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Reef monitoring programmes often focus on limited sites, predominantly on reef slope areas, which do not capture compositional variability across zones. This study assessed spatial and temporal changes in hard coral cover at four hierarchical spatial scales. ~ 55,000, geo-referenced photoquadrats were collected annually from 2002 to 2018 and analysed using artificial intelligence for 31 sites across reef flat and reef slope zones on Heron Reef, Southern Great Barrier Reef, Australia. Trends in hard coral cover were examined at three spatial scales: (1) “reef scale”, all data; (2) “geomorphic zone scale”—north/south reef slope, inner/outer reef flat; and (3) “site scale”—31 sites. Coral cover trajectories were also examined at: (4) “sub-site scale”—sub-division of sites into 567 sub-sites, to estimate variability in coral cover trajectories via spatial statistical modelling. At reef scale coral cover increased over time to 25.6 ± 0.4 SE % in 2018 but did not recover following disturbances caused by disease (2004–2008), cyclonic conditions (2009) or severe storms (2015) to the observed pre-disturbance level (44.0 ± 0.7 SE %) seen in 2004. At geomorphic zone scale, the reef slope had significantly higher coral cover than the reef flat. Trends of decline and increase were visible in the slope zones, and the southern slope recovered to pre-decline levels. Variable coral cover trends were visible at site scale. Furthermore, sub-site spatial modelling captured eight years of coral recovery that occurred at different times and magnitudes across the four geomorphic zones, effectively estimating variability in the trajectory of the reef’s coral community. Derived spatial predictions for the entire reef show patchy coral recovery, particularly on the southern slope, and that recovery hotspots are distributed across the reef. These findings suggest that to fully understand and interpret coral decline or recovery on a reef, more accurate assessment can be achieved by examining sites distributed within different geomorphic zones to capture variation in exposure, depth and consolidation.

Although resource availability is important for coral reef nutrient cycling and trophic ecology, it is poorly understood how particulate resources may change following an oceanic heat stress event. Here, carbon and nitrogen concentrations and stable isotope values (δ13C and δ15N) of particulate organic matter (POM; 10 and 30 m) were compared from before and after the 2016 mass coral bleaching event in the Maldives, Indian Ocean. To characterize the trophic status of the post-bleaching water column, dissolved inorganic nutrients across shallow to mesophotic coral reefs (10–50 m) and plankton δ13C and δ15N were measured. Eight months after the mass bleaching, an oligotrophic water column with decreased particulate organic nitrogen and variable yet increased mean δ13C of POM was observed. Elemental and isotopic data of particulate resources from pre- and post-bleaching revealed three oceanographic regimes related to ocean mixing. This study highlights the importance of characterizing water column biogeochemistry to understand nutrient cycling in coral reef ecosystems especially post-disturbance.

Carbonate budgets are increasingly being used as a key metric to establish reef condition. To better under-stand spatial variations in framework and sediment net carbonate budgets, we quantied biogenic carbonateproduction, erosion, and dissolution within and between ve distinct geomorphological habitats of Heron Reefon the southern Great Barrier Reef. The protected reef slope had the greatest estimated net framework carbonatebudget (22.6 kgCaCO3m−2yr−1 2.4 SE), driven by abundant, fast-growing acroporid corals coupled with lowlevels of macro- and micro-bioerosion. The estimate of the exposed reef slope was signicantly lower due tolocalized damage from a single tropical cyclone that occurred 7 years prior to this study (9.7kgCaCO3m−2yr−1 2.8 SE). Within the extensive lagoon, net framework carbonate budgets ranged from0.24 kgCaCO3m−2yr−1( 0.1 SE) to 3.0 kgCaCO3m−2yr−1( 0.7 SE). The greatest net sediment carbonatebudget was estimated within the reef crest (6.0 kgCaCO3m−2yr−1 1.1 SE) and the lowest in the shallowlagoon (1.2 kgCaCO3m−2yr−1 0.2 SE). Chemical dissolution of the sediments exhibited spatial variability,with reef crest and reef  at sediments in a state of net production. Considering the area of each habitat, the netreef framework and sediment budgets across Heron Reef were 4.06 kgCaCO3m−2yr−1and2.82 kgCaCO3m−2yr−1, respectively. The results of this study improve our understanding of spatial variabilityin carbonate production and bioerosion and provide a comprehensive reef-scale carbonate budget for a rela-tively undisturbed coral reef ecosystem.

Anticipating future changes of an ecosystem's dynamics requires knowledge of how its key communities respond to current environmental regimes. The Great Barrier Reef (GBR) is under threat, with rapid changes of its reef-building hard coral (HC) community structure already evident across broad spatial scales. While several underlying relationships between HC and multiple disturbances have been documented, responses of other benthic communities to disturbances are not well understood. Here we used statistical modelling to explore the effects of broad-scale climate-related disturbances on benthic communities to predict their structure under scenarios of increasing disturbance frequency. We parameterized a multivariate model using the composition of benthic communities estimated by 145,000 observations from the northern GBR between 2012 and 2017. During this time, surveyed reefs were variously impacted by two tropical cyclones and two heat stress events that resulted in extensive HC mortality. This unprecedented sequence of disturbances was used to estimate the effects of discrete versus interacting disturbances on the compositional structure of HC, soft corals (SC) and algae. Discrete disturbances increased the prevalence of algae relative to HC while the interaction between cyclones and heat stress was the main driver of the increase in SC relative to algae and HC. Predictions from disturbance scenarios included relative increases in algae versus SC that varied by the frequency and types of disturbance interactions. However, high uncertainty of compositional changes in the presence of several disturbances shows that responses of algae and SC to the decline in HC needs further research. Better understanding of the effects of multiple disturbances on benthic communities as a whole is essential for predicting the future status of coral reefs and managing them in the light of new environmental regimes. The approach we develop here opens new opportunities for reaching this goal.

Long-term monitoring studies are central to coral reef ecology and conservation management. However, ongoing monitoring programs are almost exclusively focused on shallow depths, and it remains unclear to what extent those are representative of the whole ecosystem. Here, we present a temporal comparison (2012-2017) of directly adjacent shallow and mesophotic benthic communities across seven sites from the Great Barrier Reef and Western Coral Sea. We found a positive correlation initially between shallow and mesophotic coral cover, with higher cover at shallow depths. However, this correlation broke down after multiple disturbances, with coral cover declining only at shallow depths. Point-based tracking revealed the dynamic nature of mesophotic communities, with their consistent coral cover reflecting a net balance between substantial growth and mortality. Overall, the divergent trajectories highlight the urgency to expand monitoring efforts into mesophotic depths, to decipher the processes governing these habitats and enable better-informed management of the overall ecosystem.

Elevated ocean temperatures can cause coral bleaching, the loss of colour from reef-building corals because of a breakdown of the symbiosis with the dinoflagellate Symbiodinium. Recent studies have warned that global climate change could increase the frequency of coral bleaching and threaten the long-term viability of coral reefs. These assertions are based on projecting the coarse output from atmosphere-ocean general circulation models (GCMs) to the local conditions around representative coral reefs. Here, we conduct the first comprehensive global assessment of coral bleaching under climate change by adapting the NOAA Coral Reef Watch bleaching prediction method to the output of a low- and high-climate sensitivity GCM. First, we develop and test algorithms for predicting mass coral bleaching with GCM-resolution sea surface temperatures for thousands of coral reefs, using a global coral reef map and 1985-2002 bleaching prediction data. We then use the algorithms to determine the frequency of coral bleaching and required thermal adaptation by corals and their endosymbionts under two different emissions scenarios. The results indicate that bleaching could become an annual or biannual event for the vast majority of the world's coral reefs in the next 30-50 years without an increase in thermal tolerance of 0.2-1.0°C per decade. The geographic variability in required thermal adaptation found in each model and emissions scenario suggests that coral reefs in some regions, like Micronesia and western Polynesia, may be particularly vulnerable to climate change. Advances in modelling and monitoring will refine the forecast for individual reefs, but this assessment concludes that the global prognosis is unlikely to change without an accelerated effort to stabilize atmospheric greenhouse gas concentrations.

