. Monitoring programs can provide tests of alternative potential causes of outbreaks if they specifically monitor all key taxa at reefs that are exposed to appropriate combinations of potential causal factors. [ABSTRACT FROM AUTHOR]

Studies on the population and community dynamics of scleractinian corals typically focus on catastrophic mortality associated with acute disturbances (e.g., coral bleaching and outbreaks of crown-of-thorns starfish), though corals are subject to high levels of background mortality and injuries caused by routine and chronic processes. This study quantified prevalence (proportion of colonies with injuries) and severity (areal extent of injuries on individual colonies) of background mortality and injuries for four common coral taxa (massive Porites, encrusting Montipora, Acropora hyacinthus and branching Pocillopora) on the Great Barrier Reef, Australia. Sampling was conducted over three consecutive years during which there were no major acute disturbances. A total of 2276 adult colonies were surveyed across 27 sites, within nine reefs and three distinct latitudinal sectors. The prevalence of injuries was very high (>83%) across all four taxa, but highest for Porites (91%) and Montipora (85%). For these taxa ( Montipora and Pocillopora), there was also significant temporal and spatial variation in prevalence of partial mortality. The severity of injuries ranged from 3% to more than 80% and varied among coral taxa, but was fairly constant spatially and temporally. This shows that some injuries have considerable longevity and that corals may invest relatively little in regenerating tissue over sites of previous injuries. Inter-colony variation in the severity of injury also had no apparent effect on the realized growth of individual colonies, suggesting that energy diverted to regeneration has a limited bearing on overall energetic allocation, or impacts on other life-history processes (e.g., reproduction) rather than growth. Establishing background levels of injury and regeneration is important for understanding energy investment and life-history consequences for reef-building corals as well as for predicting susceptibility to, and capacity to recover from, acute disturbances. [ABSTRACT FROM AUTHOR]

Large tropical and sub-tropical marine animals must meet their energetic requirements in a largely oligotrophic environment. Many planktivorous elasmobranchs, whose thermal ecologies prevent foraging in nutrient-rich polar waters, aggregate seasonally at predictable locations throughout tropical oceans where they are observed feeding. Here we investigate the foraging and oceanographic environment around Lady Elliot Island, a known aggregation site for reef manta rays Manta alfredi in the southern Great Barrier Reef. The foraging behaviour of reef manta rays was analysed in relation to zooplankton populations and local oceanography, and compared to long-term sighting records of reef manta rays from the dive operator on the island. Reef manta rays fed at Lady Elliot Island when zooplankton biomass and abundance were significantly higher than other times. The critical prey density threshold that triggered feeding was 11.2 mg m-3 while zooplankton size had no significant effect on feeding. The community composition and size structure of the zooplankton was similar when reef manta rays were feeding or not, with only the density of zooplankton changing. Higher zooplankton biomass was observed prior to low tide, and long-term (~5 years) sighting data confirmed that more reef manta rays are also observed feeding during this tidal phase than other times. This is the first study to examine prey availability at an aggregation site for reef manta rays and it indicates that they feed in locations and at times of higher zooplankton biomass. [ABSTRACT FROM AUTHOR]

River runoff and associated flood plumes (hereafter river plumes) are a major source of land-sourced contaminants to the marine environment, and are a significant threat to coastal and marine ecosystems worldwide. Remote sensing monitoring products have been developed to map the spatial extent, composition and frequency of occurrence of river plumes in the Great Barrier Reef (GBR), Australia. There is, however, a need to incorporate these monitoring products into Risk Assessment Frameworks as management decision tools. A simple Satellite Risk Framework has been recently proposed to generate maps of potential risk to seagrass and coral reef ecosystems in the GBR focusing on the Austral tropical wet season. This framework was based on a "magnitude × likelihood" risk management approach and GBR plume water types mapped from satellite imagery. The GBR plume water types (so called "Primary" for the inshore plume waters, "Secondary" for the midshelf-plume waters and "Tertiary" for the offshore plume waters) represent distinct concentrations and combinations of land-sourced and marine contaminants. The current study aimed to test and refine the methods of the Satellite Risk Framework. It compared predicted pollutant concentrations in plume water types (multi-annual average from 2005-2014) to published ecological thresholds, and combined this information with similarly long-term measures of seagrass and coral ecosystem health. The Satellite Risk Framework and newly-introduced multi-annual risk scores were successful in demonstrating where water conditions were, on average, correlated to adverse biological responses. Seagrass meadow abundance (multi-annual change in % cover) was negatively correlated to the multi-annual risk score at the site level (R² = 0.47, p < 0.05). Relationships between multi-annual risk scores and multi-annual changes in proportional macroalgae cover (as an index for coral reef health) were more complex (R² = 0.04, p > 0.05), though reefs incurring higher risk scores showed relatively higher proportional macroalgae cover. Multi-annual risk score thresholds associated with loss of seagrass cover were defined, with lower risk scores (≤0.2) associated with a gain or little loss in seagrass cover (gain/-12%), medium risk scores (0.2-0.4) associated with moderate loss (-12/-30%) and higher risk scores (>0.4) with the greatest loss in cover (>-30%). These thresholds were used to generate an intermediate river plume risk map specifically for seagrass meadows of the GBR. An intermediate river plume risk map for coral reefs was also developed by considering a multi-annual risk score threshold of 0.2--above which a higher proportion of macroalgae within the algal communities can be expected. These findings contribute to a long-term and adaptive approach to set relevant risk framework and thresholds for adverse biological responses in the GBR. The ecological thresholds and risk scores used in this study will be refined and validated through ongoing monitoring and assessment. As uncertainties are reduced, these risk metrics will provide important information for the development of strategies to manage water quality and ecosystem health. [ABSTRACT FROM AUTHOR]

