Reduced thermal tolerance in a coral carrying CRISPR-induced mutations in the gene for a heat-shock transcription factor

Transcription of genes involved in bleaching of a coral reef species Acropora downingi (Wallace, 1999) in response to high temperature

Anthropogenic-induced global warming poses a significant threat to coral reef ecosystems worldwide. However, certain species within the Persian Gulf exhibit remarkable resilience to elevated temperatures compared to their counterparts in other reef systems. To understand the thermal tolerance in Persian Gulf corals and their molecular responses to extreme warm temperatures, Acropora downingi specimens collected from Larak Island were subjected to a heat shock of 34 ± 1 °C. We evaluated coral coloration, bleaching, and mRNA expression of biomarkers related to heat shock proteins (HSPs) such as Hsp70 and Hsp90, oxidative stress markers like Catalase and manganese superoxide dismutase (Cat and Mn-Sod), anti-apoptotic factors exemplified by B-cell lymphoma 2 (Bcl-2), and calcification-related genes including galaxin (Gal) after 24 h and 48 h of thermal shock exposure. Exposure of A. downingi to a 48-h heat shock at 34 °C resulted in noticeable fading of coral coloration compared to the control group. Despite this, the corals demonstrated resilience and did not undergo complete bleaching. Our findings also revealed significant increase of Hsp70, Hsp90, Cat, Mn-Sod, Bcl-2, and Gal mRNA expression after 24 h of thermal stress. However, after 48 h, transcripts for Hsp90, Cat, and Gal were observed to be decreased. These results suggest the pivotal roles played by genes involved in HSP signaling pathways, oxidative stress responses, anti-apoptosis processes, and calcification processes in the Persian Gulf coral's adaptation to thermal stress and its resistance to bleaching.

Transcriptomics of the Anthopleura Sea Anemone Reveals Unique Adaptive Strategies to Shallow-Water Hydrothermal Vent

The nonsymbiotic sea anemone Anthopleura nigrescens dominates the shallow-water hydrothermal vents off the coast of Kueishan Island, Taiwan. These vents represent some of the world's most extreme environments, with recorded pH values as low as 1.52 and temperatures reaching 121°C. To investigate the adaptations of A. nigrescens to these extreme conditions, transcriptomic analyses were conducted to compare populations inhabiting vent and non-vent areas. To identify shared genetic mechanisms in vent-dwelling anemones, specific orthologs conserved in vent sea anemones were identified by comparing the genomic data of Anthopleura species and other sea anemones. Tank experiments with elevated temperatures were also performed to evaluate the expression profiles of genes associated with heat resistance. The transcriptomic analysis revealed that enriched genes in vent populations are involved in H2S homeostasis and stress resistance, suggesting that detoxification and thermal stress resistance are critical adaptive strategies. Two significantly upregulated genes encoding hydroxyacylglutathione hydrolase and thiosulfate sulfurtransferase may play a role in managing sulfur toxicity and maintaining redox balance. The enriched genes and vent-specific gene expression patterns also suggest that efficient DNA repair mechanisms play a crucial role in the thermal stress resistance of vent populations. Interestingly, some genes associated with circadian rhythms were upregulated in vent populations, suggesting these genes may help vent anemones adapt to the highly dynamic conditions of hydrothermal vents. Furthermore, the expression profiles of stress-resistance-related genes reveal that vent anemones have developed unique molecular regulatory mechanisms to cope with elevated temperatures, as observed in the tank experiment. These transcriptomic findings advance our understanding of the life adaptations in shallow-water hydrothermal vent environments.

Living Coral Displays, Research Laboratories, and Biobanks as Important Reservoirs of Chemodiversity with Potential for Biodiscovery