Conserving coral reefs is critical for maintaining marine biodiversity, protecting coastlines, and supporting livelihoods in many coastal communities. Climate change threatens coral reefs globally, but researchers have identified a portfolio of coral reefs (bioclimatic units [BCUs]) that are relatively less exposed to climate impacts and strongly connected to other coral reef systems. These reefs provide a proactive opportunity to secure a long-term future for coral reefs under climate change. To help guide local management efforts, we quantified marine cumulative human impact (CHI) from climate, marine, and land pressures (2013 and from 2008 to 2013) in BCUs and across countries tasked with BCU management. Additionally, we created a management index based on common management measures and policies for each pressure source (climate, marine, and land) to identify a country's intent and commitment to effectively manage these pressures. Twenty-two countries (79%) had increases in CHI from 2008 to 2013. Climate change pressures had the highest proportional contribution to CHI across all reefs and in all but one country (Singapore), but 18 BCUs (35%) and nine countries containing BCUs (32%) had relatively high land and marine impacts. There was a significant positive relationship between climate impact and the climate management index across countries (RIdentificación de Oportunidades de Gestión para Combatir las Amenazas Climáticas, Marinas y Terrestres en los Arrecifes de Coral Menos Expuestos al Clima Resumen La conservación de los arrecifes de coral es de suma importancia para mantener la biodiversidad marina y para sostener el medio de vida en muchas comunidades costeras. El cambio climático es una amenaza mundial para los arrecifes de coral; aun así, los investigadores han identificado un portafolio de arrecifes de coral (unidades bioclimáticas[UBCs]) que se encuentran relativamente menos expuestos a los impactos climáticos y están conectados a otros sistemas arrecifales. Estos arrecifes proporcionan una oportunidad proactiva de asegurar un futuro a largo plazo para los arrecifes de coral frente al cambio climático. Para ayudar a guiar los esfuerzos locales de manejo, cuantificamos el impacto humano acumulativo (IHA) sobre los ambientes marinos a partir de las presiones climáticas, marinas y terrestres (del 2008 al 2013) en las UBCs y en los países encargados del manejo de estas. Además, creamos un índice de manejo con base en las medidas y políticas comunes de gestión para cada fuente de presión (clima, ambiente marino, suelo) para identificar la intención y el compromiso de cada país para manejar de manera efectiva estas presiones. Veintidós países (79%) tuvieron incrementos en el IHA entre 2008 y 2013. Las presiones por el cambio climático tuvieron la contribución proporcional más alta al IHA en todos los arrecifes y en todos los países excepto uno (Singapur), pero 18 UBCs (35%) y nueve países que cuentan con UBCs (32%) tuvieron impactos terrestres y marinos relativamente altos. Hubo una relación positiva significativa entre el impacto climático y el índice de manejo climático entre los países (R

Despite recent efforts to curtail greenhouse gas emissions, current global emission trajectories are still following the business-as-usual representative concentration pathway (RCP) 8.5 emission pathway. The resulting ocean warming and acidification have transformative impacts on coral reef ecosystems, detrimentally affecting coral physiology and health, and these impacts are predicted to worsen in the near future. In this study, we kept fragments of the symbiotic corals Acropora intermedia (thermally sensitive) and Porites lobata (thermally tolerant) for 7 weeks under an orthogonal design of predicted end-of-century RCP8.5 conditions for temperature and pCO(2) (3.5 degrees C and 570 ppm above present-day, respectively) to unravel how temperature and acidification, individually or interactively, influence metabolic and physiological performance. Our results pinpoint thermal stress as the dominant driver of deteriorating health in both species because of its propensity to destabilize coral-dinoflagellate symbiosis (bleaching). Acidification had no influence on metabolism but had a significant negative effect on skeleton growth, particularly when photosynthesis was absent such as in bleached corals or under dark conditions. Total loss of photosynthesis after bleaching caused an exhaustion of protein and lipid stores and collapse of calcification that ultimately led to A. intermedia mortality. Despite complete loss of symbionts from its tissue, P. lobata maintained small amounts of photosynthesis and experienced a weaker decline in lipid and protein reserves that presumably contributed to higher survival of this species. Our results indicate that ocean warming and acidification under business-as-usual CO2 emission scenarios will likely extirpate thermally sensitive coral species before the end of the century, while slowing the recovery of more thermally tolerant species from increasingly severe mass coral bleaching and mortality. This could ultimately lead to the gradual disappearance of tropical coral reefs globally, and a shift on surviving reefs to only the most resilient coral species.

Climate change is causing major changes to marine ecosystems globally, with ocean acidification of particular concern for coral reefs. Using a 200 d in situ carbon dioxide enrichment study on Heron Island, Australia, we simulated future ocean acidification conditions, and found reduced pH led to a drastic decline in net calcification of living corals to no net growth, and accelerated disintegration of dead corals. Net calcification declined more severely than in previous studies due to exposure to the natural community of bioeroding organisms in this in situ study and to a longer experimental duration. Our data suggest that reef flat corals reach net dissolution at an aragonite saturation state (ΩAR) of 2.3 (95% confidence interval: 1.8–2.8) with 100% living coral cover and at ΩAR > 3.5 with 30% living coral cover. This model suggests that areas of the reef with relatively low coral mortality, where living coral cover is high, are likely to be resistant to carbon dioxide-induced reef dissolution. A Free Ocean Carbon Enrichment study on the Great Barrier Reef finds that elevated carbon dioxide impairs net calcification of living corals and may accelerate dissolution of dead corals.

Photosynthesis is an important driver of calcium carbonate deposition on tropical coral reefs largely due to the symbiosis of numerous invertebrates with photosynthetic dinoflagellates in the family Symbiodiniaceae. In bioeroding sponges, however, similar symbioses appear to support the decalcification of carbonate substrates. Compared to its role in calcification, the relative importance of photosynthesis to decalcification processes is less known. Here, the daytime and night-time chemical bioerosion rates of the common Indo-Pacific sponge Cliona orientalis were examined under varying levels of photosynthetic activity and/or varying abundances of intracellular dinoflagellates. Photosynthesis was manipulated either by preconditioning the sponges with the photosynthetic inhibitor diuron (DCMU), or by exposing them to short-term heat stress to achieve bleaching (loss of symbionts). DCMU reduced symbiont numbers and diminished their ability to evolve oxygen. Thermal stress caused a significantly greater loss of symbionts, but photosynthesis was less inhibited. In both cases, decreases in photosynthetic activity and symbiont densities led to proportionately lowered daytime chemical bioerosion rates. Moreover, increased rates of night-time bioerosion were linked to greater daytime rates of photosynthesis, rather than to the night-time respiration of the sponge holobiont. Our findings support the conclusion that photosynthetic products (photosynthates) and/or by-products (oxygen) stimulate sponge bioerosion. This work further reveals the importance of symbionts in the ecology of such sponges and in their ability to sustain high bioerosion activity in otherwise nutrient-poor ecosystems.

