Rapid Acclimation Ability Mediated by Transcriptome Changes in Reef-Building Corals

Urbanisation-associated shifts in the avian metabolome within the annual cycle

While organisms have evolved to cope with predictable changes in the environment, the rapid rate of current global change presents numerous novel and unpredictable stressors to which organisms have had less time to adapt. To persist in the urban environment, organisms must modify their physiology, morphology and behaviour accordingly. Metabolomics offers great potential for characterising organismal responses to natural and anthropogenic stressors at the systems level and can be applied to any species, even without genomic knowledge. Using metabolomic profiling of blood, we investigated how two closely related species of passerine bird respond to the urban environment. Great tits Parus major and blue tits Cyanistes caeruleus residing in urban and forest habitats were sampled during the breeding (spring) and non-breeding (winter) seasons across replicated sites in southern Sweden. During breeding, differences in the plasma metabolome between urban and forest birds were characterised by higher levels of amino acids in urban-dwelling tits and higher levels of fatty acyls in forest-dwelling tits. The suggested higher rates of fatty acid oxidation in forest tits could be driven by habitat-associated differences in diet and could explain the higher reproductive investment and success of forest tits. High levels of amino acids in breeding urban tits could reflect the lack of lipid-rich caterpillars in the urban environment and a dietary switch to protein-rich spiders, which could be of benefit for tackling inflammation and oxidative stress associated with pollution. In winter, metabolomic profiles indicated lower overall levels of amino acids and fatty acyls in urban tits, which could reflect relaxed energetic demands in the urban environment. Our metabolomic profiling of two urban-adapted species suggests that their metabolism is modified by urban living, though whether these changes represent adaptative or non-adaptive mechanisms to cope with anthropogenic challenges remains to be determined.

Life-stage specificity and temporal variations in transcriptomes and DNA methylomes of the reef coral Pocillopora damicornis in response to thermal acclimation

Understanding the acclimation capacity of reef corals across generations to thermal stress and its underlying molecular underpinnings could provide insights into their resilience and adaptive responses to future climate change. Here, we acclimated adult brooding coral Pocillopora damicornis to high temperature (32 °C vs. 29 °C) for three weeks and analyzed the changes in phenotypes, transcriptomes and DNA methylomes of adult corals and their brooded larvae. Results showed that although adult corals did not show noticeable bleaching after thermal exposure, they released fewer but larger larvae. Interestingly, larval cohorts from two consecutive lunar days exhibited contrasting physiological resistance to thermal stress, as evidenced by the divergent responses of area-normalized symbiont densities and photochemical efficiency to thermal stress. RNA-seq and whole-genome bisulfite sequencing revealed that adult and larval corals mounted distinct transcriptional and DNA methylation changes in response to thermal stress. Remarkably, larval transcriptomes and DNA methylomes also varied greatly among lunar days and thermal treatments, aligning well with their physiological metrics. Overall, our study shows that changes in transcriptomes and DNA methylomes in response to thermal acclimation can be highly life stage-specific. More importantly, thermally-acclimated adult corals could produce larval offspring with temporally contrasting photochemical performance and thermal resilience, and such variations in larval phenotypes are associated with differential transcriptomes and DNA methylomes, and are likely to increase the likelihood of reproductive success and plasticity of larval propagules under thermal stress.

Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont

Since their radiation in the Middle Triassic period ∼240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.

Synergistic response to climate stressors in coral is associated with genotypic variation in baseline expression

As environments are rapidly reshaped due to climate change, phenotypic plasticity plays an important role in the ability of organisms to persist and is considered an especially important acclimatization mechanism for long-lived sessile organisms such as reef-building corals. Often, this ability of a single genotype to display multiple phenotypes depending on the environment is modulated by changes in gene expression, which can vary in response to environmental changes via two mechanisms: baseline expression and expression plasticity. We used transcriptome-wide expression profiling of eleven genotypes of common-gardened Acropora cervicornis to explore genotypic variation in the expression response to thermal and acidification stress, both individually and in combination. We show that the combination of these two stressors elicits a synergistic gene expression response, and that both baseline expression and expression plasticity in response to stress show genotypic variation. Additionally, we demonstrate that frontloading of a large module of coexpressed genes is associated with greater retention of algal symbionts under combined stress. These results illustrate that variation in the gene expression response of individuals to climate change stressors can persist even when individuals have shared environmental histories, affecting their performance under future climate change scenarios.

Genomics for monitoring and understanding species responses to global climate change

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.

Physiological and microbiome adaptation of coral Turbinaria peltata in response to marine heatwaves

Against the backdrop of global warming, marine heatwaves are projected to become increasingly intense and frequent. This trend poses a potential threat to the survival of corals and the maintenance of entire coral reef ecosystems. Despite extensive evidence for the resilience of corals to heat stress, their ability to withstand repeated heatwave events has not been determined. In this study, we examined the responses and resilience of Turbinaria peltata to repeated exposure to marine heatwaves, with a focus on physiological parameters and symbiotic microorganisms. In the first heatwave, from a physiological perspective, T. peltata showed decreases in the Chl a content and endosymbiont density and significant increases in GST, caspase-3, CAT, and SOD levels (p < .05), while the effects of repeated exposure on heatwaves were weaker than those of the initial exposure. In terms of bacteria, the abundance of Leptospira, with the potential for pathogenicity and intracellular parasitism, increased significantly during the initial exposure. Beneficial bacteria, such as Achromobacter arsenitoxydans and Halomonas desiderata increased significantly during re-exposure to the heatwave. Overall, these results indicate that T. peltata might adapt to marine heatwaves through physiological regulation and microbial community alterations.

Adaptation strategies of relatively high-latitude marginal reef corals in response to severe temperature fluctuations

The large seasonal temperature fluctuations caused by global warming and frequent marine heatwaves pose new challenges to survival of relatively high-latitude marginal reef corals. However, the adaptation strategies of high-latitude marginal corals are not fully understood. We employed integrated approach to investigate the response mechanism of hosts, Symbiodiniaceae, and symbiotic bacteria of marginal reef corals Acropora pruinosa and Pavona decussate in response to large seasonal temperature fluctuations. The coral holobiont maintained a high level of immunity to adapt to seasonal pressure by increasing Symbiodiniaceae energy supply. The symbiotic Symbiodiniaceae of two coral was dominated by C1 subgroup, and was stable across seasons. The α-diversity of symbiotic bacteria P. decussata and A. pruinosa in summer was higher than that in winter. The symbiotic bacterial community of two coral reorganized during different seasons. Scleractinian corals improve adaptability to seasonal stress by increasing energy supply to maintain high levels of immunity, increasing symbiotic bacterial α-diversity, and changing dominant bacteria. This study demonstrates the adaptation strategies of marginal reef corals to seasonal temperature fluctuations and provides novel insights into the study of the adaptation of corals and relatively high-latitude coral refuges in the context of global warming and intensified marine heatwaves.