Over the last decades, bioprospecting of tropical corals has revealed numerous bioactive compounds with potential for biotechnological applications. However, this search involves sampling in natural reefs, and this is currently hampered by multiple ethical and technological constraints. Living coral displays, research laboratories, and biobanks currently offer an opportunity to continue to unravel coral chemodiversity, acting as "Noah's Arks" that may continue to support the bioprospecting of molecules of interest. This issue is even more relevant if one considers that tropical coral reefs currently face unprecedent threats and irreversible losses that may impair the biodiscovery of molecules with potential for new products, processes, and services. Living coral displays provide controlled environments for studying corals and producing both known and new metabolites under varied conditions, and they are not prone to common bottlenecks associated with bioprospecting in natural coral reefs, such as loss of the source and replicability. Research laboratories may focus on a particular coral species or bioactive compound using corals that were cultured ex situ, although they may differ from wild conspecifics in metabolite production both in quantitative and qualitative terms. Biobanks collect and preserve coral specimens, tissues, cells, and/or information (e.g., genes, associated microorganisms), which offers a plethora of data to support the study of bioactive compounds' mode of action without having to cope with issues related to access, standardization, and regulatory compliance. Bioprospecting in these settings faces several challenges and opportunities. On one hand, it is difficult to ensure the complexity of highly biodiverse ecosystems that shape the production and chemodiversity of corals. On the other hand, it is possible to maximize biomass production and fine tune the synthesis of metabolites of interest under highly controlled environments. Collaborative efforts are needed to overcome barriers and foster opportunities to fully harness the chemodiversity of tropical corals before in-depth knowledge of this pool of metabolites is irreversibly lost due to tropical coral reefs' degradation.

A Genetic Variant of Delta-9 Desaturase Is Associated With Latitudinal Adaptation in a Coral from the Great Barrier Reef

Coral populations across the Great Barrier Reef (GBR) could rapidly adapt to the warming climate if they have standing genetic variation for thermal tolerance. Here, we describe a locus likely involved in latitudinal adaptation of Acropora millepora. This locus shows a steep latitudinal gradient of derived allele frequency increasing at higher latitudes, and harbours a cluster of eight tandemly repeated Δ9-desaturase genes adjacent to a region in the genome where a hard selective sweep likely occurred. In colonies reciprocally transplanted across 4.5° of latitude, the expression of Δ9-desaturase is upregulated at the high-latitude reef. Furthermore, corals from the low-latitude reef bearing the derived Δ9-desaturase allele express the gene more and grow faster than their peers when transplanted to the high-latitude reef. In other organisms ranging from bacteria to fish, Δ9-desaturase is upregulated under cold conditions to adjust membrane fluidity by introducing double bonds into fatty acid chains of membrane lipids. It is therefore plausible that the signal of latitudinal adaptation at the Δ9-desaturase locus is due to its involvement in adaptation to cooler temperatures at higher latitudes.

The predictability of fluctuating environments shapes the thermal tolerance of marine ectotherms and compensates narrow safety margins

Aquatic species living in productive coastal habitats with abundant primary producers have evolved in highly dynamic diel and seasonally fluctuating environments in terms of, for example, water temperature and dissolved oxygen. However, how environmental fluctuations shape the thermal tolerance of marine species is still poorly understood. Here we hypothesize that the degree of predictability of the diel environmental fluctuations in the coastal area can explain the thermal response of marine species. To test this hypothesis, we measured the thermal tolerance of 17 species of marine ectotherm from tropical, warm temperate and cold temperate latitudes under two levels of oxygen (around saturation and at supersaturation), and relate the results to their site-specific temperature and oxygen fluctuation and their environmental predictability. We demonstrate that oxygen and temperature fluctuations at tropical latitudes have a higher predictability than those at warm and cold temperate latitudes. Further, we show that marine species that are adapted to high predictability have the potential to tune their thermal performance when exposed to oxygen supersaturation, despite being constrained within a narrow safety margin. We advocate that the predictability of the environmental fluctuation needs to be considered when measuring and forecasting the response of marine animals to global warming.

Plant conservation in the age of genome editing: opportunities and challenges

Numerous plant taxa are threatened by habitat destruction or overexploitation. To overcome these threats, new methods are urgently needed for rescuing threatened and endangered plant species. Here, we review the genetic consequences of threats to species populations. We highlight potential advantages of genome editing for mitigating negative effects caused by new pathogens and pests or climate change where other approaches have failed. We propose solutions to protect threatened plants using genome editing technology unless absolutely necessary. We further discuss the challenges associated with genome editing in plant conservation to mitigate the decline of plant diversity.