Oceanographic processes shape coral reefs worldwide by redistributing inorganic nutrients and particulate resources over depth. Deep-water upwelling occurs frequently in coral reef ecosystems, but its impact on coral nutrition remains unclear. This study investigated the influence of upwelling on the trophic ecology of three common reef-building corals (Galaxea fascicularis, Pachyseris speciosa and Pocillopora verrucosa) from different reef depths (shallow reef, 10 m, vs. deep reef, 30 m) and reef exposures (oceanic rim vs. Inner Sea) across > 250 km of the Maldives archipelago, Indian Ocean. Carbon and nitrogen stable isotope ratios (δ C and δ N) of coral hosts, their symbionts and particulate organic matter (POM) were used to characterize coral trophic strategies. Across the Maldives, consistent mean δ N values were recorded in hosts (5.5‰) and symbionts (5.2‰) of the three coral species from shallow and deep reefs of oceanic and Inner Sea reef exposures. Coral hosts, symbionts and POM from both depths had δ N values that were consistent with the isotopic signature of a deep-water nitrate source transported to surface waters via upwelling. In contrast, a wide range of δ C values (~10‰) revealed different trophic strategies and isotopic niches among the coral species. Different mean δ C values of G. fascicularis indicated greater symbiont autotrophy in corals from shallow (-15.5‰) compared to deep reefs (-17.6‰). Conversely, the mean δ C values of P. speciosa (-15.1‰) and P. verrucosa (-17.7‰) were not affected by reef depth. These corals maintained consistent trophic strategies over depth, with P. speciosa relying more on autotrophy compared to P. verrucosa. Despite different reef exposure to oceanic waters, coral host and POM δ N and δ C values did not differ between oceanic and Inner Sea reef exposures. Nutritional resources appear to be homogenous in the central Maldives due to atoll-wide water circulation. However, species-specific trophic strategies resulted in diverse patterns of δ C values over depth. Because heterotrophic feeding has been linked to coral host survival through coral bleaching events, understanding the trophic ecology of corals within the reef assemblage can provide insight into species resilience under ocean warming conditions. As a member of the typically competitive Pocilloporidae family, the dependence of P. verrucosa on heterotrophy may help this coral be a future “winner” under sustained ocean warming. A plain language summary is available for this article.

Coral reefs, especially those located near-shore, are increasingly exposed to anthropogenic, eutrophic conditions that are often chronic. Yet, corals under unperturbed conditions may frequently receive natural and usually temporary nutrient supplementation through biological sources such as fishes. We compared physiological parameters indicative of long- and short-term coral health (day and night calcification, fragment surface area, productivity, energy reserves, and tissue stoichiometry) under continuous and temporary nutrient enrichment. The symbiotic coral Acropora intermedia was grown for 7 weeks under continuously elevated (press) levels of ammonium (14 µmol L−1) and phosphate (10 µmol L−1) as separate and combined treatments, to discern the individual and interactive nutrient effects. Another treatment exposed A. intermedia twice-daily to an ammonium and phosphate pulse of the same concentrations as the press treatments to simulate natural biotic supplementation. Press exposure to elevated ammonium or phosphate produced mixed effects on physiological responses, with little interaction between the nutrients in the combined treatment. Overall, corals under press exposure transitioned resources away from calcification. However, exposure to nutrient pulses often enhanced physiological responses. Our findings indicate that while continuous nutrient enrichment may pose a threat to coral health, episodic nutrient pulses that resemble natural nutrient supplementation may significantly benefit coral health and physiology.

Sediment runoff from disturbed coastal catchments is a major threat to marine ecosystems. Understanding where sediments are produced and where they are delivered enables managers to design more effective strategies for improving water quality. A management strategy is targeted restoration of degraded terrestrial areas, as it provides opportunities to reduce land-based runoff from coastal areas and consequently foster coral reef conservation. To do this strategically, a systematic approach is needed to identify watersheds where restoration actions will provide the highest conservation benefits for coral reefs. Here, we develop a systematic approach for identifying global forest restoration opportunities that would also result in large decreases in the flux of sediments to coral reefs. We estimate how land-use change affects sediment runoff globally using high-resolution spatial data and determine the subsequent risk of sediment exposure on coral reefs using a diffusion-based ocean transport model. Our results reveal that sediment export is a major issue affecting 41% of coral reefs globally. The main coastal watersheds with the highest sediment export are predominantly located in Southeast Asian countries, with Indonesia and the Philippines accounting for 52% of the sediment export in coastal areas near coral reefs. We show how restoring forest across multiple watersheds could help to reduce sediment export to 63,000km2 of coral reefs. Although reforestation opportunities in areas that discharge onto coral reefs are relatively small across watersheds, it is possible to achieve large sediment reduction benefits by strategically targeting watersheds located in regions with a high density of corals near to the coast. Thus, reforestation benefits on coral reefs do not necessarily come from the watersheds that produce the highest sediment export. These analyses are key for generating informed action to support both international conservation policy and national restoration activities.

International audience; Maintaining coral reef ecosystems is a social imperative, because so many people depend on coral reefs for food production, shoreline protection, and livelihoods. The survival of reefs this century, however, is threatened by the mounting effects of climate change. Climate mitigation is the foremost and essential action to prevent coral reef ecosystem collapse. Without it, reefs will become extremely diminished within the next 20-30 years. Even with strong climate mitigation, however, existing conservation measures such as marine protected areas and fisheries management are no longer sufficient to sustain the ecosystem and many additional and innovative actions to increase reef resilience must also be taken. In this paper we assess the suite of protections and actions in terms of their potential be effective according to a set of criteria that include effectiveness, readiness, co-benefits and disbenefits. Even with the best scientific innovation, saving coral reefs will require a well-funded, welldesigned, and rapidly executed strategy with political and social commitments at the level of other grand challenges.

Global climate change will drive declines in coral reefs over coming decades. Yet, the relative role of temperature versus acidification, and the ability of resultant ecosystems to retain core services such as coastal protection, are less clear. Here, we investigate changes to the net chemical balances of calcium carbonate within complex experimental coral reefs over 18 months under conditions projected for 2100 if CO2 emissions continue unmitigated. We reveal a decoupling of calcifier biomass and calcification under the synergistic impact of warming and acidification, that combined with increased night-time dissolution, leads to an accelerated loss of carbonate frameworks. Climate change induced degradation will limit the ability of coral reefs to keep-up with sea level rise, possibly for thousands of years. We conclude that instead of simply transitioning to alternate states that are capable of buffering coastlines, reefs are at risk of drowning leading to critical losses in ecosystem functions. Uncoupling of calcification from calcifier biomass could accelerate coral reef degradation under the combined impact of warming and ocean acidification, suggests an 18-month long mesocosm experiment.

Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa), and uncover through a comprehensive genomic and phenotypic assessment that it comprises morphologically indistinguishable, but ecologically divergent cryptic lineages. Demographic modelling based on whole-genome resequencing disproved that morphological crypsis was due to recent divergence, and instead indicated ancient morphological stasis. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid diagnostic assay revealed differentiation of their ecological distributions. Leveraging “common garden” conditions facilitated by the overlapping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate how ecologically and phenotypically divergent coral species can evolve despite morphological stasis, and provide new leads into the potential mechanisms facilitating such divergence in sympatry. More broadly, they indicate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively.

