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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]

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]

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]

In a stated preference valuation survey, the expected benefits of environmental policies are generally presented to respondents without reference to the fact that the predicted outcomes are rarely known with certainty. This omission may reduce the credibility of the valuation scenario and contribute to hypothetical bias. In the study outlined in this paper, a choice experiment was conducted to elicit values for environmental improvements in the Great Barrier Reef (Australia), with outcome certainty included as a separate attribute. Different specifications of the utility functions, which imply different behavioural assumptions about the way choices have been made, generate variations in value estimates. Results showed that respondents incorporate outcome certainty into their decisions, but that an expected utility formulation, represented by the interaction between environmental protection and likelihood of occurrence, underestimated environmental values. Some environmental protection values appear to be independent of outcome certainty, which may be consistent with existence values and other non-use categories. A partial expected utility model is cautiously recommended. [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]

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]

Low-lying reef islands are among the most vulnerable environments on earth to anthropogenic-induced climate change and sea-level rise over the next century because they are low, composed of unconsolidated sediment that is able to be mobilised by waves and currents, and depend on sediments supplied by reef organisms that are particularly sensitive to environmental changes (e.g. ocean temperatures and chemistry). Therefore, the spatial and temporal links between active carbonate production and island formation and dynamics are fundamental to predicting future island resilience, yet remain poorly quantified. In this paper we present results of a detailed geomorphological and sedimentological study of a reef and sand cay on the northern Great Barrier Reef. We provide an empirical investigation of the temporal linkages between sediment production and reef island development using a large collection of single grain AMS 14C dates. Large benthic foraminifera (LBF) are the single most important contributor to contemporary island sand mass (47%; ranging from 36% to 63%) at Raine Island, reflecting rapid rates of sediment production and delivery. Standing stock data reveal extremely high production rates on the reef (1.8 kg m-2 yr-1), while AMS 14C dates of single LBF tests indicate rapid rates of sediment transferral across the reef. We also demonstrate that age is statistically related to preservation and taphonomic grade (severely abraded tests > moderately abraded tests > pristine tests). We construct a contemporary reef and island sediment budget model for Raine Island that shows that LBF (Baculogypsina, Marginopora and Amphistegina) contribute 55% of the sediment produced on the reef annually, of which a large proportion (54%) contribute to the net annual accretion of the island. The tight temporal coupling between LBF growth and island sediment supply combined with the sensitivity of LBF to bleaching and ocean acidification suggests that islands dominated by LBF are likely to be very sensitive to short and long term climate change projections. Potential outcomes of this work relate to improving the understanding of the future change dynamics of reef islands in response to climate change. [ABSTRACT FROM AUTHOR]

Innovative partnerships for conservation are required to stem the tide of continued ecosystem degradation. Nature-based tourism is one such partnership. Yet the natural attractions that nature-based tourism depends on are under increasing anthropogenic threat. Because of their dependence on international visitors, nature-based tourism enterprises are under additional pressure from socioeconomic and political crises in a globalized world. Recent research shows that lifestyle values, the motives that entice owners and staff of tourism enterprises to live and work in a chosen natural attraction, strengthen the resilience of enterprises to crises. This paper empirically explores the relationship between the lifestyle values of nature-based tourism enterprises, their resilience, and their support of and contribution to conservation of Australia's Great Barrier Reef. Semi-structured interviews with the owners and senior managers of 48 reef tourism enterprises showed that those that reported high lifestyle values had higher levels of conservation ethic and participated more extensively in conservation actions. The relationship between resilience and conservation ethic was not statistically significant. Bureaucratic, regulatory and cost constraints, and a lack of knowledge, limit enterprise participation in conservation. Conservation agencies can work to reduce some of these constraints to ensure that conservation benefits from nature-based tourism enterprises are maximized. [ABSTRACT FROM PUBLISHER]