Climate adaptive loci revealed by seascape genomics correlate with phenotypic variation in heat tolerance of the coral Acropora millepora

One of the main challenges in coral reef conservation and restoration is the identification of coral populations resilient under global warming. Seascape genomics is a powerful tool to uncover genetic markers potentially involved in heat tolerance among large populations without prior information on phenotypes. Here, we aimed to provide first insights on the role of candidate heat associated loci identified using seascape genomics in driving the phenotypic response of Acropora millepora from New Caledonia to thermal stress. We subjected 7 colonies to a long-term ex-situ heat stress assay (4 °C above the maximum monthly mean) and investigated their physiological response along with their Symbiodiniaceae communities and genotypes. Despite sharing similar thermal histories and associated symbionts, these conspecific individuals differed greatly in their tolerance to heat stress. More importantly, the clustering of individuals based on their genotype at heat-associated loci matched the phenotypic variation in heat tolerance. Colonies that sustained on average lower mortality, higher Symbiodiniaceae/chlorophyll concentrations and photosynthetic efficiency under prolonged heat stress were also the closest based on their genotypes, although the low sample size prevented testing loci predictive accuracy. Together these preliminary results support the relevance of coupling seascape genomics and long-term heat stress experiments in the future, to evaluate the effect size of candidate heat associated loci and pave the way for genomic predictive models of corals heat tolerance.

Naturally segregating genetic variants contribute to thermal tolerance in a Drosophila melanogaster model system

Thermal tolerance is a fundamental physiological complex trait for survival in many species. For example, everyday tasks such as foraging, finding a mate, and avoiding predation are highly dependent on how well an organism can tolerate extreme temperatures. Understanding the general architecture of the natural variants within the genes that control this trait is of high importance if we want to better comprehend thermal physiology. Here, we take a multipronged approach to further dissect the genetic architecture that controls thermal tolerance in natural populations using the Drosophila Synthetic Population Resource as a model system. First, we used quantitative genetics and Quantitative Trait Loci mapping to identify major effect regions within the genome that influences thermal tolerance, then integrated RNA-sequencing to identify differences in gene expression, and lastly, we used the RNAi system to (1) alter tissue-specific gene expression and (2) functionally validate our findings. This powerful integration of approaches not only allows for the identification of the genetic basis of thermal tolerance but also the physiology of thermal tolerance in a natural population, which ultimately elucidates thermal tolerance through a fitness-associated lens.

Photosynthesis and other factors affecting the establishment and maintenance of cnidarian-dinoflagellate symbiosis

Coral growth depends on the partnership between the animal hosts and their intracellular, photosynthetic dinoflagellate symbionts. In this study, we used the sea anemone Aiptasia, a laboratory model for coral biology, to investigate the poorly understood mechanisms that mediate symbiosis establishment and maintenance. We found that initial colonization of both adult polyps and larvae by a compatible algal strain was more effective when the algae were able to photosynthesize and that the long-term maintenance of the symbiosis also depended on photosynthesis. In the dark, algal cells were taken up into host gastrodermal cells and not rapidly expelled, but they seemed unable to reproduce and thus were gradually lost. When we used confocal microscopy to examine the interaction of larvae with two algal strains that cannot establish stable symbioses with Aiptasia, it appeared that both pre- and post-phagocytosis mechanisms were involved. With one strain, algae entered the gastric cavity but appeared to be completely excluded from the gastrodermal cells. With the other strain, small numbers of algae entered the gastrodermal cells but appeared unable to proliferate there and were slowly lost upon further incubation. We also asked if the exclusion of either incompatible strain could result simply from their cells' being too large for the host cells to accommodate. However, the size distributions of the compatible and incompatible strains overlapped extensively. Moreover, examination of macerates confirmed earlier reports that individual gastrodermal cells could expand to accommodate multiple algal cells. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

Conservation Mitonuclear Replacement: Facilitated mitochondrial adaptation for a changing world

Most species will not be able to migrate fast enough to cope with climate change, nor evolve quickly enough with current levels of genetic variation. Exacerbating the problem are anthropogenic influences on adaptive potential, including the prevention of gene flow through habitat fragmentation and the erosion of genetic diversity in small, bottlenecked populations. Facilitated adaptation, or assisted evolution, offers a way to augment adaptive genetic variation via artificial selection, induced hybridization, or genetic engineering. One key source of genetic variation, particularly for climatic adaptation, are the core metabolic genes encoded by the mitochondrial genome. These genes influence environmental tolerance to heat, drought, and hypoxia, but must interact intimately and co-evolve with a suite of important nuclear genes. These coadapted mitonuclear genes form some of the important reproductive barriers between species. Mitochondrial genomes can and do introgress between species in an adaptive manner, and they may co-introgress with nuclear genes important for maintaining mitonuclear compatibility. Managers should consider the relevance of mitonuclear genetic variability in conservation decision-making, including as a tool for facilitating adaptation. I propose a novel technique dubbed Conservation Mitonuclear Replacement (CmNR), which entails replacing the core metabolic machinery of a threatened species-the mitochondrial genome and key nuclear loci-with those from a closely related species or a divergent population, which may be better-adapted to climatic changes or carry a lower genetic load. The most feasible route to CmNR is to combine CRISPR-based nuclear genetic editing with mitochondrial replacement and assisted reproductive technologies. This method preserves much of an organism's phenotype and could allow populations to persist in the wild when no other suitable conservation options exist. The technique could be particularly important on mountaintops, where rising temperatures threaten an alarming number of species with almost certain extinction in the next century.