El Niño Southern Oscillation global coral bleaching events are increasing in frequency; however, the severity of bleaching is not geographically uniform. There were two major objectives of the present project: 1) assess the state of reefs and coral health at several sites and 2) explore water quality and climate change impacts on Timorese reefs. The impacts of climate change (principally by following coral mortality) were surveyed on coral reefs before and after the 2016–2017 underwater heatwave, using temperature loggers deployed between surveys which were compared to Coral Reef Watch (CRW) experimental virtual station sea surface temperature (SST). CRW is an important and widely used tool; however, we found the SST was significantly warmer (> 1°C) than in situ temperature during the austral summer accruing 5.79 degree heating weeks. In situ temperature showed no accumulation. Change in coral cover between surveys was attributed to reef heterogeneity. There were significant differences in coral cover, coral diversity, and nutrient concentrations between site and depth and a low prevalence of disease recorded in both years. The comparison of temperature and SST indicate that bleaching stress in Timor-Leste is potentially mitigated by seasonal and oceanographic dynamics. This is corroborated by Timor-Leste’s location within the Indonesian ThroughFlow. Timor-Leste is a climate refugium and the immediate conservation work lies in the management of localized anthropogenic impacts on coral reefs such as sedimentation and fishing.

This paper describes benthic coral reef community composition point-based field data sets derived from georeferenced photoquadrats using machine learning. Annually over a 17 year period (2002–2018), data were collected using downward-looking photoquadrats that capture an approximately 1 m2 footprint along 100 m–1500 m transect surveys distributed along the reef slope and across the reef flat of Heron Reef (28 km2), Southern Great Barrier Reef, Australia. Benthic community composition for the photoquadrats was automatically interpreted through deep learning, following initial manual calibration of the algorithm. The resulting data sets support understanding of coral reef biology, ecology, mapping and dynamics. Similar methods to derive the benthic data have been published for seagrass habitats, however here we have adapted the methods for application to coral reef habitats, with the integration of automatic photoquadrat analysis. The approach presented is globally applicable for various submerged and benthic community ecological applications, and provides the basis for further studies at this site, regional to global comparative studies, and for the design of similar monitoring programs elsewhere., Measurement(s) marine benthic feature Technology Type(s) photoquadrat transect surveys Factor Type(s) benthic composition Sample Characteristic - Organism benthic communities Sample Characteristic - Environment coral reef • marine coral reef flat zone • marine coral reef crest • marine coral reef back reef • marine coral reef fore reef Sample Characteristic - Location Heron Island Reef, 23–052 Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.14034320

Understanding the effects of natural processes on coral–algal competition is an important step in identifying the role of macroalgae in perturbed coral reef ecosystems. However, studies investigating coral–algal interactions are often conducted in response to a disturbance, and rarely incorporate seasonal variability. Here, naturally occurring coral–algal interactions were assessed in situ four times a year over 2 years across eight sites spanning diverse benthic communities. In over 6500 recorded coral–algal interactions, cyanobacteria and turf algae were found to be the most damaging regardless of season, resulting in visible damage to coral in greater than 95% of interactions. Macroalgae that primarily compete using chemical mechanisms were found to be more damaging than those that compete using physical mechanisms (e.g. abrasion), with both groups demonstrating decreased competitive ability in summer. While crustose coralline algae were the least damaging to competing coral, during summer, it became three times more competitive. Our results demonstrate that the competitive ability of macroalgae and the outcomes of coral–algal competition can fluctuate in seasonal cycles that may be related to biomass, production of chemical defences and/or physical toughness. The results of this study have important implications for understanding the trajectory and resilience of coral reef ecosystems into the future.

Addressing the global decline of coral reefs requires effective actions from managers, policymakers and society as a whole. Coral reef scientists are therefore challenged with the task of providing prompt and relevant inputs for science-based decision-making. Here, we provide a baseline dataset, covering 1300 km of tropical coral reef habitats globally, and comprised of over one million geo-referenced, high-resolution photo-quadrats analysed using artificial intelligence to automatically estimate the proportional cover of benthic components. The dataset contains information on five major reef regions, and spans 2012–2018, including surveys before and after the 2016 global bleaching event. The taxonomic resolution attained by image analysis, as well as the spatially explicit nature of the images, allow for multi-scale spatial analyses, temporal assessments (decline and recovery), and serve for supporting image recognition developments. This standardised dataset across broad geographies offers a significant contribution towards a sound baseline for advancing our understanding of coral reef ecology and thereby taking collective and informed actions to mitigate catastrophic losses in coral reefs worldwide., Measurement(s) ecosystem • coral reef • composition Technology Type(s) automated image annotation • machine learning Factor Type(s) year of data collection • geographic location Sample Characteristic - Organism Anthozoa • Algae • Porifera Sample Characteristic - Environment marine coral reef biome • marine coral reef fore reef Sample Characteristic - Location Atlantic Ocean • Eastern Australia • Indian Ocean • Southeast Asia • Pacific Ocean • Great Barrier Reef Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13007516

Global change causes widespread decline of coral reefs. In order to counter the anticipated disappearance of coral reefs by the end of this century, many initiatives are emerging, including creation of marine protected areas (MPAs), reef restoration projects, and assisted evolution initiatives. Such efforts, although critically important, are locally constrained. We propose to build a “Noah's Ark” biological repository for corals that taps into the network of the world’s public aquaria and coral reef scientists. Public aquaria will serve not only as a reservoir for the purpose of conservation, restoration, and research of reef-building corals but also as a laboratory for the implementation of operations for the selection of stress-resilient and resistant genotypes. The proposed project will provide a global dimension to coral reef education and protection as a result of the involvement of a network of public and private aquaria., Global change is causing a widespread decline in coral reefs. This Community Page article proposes to build the World Coral Conservatory, a “Noah's Ark” biological repository that taps into the network of the world’s public aquaria and coral reef scientists, in order to preserve the fast-disappearing biodiversity of coral reefs.

While there is an ever-expanding list of impacts on coral reefs as a result of ocean warming and acidification, there is little information on how these global changes influence coral–algal competition. The present study assessed the impact of business-as-usual ocean warming and acidification conditions on the survivorship, calcification, photosynthesis and respiration of the coral–algal interaction between the macroalga Halimeda heteromorpha and the coral Acropora intermedia over 8 weeks in two seasons. The physiological responses of A. intermedia and H. heteromorpha were highly dependent on season, with both organisms demonstrating optimal rates of calcification and photosynthesis under present-day conditions in summer. Contact with H. heteromorpha did not influence A. intermedia survivorship, however did reduce long-term calcification rates. Photosynthetic rates of A. intermedia were influenced by algal contact temporally in opposing directions, with rates reduced in winter and increased in summer. Enhanced photosynthetic rates as a result of algal contact were not enough to offset the combined effects of ocean warming and acidification, which regardless of coral–algal contact, reduced survivorship, calcification and photosynthesis of A. intermedia and the calcification rates of H. heteromorpha. These findings provide experimental support for the idea that the effects of coral–algal competition are temporally variable, and help improve our understanding of how future ocean warming and acidification may alter the dynamics of coral–algal interactions.

Rapid ocean warming as a result of climate change poses a key risk for coral reefs. Even if the goals of the Paris Climate Agreement are achieved, coral reefs are likely to decline by 70–90% relative to their current abundance by midcentury. Although alarming, coral communities that survive will play a key role in the regeneration of reefs by mid-to-late century. Here, we argue for a coordinated, global coral reef conservation strategy that is centred on 50 large (500km2) regions that are the least vulnerable to climate change and which are positioned to facilitate future coral reef regeneration. The proposed strategy and actions should strengthen and expand existing conservation efforts for coral reefs as we face the long-term consequences of intensifying climate change.