A spatially-structured simulation model of the metapopulation dynamics of common coral trout (Plectropomus leopardus) and their harvest by line fishing was developed to evaluate potential management options on the Great Barrier Reef (GBR), including closing areas to fishing. The effects of line fishing simulator (ELFSim) incorporates a spatially-structured model of the life-history of common coral trout, including larval dispersal, harvest by multiple fishing sectors (commercial, charter and recreational), and a range of mechanisms for regulating harvest. The model is designed to allow considerable flexibility in biological and fishery dynamics, to be portable to contexts other than the GBR, and to be modular to allow comparison of different implementations of biological and harvest model components. In this paper, we describe the details of the model and discuss its utility as a tool for evaluating fishery management strategies in the context of diverse stakeholder expectations. We illustrate a simple application by changing the rate at which larvae settle on the reef from which they were spawned, under a range of spatial closures and a scenario of steadily increasing fishing effort. The results identify the conditions under which a “larval subsidy effect” may be important to the performance of fishery management strategies. This effect was manifest as increased catches outside of areas closed to fishing when larvae were freely exchanged among reefs compared to when larval exchange was diminished or absent. [Copyright &y& Elsevier]

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]

Much research on coral reefs has documented differential declines in coral and associated organisms. In order to contextualise this general degradation, research on community composition is necessary in the context of varied disturbance histories and the biological processes and physical features thought to retard or promote recovery. We conducted a spatial assessment of coral reef communities across five reefs of the central Great Barrier Reef, Australia, with known disturbance histories, and assessed patterns of coral cover and community composition related to a range of other variables thought to be important for reef dynamics. Two of the reefs had not been extensively disturbed for at least 15 years prior to the surveys. Three of the reefs had been severely impacted by crown-of-thorns starfish outbreaks and coral bleaching approximately a decade before the surveys, from which only one of them was showing signs of recovery based on independent surveys. We incorporated wave exposure (sheltered and exposed) and reef zone (slope, crest and flat) into our design, providing a comprehensive assessment of the spatial patterns in community composition on these reefs. Categorising corals into life history groupings, we document major coral community differences in the unrecovered reefs, compared to the composition and covers found on the undisturbed reefs. The recovered reef, despite having similar coral cover, had a different community composition from the undisturbed reefs, which may indicate slow successional processes, or a different natural community dominance pattern due to hydrology and other oceanographic factors. The variables that best correlated with patterns in the coral community among sites included the density of juvenile corals, herbivore fish biomass, fish species richness and the cover of macroalgae. Given increasing impacts to the Great Barrier Reef, efforts to mitigate local stressors will be imperative to encouraging coral communities to persist into the future. [ABSTRACT FROM AUTHOR]

Despite extensive work on the genetic diversity of reef invertebrate-dinoflagellate symbioses on the Great Barrier Reef ( GBR; Australia), large information gaps exist from northern and inshore regions. Therefore, a broad survey was done comparing the community of inshore, mid-shelf and outer reefs at the latitude of Lizard Island. Symbiodinium ( Freudenthal) diversity was characterized using denaturing gradient gel electrophoresis fingerprinting and sequencing of the ITS2 region of the ribosomal DNA. Thirty-nine distinct Symbiodinium types were identified from four subgeneric clades (B, C, D, and G). Several Symbiodinium types originally characterized from the Indian Ocean were discovered as well as eight novel types (C1kk, C1 LL, C3nn, C26b, C161a, C162, C165, C166). Multivariate analyses on the Symbiodinium species diversity data showed a strong link with host identity, consistent with previous findings. Of the four environmental variables tested, mean austral winter sea surface temperature ( SST) influenced Symbiodinium distribution across shelves most significantly. A similar result was found when the analysis was performed on Symbiodinium diversity data of genera with an open symbiont transmission mode separately with chl a and PAR explaining additional variation. This study underscores the importance of SST and water quality related variables as factors driving Symbiodinium distribution on cross-shelf scales. Furthermore, this study expands our knowledge on Symbiodinium species diversity, ecological partitioning (including host-specificity) and geographic ranges across the GBR. The accelerating rate of environmental change experienced by coral reef ecosystems emphasizes the need to comprehend the full complexity of cnidarian symbioses, including the biotic and abiotic factors that shape their current distributions. [ABSTRACT FROM AUTHOR]