Acute heat priming promotes short-term climate resilience of early life stages in a model sea anemone

Across diverse taxa, sublethal exposure to abiotic stressors early in life can lead to benefits such as increased stress tolerance upon repeat exposure. This phenomenon, known as hormetic priming, is largely unexplored in early life stages of marine invertebrates, which are increasingly threatened by anthropogenic climate change. To investigate this phenomenon, larvae of the sea anemone and model marine invertebrate Nematostella vectensis were exposed to control (18 °C) or elevated (24 °C, 30 °C, 35 °C, or 39 °C) temperatures for 1 h at 3 days post-fertilization (DPF), followed by return to control temperatures (18 °C). The animals were then assessed for growth, development, metabolic rates, and heat tolerance at 4, 7, and 11 DPF. Priming at intermediately elevated temperatures (24 °C, 30 °C, or 35 °C) augmented growth and development compared to controls or priming at 39 °C. Indeed, priming at 39 °C hampered developmental progression, with around 40% of larvae still in the planula stage at 11 DPF, in contrast to 0% for all other groups. Total protein content, a proxy for biomass, and respiration rates were not significantly affected by priming, suggesting metabolic resilience. Heat tolerance was quantified with acute heat stress exposures, and was significantly higher for animals primed at intermediate temperatures (24 °C, 30 °C, or 35 °C) compared to controls or those primed at 39 °C at all time points. To investigate a possible molecular mechanism for the observed changes in heat tolerance, the expression of heat shock protein 70 (HSP70) was quantified at 11 DPF. Expression of HSP70 significantly increased with increasing priming temperature, with the presence of a doublet band for larvae primed at 39 °C, suggesting persistent negative effects of priming on protein homeostasis. Interestingly, primed larvae in a second cohort cultured to 6 weeks post-fertilization continued to display hormetic growth responses, whereas benefits for heat tolerance were lost; in contrast, negative effects of short-term exposure to extreme heat stress (39 °C) persisted. These results demonstrate that some dose-dependent effects of priming waned over time while others persisted, resulting in heterogeneity in organismal performance across ontogeny following priming. Overall, these findings suggest that heat priming may augment the climate resilience of marine invertebrate early life stages via the modulation of key developmental and physiological phenotypes, while also affirming the need to limit further anthropogenic ocean warming.

Response of resistant larvae of the coral Acropora tenuis to future thermal stress

Seawater temperatures are rising rapidly and severely due to climate change, negatively affecting coral reef communities. The persistence of coral populations depends on their success during the early life stages. Thermal conditioning during the larval stage can increase coral larvae's ability to tolerate high temperatures in subsequent stages. We studied the response of resistant larvae of Acropora tenuis to thermal stress to increase their thermal tolerance during the juvenile stage. Larvae were exposed to ambient (∼26 °C) and thermal stress (∼31 °C) temperatures. Then, settlement success on preconditioned tiles was determined. After 28 days at ambient temperature, the juveniles were exposed to thermal stress for 14 days, and their survival was assessed. Our results showed that thermal stress in the larval stage did not alter the thermal tolerance of juveniles, and they could not acclimate to heat stress. As a result, the summer's heat waves could potentially threaten their resilience.

Metabolomic signatures of corals thriving across extreme reef habitats reveal strategies of heat stress tolerance

Anthropogenic stressors continue to escalate worldwide, driving unprecedented declines in reef environmental conditions and coral health. One approach to better understand how corals can function in the future is to examine coral populations that thrive within present day naturally extreme habitats. We applied untargeted metabolomics (gas chromatography-mass spectrometry (GC-MS)) to contrast metabolite profiles of Pocillopora acuta colonies from hot, acidic and deoxygenated mangrove environments versus those from adjacent reefs. Under ambient temperatures, P. acuta predominantly associated with endosymbionts of the genera Cladocopium (reef) or Durusdinium (mangrove), exhibiting elevated metabolism in mangrove through energy-generating and biosynthesis pathways compared to reef populations. Under transient heat stress, P. acuta endosymbiont associations were unchanged. Reef corals bleached and exhibited extensive shifts in symbiont metabolic profiles (whereas host metabolite profiles were unchanged). By contrast, mangrove populations did not bleach and solely the host metabolite profiles were altered, including cellular responses in inter-partner signalling, antioxidant capacity and energy storage. Thus mangrove P. acuta populations resist periodically high-temperature exposure via association with thermally tolerant endosymbionts coupled with host metabolic plasticity. Our findings highlight specific metabolites that may be biomarkers of heat tolerance, providing novel insight into adaptive coral resilience to elevated temperatures.

The Influence of Symbiosis on the Proteome of the Exaiptasia Endosymbiont Breviolum minutum

The cellular mechanisms responsible for the regulation of nutrient exchange, immune response, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved. Here, we employed liquid chromatography-mass spectrometry to elucidate proteomic changes associated with symbiosis in Breviolum minutum, a native symbiont of the sea anemone Exaiptasia diaphana ('Aiptasia'). We manipulated nutrients available to the algae in culture and to the holobiont in hospite (i.e., in symbiosis) and then monitored the impacts of our treatments on host-endosymbiont interactions. Both the symbiotic and nutritional states had significant impacts on the B. minutum proteome. B. minutum in hospite showed an increased abundance of proteins involved in phosphoinositol metabolism (e.g., glycerophosphoinositol permease 1 and phosphatidylinositol phosphatase) relative to the free-living alga, potentially reflecting inter-partner signalling that promotes the stability of the symbiosis. Proteins potentially involved in concentrating and fixing inorganic carbon (e.g., carbonic anhydrase, V-type ATPase) and in the assimilation of nitrogen (e.g., glutamine synthase) were more abundant in free-living B. minutum than in hospite, possibly due to host-facilitated access to inorganic carbon and nitrogen limitation by the host when in hospite. Photosystem proteins increased in abundance at high nutrient levels irrespective of the symbiotic state, as did proteins involved in antioxidant defences (e.g., superoxide dismutase, glutathione s-transferase). Proteins involved in iron metabolism were also affected by the nutritional state, with an increased iron demand and uptake under low nutrient treatments. These results detail the changes in symbiont physiology in response to the host microenvironment and nutrient availability and indicate potential symbiont-driven mechanisms that regulate the cnidarian-dinoflagellate symbiosis.

Short-term improvement of heat tolerance in naturally growing Acropora corals in Okinawa

Mass bleaching and subsequent mortality of reef corals by heat stress has increased globally since the late 20th century, due to global warming. Some experimental studies have reported that corals may increase heat tolerance for short periods, but only a few such studies have monitored naturally-growing colonies. Therefore, we monitored the survival, growth, and bleaching status of Acropora corals in fixed plots by distinguishing individual colonies on a heat-sensitive reef flat in Okinawa, Japan. The level of heat stress, assessed by the modified version of degree heating week duration in July and August, when the seawater temperature was the highest, was minimally but significantly higher in 2017 than in 2016; however, the same colonies exhibited less bleaching and mortality in 2017 than in 2016. Another study conducted at the same site showed that the dominant unicellular endosymbiotic algal species did not change before and after the 2016 bleaching, indicating that shifting and switching of the Symbiodiniaceae community did not contribute to improved heat tolerance. Colonies that suffered from partial mortality in 2016 were completely bleached at higher rates in 2017 than those without partial mortality in 2016. The present results suggest that either genetic or epigenetic changes in coral hosts and/or algal symbionts, or the shifting or switching of microbes other than endosymbionts, may have improved coral holobiont heat tolerance.

