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Survival of symbiotic reef-building corals under global warming requires rapid acclimation or adaptation. The impact of accumulated heat stress was compared across 1643 symbiont communities before and after the 2016 mass bleaching in three coral species and free-living in the environment across ~900 kilometers of the Great Barrier Reef. Resilient reefs (less aerial bleaching than predicted from high satellite sea temperatures) showed low variation in symbioses. Before 2016, heat-tolerant environmental symbionts were common in ~98% of samples and moderately abundant (9 to 40% in samples). In corals, heat-tolerant symbionts were at low abundances (0 to 7.3%) but only in a minority (13 to 27%) of colonies. Following bleaching, environmental diversity doubled (including heat-tolerant symbionts) and increased in one coral species. Communities were dynamic ( Acropora millepora ) and conserved ( Acropora hyacinthus and Acropora tenuis ), including symbiont community turnover and redistribution. Symbiotic restructuring after bleaching occurs but is a taxon-specific ecological opportunity.

The metabolic capabilities of animals have been derived from well-studied model organisms and are generally considered to be well understood. In animals, cysteine is an important amino acid thought to be exclusively synthesized through the transsulfuration pathway. Corals of the genus

The metabolic capabilities of animals have been derived from well-studied model organisms and are generally considered to be well understood. In animals, cysteine is an important amino acid thought to be exclusively synthesized through the transsulfuration pathway. Corals of the genus Acropora have lost cystathionine β-synthase, a key enzyme of the transsulfuration pathway, and it was proposed that Acropora relies on the symbiosis with dinoflagellates of the family Symbiodiniaceae for the acquisition of cysteine. Here, we identify the existence of an alternative pathway for cysteine biosynthesis in animals through the analysis of the genome of the coral Acropora loripes . We demonstrate that these coral proteins are functional and synthesize cysteine in vivo, exhibiting previously unrecognized metabolic capabilities of animals. This pathway is also present in most animals but absent in mammals, arthropods, and nematodes, precisely the groups where most of the animal model organisms belong to, highlighting the risks of generalizing findings from model organisms.

Scleractinian coral populations are increasingly exposed to conditions above their upper thermal limits due to marine heatwaves, contributing to global declines of coral reef ecosystem health. However, historic mass bleaching events indicate there is considerable inter- and intra-specific variation in thermal tolerance whereby species, individual coral colonies and populations show differential susceptibility to exposure to elevated temperatures. Despite this, we lack a clear understanding of how heat tolerance varies across large contemporary and historical environmental gradients, or the selective pressures that underpin this variation. Here we conducted standardised acute heat stress experiments to identify variation in heat tolerance among species and isolated reefs spanning a large environmental gradient across the Coral Sea Marine Park. We quantified the photochemical yield (F

Climate change induced increases in global ocean temperature represent the greatest threat to the persistence of reef ecosystems and most coral populations are projected to experience temperatures above their current bleaching thresholds annually by 2050. Adaptation to higher temperatures is necessary if corals are to persist in a warming future. While many aspects of heat stress have been well studied, few data are available for predicting the capacity for adaptive cross-generational responses in corals. Consistent sets of heat tolerant genomic markers that reliably predict thermal tolerance have yet to be identified. To address this knowledge gap, we quantified the heritability and genetic variation associated with heat tolerance in Platygyra daedalea from the Great Barrier Reef. We tracked the survival of quantitative genetic crosses of larvae in a heat tolerance selection experiment. We also identified allelic shifts in heat-selected survivors compared with paired, non-selected controls. The narrow-sense heritability of survival under heat stress was 0.66 and a total of 1,069 single nucleotide polymorphisms (SNPs) were associated with different survival probabilities. While 148 SNPs were shared between several experimental crosses, no common SNPs were identified for all crosses suggesting that specific combinations of many markers are responsible for heat tolerance. However, we found two regions that overlap with previously identified loci associated with heat tolerance in Persian Gulf populations of P. daedalea reinforcing the importance of these markers for heat tolerance. These results illustrate the importance of high heritability and the complexity of the genomic architecture underpinning host heat tolerance. These findings suggest that this P. daedalea population has the genetic prerequisites for adaptation to increasing temperatures. This study also provides knowledge for the development of high throughput genomic tools to screen for variation within and across populations to enhance adaptation through assisted gene flow and assisted migration.