Long-term monitoring data show that hard coral cover on the Great Barrier Reef (GBR) has reduced by >70 % over the past century. Although authorities and many marine scientists were in denial for many years, it is now widely accepted that this reduction is largely attributable to the chronic state of eutrophication that exists throughout most of the GBR. Some reefs in the far northern GBR where the annual mean chlorophyll a (Chl a) is in the lower range of the proposed Eutrophication Threshold Concentration for Chl a (~0.2-0.3 mg m) show little or no evidence of degradation over the past century. However, the available evidence suggests that coral diseases and the crown-of-thorns starfish will proliferate in such waters and hence the mandated eutrophication Trigger values for Chl a (~0.4-0.45 mg m) will need to be decreased to ~0.2 mg m for sustaining coral reef communities. [ABSTRACT FROM AUTHOR]

Mass coral bleaching affected large parts of the Great Barrier Reef (GBR) in 1998 and 2002. In this study, we assessed if signatures of these major thermal stress events were recorded in the growth characteristics of massive Porites colonies. In 2005 a suite of short (<50 cm) cores were collected from apparently healthy, surviving Porites colonies, from reefs in the central GBR (18–19°S) that have documented observations of widespread bleaching. Sites included inshore (Nelly Bay, Pandora Reef), annually affected by freshwater flood events, midshelf (Rib Reef), only occasionally affected by freshwater floods and offshore (Myrmidon Reef) locations primarily exposed to open ocean conditions. Annual growth characteristics (extension, density and calcification) were measured in 144 cores from 79 coral colonies and analysed over the common 24-year period, 1980–2003. Visual examination of the annual density bands revealed growth hiatuses associated with the bleaching years in the form of abrupt decreases in annual linear extension rates, high density stress bands and partial mortality. The 1998 mass-bleaching event reduced Porites calcification by 13 and 18% on the two inshore locations for 4 years, followed by recovery to baseline calcification rates in 2002. Evidence of partial mortality was apparent in 10% of the offshore colonies in 2002; however no significant effects of the bleaching events were evident in the calcification rates at the mid shelf and offshore sites. These results highlight the spatial variation of mass bleaching events and that all reef locations within the GBR were not equally stressed by the 1998 and 2002 mass bleaching events, as some models tend to suggest, which enabled recovery of calcification on the GBR within 4 years. The dynamics in annual calcification rates and recovery displayed here should be used to improve model outputs that project how coral calcification will respond to ongoing warming of the tropical oceans. [ABSTRACT FROM AUTHOR]

Current velocity in aquatic environments has major implications for the diversity, abundance and ecology of aquatic organisms, but quantifying these currents has proven difficult. This study utilises a simple and inexpensive instrument (<$150) to provide a detailed current velocity profile of the coral-reef system around Lizard Island (Great Barrier Reef, Australia) at a spatial and temporal scale relevant to the ecology of individual benthos and fish. The instrument uses load-cell sensors to provide a correlation between sensor output and ambient current velocity of 99%. Each instrument is able to continuously record current velocities to >500 cms−1 and wave frequency to >100 Hz over several weeks. Sensor data are registered and processed at 16 MHz and 10 bit resolution, with a measuring precision of 0.06±0.04%, and accuracy of 0.51±0.65% (mean ±S.D.). Each instrument is also pressure rated to 120 m and shear stresses ≤20 kNm−2 allowing deployment in harsh environments. The instrument was deployed across 27 coral reef sites covering the crest (3 m), mid-slope (6 m) and deep-slope (9 m depth) of habitats directly exposed, oblique or sheltered from prevailing winds. Measurements demonstrate that currents over the reef slope and crest varies immensely depending on depth and exposure: Currents differ up to 9-fold within habitats only separated by 3 m depth and 15-fold between exposed, oblique and sheltered habitats. Comparisons to ambient weather conditions reveal that currents around Lizard Island are largely wind driven. Zero to 22.5 knot winds correspond directly to currents of 0 to >82 cms−1, while tidal currents rarely exceed 5.5 cms−1. Rather, current velocity increases exponentially as a function of wave height (0 to 1.6 m) and frequency (0.54 to 0.20 Hz), emphasizing the enormous effect of wind and waves on organisms in these shallow coral reef habitats. [ABSTRACT FROM AUTHOR]