Learning from the past is not enough to survive present and future bleaching threshold temperatures

In the past decade, the frequency of mass coral bleaching events has increased due to seawater temperature anomalies persisting for longer periods. Coral survival from temperature anomalies has been based on how each species in each location responds to stress, which is unique to individual species and may be due to the way stressful experiences accumulate through time in the form of ecological and physiological memory. A deeper understanding of ecological and physiological memory in corals is necessary to understand their survival strategies into the future. Laboratory experiments can help us simulate seawater temperatures experienced by corals in the past and compare their responses to those of the present and future. In this study, we sampled corals with different life history traits from one location perturbed by seawater temperature incursions (variable site) and from a second, relatively undisturbed location (stable site). We sampled across two seasons to observe the responses to bleaching threshold temperatures in the past (1998-29 °C), present (2018-31 °C), and future (2050-33 °C). Corals were healthy at 29 °C and 31 °C, but a fast-growing, temperature-susceptible coral species experienced high mortality at 33 °C compared to a slow-growing, temperature-resistant coral species. Moreover, corals from the variable site and during the spring season fared better under temperature stress. The results of this study provide insight into the possible role of life-history traits on coral's response to seasons and locations in terms of memory to long-term and short-term thermal anomalies and climate change.

Exploring the response of a key Mediterranean gorgonian to heat stress across biological and spatial scales

Understanding the factors and processes that shape intra-specific sensitivity to heat stress is fundamental to better predicting the vulnerability of benthic species to climate change. Here, we investigate the response of a habitat-forming Mediterranean octocoral, the red gorgonian Paramuricea clavata (Risso, 1826) to thermal stress at multiple biological and geographical scales. Samples from eleven P. clavata populations inhabiting four localities separated by hundreds to more than 1500 km of coast and with contrasting thermal histories were exposed to a critical temperature threshold (25 °C) in a common garden experiment in aquaria. Ten of the 11 populations lacked thermotolerance to the experimental conditions provided (25 days at 25 °C), with 100% or almost 100% colony mortality by the end of the experiment. Furthermore, we found no significant association between local average thermal regimes nor recent thermal history (i.e., local water temperatures in the 3 months prior to the experiment) and population thermotolerance. Overall, our results suggest that local adaptation and/or acclimation to warmer conditions have a limited role in the response of P. clavata to thermal stress. The study also confirms the sensitivity of this species to warm temperatures across its distributional range and questions its adaptive capacity under ocean warming conditions. However, important inter-individual variation in thermotolerance was found within populations, particularly those exposed to the most severe prior marine heatwaves. These observations suggest that P. clavata could harbor adaptive potential to future warming acting on standing genetic variation (i.e., divergent selection) and/or environmentally-induced phenotypic variation (i.e., intra- and/or intergenerational plasticity).

Evidence for adaptive morphological plasticity in the Caribbean coral, Acropora cervicornis

Genotype-by-environment interactions (GxE) indicate that variation in organismal traits cannot be explained by fixed effects of genetics or site-specific plastic responses alone. For tropical coral reefs experiencing dramatic environmental change, identifying the contributions of genotype, environment, and GxE on coral performance will be vital for both predicting persistence and developing restoration strategies. We quantified the impacts of G, E, and GxE on the morphology and survival of the endangered coral, Acropora cervicornis, through an in situ transplant experiment exposing common garden (nursery)-raised clones of ten genotypes to nine reef sites in the Florida Keys. By fate-tracking outplants over one year with colony-level 3D photogrammetry, we uncovered significant GxE on coral size, shape, and survivorship, indicating that no universal winner exists in terms of colony performance. Rather than differences in mean trait values, we found that individual-level morphological plasticity is adaptive in that the most plastic individuals also exhibited the fastest growth and highest survival. This indicates that adaptive morphological plasticity may continue to evolve, influencing the success of A. cervicornis and resulting reef communities in a changing climate. As focal reefs are active restoration sites, the knowledge that variation in phenotype is an important predictor of performance can be directly applied to restoration planning. Taken together, these results establish A. cervicornis as a system for studying the ecoevolutionary dynamics of phenotypic plasticity that also can inform genetic- and environment-based strategies for coral restoration.

Compound Extreme Events Induce Rapid Mortality in a Tropical Sea Urchin

AbstractThe frequency, magnitude, and duration of marine heatwaves and deoxygenation events are increasing globally. Recent research suggests that their co-occurrence is more common than previously thought and that their combination can have rapid, dire biological impacts. We used the sea urchin Echinometra lucunter to determine whether mortality occurs faster when deoxygenation events are combined with extreme heating (compound events), compared to deoxygenation events alone. We also tested whether prior exposure to local heatwave conditions accentuates the impacts of compound events. Animals were first exposed for five days to either ambient temperature (28 °C) or a warmer temperature that met the minimum criteria for a local heatwave (30.5 °C). Animals were then exposed to hypoxia, defined as oxygen levels 35% below their average critical oxygen limit, combined with ambient or extreme field temperatures (28 °C, 32 °C). Subsets of animals were removed from the hypoxic treatments every 3 hours for 24 hours to determine how long they could survive. Prior exposure to heatwave conditions did not help or hinder survival under hypoxic conditions, and animals exposed to hypoxia under ambient temperatures experienced little mortality. However, when hypoxia was coupled with extreme temperatures (32 °C), 55% of the animals died within 24 hours. On the reefs at our Panama study site, we found that extreme hypoxic conditions only ever occurred during marine heatwave events, with four compound events occurring in 2018. These results show that short durations (∼1 day) of compound events can be catastrophic and that increases in their duration will severely threaten sea urchin populations.

Expression plasticity regulates intraspecific variation in the acclimatization potential of a reef-building coral

Phenotypic plasticity is an important ecological and evolutionary response for organisms experiencing environmental change, but the ubiquity of this capacity within coral species and across symbiont communities is unknown. We exposed ten genotypes of the reef-building coral Montipora capitata with divergent symbiont communities to four thermal pre-exposure profiles and quantified gene expression before stress testing 4 months later. Here we show two pre-exposure profiles significantly enhance thermal tolerance despite broadly different expression patterns and substantial variation in acclimatization potential based on coral genotype. There was no relationship between a genotype’s basal thermal sensitivity and ability to acquire heat tolerance, including in corals harboring naturally tolerant symbionts, which illustrates the potential for additive improvements in coral response to climate change. These results represent durable improvements from short-term stress hardening of reef-building corals and substantial cryptic complexity in the capacity for plasticity.

Phenotypic plasticity is an important response for organisms experiencing climate change. Here, Drury et al. show that stress-hardening can produce durable improvements in coral thermal tolerance, masking substantial variation between individuals.