To understand how environmental conditions and reproductive events affect coral energetic status, seasonal variations in lipid and fatty acid profiles of the common scleractinian coral, Acropora millepora, were studied from pre-spawning in November 2009 until post-spawning in November 2010 at Halfway Island (in the Keppel Island Group, Southern Great Barrier Reef, Australia). Seasonal chlorophyll levels, photosynthetically active radiation (PAR), rainfall and water temperature were major drivers of the overall coral lipid profile, and this was particularly pronounced in correlations with the important, high-energy lipid, triacylglycerol. This likely reflected changing food sources and feeding modes (i.e. phototrophy vs heterotrophy), which corresponds to the opportunistic feeding behaviour of corals. Water temperature was also a major influencer of the coral fatty acid profile. In particular, saturated fatty acids correlated positively with water temperature, while polyunsaturated fatty acids correlated negatively, reflecting cell membrane fluidity regulation, which is necessary for coral to tolerate changing temperatures. Spawning and maternal provisioning also proved to be a major driver of change in the coral lipid profile. The mass spawning events in spring for both 2009 and 2010 caused reductions in the important coral egg constituents: wax ester, triacylglycerol, phosphatidylcholine and fatty acid 10:0. Interestingly, lipid accumulation was significantly lower in the 2010 spawn compared to 2009, possibly due to lower PAR and chlorophyll levels, reflecting reduced photosynthetic activity and phytoplankton availability. Regardless, in 2010, resource provisioning to egg production was greater than in 2009, suggesting increased reproductive effort in the face of environmental stress. This study demonstrates the strong influence of opportunistic heterotrophy and autotrophy and maternal provisioning on the coral lipid profile. Such information is fundamental to understanding the environmental and biochemical processes underlying coral health and predicting how anomalous events and climate-driven changes will affect coral reef assemblages.

Coral-reef ecosystems are experiencing frequent and severe disturbance events that are reducing global coral abundance and potentially overwhelming the natural capacity for reefs to recover. While mitigation strategies for climate warming and other anthropogenic disturbances are implemented, coral restoration programmes are being established worldwide as an additional conservation measure to minimise coral loss and enhance coral recovery. Current restoration efforts predominantly rely on asexually produced coral fragments—a process with inherent practical constraints on the genetic diversity conserved and the spatial scale achieved. Because the resilience of coral communities has hitherto relied on regular renewal with natural recruits, the scaling-up of restoration programmes would benefit from greater use of sexually produced corals, which is an approach that is gaining momentum. Here we review the present state of knowledge of scleractinian coral sexual reproduction in the context of reef restoration, with a focus on broadcast-spawning corals. We identify key knowledge gaps and bottlenecks that currently constrain the sexual production of corals and consider the feasibility of using sexually produced corals for scaling-up restoration to the reef- and reef-system scales.

Reef-forming corals are under threat globally from climate change, leading to changes in sea temperatures with both hot and cold events recorded and projected to increase in frequency and severity in the future. Tolerance to heat and cold exposure has been found to be mutually exclusive in other marine invertebrates, but it is currently unclear whether a trade-off exists between hot and cold thermal tolerance in tropical corals. This study quantified the changes in physiology in Acropora millepora from the central Great Barrier Reef subjected to three temperature treatments; sub-lethal cold, ambient and sub-lethal heat (23.0 °C, 27.0 °C and 29.5 °C, respectively). After 10 weeks, pigment content and Symbiodiniaceae density increased in cold-treated corals but decreased in heat-treated corals relative to corals at ambient conditions. Heat-treated corals gained less mass relative to both ambient and cold-treated corals. These results indicate that the physiological condition of A. millepora corals examined here improved in response to mild cold exposure compared to ambient exposure and decreased under mild heat exposure despite both these temperatures occurring in situ around 15% of the year. The energetic condition of corals in the hotter treatment was reduced compared to both ambient and cooler groups, indicating that corals may be more resilient to mild cold exposure relative to mild heat exposure. The results indicate that the corals shifted their resource allocation in response to temperature treatment, investing more energy into skeletal extension rather than maintenance. No evidence of thermal tolerance trade-offs was found, and cold thermal tolerance was not lost in more heat-tolerant individuals. An enhanced understanding of physiological responses of corals at both ends of the thermal spectrum is important for predicting the resilience of corals under projected climate change conditions.