Finding genes and pathways that underlie coral adaptation

Mass coral bleaching is one of the clearest threats of climate change to the persistence of marine biodiversity. Despite the negative impacts of bleaching on coral health and survival, some corals may be able to rapidly adapt to warming ocean temperatures. Thus, a significant focus in coral research is identifying the genes and pathways underlying coral heat adaptation. Here, we review state-of-the-art methods that may enable the discovery of heat-adaptive loci in corals and identify four main knowledge gaps. To fill these gaps, we describe an experimental approach combining seascape genomics with CRISPR/Cas9 gene editing to discover and validate heat-adaptive loci. Finally, we discuss how information on adaptive genotypes could be used in coral reef conservation and management strategies.

Impacts of Climate Change on Marine Foundation Species

Marine foundation species are the biotic basis for many of the world's coastal ecosystems, providing structural habitat, food, and protection for myriad plants and animals as well as many ecosystem services. However, climate change poses a significant threat to foundation species and the ecosystems they support. We review the impacts of climate change on common marine foundation species, including corals, kelps, seagrasses, salt marsh plants, mangroves, and bivalves. It is evident that marine foundation species have already been severely impacted by several climate change drivers, often through interactive effects with other human stressors, such as pollution, overfishing, and coastal development. Despite considerable variation in geographical, environmental, and ecological contexts, direct and indirect effects of gradual warming and subsequent heatwaves have emerged as the most pervasive drivers of observed impact and potent threat across all marine foundation species, but effects from sea level rise, ocean acidification, and increased storminess are expected to increase. Documented impacts include changes in the genetic structures, physiology, abundance, and distribution of the foundation species themselves and changes to their interactions with other species, with flow-on effects to associated communities, biodiversity, and ecosystem functioning. We discuss strategies to support marine foundation species into the Anthropocene, in order to increase their resilience and ensure the persistence of the ecosystem services they provide.

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects

Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of 'dark' genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.

Thermal tolerance traits of individual corals are widely distributed across the Great Barrier Reef

Adaptation of reef-building corals to global warming depends upon standing heritable variation in tolerance traits upon which selection can act. Yet limited knowledge exists on heat-tolerance variation among conspecific individuals separated by metres to hundreds of kilometres. Here, we performed standardized acute heat-stress assays to quantify the thermal tolerance traits of 709 colonies of Acropora spathulata from 13 reefs spanning 1060 km (9.5° latitude) of the Great Barrier Reef. Thermal thresholds for photochemical efficiency and chlorophyll retention varied considerably among individual colonies both among reefs (approximately 6°C) and within reefs (approximately 3°C). Although tolerance rankings of colonies varied between traits, the most heat-tolerant corals (i.e. top 25% of each trait) were found at virtually all reefs, indicating widespread phenotypic variation. Reef-scale environmental predictors explained 12-62% of trait variation. Corals exposed to high thermal averages and recent thermal stress exhibited the greatest photochemical performance, probably reflecting local adaptation and stress pre-acclimatization, and the lowest chlorophyll retention suggesting stress pre-sensitization. Importantly, heat tolerance relative to local summer temperatures was the greatest on higher latitude reefs suggestive of higher adaptive potential. These results can be used to identify naturally tolerant coral populations and individuals for conservation and restoration applications.

A landmark environmental law looks ahead

In late December 1973, the United States enacted what some would come to call "the pitbull of environmental laws." In the 50 years since, the formidable regulatory teeth of the Endangered Species Act (ESA) have been credited with considerable successes, obliging agencies to draw upon the best available science to protect species and habitats. Yet human pressures continue to push the planet toward extinctions on a massive scale. With that prospect looming, and with scientific understanding ever changing, Science invited experts to discuss how the ESA has evolved and what its future might hold. -Brad Wible.