Microbiota mediated plasticity promotes thermal adaptation in the sea anemone Nematostella vectensis

At the current rate of climate change, it is unlikely that multicellular organisms will be able to adapt to changing environmental conditions through genetic recombination and natural selection alone. Thus, it is critical to understand alternative mechanisms that allow organisms to cope with rapid environmental changes. Here, we use the sea anemone Nematostella vectensis, which has evolved the capability of surviving in a wide range of temperatures and salinities, as a model to investigate the microbiota as a source of rapid adaptation. We long-term acclimate polyps of Nematostella to low, medium, and high temperatures, to test the impact of microbiota-mediated plasticity on animal acclimation. Using the same animal clonal line, propagated from a single polyp, allows us to eliminate the effects of the host genotype. The higher thermal tolerance of animals acclimated to high temperature can be transferred to non-acclimated animals through microbiota transplantation. The offspring fitness is highest from F0 females acclimated to high temperature and specific members of the acclimated microbiota are transmitted to the next generation. These results indicate that microbiota plasticity can contribute to animal thermal acclimation and its transmission to the next generation may represent a rapid mechanism for thermal adaptation.

This study shows that sea anemones acclimated to high temperatures exhibit increased resistance to thermal stress and that this improved fitness can be transferred by microbiome transplantation. These results indicate that plasticity mediated by the microbiota might be an important factor facilitating thermal adaptations in animals.

Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience

Coral reefs are home to over two million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic, and other omics data is becoming increasingly available from different species of reef-building corals, the unicellular dinoflagellates, and the coral microbiome (bacteria, archaea, viruses, fungi, etc.). Such new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Two decades of seawater acidification experiments on tropical scleractinian corals: Overview, meta-analysis and perspectives

Ocean acidification has emerged as a major concern in the last fifteen years and studies on the impacts of seawater acidification on marine organisms have multiplied accordingly. This review aimed at synthesizing the literature on the effects of seawater acidification on tropical scleractinians under laboratory-controlled conditions. We identified 141 articles (published between 1999 and 2021) and separated endpoints into 22 biological categories to identify global trends for mitigation and gaps in knowledge and research priorities for future investigators. The relative number of affected endpoints increased with pH intensity (particularly for endpoints associated to calcification and reproduction). When exposed to pH 7.6-7.8 (compared to higher pH), 49% of endpoints were affected. The diversity in experimental designs prevented deciphering the modulating role of coral life stages, genera or duration of exposure. Finally, important bias in research efforts included most experiments on adult corals (68.5%), in 27 out of 150 (18%) coral ecoregions and exclusively from shallow-waters.

Adaptive Variation in Homolog Number Within Transcript Families Promotes Expression Divergence in Reef-Building Coral

Gene expression, especially in multi-species experiments, is used to gain insight into the genetic basis of how organisms adapt and respond to changing environments. However, evolutionary processes which can influence gene expression patterns between species such as the presence of paralogs which arise from gene duplication events are rarely accounted for. Paralogous transcripts can alter the transcriptional output of a gene and thus exclusion of these transcripts can obscure important biological differences between species. To address this issue, we investigated how differences in transcript family size is associated with divergent gene expression patterns in five species of Caribbean reef-building corals. We demonstrate that transcript families that are rapidly evolving in terms of size have increased levels of expression divergence. Additionally, these rapidly evolving transcript families are enriched for multiple biological processes, with genes involved in the coral innate immune system demonstrating pronounced variation in homolog number between species. Overall, this investigation demonstrates the importance of incorporating paralogous transcripts when comparing gene expression across species by influencing both transcriptional output and the number of transcripts within biological processes. As this investigation was based on transcriptome assemblies, additional insights into the relationship between gene duplications and expression patterns will likely emergence once more genome assemblies are available for study.

Impacts of ocean warming and acidification on calcifying coral reef taxa: mechanisms responsible and adaptive capacity

Ocean warming (OW) and acidification (OA) are two of the greatest global threats to the persistence of coral reefs. Calcifying reef taxa such as corals and coralline algae provide the essential substrate and habitat in tropical reefs but are at particular risk due to their susceptibility to both OW and OA. OW poses the greater threat to future reef growth and function, via its capacity to destabilise the productivity of both taxa, and to cause mass bleaching events and mortality of corals. Marine heatwaves are projected to increase in frequency, intensity, and duration over the coming decades, raising the question of whether coral reefs will be able to persist as functioning ecosystems and in what form. OA should not be overlooked, as its negative impacts on the calcification of reef-building corals and coralline algae will have consequences for global reef accretion. Given that OA can have negative impacts on the reproduction and early life stages of both coralline algae and corals, the interdependence of these taxa may result in negative feedbacks for reef replenishment. However, there is little evidence that OA causes coral bleaching or exacerbates the effects of OW on coral bleaching. Instead, there is some evidence that OA alters the photo-physiology of both taxa. Tropical coralline algal possess shorter generation times than corals, which could enable more rapid evolutionary responses. Future reefs will be dominated by taxa with shorter generation times and high plasticity, or those individuals inherently resistant and resilient to both marine heatwaves and OA.

Rebuilding relationships on coral reefs: Coral bleaching knowledge-sharing to aid adaptation planning for reef users: Bleaching emergence on reefs demonstrates the need to consider reef scale and accessibility when preparing for, and responding to, coral bleaching

Coral bleaching has impacted reefs worldwide and the predictions of near-annual bleaching from over two decades ago have now been realized. While technology currently provides the means to predict large-scale bleaching, predicting reef-scale and within-reef patterns in real-time for all reef users is limited. In 2020, heat stress across the Great Barrier Reef underpinned the region's third bleaching event in 5 years. Here we review the heterogeneous emergence of bleaching across Heron Island reef habitats and discuss the oceanographic drivers that underpinned variable bleaching emergence. We do so as a case study to highlight how reef end-user groups who engage with coral reefs in different ways require targeted guidance for how, and when, to alter their use of coral reefs in response to bleaching events. Our case study of coral bleaching emergence demonstrates how within-reef scale nowcasting of coral bleaching could aid the development of accessible and equitable bleaching response strategies on coral reefs.

Coral environmental memory: causes, mechanisms, and consequences for future reefs

The apparent ability of corals to acquire and maintain enhanced stress tolerance through a dose-dependent environmental memory, which may persist for multiple years, has critical implications for coral reef conservation research. Such responses are variable across coral species and environmental stressors, with primed corals exhibiting a modified response to secondary stress exposures. While the mechanisms underlying coral memory responses are poorly understood, they likely involve both the coral host and microbiome. With advances in molecular technologies, it is now possible to investigate potential memory mechanisms in non-model organisms, including transcriptional regulation through epigenetic modifications. We integrate evidence of coral environmental memory and suggest future research directions to evaluate the potential for this process to enhance coral resilience under climate change.