Coral reefs are likely to be exposed to more intense cyclones under climate change. Cyclone impacts are spatially highly variable given complex hydrodynamics, and coral-specific sensitivity to wave impacts. Predicting reef vulnerability to cyclones is critical to management but requires high resolution environmental data that are difficult to obtain over broad spatial scales. Using 30m-resolution wave modelling, we tested cyclonic and non-cyclonic wave metrics as predictors of coral damage on 22 reefs after severe cyclone Ita impacted the northern Great Barrier Reef, Australia in 2014. Analyses of coral cover change accounting for the type of coral along a gradient of vulnerability to wave damage (e.g., massive, branching, Acroporids) excluded cyclone-generated surface wave metrics (derived from wave height) as important predictors. Increased bottom stress wave environment (near-bed wave orbital velocity) due to Ita (Ita-Ub) explained spatial patterns of 17% to 46% total coral cover loss only when the initial abundance of Acroporids was accounted for, and only when exceeding 35% cover. Greater coral losses occurred closer to the cyclone path irrespective of coral type. Massive and encrusting corals, however, had losses exacerbated in higher non-cyclonic bottom-wave energy environments (nc-Ub). The effect of community composition on structural vulnerability to wave damage was more important predicting damage that the magnitude of the cyclone-generated waves, especially when reefs are surveyed well beyond where damaging waves are expected to occur. Exposure to Ita-Ub was greater in typically high nc-Ub environments with relatively low cover of the most fragile morphologies explaining why these were the least affected overall. We reveal that the common surface-wave metrics of cyclone intensity may not always be able to predict spatial impacts and conclude that reef vulnerability assessments need to account for chronic wave patterns and differences in community composition in order to provide predictive tools for future conservation and restoration.

We use a multi-tracer approach to identify catchment sources of nitrogen (N) in the skeletons of nearshore Porites corals within the Great Barrier Reef. We measured δ15N, δ13C and C:N ratios of particulate organic matter (POM) sampled from the Pioneer River catchment and identified five distinct end-members: (1) marine planktonic and algal-dominated matter with higher δ15N values from the river mouth and coastal waters; (2) estuarine planktonic and algal matter with lower δ15N values associated with estuarine mixing; (3) lower river freshwater phytoplankton and algal-dominated matter in stratified reservoirs adjacent to catchment weirs, with the 15N-enriched source likely caused by microbial remineralization and denitrification; (4) upper river low δ15N terrigenous soil matter eroded from cane fields bordering waterways; and (5) terrestrial plant detrital matter in forest streams, representing a low δ15N fixed atmospheric nitrogen source. The δ15N values of adjacent, nearshore Porites coral skeletons is reflective of POM composition in coastal waters, with 15N-enriched values reflective of transformed N during flood pulses from the Pioneer River.

Competitive processes and their outcomes, such as interactions between scleractinian corals and macroalgae, are important drivers of the structure and function of coral reef ecosystems. Human communities can alter the dynamics of coral-algal interactions by changing species abundance and by affecting competitive ability. Here, we investigated how a natural human population gradient in the Maldives influences the relative abundance of benthic organisms, and if changes in benthic cover can influence the diversity, frequency and outcomes of coral-algal interactions. We observed a decline in some coral assemblages and an increase in coral mortality and filamentous algae on reefs with the highest human population pressures. At the highest level of human population, the diversity of coral-algal interactions was significantly reduced, with some genera of plating corals locally sparse. Human population pressures did not increase the frequency of coral-algal interactions or the competitive ability of macroalgal types. Regardless of human population, interactions between filamentous algae and cyanobacteria were the most damaging to competing corals. Interactions between crustose coralline algae and Halimeda were not only the most common and least harmful to coral, but were also positively correlated with coral cover, emphasizing the role that positive species interactions can play in regulating community structure and function.

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.

Ecosystem monitoring is central to effective management, where rapid reporting is essential to provide timely advice. While digital imagery has greatly improved the speed of underwater data collection for monitoring benthic communities, image analysis remains a bottleneck in reporting observations. In recent years, a rapid evolution of artificial intelligence in image recognition has been evident in its broad applications in modern society, offering new opportunities for increasing the capabilities of coral reef monitoring. Here, we evaluated the performance of Deep Learning Convolutional Neural Networks for automated image analysis, using a global coral reef monitoring dataset. The study demonstrates the advantages of automated image analysis for coral reef monitoring in terms of error and repeatability of benthic abundance estimations, as well as cost and benefit. We found unbiased and high agreement between expert and automated observations (97%). Repeated surveys and comparisons against existing monitoring programs also show that automated estimation of benthic composition is equally robust in detecting change and ensuring the continuity of existing monitoring data. Using this automated approach, data analysis and reporting can be accelerated by at least 200x and at a fraction of the cost (1%). Combining commonly used underwater imagery in monitoring with automated image annotation can dramatically improve how we measure and monitor coral reefs worldwide, particularly in terms of allocating limited resources, rapid reporting and data integration within and across management areas.

Rapid ocean warming due to climate change poses a serious risk to the survival of coral reefs. It is estimated that 70–90 percent of all reefs will be severely degraded by mid-century even if the 1.5°C goal of the Paris Climate Agreement is achieved. However, one coral reef ecosystem seems to be more resilient to rising sea temperatures than most others. The Red Sea’s reef ecosystem is one of the longest continuous living reefs in the world, and its northernmost portion extends into the Gulf of Aqaba. The scleractinian corals in the Gulf have an unusually high tolerance for the rapidly warming seawater in the region. They withstand water temperature anomalies that cause severe bleaching or mortality in most hard corals elsewhere. This uniquely resilient reef employs biological mechanisms which are likely to be important for coral survival as the planet’s oceans warm. The Gulf of Aqaba could potentially be one of the planet’s largest marine refuges from climate change. However, this unique portion of the Red Sea’s reef will only survive and flourish if serious regional environmental challenges are addressed. Localized anthropogenic stressors compound the effects of warming seawater to damage corals and should be mitigated immediately. Reefs in the rest of the Red Sea are already experiencing temperatures above their thermal tolerance and have had significant bleaching, though they too would benefit from fewer local anthropogenic stressors. The countries bordering the entire Red Sea will need to cooperate to enable effective scientific research and conservation. The newly established Transnational Red Sea Center, based at the Ecole Polytechnique Fédérale de Lausanne (EPFL), can serve as the regionally inclusive, neutral organization to foster crucial regional scientific collaboration. published

Marine sponges are set to become more abundant in many near-future oligotrophic environments, where they play crucial roles in nutrient cycling. Of high importance is their mass turnover of dissolved organic matter (DOM), a heterogeneous mixture that constitutes the largest fraction of organic matter in the ocean and is recycled primarily by bacterial mediation. Little is known, however, about the mechanism that enables sponges to incorporate large quantities of DOM in their nutrition, unlike most other invertebrates. Here, we examine the cellular capacity for direct processing of DOM, and the fate of the processed matter, inside a dinoflagellate-hosting bioeroding sponge that is prominent on Indo-Pacific coral reefs. Integrating transmission electron microscopy with nanoscale secondary ion mass spectrometry, we track 15 N- and 13 C-enriched DOM over time at the individual cell level of an intact sponge holobiont. We show initial high enrichment in the filter-feeding cells of the sponge, providing visual evidence of their capacity to process DOM through pinocytosis without mediation of resident bacteria. Subsequent enrichment of the endosymbiotic dinoflagellates also suggests sharing of host nitrogenous wastes. Our results shed light on the physiological mechanism behind the ecologically important ability of sponges to cycle DOM via the recently described sponge loop.