The Great Barrier Reef (GBR) is the world's largest coral reef ecosystem. Crustose coralline algae (CCA) are important contributors to reef calcium carbonate and can facilitate coral recruitment. Despite the importance of CCA, little is known about species-level distribution, abundance, and diversity, and how these vary across the continental shelf and key habitat zones within the GBR. We quantified CCA species distributions using line transects ( n = 127) at 17 sites in the northern and central regions of the GBR, distributed among inner-, mid-, and outer-shelf regions. At each site, we identified CCA along replicate transects in three habitat zones: reef flat, reef crest, and reef slope. Taxonomically, CCA species are challenging to identify (especially in the field), and there is considerable disagreement in approach. We used published, anatomically based taxonomic schemes for consistent identification. We identified 30 CCA species among 12 genera; the most abundant species were Porolithon onkodes, Paragoniolithon conicum (sensu Adey), Neogoniolithon fosliei, and Hydrolithon reinboldii. Significant cross-shelf differences were observed in CCA community structure and CCA abundance, with inner-shelf reefs exhibiting lower CCA abundance than outer-shelf reefs. Shelf position, habitat zone, latitude, depth, and the interaction of shelf position and habitat were all significantly associated with variation in composition of CCA communities. Collectively, shelf position, habitat, and their interaction contributed to 22.6 % of the variation in coralline communities. Compared to mid- and outer-shelf sites, inner-shelf sites exhibited lower relative abundances of N. fosliei and Lithophyllum species. Reef crest habitats exhibited greater abundance of N. fosliei than reef flat and reef slope habitats. Reef slope habitats exhibited lower abundance of P. onkodes, but greater abundance of Neogoniolithon clavycymosum than reef crest and reef slope habitats. These findings provide important data on CCA distribution within the GBR and reinforce the fundamental role of cross-shelf variation and diverse habitat zones as contributors to the biodiversity of the GBR. [ABSTRACT FROM AUTHOR]

Scleractinian corals often exhibit high levels of morphological plasticity, which is potentially important in enabling individual species to occupy benthic spaces across a wide range of environmental gradients. This study tested for differences in the three-dimensional (3D) geometry of three branching corals, Acropora nasuta, Pocillopora spp. and Stylophora pistillata among inner-, mid- and outer-shelf reefs in the central Great Barrier Reef, Australia. Important attributes of coral morphology (e.g., surface area to volume ratio) were expected to vary linearly across the shelf in accordance with marked gradients in environmental conditions, but instead, we detected non-linear trends in the colony structure of A. nasuta and Pocillopora spp. The surface area to volume ratio of both A. nasuta and Pocillopora spp. was highest at mid-shelf locations, (reflecting higher colony complexity) and was significantly lower at both inner-shelf and outer-shelf reefs. The branching structure of these corals was also far more tightly packed at inner-shelf and outer-shelf reefs, compared to mid-shelf reefs. Apparent declines in complexity and inter-branch spacing at inner and outer-shelf reefs (compared to conspecifics from mid-shelf reefs) may reflect changes driven by gradients of sedimentation and hydrodynamics. The generality and explanations of observed patterns warrant further investigation, which is very feasible using the 3D-photogrammetry techniques used in this study. [ABSTRACT FROM AUTHOR]