Humans have long sought to restore species, but little attention has been directed at how to best select a subset of foundation species for maintaining rich assemblages that support ecosystems, like coral reefs and rainforests that are increasingly threatened by environmental change.We propose a two-part hedging approach that selects optimized sets of species for restoration. The first part acknowledges that biodiversity supports ecosystem functions and services, and so it takes precaution against loss by ensuring an even spread of phenotypic traits. The second part maximizes species and ecosystem persistence by weighting species based on characteristics that are known to improve ecological persistence—e.g., abundance, species range and tolerance to environmental change.Using existing phenotypic trait and ecological characteristic data for reef building corals, we identified sets of ecologically persistent species by examining marginal returns in occupancy of phenotypic trait space. We compared optimal sets of species with those from the world’s southern-most coral reef which naturally harbors low coral diversity to show these occupy much of the trait space. Comparison with an existing coral restoration program indicated that current corals used for restoration only cover part of the desired trait space and may be improved by including species with different traits.Synthesis and applications. While there are many possible criteria for selecting species for restoration, the approach proposed here addresses the need to insure against unpredictable losses of ecosystem services by focusing on a wide range of phenotypic traits and ecological characteristics. Furthermore, the flexibility of the approach enables the functional goals of restoration to vary depending on environmental context, stakeholder values, and the spatial and temporal scales at which meaningful impacts can be achieved.

Natural bleaching events provide an opportunity to examine how local scale environmental variation influences bleaching severity and recovery. During the 2020 marine heatwave, we documented widespread and severe coral bleaching (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 owing 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 an 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.Open Research StatementData are not yet provided but are being compiled. Upon acceptance data will be archived on GitHub.

The ability of corals to adapt to global warming may involve trade-offs among the traits that influence their success as the foundational species of coral reefs.

The Great Barrier Reef (GBR), located off the coast of Queensland, Australia, is a UNESCO1 World Heritage site, one of the seven natural wonders of the world and the world’s largest living structure. Spanning 2300 km, it has more than 450 species of corals, 1600 types of fish, and is one of the world’s unique and most biodiverse environments (AIMS 2018). It is estimated that the GBR supports more than 64,000 jobs and contributes more than AU $6.4B/yr to the Australian economy (Deloitte 2017). However, the unprecedented back-to-back bleaching events of 2016 and 2017 led to widespread mortality of shallow water corals (Hughes et al. 2018). While the Great Barrier Reef is still resilient, the projected increase in sea temperatures, forecasts for more frequent coral bleaching, continued outbreaks of crown-of-thorns starfish (COTS) and increasing intensity and frequency of cyclones puts the Great Barrier Reef’s future recovery at high risk. With the relatively recent recognition of a need for urgent activity around GBR coral restoration, the low information base from which we were operating, and the recognised need to learn from the international community on best practice restoration, the first Great Barrier Reef Restoration Symposium (the symposium) was initiated. The symposium brought together restoration practitioners, scientists, engineers, environmental managers, NGOs and industry partners to share experiences, insights and ideas about what worked, what did not, and the knowledge gaps that needed filling in order to help the GBR. The symposium was a collaborative effort between the Tropical Water Quality Hub of the Australian Government’s National Environmental Science Program, the Reef and Rainforest Research Centre, the Reef Restoration and Adaptation Program and the Association of Marine Park Tourism Operators. Additional partners included James Cook University, Reef Ecologic and the Reef Restoration Foundation.

Fatty acids (FA) play a vital role in coral physiology, metabolism and stress resistance. Optimal health requires a balance of fatty acids, and more specifically essential polyunsaturated fatty acids (PUFA), for efficient biochemical and physiological functioning. Therefore, it is necessary to fully assess and evaluate the viability of FA as biomarkers for monitoring the health of coral populations. This study explores seasonal and spatial variation in the abundance of 17 FA in the coral Acropora tenuis, along two water quality gradients on the central Great Barrier Reef. Ratios of key FA varied similarly along the two water quality gradients and were highest in corals from comparatively good water quality conditions. Strong differences in PUFA composition were found between wet and dry seasons, with high percentage n-3 PUFA defining the dry seasons (June 2013 and October 2013) and high percentage n-6 PUFA defining the wet seasons (February 2013 and 2014). Saturated FA and monounsaturated FA concentrations varied with season, positively correlated with Symbiodinium density, and had highest concentrations in corals exposed to relatively poor water quality. Overall, results demonstrate that essential FA and their derived ratios support FA as a potential indicator of coral holobiont health; however, strong seasonal variation may negate FA and their derived ratios as water quality indicators.