Unlocking the Complex Cell Biology of Coral-Dinoflagellate Symbiosis: A Model Systems Approach

Symbiotic interactions occur in all domains of life, providing organisms with resources to adapt to new habitats. A prime example is the endosymbiosis between corals and photosynthetic dinoflagellates. Eukaryotic dinoflagellate symbionts reside inside coral cells and transfer essential nutrients to their hosts, driving the productivity of the most biodiverse marine ecosystem. Recent advances in molecular and genomic characterization have revealed symbiosis-specific genes and mechanisms shared among symbiotic cnidarians. In this review, we focus on the cellular and molecular processes that underpin the interaction between symbiont and host. We discuss symbiont acquisition via phagocytosis, modulation of host innate immunity, symbiont integration into host cell metabolism, and nutrient exchange as a fundamental aspect of stable symbiotic associations. We emphasize the importance of using model systems to dissect the cellular complexity of endosymbiosis, which ultimately serves as the basis for understanding its ecology and capacity to adapt in the face of climate change.

CRISPR-Cas9 genome editing in Steinernema entomopathogenic nematodes

Molecular tool development in traditionally non-tractable animals opens new avenues to study gene functions in the relevant ecological context. Entomopathogenic nematodes (EPN) Steinernema and their symbiotic bacteria of Xenorhabdus spp are a valuable experimental system in the laboratory and are applicable in the field to promote agricultural productivity. The infective juvenile (IJ) stage of the nematode packages mutualistic symbiotic bacteria in the intestinal pocket and invades insects that are agricultural pests. The lack of consistent and heritable genetics tools in EPN targeted mutagenesis severely restricted the study of molecular mechanisms underlying both parasitic and mutualistic interactions. Here, I report a protocol for CRISPR-Cas9 based genome-editing that is successful in two EPN species, S. carpocapsae and S. hermaphroditum . I adapted a gonadal microinjection technique in S. carpocapsae , which created on-target modifications of a homologue Sc-dpy-10 (cuticular collagen) by homology-directed repair. A similar delivery approach was used to introduce various alleles in S. hermaphroditum including Sh-dpy-10 and Sh-unc-22 (a muscle gene), resulting in visible and heritable phenotypes of dumpy and twitching, respectively. Using conditionally dominant alleles of Sh-unc-22 as a co-CRISPR marker, I successfully modified a second locus encoding Sh-Daf-22 (a homologue of human sterol carrier protein SCPx), predicted to function as a core enzyme in the biosynthesis of nematode pheromone that is required for IJ development. As a proof of concept, Sh-daf-22 null mutant showed IJ developmental defects in vivo ( in insecta) . This research demonstrates that Steinernema spp are highly tractable for targeted mutagenesis and has great potential in the study of gene functions under controlled laboratory conditions within the relevant context of its ecological niche.

Reconciling the variability in the biological response of marine invertebrates to climate change

As climate change increases the rate of environmental change and the frequency and intensity of disturbance events, selective forces intensify. However, given the complicated interplay between plasticity and selection for ecological - and thus evolutionary - outcomes, understanding the proximate signals, molecular mechanisms and the role of environmental history becomes increasingly critical for eco-evolutionary forecasting. To enhance the accuracy of our forecasting, we must characterize environmental signals at a level of resolution that is relevant to the organism, such as the microhabitat it inhabits and its intracellular conditions, while also quantifying the biological responses to these signals in the appropriate cells and tissues. In this Commentary, we provide historical context to some of the long-standing challenges in global change biology that constrain our capacity for eco-evolutionary forecasting using reef-building corals as a focal model. We then describe examples of mismatches between the scales of external signals relative to the sensors and signal transduction cascades that initiate and maintain cellular responses. Studying cellular responses at this scale is crucial because these responses are the basis of acclimation to changing environmental conditions and the potential for environmental 'memory' of prior or historical conditions through molecular mechanisms. To challenge the field, we outline some unresolved questions and suggest approaches to align experimental work with an organism's perception of the environment; these aspects are discussed with respect to human interventions.

Management approaches to conserve Australia's marine ecosystem under climate change

Australia's coastal marine ecosystems have a deep cultural significance to Indigenous Australians, include multiple World Heritage sites, and support the nation's rapidly growing blue economy. Yet, increasing local pressures and global climate change are expected to undermine the biological, social, cultural, and economic value of these ecosystems within a human generation. Mitigating the causes of climate change is the most urgent action to secure their future; however, conventional and new management actions will play roles in preserving ecosystem function and value until that is achieved. This includes strategies codeveloped with Indigenous Australians that are guided by traditional ecological knowledge and a modeling and decision support framework. We provide examples of developments at one of Australia's most iconic ecosystems, the Great Barrier Reef, where recent, large block funding supports research, governance, and engagement to accelerate the development of tools for management under climate change.