Preconditioning improves bleaching tolerance in the reef-building coral Pocillopora acuta through modulations in the programmed cell death pathways

Reef-building corals rely on intracellular algal symbionts to meet energetic demands. Increasing extreme weather driven by climate change often leads to disruption of this symbiosis and to coral death. Corals can better withstand stress after previous exposure to sublethal conditions, but the mechanisms for this resilience remain unclear. Here, we show that a three-day thermal preconditioning increases tolerance of acute heat stress through modulations in cell death pathways in the stony coral Pocillopora acuta. In preconditioned corals, the ratio of pro-survival (pa-Bcl-2 and pa-BI-1) to pro-death (pa-BAK and pa-BAX) gene expression increased and the corals underwent significantly less bleaching. When treated with Bcl-2 inhibitor, corals lost the improved thermal tolerance, suggesting an important role of programmed cell death in coral bleaching and acclimatization. During heat stress, the activity of acid phosphatase increased but caspase-3 did not, suggesting the involvement of autophagy/symbiophagy rather than apoptosis in this process. A similar shift in gene expression also occurs in thermally stressed corals that have been exposed to naturally higher temperatures during summer thermal maxima in Kāne'ohe Bay, Hawai'i, suggesting that corals can increase their resilience to realistic warming events during high-risk periods through alterations in cell signalling. These data suggest that programmed cell death pathways underly coral acclimatization and resilience and may be important for coral reef conservation and management.

Marine heatwaves depress metabolic activity and impair cellular acid-base homeostasis in reef-building corals regardless of bleaching susceptibility

Ocean warming is causing global coral bleaching events to increase in frequency, resulting in widespread coral mortality and disrupting the function of coral reef ecosystems. However, even during mass bleaching events, many corals resist bleaching despite exposure to abnormally high temperatures. While the physiological effects of bleaching have been well documented, the consequences of heat stress for bleaching-resistant individuals are not well understood. In addition, much remains to be learned about how heat stress affects cellular-level processes that may be overlooked at the organismal level, yet are crucial for coral performance in the short term and ecological success over the long term. Here we compared the physiological and cellular responses of bleaching-resistant and bleaching-susceptible corals throughout the 2019 marine heatwave in Hawai'i, a repeat bleaching event that occurred 4 years after the previous regional event. Relative bleaching susceptibility within species was consistent between the two bleaching events, yet corals of both resistant and susceptible phenotypes exhibited pronounced metabolic depression during the heatwave. At the cellular level, bleaching-susceptible corals had lower intracellular pH than bleaching-resistant corals at the peak of bleaching for both symbiont-hosting and symbiont-free cells, indicating greater disruption of acid-base homeostasis in bleaching-susceptible individuals. Notably, cells from both phenotypes were unable to compensate for experimentally induced cellular acidosis, indicating that acid-base regulation was significantly impaired at the cellular level even in bleaching-resistant corals and in cells containing symbionts. Thermal disturbances may thus have substantial ecological consequences, as even small reallocations in energy budgets to maintain homeostasis during stress can negatively affect fitness. These results suggest concern is warranted for corals coping with ocean acidification alongside ocean warming, as the feedback between temperature stress and acid-base regulation may further exacerbate the physiological effects of climate change.

Fast and pervasive transcriptomic resilience and acclimation of extremely heat-tolerant coral holobionts from the northern Red Sea

Corals from the northern Red Sea and Gulf of Aqaba exhibit extreme thermal tolerance. To examine the underlying gene expression dynamics, we exposed Stylophora pistillata from the Gulf of Aqaba to short-term (hours) and long-term (weeks) heat stress with peak seawater temperatures ranging from their maximum monthly mean of 27 °C (baseline) to 29.5 °C, 32 °C, and 34.5 °C. Corals were sampled at the end of the heat stress as well as after a recovery period at baseline temperature. Changes in coral host and symbiotic algal gene expression were determined via RNA-sequencing (RNA-Seq). Shifts in coral microbiome composition were detected by complementary DNA (cDNA)-based 16S ribosomal RNA (rRNA) gene sequencing. In all experiments up to 32 °C, RNA-Seq revealed fast and pervasive changes in gene expression, primarily in the coral host, followed by a return to baseline gene expression for the majority of coral (>94%) and algal (>71%) genes during recovery. At 34.5 °C, large differences in gene expression were observed with minimal recovery, high coral mortality, and a microbiome dominated by opportunistic bacteria (including Vibrio species), indicating that a lethal temperature threshold had been crossed. Our results show that the S. pistillata holobiont can mount a rapid and pervasive gene expression response contingent on the amplitude and duration of the thermal stress. We propose that the transcriptomic resilience and transcriptomic acclimation observed are key to the extraordinary thermal tolerance of this holobiont and, by inference, of other northern Red Sea coral holobionts, up to seawater temperatures of at least 32 °C, that is, 5 °C above their current maximum monthly mean.

Metabolomic signatures of coral bleaching history

Coral bleaching has a profound impact on the health and function of reef ecosystems, but the metabolomic effects of coral bleaching are largely uncharacterized. Here, untargeted metabolomics was used to analyse pairs of adjacent Montipora capitata corals that had contrasting bleaching phenotypes during a severe bleaching event in 2015. When these same corals were sampled four years later while visually healthy, there was a strong metabolomic signature of bleaching history. This was primarily driven by betaine lipids from the symbiont, where corals that did not bleach were enriched in saturated lyso-betaine lipids. Immune modulator molecules were also altered by bleaching history in both the coral host and the algal symbiont, suggesting a shared role in partner choice and bleaching response. Metabolomics from a separate set of validation corals was able to predict the bleaching phenotype with 100% accuracy. Experimental temperature stress induced phenotype-specific responses, which magnified differences between historical bleaching phenotypes. These findings indicate that natural bleaching susceptibility is manifested in the biochemistry of both the coral animal and its algal symbiont. This metabolome difference is stable through time and results in different physiological responses to temperature stress. This work provides insight into the biochemical mechanisms of coral bleaching and presents a valuable new tool for resilience-based reef restoration.

De novo assembly of the transcriptome of scleractinian coral, Anomastraea irregularis and analyses of its response to thermal stress

Rising seawater temperatures cause coral bleaching. The molecular responses of the coral holobiont under stress conditions, determine the success of the symbiosis. Anomastraea irregularis is a hard coral commonly found in the harsh intertidal zones of the south coast of KwaZulu-Natal (KZN), South Africa, where it thrives at the very margins of hard coral distribution in the Western Indian Ocean. To identify the possible molecular and cellular mechanisms underlying its resilience to heat stress, experimental and control nubbins were exposed to temperatures of 29 and 19 °C respectively for 24 h. The transcriptome was assembled de novo from 42.8 million quality controlled 63 bp paired-end short sequence reads obtained via RNA sequencing (RNA-seq). The assembly yielded 333,057 contigs (> 500 bp = 55,626, Largest = 6341 bp N₅₀ = 747 bp). 1362 (1.23%) of the transcripts were significantly differentially expressed between heat stressed and control samples. Log fold change magnitudes among individual genes ranged from - 4.6 to 7.2. Overall, the heat stress response in the A. irregularis constituted a protective response involving up regulation of apoptosis and SUMOylation. Gene ontology (GO) analyses revealed that heat stress in the coral affected the metabolism, protein synthesis, photosynthesis, transport and cytoskeleton. This is the first study to produce a reference transcriptome of this coral species and analyze its response to heat stress. The assembled transcriptome also presents a valuable resource for further transcriptomic and genomic studies.