To investigate plasticity in biochemical and physiological health attributes of corals, identical colony fragments of the coral Acropora tenuis, from two inshore populations, were exposed to native and novel environmental regimes. Variation in global gene expression (GE) and lipid and fatty acid (FA) composition of surviving colony fragments were quantified after four months. Major FA classes, with the exception of short-chain (C18) polyunsaturated fatty acids (PUFA), decreased in concentration when coral fragments were exposed to lower water quality regardless of their source population. In contrast, a strong effect of source population was detected in the GE profiles of all coral fragments and was enriched with genes associated with translation, ribosome biogenesis and ribosome cellular components. One cluster of co-expressed genes positively correlated with multiple individual FA and included genes involved in developmental processes and cellular pathways. This study demonstrates the strong influence of a source effect defining gene expression relating to basic biological functions, including biosynthetic processing, translation and ribosome biogenesis. However, there is plasticity in FA composition and specific genes relating to elevated health and immunity, which can respond to changes in environmental conditions. These findings suggest hope for future corals, if we can reduce anthropogenic water quality stressors.

Ecosystem-based management on coral reefs has historically focussed on biodiversity conservation through the establishment of marine reserves, but it is increasingly recognised that a subset of species can be key to the maintenance of ecosystem processes and functioning. Specific provisions for these key taxa are essential to biodiversity conservation and resilience-based adaptive management. While a wealth of literature addresses ecosystem functioning on coral reefs, available information covers only a subset of specific taxa, ecological processes and environmental stressors. What is lacking is a comparative assessment across the diverse range of coral reef species to synthesise available knowledge to inform science and management. Here we employed expert elicitation coupled with a literature review to generate the first comprehensive assessment of 70 taxonomically diverse and functionally distinct coral reef species from microbes to top predators to summarise reef functioning. Although our synthesis is largely through the lens of the Great Barrier Reef, Australia, a particularly data-rich system, it is relevant to coral reefs in general. We use this assessment to evaluate which taxa drive processes that maintain a healthy reef and whether management of these taxa is considered a priority (i.e. are they vulnerable?) or is feasible (i.e. can they be managed?). Scientific certainty was scored to weight our recommendations, particularly when certainty was low. We use five case studies to highlight critical gaps in knowledge that limit our understanding of ecosystem functioning. To inform the development of novel management strategies and research objectives, we identify taxa that support positive interactions and enhance ecosystem performance, including those where these roles are currently underappreciated. We conclude that current initiatives effectively capture many priority taxa but that there is significant room to increase opportunities for underappreciated taxa in both science and management to maximally safeguard coral reef functioning.

Reef-building corals are keystone species that are threatened by anthropogenic stresses including climate change. To investigate corals’ responses to stress and other aspects of their biology, numerous genomic and transcriptomic studies have been performed, generating many hypotheses about the roles of particular genes and molecular pathways. However, it has not generally been possible to test these hypotheses rigorously because of the lack of genetic tools for corals or closely related cnidarians. CRISPR technology seems likely to alleviate this problem. Indeed, we show here that microinjection of single-guide RNA/Cas9 ribonucleoprotein complexes into fertilized eggs of the coral Acropora millepora can produce a sufficiently high frequency of mutations to detect a clear phenotype in the injected generation. Based in part on experiments in a sea-anemone model system, we targeted the gene encoding Heat Shock Transcription Factor 1 (HSF1) and obtained larvae in which >90% of the gene copies were mutant. The mutant larvae survived well at 27 °C but died rapidly at 34 °C, a temperature that did not produce detectable mortality over the duration of the experiment in wild-type (WT) larvae or larvae injected with Cas9 alone. We conclude that HSF1 function (presumably its induction of genes in response to heat stress) plays an important protective role in corals. More broadly, we conclude that CRISPR mutagenesis in corals should allow wide-ranging and rigorous tests of gene function in both larval and adult corals.