A new species of Numbakulla Guţu & Heard, 2002 (Tanaidacea) is described from Heron Island (southern Great Barrier Reef, Queensland) collected during the Census of Coral Reefs Ecosystem (CReefs) program. The new species is the third member of the family and can be recognized by the combination of characters as: length/width ratio of the body, which is 6:7, pereonite 4 longer than the rest, the presence of eyes, a blunt rostrum, antenna article 2 elongated, cheliped carpus with row of inner setae, pereopod 6 carpus with spines, pleopod endopod with denticles. [ABSTRACT FROM AUTHOR]

Ocean acidification, via an anthropogenic increase in seawater carbon dioxide ( CO2), is potentially a major threat to coral reefs and other marine ecosystems. However, our understanding of how natural short-term diurnal CO2 variability in coral reefs influences longer term anthropogenic ocean acidification remains unclear. Here, we combine observed natural carbonate chemistry variability with future carbonate chemistry predictions for a coral reef flat in the Great Barrier Reef based on the RCP8.5 CO2 emissions scenario. Rather than observing a linear increase in reef flat partial pressure of CO2 ( p CO2) in concert with rising atmospheric concentrations, the inclusion of in situ diurnal variability results in a highly nonlinear threefold amplification of the p CO2 signal by the end of the century. This significant nonlinear amplification of diurnal p CO2 variability occurs as a result of combining natural diurnal biological CO2 metabolism with long-term decreases in seawater buffer capacity, which occurs via increasing anthropogenic CO2 absorption by the ocean. Under the same benthic community composition, the amplification in the variability in p CO2 is likely to lead to exposure to mean maximum daily p CO2 levels of ca. 2100 μatm, with corrosive conditions with respect to aragonite by end-century at our study site. Minimum p CO2 levels will become lower relative to the mean offshore value (ca. threefold increase in the difference between offshore and minimum reef flat p CO2) by end-century, leading to a further increase in the p CO2 range that organisms are exposed to. The biological consequences of short-term exposure to these extreme CO2 conditions, coupled with elevated long-term mean CO2 conditions are currently unknown and future laboratory experiments will need to incorporate natural variability to test this. The amplification of p CO2 that we describe here is not unique to our study location, but will occur in all shallow coastal environments where high biological productivity drives large natural variability in carbonate chemistry. [ABSTRACT FROM AUTHOR]

Pocillopora damicornis (Linnaeus, 1758; Scleractinia, Pocilloporidae) has recently been found to comprise at least five distinct genetic lineages in Eastern Australia, some of which likely represent cryptic species. Due to similar and plastic gross morphology of these lineages, field identification is often difficult. Here we present a quick, cost effective genetic assay as well as three novel microsatellite markers that distinguish the two most common lineages found on the Great Barrier Reef. The assay is based on PCR amplification of two regions within the mitochondrial putative control region, which show consistent and easily identifiable fragment size differences for the two genetic lineages after Alu1 restriction enzyme digestion of the amplicons. [ABSTRACT FROM AUTHOR]

For species with complex life histories such as scleractinian corals, processes occurring early in life can greatly influence the number of individuals entering the adult population. A plethora of studies have examined settlement patterns of coral larvae, mostly on artificial substrata, and the composition of adult corals across multiple spatial and temporal scales. However, relatively few studies have examined the spatial distribution of small (≤50 mm diameter) sexually immature corals on natural reef substrata. We, therefore, quantified the variation in the abundance, composition and size of juvenile corals (≤50 mm diameter) among 27 sites, nine reefs, and three latitudes spanning over 1000 km on Australia’s Great Barrier Reef. Overall, 2801 juveniles were recorded with a mean density of 6.9 (±0.3 SE) ind.m−2, with Acropora, Pocillopora, and Porites accounting for 84.1% of all juvenile corals surveyed. Size-class structure, orientation on the substrate and taxonomic composition of juvenile corals varied significantly among latitudinal sectors. The abundance of juvenile corals varied both within (6–13 ind.m−2) and among reefs (2.8–11.1 ind.m−2) but was fairly similar among latitudes (6.1–8.2 ind.m−2), despite marked latitudinal variation in larval supply and settlement rates previously found at this scale. Furthermore, the density of juvenile corals was negatively correlated with the biomass of scraping and excavating parrotfishes across all sites, revealing a potentially important role of parrotfishes in determining distribution patterns of juvenile corals on the Great Barrier Reef. While numerous studies have advocated the importance of parrotfishes for clearing space on the substrate to facilitate coral settlement, our results suggest that at high biomass they may have a detrimental effect on juvenile coral assemblages. There is, however, a clear need to directly quantify rates of mortality and growth of juvenile corals to understand the relative importance of these mechanisms in shaping juvenile, and consequently adult, coral assemblages. [ABSTRACT FROM AUTHOR]