As living carbonate-based structures, coral reefs are highly vulnerable to ocean acidification. The Great Barrier Reef (GBR) is the largest continuous coral reef system in the world. Its economic, social, and icon assets are valued at AU$56 billion (Deloitte Access Economics, 2017), owing to its vast biodiversity and services related to commercial and recreational fisheries, shoreline protection, and reef-related tourism and recreation. Ocean acidification poses a significant risk to these ecological and socioeconomic services, threatening not only the structural foundation of the GBR but the livelihoods of reef-dependent sectors of society. To assess the vulnerabilities of the GBR to ocean acidification, we review the characteristics of the GBR and the current valuation and factors affecting potential losses across three major areas of socioeconomic concern: fisheries, shoreline protection, and reef-related tourism and recreation. We then discuss potential solutions, both conventional and unconventional, for mitigating ocean acidification impacts on the GBR and propose a suite of actions that would help assess and increase the region's preparedness for the effects of ocean acidification.

Coral reefs are spectacular ecosystems found along tropical coastlines where they provide goods and services to hundreds of millions of people. While under threat from local factors, coral reefs are increasingly susceptible to ocean warming from anthropogenic climate change. One of the signature disturbances is the large-scale, and often deadly, breakdown of the symbiosis between corals and dinoflagellates. This is referred to as mass coral bleaching and often causes mass mortality. The first scientific records of mass bleaching date to the early 1980s (Hoegh-Guldberg et al., 2017). Kamenos and Hennige (2018, hereafter KH18), however, claim to show that mass coral bleaching is not a recent phenomenon, and has occurred regularly over the past four centuries (1572–2001) on the Great Barrier Reef (GBR), Australia. They support their claim by developing a putative proxy for coral bleaching that uses the suggested relationship between elevated sea surface temperatures (SSTs) and reduced linear extension rates of 44 Porites spp. coral cores from 28 GBR reefs. If their results are correct, then mass coral bleaching events have been a frequent feature for hundreds of years in sharp contrast to the vast majority of scientific evidence. There are, however, major flaws in the KH18 methodology. Their use of the Extended Reconstructed Sea Surface Temperature (ERSST) dataset (based on ship and buoy observations) for reef temperatures from 1854 to 2001, ignores the increasing unreliability of these data which become sparse, less rigorous, and more interpolated going back in time. To demonstrate how the quality of these data degrades, we plot the average number of SST observations per month that contribute to each 200 x 200 km ERSST pixel (Figure 1A, black line). Note that from 1854 to 1900 the four ERSST pixels used by KH18 averaged only 0.85 observations per month, and 82% of these months had no observations at all. Given the heterogeneous nature of SST at local and regional levels, using such broad-scale data as ERSST, is likely to produce substantial errors at reef scales (Figure 1A, red line prior to 1900).

Coral reefs are highly vulnerable habitats, threatened by climate change and local anthropogenic impacts. Management is imperative, and spatial prioritisation apportions the area of interest to inform investments of scarce conservation resources. Spatially delineated planning units used to make management decisions are typically large enough to contain significant natural variabilities, but the ecological significance of such variance is seldom considered in planning decisions. On coral reefs, the patchiness of habitat quality within planning units matters both ecologically and functionally. Here, we show that considering within-planning unit variance in spatial prioritisation influences the location and design of reserve networks. Studying Timor-Leste, we statistically model the average and variance in coral cover. We compare conservation priority areas for scenarios informed by coral cover and variance to a baseline scenario with the spatial prioritisation software Marxan. To further explain these differences, and to show the value of including coral variance as a metric in spatial prioritisation, we created a reserve quality score. We show that the similarity between reserve networks was only 57% for protection, and 44% for restoration objectives. For both objectives, the inclusion of cover variance improves the conservation benefit of management. This project has shown a novel way to target areas for restoration. These results demonstrate that not only is mean coral cover (and, by extension, reef condition) a key criterion in selecting marine conservation actions, but its variance must be considered in spatial conservation prioritisation to improve both the efficiency and benefit of management actions within marine reserve networks.

Competition between corals and macroalgae is frequently observed on reefs with the outcome of these interactions affecting the relative abundance of reef organisms and therefore reef health. Anthropogenic activities have resulted in increased atmospheric CO2 levels and a subsequent rise in ocean temperatures. In addition to increasing water temperature, elevated CO2 levels are leading to a decrease in oceanic pH (ocean acidification). These two changes have the potential to alter ecological processes within the oceans, including the outcome of competitive coral-macroalgal interactions. In our study, we explored the combined effect of temperature increase and ocean acidification on the competition between the coral Porites lobata and on the Great Barrier Reef abundant macroalga Chlorodesmis fastigiata. A temperature increase of +1 °C above present temperatures and CO2 increase of +85 ppm were used to simulate a low end emission scenario for the mid- to late 21st century, according to the Representative Concentration Pathway 2.6 (RCP2.6). Our results revealed that the net photosynthesis of P. lobata decreased when it was in contact with C. fastigiata under ambient conditions, and that dark respiration increased under RCP2.6 conditions. The Photosynthesis to Respiration (P:R) ratios of corals as they interacted with macroalgal competitors were not significantly different between scenarios. Dark calcification rates of corals under RCP2.6 conditions, however, were negative and significantly decreased compared to ambient conditions. Light calcification rates were negatively affected by the interaction of macroalgal contact in the RCP2.6 scenario, compared to algal mimics and to coral under ambient conditions. Chlorophyll a, and protein content increased in the RCP2.6 scenario, but were not influenced by contact with the macroalga. We conclude that the coral host was negatively affected by RCP2.6 conditions, whereas the productivity of its symbionts (zooxanthellae) was enhanced. While a negative effect of the macroalga (C. fastigiata) on the coral (P. lobata) was observed for the P:R ratio under control conditions, it was not enhanced under RCP2.6 conditions.

Karimunjawa National Park is one of Indonesia&rsquo, s oldest established marine parks. Coral reefs across the park are being impacted by fishing, tourism and declining water quality (local stressors), as well as climate change (global pressures). In this study, we apply a multivariate statistical model to detailed benthic ecological datasets collected across Karimunjawa&rsquo, s coral reefs, to explore drivers of community change at the park level. Eighteen sites were surveyed in 2014 and 2018, before and after the 2016 global mass coral bleaching event. Analyses revealed that average coral cover declined slightly from 29.2 &plusmn, 0.12% (Standard Deviation, SD) to 26.3 &plusmn, 0.10% SD, with bleaching driving declines in most corals. Management zone was unrelated to coral decline, but shifts from massive morphologies toward more complex foliose and branching corals were apparent across all zones, reflecting a park-wide reduction in damaging fishing practises. A doubling of sponges and associated declines in massive corals could not be related to bleaching, suggesting another driver, likely declining water quality associated with tourism and mariculture. Further investigation of this potentially emerging threat is needed. Monitoring and management of water quality across Karimunjawa may be critical to improving resilience of reef communities to future coral bleaching.