Naturally segregating genetic variants contribute to thermal tolerance in a D. melanogaster model system

Thermal tolerance is a fundamental physiological complex trait for survival in many species. For example, everyday tasks such as foraging, finding a mate, and avoiding predation, are highly dependent on how well an organism can tolerate extreme temperatures. Understanding the general architecture of the natural variants of the genes that control this trait is of high importance if we want to better comprehend how this trait evolves in natural populations. Here, we take a multipronged approach to further dissect the genetic architecture that controls thermal tolerance in natural populations using the Drosophila Synthetic Population Resource (DSPR) as a model system. First, we used quantitative genetics and Quantitative Trait Loci (QTL) mapping to identify major effect regions within the genome that influences thermal tolerance, then integrated RNA-sequencing to identify differences in gene expression, and lastly, we used the RNAi system to 1) alter tissue-specific gene expression and 2) functionally validate our findings. This powerful integration of approaches not only allows for the identification of the genetic basis of thermal tolerance but also the physiology of thermal tolerance in a natural population, which ultimately elucidates thermal tolerance through a fitness-associated lens.

Role of the bicarbonate transporter SLC4γ in stony-coral skeleton formation and evolution

Coral reefs are highly diverse ecosystems of immense ecological, economic, and aesthetic importance built on the calcium-carbonate-based skeletons of stony corals. The formation of these skeletons is threatened by increasing ocean temperatures and acidification, and a deeper understanding of the molecular mechanisms involved may assist efforts to mitigate the effects of such anthropogenic stressors. In this study, we focused on the role of the predicted bicarbonate transporter SLC4γ, which was suggested in previous studies to be a product of gene duplication and to have a role in coral-skeleton formation. Our comparative-genomics study using 30 coral species and 15 outgroups indicates that SLC4γ is present throughout the stony corals, but not in their non-skeleton-forming relatives, and apparently arose by gene duplication at the onset of stony-coral evolution. Our expression studies show that SLC4γ, but not the closely related and apparently ancestral SLC4β, is highly upregulated during coral development coincident with the onset of skeleton deposition. Moreover, we show that juvenile coral polyps carrying CRISPR/Cas9-induced mutations in SLC4γ are defective in skeleton formation, with the severity of the defect in individual animals correlated with their frequencies of SLC4γ mutations. Taken together, the results suggest that the evolution of the stony corals involved the neofunctionalization of the newly arisen SLC4γ for a unique role in the provision of concentrated bicarbonate for calcium-carbonate deposition. The results also demonstrate the feasibility of reverse-genetic studies of ecologically important traits in adult corals.

Harnessing the omics revolution to address the global biodiversity crisis

Human disturbances are altering global biodiversity in unprecedented ways. We identify three fundamental challenges underpinning our understanding of global biodiversity (namely discovery, loss, and preservation), and discuss how the omics revolution (e.g. genomics, transcriptomics, proteomics, metabolomics, and meta-omics) can help address these challenges. We also discuss how omics tools can illuminate the major drivers of biodiversity loss, including invasive species, pollution, urbanization, overexploitation, and climate change, with a special focus on highly diverse tropical environments. Although omics tools are transforming the traditional toolkit of biodiversity research, their application to addressing the current biodiversity crisis remains limited and may not suffice to offset current rates of biodiversity loss. Despite technical and logistical challenges, omics tools need to be fully integrated into global biodiversity research, and better strategies are needed to improve their translation into biodiversity policy and practice. It is also important to recognize that although the omics revolution can be considered the biologist's dream, socioeconomic disparity limits their application in biodiversity research.

The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions

Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.

Advancing the protection of marine life through genomics

The rapid growth in genomic techniques provides the potential to transform how we protect, manage, and conserve marine life. Further, solutions to boost the resilience of marine species to climate change and other disturbances that characterize the Anthropocene require transformative approaches, made more effective if guided by genomic data. Although genetic techniques have been employed in marine conservation for decades and the availability of genomic data is rapidly expanding, widespread application still lags behind other data types. This Essay reviews how genetics and genomics have been utilized in management initiatives for ocean conservation and restoration, highlights success stories, and presents a pathway forward to enhance the uptake of genomic data for protecting our oceans.