Coral reef ecosystems are under increasing pressure from local and regional stressors and a changing climate. Current management focuses on reducing stressors to allow for natural recovery, but in many areas where coral reefs are damaged, natural recovery can be restricted, delayed or interrupted because of unstable, unconsolidated coral fragments, or rubble. Rubble fields are a natural component of coral reefs, but repeated or high-magnitude disturbances can prevent natural cementation and consolidation processes, so that coral recruits fail to survive. A suite of interventions have been used to target this issue globally, such as using mesh to stabilise rubble, removing the rubble to reveal hard substrate and deploying rocks or other hard substrates over the rubble to facilitate recruit survival. Small, modular structures can be used at multiple scales, with or without attached coral fragments, to create structural complexity and settlement surfaces. However, these can introduce foreign materials to the reef, and a limited understanding of natural recovery processes exists for the potential of this type of active intervention to successfully restore local coral reef structure. This review synthesises available knowledge about the ecological role of coral rubble, natural coral recolonisation and recovery rates and the potential benefits and risks associated with active interventions in this rapidly evolving field. Fundamental knowledge gaps include baseline levels of rubble, the structural complexity of reef habitats in space and time, natural rubble consolidation processes and the risks associated with each intervention method. Any restoration intervention needs to be underpinned by risk assessment, and the decision to repair rubble fields must arise from an understanding of when and where unconsolidated substrate and lack of structure impair natural reef recovery and ecological function. Monitoring is necessary to ascertain the success or failure of the intervention and impacts of potential risks, but there is a strong need to specify desired outcomes, the spatial and temporal context and indicators to be measured. With a focus on the Great Barrier Reef, we synthesise the techniques, successes and failures associated with rubble stabilisation and the use of small structures, review monitoring methods and indicators, and provide recommendations to ensure that we learn from past projects.

Conservation help from genomics Corals worldwide are under threat from rising sea temperatures and pollution. One response to heat stress is coral bleaching—the loss of photosynthetic endosymbionts that provide energy for the coral. Fuller et al. present a high-resolution genome of the coral Acropora millepora (see the Perspective by Bay and Guerrero). They were able to perform population genetic analyses with samples sequenced at lower coverage and conduct genome-wide association studies. These data were combined to generate a polygenic risk score for bleaching that can be used in coral conservation. Science this issue p. eaba4674 ; see also p. 249

Research with coral embryos and larvae often requires laborious manual counting and sorting of individual specimens, usually via microscopy. Because many coral species spawn only once per year during a narrow temporal window, sample processing is a time-limiting step for research on the early life-history stages of corals. Flow cytometry, an automated technique for measuring and sorting particles, cells, and cell-clusters, is a potential solution to this bottleneck. Yet most flow cytometers do not accommodate live organisms of the size of most coral embryos (> 250 µm), and sample processing is often destructive. Here we tested the ability of a large-particle flow cytometer with a gentle pneumatic sorting mechanism to process and spectrally sort live and preserved Montipora capitata coral embryos and larvae. Average survival rates of mechanically-sorted larvae were over 90% and were comparable to those achieved by careful hand-sorting. Preserved eggs and embryos remained intact throughout the sorting process and were successfully sorted based on real-time size and fluorescence detection. In-line bright-field microscopy images were captured for each sample object as it passed through the flow-cell, enabling the identification of early-stage embryos (2-cell to morula stage). Samples were counted and sorted at an average rate of 4 s larva−1 and as high as 0.2 s larva−1 for high-density samples. Results presented here suggest that large-particle flow cytometry has the potential to significantly increase efficiency and accuracy of data collection and sample processing during time-limited coral spawning events, facilitating larger-scale and higher-replication studies with an expanded number of species.