A framework for understanding gene expression plasticity and its influence on stress tolerance

Phenotypic plasticity can serve as a stepping stone towards adaptation. Recently, studies have shown that gene expression contributes to emergent stress responses such as thermal tolerance, with tolerant and susceptible populations showing distinct transcriptional profiles. However, given the dynamic nature of gene expression, interpreting transcriptomic results in a way that elucidates the functional connection between gene expression and the observed stress response is challenging. Here, we present a conceptual framework to guide interpretation of gene expression reaction norms in the context of stress tolerance. We consider the evolutionary and adaptive potential of gene expression reaction norms and discuss the influence of sampling timing, transcriptomic resilience, as well as complexities related to life history when interpreting gene expression dynamics and how these patterns relate to host tolerance. We highlight corals as a case study to demonstrate the value of this framework for non-model systems. As species face rapidly changing environmental conditions, modulating gene expression can serve as a mechanistic link from genetic and cellular processes to the physiological responses that allow organisms to thrive under novel conditions. Interpreting how or whether a species can employ gene expression plasticity to ensure short-term survival will be critical for understanding the global impacts of climate change across diverse taxa.

Physiological and molecular responses of lobe coral indicate nearshore adaptations to anthropogenic stressors

Corals in nearshore marine environments are increasingly exposed to reduced water quality, which is the primary local threat to Hawaiian coral reefs. It is unclear if corals surviving in such conditions have adapted to withstand sedimentation, pollutants, and other environmental stressors. Lobe coral populations from Maunalua Bay, Hawaii showed clear genetic differentiation between the 'polluted, high-stress' nearshore site and the 'less polluted, lower-stress' offshore site. To understand the driving force of the observed genetic partitioning, reciprocal transplant and common-garden experiments were conducted to assess phenotypic differences between these two populations. Physiological responses differed significantly between the populations, revealing more stress-resilient traits in the nearshore corals. Changes in protein profiles highlighted the inherent differences in the cellular metabolic processes and activities between the two; nearshore corals did not significantly alter their proteome between the sites, while offshore corals responded to nearshore transplantation with increased abundances of proteins associated with detoxification, antioxidant defense, and regulation of cellular metabolic processes. The response differences across multiple phenotypes between the populations suggest local adaptation of nearshore corals to reduced water quality. Our results provide insight into coral’s adaptive potential and its underlying processes, and reveal potential protein biomarkers that could be used to predict resiliency.

Genetic Constraints, Transcriptome Plasticity, and the Evolutionary Response to Climate Change

In situ adaptation to climate change will be critical for the persistence of many ectotherm species due to their relative lack of dispersal capacity. Climate change is causing increases in both the mean and the variance of environmental temperature, each of which may act as agents of selection on different traits. Importantly, these traits may not be heritable or have the capacity to evolve independently from one another. When genetic constraints prevent the "baseline" values of thermal performance traits from evolving rapidly, phenotypic plasticity driven by gene expression might become critical. We review the literature for evidence that thermal performance traits in ectotherms are heritable and have genetic architectures that permit their unconstrained evolution. Next, we examine the relationship between gene expression and both the magnitude and duration of thermal stress. Finally, we identify genes that are likely to be important for adaptation to a changing climate and determine whether they show patterns consistent with thermal adaptation. Although few studies have measured narrow-sense heritabilities of thermal performance traits, current evidence suggests that the end points of thermal reaction norms (tolerance limits) are moderately heritable and have the potential to evolve rapidly. By contrast, performance at intermediate temperatures has substantially lower evolutionary potential. Moreover, evolution in many species appears to be constrained by genetic correlations such that populations can adapt to either increases in mean temperature or temperature variability, but not both. Finally, many species have the capacity for plastic expression of the transcriptome in response to temperature shifts, with the number of differentially expressed genes increasing with the magnitude, but not the duration, of thermal stress. We use these observations to develop a conceptual model that describes the likely trajectory of genome evolution in response to changes in environmental temperature. Our results indicate that extreme weather events, rather than gradual increases in mean temperature, are more likely to drive genetic and phenotypic change in wild ectotherms.

Thermal acclimation increases heat tolerance of the scleractinian coral Acropora pruinosa

Field ecological observations indicate that scleractinian coral exposed to early thermal stress are likely to develop higher tolerance to subsequent heat stress. The causes of this phenomenon, however, remain enigmatic. To unravel the mechanisms underlying the increased heat tolerance, we applied different thermal treatments to the scleractinian coral Acropora pruinosa and studied the resulting differences in appearance, physiological index, Symbiodiniaceae and bacterial communities, and transcriptome response. We found that early heat stress improved the thermal tolerance of the coral holobiont. After thermal acclimation, the community structure and symbiotic bacterial diversity in the microbiota were reorganized, whereas those of Symbiodiniaceae remained stable. RNA-seq analysis revealed that the downregulated coral host genes were mainly involved in pathways relating to metabolism, particularly the nitrogen metabolism pathway. This indicates that thermal acclimation led to decrease in the metabolism level in the coral host, which might be a self-protection mechanism. We suggest that thermal acclimation may increase scleractinian coral thermal tolerance by slowing host metabolism, altering the dominant bacterial population, and increasing bacterial diversity. This study offers new insights into the adaptive potential of scleractinian coral to heat stress from global warming.

Standardized short-term acute heat stress assays resolve historical differences in coral thermotolerance across microhabitat reef sites

Coral bleaching is one of the main drivers of reef degradation. Most corals bleach and suffer mortality at just 1-2°C above their maximum monthly mean temperatures, but some species and genotypes resist or recover better than others. Here, we conducted a series of 18-hr short-term acute heat stress assays side-by-side with a 21-day long-term heat stress experiment to assess the ability of both approaches to resolve coral thermotolerance differences reflective of in situ reef temperature thresholds. Using a suite of physiological parameters (photosynthetic efficiency, coral whitening, chlorophyll a, host protein, algal symbiont counts, and algal type association), we assessed bleaching susceptibility of Stylophora pistillata colonies from the windward/exposed and leeward/protected sites of a nearshore coral reef in the central Red Sea, which had previously shown differential mortality during a natural bleaching event. Photosynthetic efficiency was most indicative of the expected higher thermal tolerance in corals from the protected reef site, denoted by an increased retention of dark-adapted maximum quantum yields at higher temperatures. These differences were resolved using both experimental setups, as corroborated by a positive linear relationship, not observed for the other parameters. Notably, short-term acute heat stress assays resolved per-colony (genotype) differences that may have been masked by acclimation effects in the long-term experiment. Using our newly developed portable experimental system termed the Coral Bleaching Automated Stress System (CBASS), we thus highlight the potential of mobile, standardized short-term acute heat stress assays to resolve fine-scale differences in coral thermotolerance. Accordingly, such a system may be suitable for large-scale determination and complement existing approaches to identify resilient genotypes/reefs for downstream experimental examination and prioritization of reef sites for conservation/restoration. Development of such a framework is consistent with the recommendations of the National Academy of Sciences and the Reef Restoration and Adaptation Program committees for new intervention and restoration strategies.