Climate change is expected to have profound, partly unforeseeable effects on the composition of functional traits of complex ecosystems, such as coral reefs, and some ecosystem properties are at risk of disappearing. This study applies a novel spatially explicit, individual-based model to explore three critical life history traits of corals: heat tolerance, competitiveness and growth performance under various environmental settings. Building upon these findings, we test the adaptation potential required by a coral community in order to not only survive but also retain its diversity by the end of this century under different IPCC climate scenarios. Even under the most favourable IPCC scenario (Representative Concentration Pathway, RCP 2.6), model results indicate that shifts in the trait space are likely and coral communities will mainly consist of small numbers of temperature-tolerant and fast-growing species. Species composition of coral communities is likely to be determined by heat tolerance, with competitiveness most likely playing a subordinate role. To sustain ~15% of current coral cover under a 2 °C temperature increase by the end of the century (RCP 4.5), coral systems would have to accommodate temperature increases of 0.1–0.15 °C per decade, assuming that periodic extreme thermal events occurred every 8 years. These required adaptation rates are unprecedented and unlikely, given corals’ life-history characteristics.

The ecological success of shallow water reef-building corals has been linked to the symbiosis between the coral host and its dinoflagellate symbionts (herein ‘symbionts’). As mixotrophs, symbiotic corals depend on nutrients 1) transferred from their photosynthetic symbionts (autotrophy) and 2) acquired by host feeding on particulate organic resources (heterotrophy). However, coral species differ in the extent to which they depend on heterotrophy for nutrition and these differences are typically poorly defined. Here, a multi-tracer fatty acid approach was used to evaluate the trophic strategies of three species of common reef-building coral (Galaxea fascicularis, Pachyseris speciosa, and Pocillopora verrucosa) whose trophic strategies had previously been identified using carbon stable isotopes. The composition and various indices of fatty acids were compared to examine the relative contribution of symbiont autotrophy and host heterotrophy in coral energy acquisition. A linear discriminant analysis (LDA) was used to estimate the contribution of polyunsaturated fatty acids (PUFA) derived from various potential sources to the coral hosts. The total fatty acid composition and fatty acid indices revealed differences between the more heterotrophic (P. verrucosa) and more autotrophic (P. speciosa) coral hosts, with the coral host G. fascicularis showing overlap with the other two species and greater variability overall. For the more heterotrophic P. verrucosa, the fatty acid indices and LDA results both indicated a greater proportion of copepod-derived fatty acids compared to the other coral species. Overall, the LDA estimated that PUFA derived from particulate resources (e.g., copepods and diatoms) comprised a greater proportion of coral host PUFA in contrast to the lower proportion of symbiont-derived PUFA. These estimates provide insight into the importance of heterotrophy in coral nutrition, especially in productive reef systems. The study supports carbon stable isotope results and demonstrates the utility of fatty acid analyses for exploring the trophic strategies of reef-building corals.

Our rapidly warming climate is threatening coral reefs as thermal anomalies trigger mass coral bleaching events. Deep (or “mesophotic”) coral reefs are hypothesised to act as major ecological refuges from mass bleaching, but empirical assessments are limited. We evaluated the potential of mesophotic reefs within the Great Barrier Reef (GBR) and adjacent Coral Sea to act as thermal refuges by characterising long-term temperature conditions and assessing impacts during the 2016 mass bleaching event. We found that summer upwelling initially provided thermal relief at upper mesophotic depths (40 m), but then subsided resulting in anomalously warm temperatures even at depth. Bleaching impacts on the deep reefs were severe (40% bleached and 6% dead colonies at 40 m) but significantly lower than at shallower depths (60–69% bleached and 8–12% dead at 5-25 m). While we confirm that deep reefs can offer refuge from thermal stress, we highlight important caveats in terms of the transient nature of the protection and their limited ability to provide broad ecological refuge., It has been suggested that deep coral reefs offer a refuge against warming and mass bleaching. Here Frade et al. look at the 2016 bleaching event in the northern Great Barrier Reef and found that deep reefs initially acted as thermal refuges, though this effect lessened in the late summer months.

Resilience underpins the sustainability of both ecological and social systems. Extensive loss of reef corals following recent mass bleaching events have challenged the notion that support of system resilience is a viable reef management strategy. While resilience-based management (RBM) cannot prevent the damaging effects of major disturbances, such as mass bleaching events, it can support natural processes that promote resistance and recovery. Here, we review the potential of RBM to help sustain coral reefs in the 21st century. We explore the scope for supporting resilience through existing management approaches and emerging technologies and discuss their opportunities and limitations in a changing climate. We argue that for RBM to be effective in a changing world, reef management strategies need to involve both existing and new interventions that together reduce stress, support the fitness of populations and species, and help people and economies to adapt to a highly altered ecosystem.

Globally, tropical coral reefs are being degraded by human activities, and as a result, reef-building corals have declined while macroalgae have increased. Recent work has focused on measuring macroalgal abundance in response to anthropogenic stressors. To accurately evaluate the effects of human impacts, however, it is necessary to understand the effects of natural processes on reef condition. To better understand how coral reef communities are influenced by natural processes, we investigated how spatial and seasonal changes in environmental conditions (temperature and PAR) influence benthic community structure, and the composition and frequency of coral-algal interactions across eight distinct zones and over a 23-month period at Heron reef on the southern Great Barrier Reef. Hard coral cover and macroalgal density showed distinct spatio-temporal variations, both within and between zones. Broad hard coral cover was significantly higher at the reef slope sites compared to the lagoon and was not significantly influenced by season. The composition and biomass of macroalgae increased in spring and declined in summer, with maximum macroalgal abundance corresponding with average temperatures of between 22 and 24°C and average 24 h PAR of 300–500 μmol qanta m−2 s−1. Changes in macroalgal biomass further influenced the composition and frequency of coral-algal interactions, however the incidence of coral-algal contact was best explained by coral cover. The results presented here emphasize that natural levels of macroalgae and coral-algal interactions are context-specific, and vary not only with-in zones, but in somewhat predictable seasonal cycles. Further, these results emphasize that the frequency of coral-algal interactions is dependent on hard coral, not just macroalgal cover, and an increase in coral-algal interactions does not necessarily translate to degradation of coral reefs.

© 2015 International Society for Microbial Ecology All rights reserved. Despite being one of the simplest metazoans, corals harbor some of the most highly diverse and abundant microbial communities. Differentiating core, symbiotic bacteria from this diverse hostassociated consortium is essential for characterizing the functional contributions of bacteria but has not been possible yet. Here we characterize the coral core microbiome and demonstrate clear phylogenetic and functional divisions between the micro-scale, niche habitats within the coral host. In doing so, we discover seven distinct bacterial phylotypes that are universal to the core microbiome of coral species, separated by thousands of kilometres of oceans. The two most abundant phylotypes are co-localized specifically with the corals' endosymbiotic algae and symbiont-containing host cells. These bacterial symbioses likely facilitate the success of the dinoflagellate endosymbiosis with corals in diverse environmental regimes.

Structural complexity strongly influences biodiversity and ecosystem productivity. On coral reefs, structural complexity is typically measured using a single and small-scale metric (‘rugosity’) that represents multiple spatial attributes differentially exploited by species, thus limiting a complete understanding of how fish associate with reef structure. We used a novel approach to compare relationships between fishes and previously unavailable components of reef complexity, and contrasted the results against the traditional rugosity index. This study focused on damselfish to explore relationships between fishes and reef structure. Three territorial species, with contrasting trophic habits and expected use of the reef structure, were examined to infer the potential species-specific mechanisms associated with how complexity influences habitat selection. Three-dimensional reef reconstructions from photogrammetry quantified the following metrics of habitat quality: 1) visual exposure to predators and competitors, 2) density of predation refuges and 3) substrate-related food availability. These metrics explained the species distribution better than the traditional measure of rugosity, and each species responded to different complexity components. Given that a critical effect of reef degradation is loss of structure, adopting three-dimensional technologies potentially offers a new tool to both understand species-habitat association and help forecast how fishes will be affected by the flattening of reefs.