Marine heat waves are increasing in magnitude, duration, and frequency as a result of climate change and are the principal global driver of mortality in reef-building corals. Resilience-based genetic management may increase coral heat tolerance, but it is unclear how temperature responses are regulated at the genome level and thus how corals may adapt to warming naturally or through selective breeding. Here we combine phenotypic, pedigree, and genomic marker data from colonies sourced from a warm reef on the Great Barrier Reef reproductively crossed with conspecific colonies from a cooler reef to produce combinations of warm purebreds and warm-cool hybrid larvae and juveniles. Interpopulation breeding created significantly greater genetic diversity across the coral genome compared to breeding between populations and maintained diversity in key regions associated with heat tolerance and fitness. High-density genome-wide scans of single nucleotide polymorphisms (SNPs) identified alleles significantly associated with larval families reared at 27.5°C (87-2,224 loci), including loci putatively associated with proteins involved in responses to heat stress (cell membrane formation, metabolism, and immune responses). Underlying genetics of these families explained 43% of PCoA multilocus variation in survival, growth, and bleaching responses at 27.5°C and 31°C at the juvenile stage. Genetic marker contribution to total variation in fitness traits (narrow-sense heritability) was high for survival but not for growth and bleaching in juveniles, with heritability of these traits being higher at 31°C relative to 27.5°C. While based on only a limited number of crosses, the mechanistic understanding presented here demonstrates that allele frequencies are affected by one generation of selective breeding, key information for the assessments of genetic intervention feasibility and modelling of reef futures.

The rate of coral reef degradation from climate change is accelerating and, as a consequence, a number of interventions to increase coral resilience and accelerate recovery are under consideration. Acropora spathulata coral colonies that survived mass bleaching in 2016 and 2017 were sourced from a bleaching-impacted and warmer northern reef on the Great Barrier Reef (GBR). These individuals were reproductively crossed with colonies collected from a recently bleached but historically cooler central GBR reef to produce pure and crossbred offspring groups (warm–warm, warm–cool and cool–warm). We tested whether corals from the warmer reef produced more thermally tolerant hybrid and purebred offspring compared with crosses produced with colonies sourced from the cooler reef and whether different symbiont taxa affect heat tolerance. Juveniles were infected with Symbiodinium tridacnidorum, Cladocopium goreaui and Durusdinium trenchii and survival, bleaching and growth were assessed at 27.5°C and 31°C. The contribution of host genetic background and symbiont identity varied across fitness traits. Offspring with either both or one parent from the northern population exhibited a 13- to 26-fold increase in survival odds relative to all other treatments where survival probability was significantly influenced by familial cross identity at 31°C but not 27.5°C (Kaplan–Meier P=0.001 versus 0.2). If in symbiosis with D. trenchii, a warm sire and cool dam provided the best odds of juvenile survival. Bleaching was predominantly driven by Symbiodiniaceae treatment, where juveniles hosting D. trenchii bleached significantly less than the other treatments at 31°C. The greatest overall fold-benefits in growth and survival at 31°C occurred in having at least one warm dam and in symbiosis with D. trenchii. Juveniles associated with D. trenchii grew the most at 31°C, but at 27.5°C, growth was fastest in juveniles associated with C. goreaui. In conclusion, selective breeding with warmer GBR corals in combination with algal symbiont manipulation can assist in increasing thermal tolerance on cooler but warming reefs. Such interventions have the potential to improve coral fitness in warming oceans. This article has an associated First Person interview with the first author of the paper., Summary: Survival of coral juveniles under heat stress can be significantly improved by breeding corals from historically warmer reefs with those from cooler reefs, and the provisioning with heat tolerant symbionts.

Coral cover has declined markedly in the recent past in many regions of the world, including the Great Barrier Reef (GBR), Australia. The major causes of this decline are generally considered to be mortality associated with large-scale severe disturbances (i.e. catastrophic mortality), such as Acanthaster planci outbreaks, cyclones and bleaching. However, background rates of mortality (i.e. not associated with catastrophic disturbance), are rarely quantified, but without these it is difficult to assess the relative importance of these 2 types of mortality (catastrophic and background). We quantified spatial and temporal variation in catastrophic and background whole-colony mortality of the common reef coral Acropora millepora over 24 mo at 2 sites in 3 regions separated by 700 km along the GBR. The study period included 2 cyclones and a flood. Overall mortality rates were exceptionally high. Of 180 colonies tagged in April 2009, only 36 (20%) were alive in April 2011, and 68% of this mortality occurred in intervals following the 3 large disturbances. Background mortality rates were also high in the Palm Islands, where they approached 40% yr-1 compared to