Comparative transcriptomics of two coral holobionts collected during the 2017 El Niño heat wave reveal differential stress response mechanisms

Although coral species exhibit differential susceptibility to stressors, little is known about the underlying molecular mechanisms. Here we compared scleractinian corals Montipora peltiformis and Platygyra carnosa collected during the 2017 El Niño heat wave. Zooxanthellae density and chlorophyll a content declined and increased substantially during and after heat stress event, respective. However, the magnitude of change was larger in M. peltiformis. Transcriptome analysis showed that heat-stressed corals corresponded to metabolic depression and catabolism of amino acids in both hosts which might promote their survival. However, only M. peltiformis has developed the bleached coral phenotype with corresponding strong stress- and immune-related responses in the host and symbiont, and strong suppression of photosynthesis-related genes in the symbiont. Overall, our study reveals differences among species in the homeostatic capacity to prevent the development of the bleached phenotype under environmental stressors, eventually determining their likelihood of survival in the warming ocean.

Coral-bleaching responses to climate change across biological scales

The global impacts of climate change are evident in every marine ecosystem. On coral reefs, mass coral bleaching and mortality have emerged as ubiquitous responses to ocean warming, yet one of the greatest challenges of this epiphenomenon is linking information across scientific disciplines and spatial and temporal scales. Here we review some of the seminal and recent coral-bleaching discoveries from an ecological, physiological, and molecular perspective. We also evaluate which data and processes can improve predictive models and provide a conceptual framework that integrates measurements across biological scales. Taking an integrative approach across biological and spatial scales, using for example hierarchical models to estimate major coral-reef processes, will not only rapidly advance coral-reef science but will also provide necessary information to guide decision-making and conservation efforts. To conserve reefs, we encourage implementing mesoscale sanctuaries (thousands of km² ) that transcend national boundaries. Such networks of protected reefs will provide reef connectivity, through larval dispersal that transverse thermal environments, and genotypic repositories that may become essential units of selection for environmentally diverse locations. Together, multinational networks may be the best chance corals have to persist through climate change, while humanity struggles to reduce emissions of greenhouse gases to net zero.

Heat Stress of Algal Partner Hinders Colonization Success and Alters the Algal Cell Surface Glycome in a Cnidarian-Algal Symbiosis

Corals owe their ecological success to their symbiotic relationship with dinoflagellate algae (family Symbiodiniaceae). While the negative effects of heat stress on this symbiosis are well studied, how heat stress affects the onset of symbiosis and symbiont specificity is less explored. In this work, we used the model sea anemone, Exaiptasia diaphana (commonly referred to as Aiptasia), and its native symbiont, Breviolum minutum, to study the effects of heat stress on the colonization of Aiptasia by algae and the algal cell-surface glycome. Heat stress caused a decrease in the colonization of Aiptasia by algae that were not due to confounding variables such as algal motility or oxidative stress. With mass spectrometric analysis and lectin staining, a thermally induced enrichment of glycans previously found to be associated with free-living strains of algae (high-mannoside glycans) and a concomitant reduction in glycans putatively associated with symbiotic strains of algae (galactosylated glycans) were identified. Differential enrichment of specific sialic acid glycans was also identified, although their role in this symbiosis remains unclear. We also discuss the methods used to analyze the cell-surface glycome of algae, evaluate current limitations, and provide suggestions for future work in algal-coral glycobiology. Overall, this study provided insight into how stress may affect the symbiosis between cnidarians and their algal symbionts by altering the glycome of the symbiodinian partner.

IMPORTANCE Coral reefs are under threat from global climate change. Their decline is mainly caused by the fragility of their symbiotic relationship with dinoflagellate algae which they rely upon for their ecological success. To better understand coral biology, researchers used the sea anemone, Aiptasia, a model system for the study of coral-algal symbiosis, and characterized how heat stress can alter the algae's ability to communicate to the coral host. This study found that heat stress caused a decline in algal colonization success and impacted the cell surface molecules of the algae such that it became more like that of nonsymbiotic species of algae. This work adds to our understanding of the molecular signals involved in coral-algal symbiosis and how it breaks down during heat stress.

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.

Bleaching physiology: who's the 'weakest link' - host vs. symbiont?