Genome-wide SNP analysis reveals an increase in adaptive genetic variation through selective breeding of coral

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.

Resilience in reef-building corals: The ecological and evolutionary importance of the host response to thermal stress

Coral reefs are under extreme threat due to a number of stressors, but temperature increases due to changing climate are the most severe. Rising ocean temperatures coupled with local extremes lead to extensive bleaching, where the coral-algal symbiosis breaks down and corals may die, compromising the structure and function of reefs. Although the symbiotic nature of the coral colony has historically been a focus of research on coral resilience, the host itself is a foundational component in the response to thermal stress. Fixed effects in the coral host set trait baselines through evolutionary processes, acting on many loci of small effect to create mosaics of thermal tolerance across latitudes and individual coral reefs. These genomic differences can be strongly heritable, producing wide variation among clones of different genotypes or families of a specific larval cross. Phenotypic plasticity is overlaid on these baselines and a growing body of knowledge demonstrates the potential for acclimatization of reef-building corals through a variety of mechanisms that promote resilience and stress tolerance. The long-term persistence of coral reefs will require many of these mechanisms to adjust to warmer temperatures within a generation, bridging the gap to reproductive events that allow recombination of standing diversity and adaptive change. Business-as-usual climate scenarios will probably lead to the loss of some coral populations or species in the future, so the interaction between intragenerational effects and evolutionary pressure is critical for the survival of reefs.

Differential gene expression during substrate probing in larvae of the Caribbean coral Porites astreoides

The transition from larva to adult is a critical step in the life history strategy of most marine animals. However, the genetic basis of this life history change remains poorly understood in many taxa, including most coral species. Recent evidence suggests that coral planula larvae undergo significant changes at the physiological and molecular levels throughout the development. To investigate this, we characterized differential gene expression (DGE) during the transition from planula to adult polyp in the abundant Caribbean reef-building coral Porites astreoides, that is from nonprobing to actively substrate-probing larva, a stage required for colony initiation. This period is crucial for the coral, because it demonstrates preparedness to locate appropriate substrata for settlement based on vital environmental cues. Through RNA-Seq, we identified 860 differentially expressed holobiont genes between probing and nonprobing larvae (p ≤ .01), the majority of which were upregulated in probing larvae. Surprisingly, differentially expressed genes of endosymbiotic dinoflagellate origin greatly outnumbered coral genes, compared with a nearly 1:1 ratio of coral-to-dinoflagellate gene representation in the holobiont transcriptome. This unanticipated result suggests that dinoflagellate endosymbionts may play a significant role in the transition from nonprobing to probing behaviour in dinoflagellate-rich larvae. Putative holobiont genes were largely involved in protein and nucleotide binding, metabolism and transport. Genes were also linked to environmental sensing and response and integral signalling pathways. Our results thus provide detailed insight into molecular changes prior to larval settlement and highlight the complex physiological and biochemical changes that occur in early transition stages from pelagic to benthic stages in corals, and perhaps more importantly, in their endosymbionts.

The active spread of adaptive variation for reef resilience

The speed at which species adapt depends partly on the rates of beneficial adaptation generation and how quickly they spread within and among populations. Natural rates of adaptation of corals may not be able to keep pace with climate warming. Several interventions have been proposed to fast-track thermal adaptation, including the intentional translocation of warm-adapted adults or their offspring (assisted gene flow, AGF) and the ex situ crossing of warm-adapted corals with conspecifics from cooler reefs (hybridization or selective breeding) and field deployment of those offspring. The introgression of temperature tolerance loci into the genomic background of cooler-environment corals aims to facilitate adaptation to warming while maintaining fitness under local conditions. Here we use research on selective sweeps and connectivity to understand the spread of adaptive variants as it applies to AGF on the Great Barrier Reef (GBR), focusing on the genus Acropora. Using larval biophysical dispersal modeling, we estimate levels of natural connectivity in warm-adapted northern corals. We then model the spread of adaptive variants from single and multiple reefs and assess if the natural and assisted spread of adaptive variants will occur fast enough to prepare receiving central and southern populations given current rates of warming. We also estimate fixation rates and spatial extent of fixation under multiple release scenarios to inform intervention design. Our results suggest that thermal tolerance is unlikely to spread beyond northern reefs to the central and southern GBR without intervention, and if it does, 30+ generations are needed for adaptive gene variants to reach fixation even under multiple release scenarios. We argue that if translocation, breeding, and reseeding risks are managed, AGF using multiple release reefs can be beneficial for the restoration of coral populations. These interventions should be considered in addition to conventional management and accompanied by strong mitigation of CO2 emissions.

Stress-resistant corals may not acclimatize to ocean warming but maintain heat tolerance under cooler temperatures

Naturally heat-resistant coral populations hold significant potential for facilitating coral reef survival under rapid climate change. However, it remains poorly understood whether they can acclimatize to ocean warming when superimposed on their already thermally-extreme habitats. Furthermore, it is unknown whether they can maintain their heat tolerance upon larval dispersal or translocation to cooler reefs. We test this in a long-term mesocosm experiment using stress-resistant corals from thermally-extreme reefs in NW Australia. We show that these corals have a remarkable ability to maintain their heat tolerance and health despite acclimation to 3-6 °C cooler, more stable temperatures over 9 months. However, they are unable to increase their bleaching thresholds after 6-months acclimation to + 1 °C warming. This apparent rigidity in the thermal thresholds of even stress-resistant corals highlights the increasing vulnerability of corals to ocean warming, but provides a rationale for human-assisted migration to restore cooler, degraded reefs with corals from thermally-extreme reefs.

The past, present, and future of coral heat stress studies

The global loss and degradation of coral reefs, as a result of intensified frequency and severity of bleaching events, is a major concern. Evidence of heat stress affecting corals through loss of symbionts and consequent coral bleaching was first reported in the 1930s. However, it was not until the 1998 major global bleaching event that the urgency for heat stress studies became internationally recognized. Current efforts focus not only on examining the consequences of heat stress on corals but also on finding strategies to potentially improve thermal tolerance and aid coral reefs survival in future climate scenarios. Although initial studies were limited in comparison with modern technological tools, they provided the foundation for many of today's research methods and hypotheses. Technological advancements are providing new research prospects at a rapid pace. Understanding how coral heat stress studies have evolved is important for the critical assessment of their progress. This review summarizes the development of the field to date and assesses avenues for future research.

Using naturally occurring climate resilient corals to construct bleaching-resistant nurseries

Coral reefs are threatened by global bleaching, spurring a need to improve upon reef restoration practices. Yet the strong capacity for corals and their symbionts to acclimatize to their local environment has brought into question whether or not corals that are temperature tolerant in one setting will lose that tolerance elsewhere. We show that variation in bleaching resilience among intraspecific colonies is maintained in novel environments for four species, and can be used to construct bleaching-resistant coral nurseries for restoration. By focusing on the host genotype and symbiont genus and its importance in stock selection, we demonstrate a path forward for reef restoration in the face of climate change.