An investigation into the evolution of coral rubble deposits on a coral reef platform is assessed using high-resolution remote sensing data and geospatial analysis. Digital change detection analysis techniques are applied to One Tree Reef in the southern Great Barrier Reef by analysing aerial photographs and satellite images captured between 1964 and 2009. Two main types of rubble deposits were identified: (1) rubble flats that are featureless mass accumulations of coral rubble; and, (2) rubble spits that are shore-normal linear features. While both deposits prograde in a lagoon-ward direction, rubble spits move faster (∼2 m/yr) than rubble flats (∼0.5 m/yr). The volume of rubble, the underlying substrate, the energy regime, and storm frequency control the rate of progradation. Rubble flat occurrence is restricted to the high-energy (windward) margin of the coral reef platform, while rubble spits are distributed reef wide, both in modal high energy and modal low energy regions of the reef. Rubble spit deposition is considered to be a result of enlarged spur and groove morphology of the forereef, whereby wave energy is focused through the enlarged groove formations causing the preferential deposition of coral rubble in particular zones of the adjacent reef flat. One last control is thought to be the elevation of the reef crest whereby lower areas are more prone to rubble flat development. A vertical and ocean-ward accumulation of rubble is occurring on the windward margin of the reef leading to a build-up and build-out of the reef, governing the expansion of the reef footprint. This study shows for the first time the evolution of a coral reef rubble flat and rubble spits over decadal time scales as detected through remotely sensed images spanning 45 years. [ABSTRACT FROM AUTHOR]

Biodiversity may provide insurance against ecosystem collapse by stabilizing assemblages that perform particular ecological functions (the "portfolio effect"). However, the extent to which this occurs in nature and the importance of different mechanisms that generate portfolio effects remain controversial. On coral reefs, herbivory helps maintain coral dominated states, so volatility in levels of herbivory has important implications for reef ecosystems. Here, we used an extensive time series of abundances on 35 reefs of the Great Barrier Reef of Australia to quantify the strength of the portfolio effect for herbivorous fishes. Then, we disentangled the contributions of two mechanisms that underlie it (compensatory interactions and differential responses to environmental fluctuations ["response diversity"]) by fitting a community-dynamic model that explicitly includes terms for both mechanisms. We found that portfolio effects operate strongly in herbivorous fishes, as shown by nearly independent fluctuations in abundances over time. Moreover, we found strong evidence for high response diversity, with nearly independent responses to environmental fluctuations. In contrast, we found little evidence that the portfolio effect in this system was enhanced by compensatory ecological interactions. Our results show that portfolio effects are driven principally by response diversity for herbivorous fishes on coral reefs. We conclude that portfolio effects can be very strong in nature and that, for coral reefs in particular, response diversity may help maintain herbivory above the threshold levels that trigger regime shifts. [ABSTRACT FROM AUTHOR]

Halacarsantia acuta sp. n. is described from Wistari Reef, Capricorn Group, southern Great Barrier Reef, the first record of the genus from Australia. The new species differs from its congeners in having antenna flagellum composed of 8 articles; epipod apically acute, without setae, broad maxilliped endite and pereopod 1 basis with a short projection. A key to species of the genus is provided. [ABSTRACT FROM AUTHOR]