Mass coral bleaching has emerged in the 21st century as the greatest threat to the health of the world's reefs. A sophisticated process understanding of bleaching at the polyp scale has now been achieved through laboratory and field studies, but this knowledge is yet to be applied in mechanistic models of shelf-scale reef systems. In this study we develop a mechanistic model of the coral-symbiont relationship that considers temperature-mediated build-up of reactive oxygen species due to excess light, leading to zooxanthellae expulsion. The model explicitly represents the coral host biomass, as well as zooxanthellae biomass, intracellular pigment concentration, nutrient status, and the state of reaction centres and the xanthophyll cycle. Photophysiological processes represented include photoadaptation, xanthophyll cycle dynamics, and reaction centre state transitions. The mechanistic model of the coral-symbiont relationship is incorporated into a ∼1 km resolution coupled hydrodynamic – biogeochemical model that encompasses the entire ∼2000 km length of the Great Barrier Reef. A simulation of the 2016 bleaching event shows the model is able to capture the broadscale features of the observed bleaching, but fails to capture bleaching on offshore reefs due to the model's grid being unable to resolve the bathymetry of shallow platforms surrounded by deep water. To further analyse the model behaviour, a ∼200 m resolution nested simulation of Davies Reef (18°49′ S, 147°38′ E) is undertaken. We use this nested model to demonstrate the depth gradient in zooxanthellae response to thermal stress. Finally, we discuss the uncertainties in the bleaching model, which lie primarily in quantifying the link between reactive oxygen build-up and the expulsion process. Through the mechanistic representation of environmental forcing, this model of coral bleaching applied in realistic environmental conditions has the potential to generate more detailed predictions than the presently-available satellite-based coral bleaching metrics, and can be used to evaluate proposed management strategies.

The mechanisms resulting in the breakdown of the coral symbiosis once the process of bleaching has been initiated remain unclear. Distinguishing the process of symbiont loss from the thermal stress response may shed light on the cellular and molecular pathways involved in each process. This study examined physiological changes and global gene expression patterns associated with white patch syndrome (WPS) in Porites lobata, which manifests in localized bleaching independent of thermal stress. In addition, a meta-analysis of global gene expression studies in other corals and anemones was used to contrast differential regulation as a result of disease and thermal stress from patterns correlated with symbiotic state. Symbiont density, chlorophyll a content, holobiont productivity, instant calcification rate, and total host protein content were uniformly reduced in WPS relative to healthy tissue. While expression patterns associated with WPS were secondary to fixed effects of source colony, specific functional enrichments combined with a lack of immune regulation suggest that the viral infection putatively giving rise to this condition affects symbiont rather than host cells. Expression in response to WPS also clustered independently of patterns in white syndrome impacted A. hyacinthus, further supporting a distinct aetiology of this syndrome. Expression patterns in WPS-affected tissues were significantly correlated with prior studies that examined short-term thermal stress responses independent of symbiotic state, suggesting that the majority of expression changes reflect a nonspecific stress response. Across studies, the magnitude and direction of expression change among particular functional enrichments suggests unique responses to stressor duration and highlights distinct responses to bleaching in an anemone model.

The mechanisms resulting in the breakdown of the coral symbiosis once the process of bleaching has been initiated remain unclear. Distinguishing symbiont loss from the abiotic stress response may shed light on the cellular and molecular pathways involved in each process. This study examined physiological changes and global gene expression patterns associated with white patch syndrome (WPS) in P. lobata, which manifests in localized bleaching independent of thermal stress. In addition, a meta-analysis of global gene expression studies in other corals and anemones was used to contrast differential regulation as a result of abiotic stress from expression patterns correlated with symbiotic state. Symbiont density, chlorophyll a content, holobiont productivity, instant calcification rate, and total host protein content were uniformly reduced in WPS relative to healthy tissue. While expression patterns associated with WPS were secondary to fixed effects of source colony, specific functional enrichments suggest that the viral infection putatively giving rise to this condition affects symbiont rather than host cells. The meta-analysis revealed that expression patterns in WPS-affected tissues were significantly correlated with prior studies examining short-term thermal stress responses. This correlation was independent of symbiotic state, as the strongest correlations were found between WPS adults and both symbiotic adult and aposymbiotic coral larvae experiencing thermal stress, suggesting that the majority of expression changes reflect a non-specific stress response. Across studies, the magnitude and direction of expression change among particular functional enrichments suggests unique responses to stressor duration, and highlights unique responses to bleaching in an anemone model which engages in a non-obligate symbiosis.