Ecological restoration of forests, meadows, reefs, or other foundational ecosystems during climate change depends on the discovery and use of individuals able to withstand future conditions. For coral reefs, climate-tolerant corals might not remain tolerant in different environments because of widespread environmental adjustment of coral physiology and symbionts. Here, we test if parent corals retain their heat tolerance in nursery settings, if simple proxies predict successful colonies, and if heat-tolerant corals suffer lower growth or survival in normal settings. Before the 2015 natural bleaching event in American Samoa, we set out 800 coral fragments from 80 colonies of four species selected by prior tests to have a range of intraspecific natural heat tolerance. After the event, nursery stock from heat-tolerant parents showed two to three times less bleaching across species than nursery stock from less tolerant parents. They also retained higher individual genetic diversity through the bleaching event than did less heat-tolerant corals. The three best proxies for thermal tolerance were response to experimental heat stress, location on the reef, and thermal microclimate. Molecular biomarkers were also predictive but were highly species specific. Colony genotype and symbiont genus played a similarly strong role in predicting bleaching. Combined, our results show that selecting for host and symbiont resilience produced a multispecies coral nursery that withstood multiple bleaching events, that proxies for thermal tolerance in restoration can work across species and be inexpensive, and that different coral clones within species reacted very differently to bleaching.

Thermal plasticity of a freshwater cnidarian holobiont: detection of trans-generational effects in asexually reproducing hosts and symbionts

Understanding factors affecting the susceptibility of organisms to thermal stress is of enormous interest in light of our rapidly changing climate. When adaptation is limited, thermal acclimation and deacclimation abilities of organisms are critical for population persistence through a period of thermal stress. Holobionts (hosts plus associated symbionts) are key components of various ecosystems, such as coral reefs, yet the contributions of their two partners to holobiont thermal plasticity are poorly understood. Here, we tested thermal plasticity of the freshwater cnidarian Hydra viridissima (green hydra) using individual behavior and population responses. We found that algal presence initially reduced hydra thermal tolerance. Hydra with algae (symbiotic hydra) had comparable acclimation rates, deacclimation rates, and thermal tolerance after acclimation to those without algae (aposymbiotic hydra) but they had higher acclimation capacity. Acclimation of the host (hydra) and/or symbiont (algae) to elevated temperatures increased holobiont thermal tolerance and these effects persisted for multiple asexual generations. In addition, acclimated algae presence enhanced hydra fitness under prolonged sublethal thermal stress, especially when food was limited. Our study indicates while less intense but sublethal stress may favor symbiotic organisms by allowing them to acclimate, sudden large, potentially lethal fluctuations in climate stress likely favor aposymbiotic organisms. It also suggests that thermally stressed colonies of holobionts could disperse acclimated hosts and/or symbionts to other colonies, thereby reducing their vulnerability to climate change.

Clonal diversity impacts coral cover in Acropora cervicornisthickets: Potential relationships between density, growth, and polymorphisms

As coral reefs decline, cryptic sources of resistance and resilience to stress may be increasingly important for the persistence of these communities. Among these sources, inter- and intraspecific diversity remain understudied on coral reefs but extensively impact a variety of traits in other ecosystems. We use a combination of field and sequencing data at two sites in Florida and two in the Dominican Republic to examine clonal diversity and genetic differentiation of high- and low-density aggregations of the threatened coral Acropora cervicornisin the Caribbean. We find that high-density aggregations called thickets are composed of up to 30 genotypes at a single site, but 47% of genotypes are also found as isolated, discrete colonies outside these aggregations. Genet-ramet ratios are comparable for thickets (0.636) and isolated colonies after rarefaction (0.569), suggesting the composition of each aggregation is not substantially different and highlighting interactions between colonies as a potential influence on structure. There are no differences in growth rate, but a significant positive correlation between genotypic diversity and coral cover, which may be due to the influence of interactions between colonies on survivorship or fragment retention during asexual reproduction. Many polymorphisms distinguish isolated colonies from thickets despite the shared genotypes found here, including putative nonsynonymous mutations that change amino acid sequence in 25 loci. These results highlight intraspecific diversity as a density-dependent factor that may impact traits important for the structure and function of coral reefs.

Impact of El Niño-Southern Oscillation 2015-2016 on the soluble proteomic profile and cytolytic activity of Millepora alcicornis ("fire coral") from the Mexican Caribbean

Reef-forming cnidarians are extremely susceptible to the “bleaching” phenomenon caused by global warming. The effect of elevated seawater temperature has been extensively studied on Anthozoans; however, to date the impact of thermal stress on the expression of genes and proteins in Hydrozoan species has not been investigated. The present study aimed to determine the differential proteomic profile of Millepora alcicornis, which inhabits the Mexican Caribbean, in response to the El Niño-Southern Oscillation 2015–2016. Additionally, the cytolytic activity of the soluble proteomes obtained from normal and bleached M. alcicornis was assessed. Bleached specimens showed decreased symbiont’s density and chlorophyll a and c2 levels. After bleaching, we observed a differential expression of 17 key proteins, tentatively identified as related to exocytosis, calcium homeostasis, cytoskeletal organization, and potential toxins, including a metalloprotease, a phospholipase A2 (PLA2), and an actitoxin. Although, some of the differentially expressed proteins included potential toxins, the hemolytic, PLA2, and proteolytic activities elicited by the soluble proteomes from bleached and normal specimens were not significantly different. The present study provides heretofore-unknown evidence that thermal stress produces a differential expression of proteins involved in essential cellular processes of Hydrozoan species. Even though our results showed an over-expression of some potential toxin-related proteins, the cytolytic effect (as assessed by hemolytic, PLA2, and caseinolytic activities) was not increased in bleached M. alcicornis, which suggests that the cytolysis is mainly produced by toxins whose expression was not affected by temperature stress. These findings allow hypothesizing that this hydrocoral is able to prey heterotrophically when suffering from moderate bleaching, giving it a better chance to withstand the effects of high temperature.

Cellular stress responses to chronic heat shock and shell damage in temperate Mya truncata

Acclimation, via phenotypic flexibility, is a potential means for a fast response to climate change. Understanding the molecular mechanisms underpinning phenotypic flexibility can provide a fine-scale cellular understanding of how organisms acclimate. In the last 30 years, Mya truncata populations around the UK have faced an average increase in sea surface temperature of 0.7 °C and further warming of between 1.5 and 4 °C, in all marine regions adjacent to the UK, is predicted by the end of the century. Hence, data are required on the ability of M. truncata to acclimate to physiological stresses, and most notably, chronic increases in temperature. Animals in the present study were exposed to chronic heat-stress for 2 months prior to shell damage and subsequently, only 3, out of 20 damaged individuals, were able to repair their shells within 2 weeks. Differentially expressed genes (between control and damaged animals) were functionally enriched with processes relating to cellular stress, the immune response and biomineralisation. Comparative transcriptomics highlighted genes, and more broadly molecular mechanisms, that are likely to be pivotal in this lack of acclimation. This study demonstrates that discovery-led transcriptomic profiling of animals during stress-response experiments can shed light on the complexity of biological processes and changes within organisms that can be more difficult to detect at higher levels of biological organisation.