Human activities threaten reef ecosystems globally, forcing ecological change at rates and scales regarded as unprecedented in the Holocene. These changes are so profound that a cessation of reef accretion (reef 'turn-off') and net erosion of reef structures is argued by many as the ultimate and imminent trajectory. Here, we use a regional scale reef growth dataset, based on 76 core records (constrained by 211 radiometric dates) from 22 reefs along and across the inner-shelf of the Great Barrier Reef, Australia, to examine the timing of different phases of reef initiation ('turn-on'), growth and 'turn-off' during the Holocene. This dataset delineates two temporally discrete episodes of reef-building over the last 8500 years: the first associated with the Holocene transgression-early highstand period [∼8.5-5.5 k calibrated years (cal y)]; the second since ∼2.3 k cal y. During both periods, reefs accreted rapidly to sea level before entering late evolutionary states - states naturally characterized by reduced coral cover and low accretion potential - and a clear hiatus occurs between these reef-building episodes for which no records of reef initiation exist. These transitions mimic those projected under current environmental disturbance regimes, but have been driven entirely by natural forcing factors. Our results demonstrate that, even through the late Holocene, reef health and growth has fluctuated through cycles independent of anthropogenic forcing. Consequently, degraded reef states cannot de facto be considered to automatically reflect increased anthropogenic stress. Indeed, in many cases degraded or nonaccreting reef communities may reflect past reef growth histories (as dictated by reef growth-sea level interactions) as much as contemporary environmental change. Recognizing when changes in reef condition reflect these natural 'turn-on'- growth -'turn-off' cycles and how they interact with on-going human disturbance is critical for effective coral reef management and for understanding future reef ecological trajectories. [ABSTRACT FROM AUTHOR]

The species diversity of pontoniine shrimps (Decapoda: Palaemonidae: Pontoniinae) previously recorded in the vicinity of Lizard Island, Great Barrier Reef (GBR), Australia, were compared with new records obtained during a recent three-week expedition as part of the CReefs Project, a field project of the Census of Marine Life. Few previous investigations at this location had discovered 18 species of pontoniine shrimps distributed among 12 genera. In contrast, relatively little effort, approximately 35 hours sampling (40 dives), was required to increase this list more than twice adding 20 new species records from 15 pontoniine genera for the locality including 6 species and 1 genus reported from Australian waters for the first time and 1 genus and 4 species new to science. This large increase in species was enumerated with little additional effort and the relatively low total species diversity of these shrimps known from this location compared to species known from the southern GBR (e.g. Heron Island), where overall diversity is expected to be less, strongly indicates that the enumeration of these shrimps from the northern GBR is far from complete. [ABSTRACT FROM AUTHOR]

This study focuses on a mesoscale eddy feature, the 'Capricorn Eddy', that typically forms within an indentation of the continental shelf in the southern GBR system. Satellite data at moderate resolution (1 km) are used to examine relevant mesoscale and sub-mesoscale sea surface dynamics. Available in situ measurements and model data are used to validate the satellite observations and to specify the nature of the processes occurring within the water column itself. The characteristic features are identified and physical theory employed to develop an understanding of associated processes. In particular, the effect of the eddy in raising cooler, nutrient-enriched oceanic subsurface water and transporting it to the reef zone, and eventually into the lagoon, is shown. This study demonstrates that the linkages between large-scale oceanography and the meso- and sub-mesoscale patterns are crucial to determining biologic responses on the scale of reef communities and may be key to understanding climate change impacts at the relevant spatial scales. [ABSTRACT FROM AUTHOR]

Climate change is now considered the greatest long-term threat to coral reefs, with some future change inevitable despite mitigation efforts. Managers must therefore focus on supporting the natural resilience of reefs, requiring that resilient reefs and reef regions be identified. We develop a framework for assessing resilience and trial it by applying the framework to target management responses to climate change on the southern Great Barrier Reef. The framework generates a resilience score for a site based on the evaluation of 19 differentially weighted indicators known or thought to confer resilience to coral reefs. Scores are summed, and sites within a region are ranked in terms of (1) their resilience relative to the other sites being assessed, and (2) the extent to which managers can influence their resilience. The framework was applied to 31 sites in Keppel Bay of the southern Great Barrier Reef, which has a long history of disturbance and recovery. Resilience and ‘management influence potential’ were both found to vary widely in Keppel Bay, informing site selection for the staged implementation of resilience-based management strategies. The assessment framework represents a step towards making the concept of resilience operational to reef managers and conservationists. Also, it is customisable, easy to teach and implement and effective in building support among local communities and stakeholders for management responses to climate change. [ABSTRACT FROM AUTHOR]