Although reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coralAcropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperonesacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

This manuscript was improved by constructive comments from the Responsible Editor and 2 anonymous reviewers. This study was supported by the Endeavour International and JCU Postgraduate Research Scholarship to K.M.Q., the Australian Research Council grant, through the ARC Centre of Excellence for Coral Reef Studies, to B.L.W., and by funding from the Australian Institute of Marine Science to L.K.B.

Active restoration initiatives are increasingly considered in natural resource management. Laboratory-reared coral larvae and recruits have been proposed for stock production but it is unknown if their use impacts subsequent symbiosis once transplanted to the reef. We exposed laboratory and field settled aposymbiotic recruits (recently settled

Recently, corals on the Great Barrier (GBR) have suffered mass bleaching. The link between ocean warming and coral bleaching is understood to be due to temperature-dependence of complex physiological processes in the coral host and algal symbiont. Here we use a coupled catchment-hydrodynamic-biogeochemical model, with detailed zooxanthellae photophysiology including photoadaptation, photoacclimation and reactive oxygen build-up, to investigate whether natural and anthropogenic catchment loads impact on coral bleaching on the GBR. For the wet season of 2017, simulations show the cross-shelf water quality gradient, driven by both natural and anthropogenic loads, generated a contrasting zooxanthellae physiological state on inshore versus mid-shelf reefs. The relatively small catchment flows and loads delivered during 2017, however, generated small river plumes with limited impact on water quality. Simulations show the removal of the anthropogenic fraction of the catchment loads delivered in 2017 would have had a negligible impact on bleaching rates.

Little is known about the potential for acclimatization or adaptation of corals to ocean acidification and even less about the molecular mechanisms underpinning these processes. Here, we examine global gene expression patterns in corals and their intracellular algal symbionts from two replicate population pairs in Papua New Guinea that have undergone long-term acclimatization to natural variation in pCO2 . In the coral host, only 61 genes were differentially expressed in response to pCO2 environment, but the pattern of change was highly consistent between replicate populations, likely reflecting the core expression homeostasis response to ocean acidification. Functional annotations highlight lipid metabolism and a change in the stress response capacity of corals as key parts of this process. Specifically, constitutive downregulation of molecular chaperones was observed, which may impact response to combined climate change-related stressors. Elevated CO2 has been hypothesized to benefit photosynthetic organisms but expression changes of in hospite Symbiodinium in response to acidification were greater and less consistent among reef populations. This population-specific response suggests hosts may need to adapt not only to an acidified environment, but also to changes in their Symbiodinium populations that may not be consistent among environments, adding another challenging dimension to the physiological process of coping with climate change.

This study explores how plasticity in biochemical attributes, used as indicators of health and condition, enables the coral Acropora tenuis to respond to differing water quality regimes in inshore regions of the Great Barrier Reef. Health attributes were monitored along a strong and weak water quality gradient, each with three reefs at increasing distances from a major river source. Attributes differed significantly only along the strong gradient; corals grew fastest, had the least dense skeletons, highest symbiont densities and highest lipid concentrations closest to the river mouth, where water quality was poorest. High nutrient and particulate loads were only detrimental to skeletal density, which decreased as linear extension increased, highlighting a trade-off. Our study underscores the importance of assessing multiple health attributes in coral reef monitoring. For example, autotrophic indices are poor indicators of coral health and condition, but improve when combined with attributes like lipid content and biomass.

Sexual reproduction is vital for population persistence, even in organisms that can reproduce asexually, such as corals. Yet, information on spatial and temporal variation in reproductive traits is surprisingly rare. Here, we examined spatial and temporal variation in fecundity, defined as the number of oocytes per polyp, in the staghorn coral Acropora millepora over 2 yr among 6 populations separated by over 700 km on inshore reefs on the Great Barrier Reef. Variation in fecundity was greatest at small spatial scales: there were pronounced differences in fecundity within and among colonies at each site but little variation at the site or regional scale. This suggests that fecundity is affected by environmental variables that also vary at small scales, such as light and water flow, rather than variables that vary on a regional scale, such as temperature. Colony fecundity in the first year was a good predictor of colony fecundity in the second year, suggesting that some genotypes are more fecund than others. This research suggests that factors operating at the scale of the individual, such as microhabitat differences in flow or light, or genetic identity, are the main cause of variation in fecundity among coral colonies.