Coral reefs are found in a wide range of environments, where they provide food and habitat to a large range of organisms as well as providing many other ecological goods and services. Warm-water coral reefs, for example, occupy shallow sunlit, warm, and alkaline waters in order to grow and calcify at the high rates necessary to build and maintain their calcium carbonate structures. At deeper locations (40–150 m), “mesophotic” (low light) coral reefs accumulate calcium carbonate at much lower rates (if at all in some cases) yet remain important as habitat for a wide range of organisms, including those important for fisheries. Finally, even deeper, down to 2,000 m or more, the so-called “cold-water” coral reefs are found in the dark depths. Despite their importance, coral reefs are facing significant challenges from human activities including pollution, over-harvesting, physical destruction, and climate change. In the latter case, even lower greenhouse gas emission scenarios (such as Representative Concentration Pathway RCP 4.5) are likely drive the elimination of most warm-water coral reefs by 2040–2050. Cold-water corals are also threatened by warming temperatures and ocean acidification although evidence of the direct effect of climate change is less clear. Evidence that coral reefs can adapt at rates which are sufficient for them to keep up with rapid ocean warming and acidification is minimal, especially given that corals are long-lived and hence have slow rates of evolution. Conclusions that coral reefs will migrate to higher latitudes as they warm are equally unfounded, with the observations of tropical species appearing at high latitudes “necessary but not sufficient” evidence that entire coral reef ecosystems are shifting. On the contrary, coral reefs are likely to degrade rapidly over the next 20 years, presenting fundamental challenges for the 500 million people who derive food, income, coastal protection, and a range of other services from coral reefs. Unless rapid advances to the goals of the Paris Climate Change Agreement occur over the next decade, hundreds of millions of people are likely to face increasing amounts of poverty and social disruption, and, in some cases, regional insecurity.

Excavating sponges are prominent bioeroders on coral reefs that in comparison to other benthic organisms may suffer less or may even benefit from warmer, more acidic and more eutrophic waters. Here, the photosymbiotic excavating sponge Cliona orientalis from the Great Barrier Reef was subjected to a prolonged simulation of both global and local environmental change: future seawater temperature, partial pressure of carbon dioxide (as for 2100 summer conditions under “business-as-usual” emissions), and diet supplementation with particulate organics. The individual and combined effects of the three factors on the bioerosion rates, metabolic oxygen and carbon flux, biomass change and survival of the sponge were monitored over the height of summer. Diet supplementation accelerated bioerosion rates. Acidification alone did not have a strong effect on total bioerosion or survival rates, yet it co-occurred with reduced heterotrophy. Warming above 30 °C (+2.7 °C above the local maximum monthly mean) caused extensive bleaching, lower bioerosion, and prevailing mortality, overriding the other factors and suggesting a strong metabolic dependence of the sponge on its resident symbionts. The growth, bioerosion capacity and likelihood of survival of C. orientalis and similar photosymbiotic excavating sponges could be substantially reduced rather than increased on end-of-the-century reefs under “business-as-usual” emission profiles.

In recent decades, coral reefs worldwide have undergone significant changes in response to various environmental and anthropogenic impacts. Among the numerous causes of reef degradation, coral disease is one factor that is to a large extent still poorly understood. Here, we characterize the physiology of white patch syndrome (WPS), a disease affecting poritid corals on the Great Barrier Reef. WPS manifests as small, generally discrete patches of tissue discolouration. Physiological analysis revealed that chlorophyll a content was significantly lower in lesions than in healthy tissues, while host protein content remained constant, suggesting that host tissue is not affected by WPS. This was confirmed by transmission electron microscope (TEM) examination, which showed intact host tissue within lesions. TEM also revealed that Symbiodinium cells are lost from the host gastrodermis with no apparent harm caused to the surrounding host tissue. Also present in the electron micrographs were numerous virus-like particles (VLPs), in both coral and Symbiodinium cells. Small (

Linkages between neighbouring ecosystems are rarely considered when seeking to predict ecological responses to climate change. However, the finding that the impact of climate change on seagrass beds is mediated by the response of neighbouring coral reef habitats highlights the need for a broader-scale view of climate change impacts on ecosystems.

Coral reefs are highly threatened by human activities at both global (ocean warming and acidification) and local scales (overfishing, pollution, and physical destruction) especially given that current rates of environmental change exceed those seen for tens of millions of years. Recent authors, however, have suggested that coral reefs might increase their tolerance to these rapid environmental changes through acclimatisation, genetic adaptation, and migration. While there is evidence of all three responses acting within coral populations, there is little basis for the conclusion that reef-building corals and coral reefs will become more sustainable and resilient over time under current high rates of change. Most studies that make this claim have correctly identified components and mechanisms but have otherwise incorrectly extended this evidence which is otherwise necessary but not sufficient to support the conclusion that coral reefs will survive due to their ability to acclimatise, adapt and/or migrate to the current rapid environmental changes.

Coral reefs are biodiverse and productive ecosystems but are threatened by local and global stresses. The resulting loss of coral reefs is threatening coastal food and livelihoods. Climate projections suggest that coral reefs will continue to undergo major changes even if the goals of the Paris Agreement (Dec 2015) are successfully implemented. Ecological changes include modified food webs, shifts in community structure, reduced habitat complexity, decreased fecundity and recruitment, changes to fisheries productivity/opportunity, and a shift in the carbonate budget of some ecosystems toward dissolution and erosion of calcium carbonate stocks. Broad estimates of the long-term (present value) of services provided by the ocean’s ecological assets exist and are useful in highlighting the value of reefs yet must be contextualised by how people respond under ecosystem change. The dynamic nature of the relationship between people, economies, and the environment complicates estimation of human consequences and economic outcomes of changing environmental and ecological capital. Challenges have increased given lack of baseline data and our inability to predict (with any precision) how people respond to changing coral reef conditions, especially given the variability, flexibility, and creativity shown by human communities and economies under change. Here, we explore how the changes to the three-dimensional structure of coral reefs affect benefits for people, specifically coastal protection, fisheries habitat, and tourism. Based on a review of available data and literature, we make a series of key recommendations that are required to better understanding of how global change will affect people dependent on coral reefs. These include: (1) baseline studies and frameworks for understanding human responses to climate change within complex social and ecological setting such as coral reefs, (2) better tools for exploring environmental benefits, markets, and financial systems faced by change, and (3) the integration of these insights into more effective policy making.

Tropical coastal ecosystems such as coral reefs have provided food, income and resources to humans for millennia. The first interactions that people had with coral reef ecosystems left little signature or impact, most probably due to the restricted access, as well as the challenges and ephemeral technologies that people used to exploit these important ecosystems. As human populations expanded along tropical coastal areas, however, the influence of coastal people on coral reefs grew rapidly. Deforestation and coastal agriculture reduced coastal water quality, with many fringing coral reefs disappearing as impacts grew. Increasing numbers of fishers with increasingly advanced technologies exploited tropical coastal fisheries so that many marine species declined dramatically. These activities have removed some functional groups to the point where ecological transformations away from coral-dominated communities increasingly occurred. Shipping and marine pollution, as well as ocean warming and acidification from the burning of fossil fuels, have added further stress on tropical marine ecosystems. The latter represents a major threat with even small amounts of change potentially driving the ecological extinction of coral reefs and other marine ecosystems. Given inaction on the core drivers of these changes, the future does not look bright for coral reef ecosystems as we move into the critical phase of the Anthropocene Epoch.