Environmental stress, such as an increase in the sea surface temperature, triggers coral bleaching, a profound dysfunction of the mutualist symbiosis between the host cnidarians and their photosynthetic dinoflagellates of the Family Symbiodiniaceae. Because of climate change, mass coral bleaching events will increase in frequency and severity in the future, threatening the persistence of this iconic marine ecosystem at global scale. Strategies adapted to coral reefs preservation and restoration may stem from the identification of the succession of events and of the different molecular and cellular contributors to the bleaching phenomenon. To date, studies aiming to decipher the cellular cascade leading to temperature-related bleaching, emphasized the involvement of reactive species originating from compromised bioenergetic pathways (e.g. cellular respiration and photosynthesis). These molecules are responsible for damage to various cellular components causing the dysregulation of cellular homeostasis and the breakdown of symbiosis. In this review, we synthesize the current knowledge available in the literature on the cellular mechanisms caused by thermal stress, which can initiate or participate in the cell cascade leading to the loss of symbionts, with a particular emphasis on the role of each partner in the initiating processes.

Techniques to save the sea

Ocean health has declined dramatically over the past few decades, threatening the rich biodiversity and ecosystem services the ocean provides. In this feature, we look at the life science techniques that could potentially save the sea.

Signatures of selection underpinning rapid coral adaptation to the world's warmest reefs

Coral populations in the world’s warmest reefs, the Persian/Arabian Gulf (PAG), represent an ideal model system to understand the evolutionary response of coral populations to past and present environmental change and to identify genomic loci that contribute to elevated thermal tolerance. Here, we use population genomics of the brain coral Platygyra daedalea to show that corals in the PAG represent a distinct subpopulation that was established during the Holocene marine transgression, and identify selective sweeps in their genomes associated with thermal adaptation. We demonstrate the presence of positive and disruptive selection and provide evidence for selection of differentially methylated haplotypes. While demographic analyses suggest limited potential for genetic rescue of neighboring Indian Ocean reefs, the presence of putative targets of selection in corals outside of the PAG offers hope that loci associated with thermal tolerance may be present in the standing genetic variation.

Tentacle patterning during Exaiptasia diaphana pedal lacerate development differs between symbiotic and aposymbiotic animals

Exaiptasia diaphana, a tropical sea anemone known as Aiptasia, is a tractable model system for studying the cellular, physiological, and ecological characteristics of cnidarian-dinoflagellate symbiosis. Aiptasia is widely used as a proxy for coral-algal symbiosis, since both Aiptasia and corals form a symbiosis with members of the family Symbiodiniaceae. Laboratory strains of Aiptasia can be maintained in both the symbiotic (Sym) and aposymbiotic (Apo, without algae) states. Apo Aiptasia allow for the study of the influence of symbiosis on different biological processes and how different environmental conditions impact symbiosis. A key feature of Aiptasia is the ease of propagating both Sym and Apo individuals in the laboratory through a process called pedal laceration. In this form of asexual reproduction, small pieces of tissue rip away from the pedal disc of a polyp, then these lacerates eventually develop tentacles and grow into new polyps. While pedal laceration has been described in the past, details of how tentacles are formed or how symbiotic and nutritional state influence this process are lacking. Here we describe the stages of development in both Sym and Apo pedal lacerates. Our results show that Apo lacerates develop tentacles earlier than Sym lacerates, while over the course of 20 days, Sym lacerates end up with a greater number of tentacles. We describe both tentacle and mesentery patterning during lacerate development and show that they form through a single pattern in early stages regardless of symbiotic state. In later stages of development, Apo lacerate tentacles and mesenteries progress through a single pattern, while variable patterns were observed in Sym lacerates. We discuss how Aiptasia lacerate mesentery and tentacle patterning differs from oral disc regeneration and how these patterning events compare to postembryonic development in Nematostella vectensis, another widely-used sea anemone model. In addition, we demonstrate that Apo lacerates supplemented with a putative nutrient source developed an intermediate number of tentacles between un-fed Apo and Sym lacerates. Based on these observations, we hypothesize that pedal lacerates progress through two different, putatively nutrient-dependent phases of development. In the early phase, the lacerate, regardless of symbiotic state, preferentially uses or relies on nutrients carried over from the adult polyp. These resources are sufficient for lacerates to develop into a functional polyp. In the late phase of development, continued growth and tentacle formation is supported by nutrients obtained from either symbionts and/or the environment through heterotrophic feeding. Finally, we advocate for the implementation of pedal lacerates as an additional resource in the Aiptasia model system toolkit for studies of cnidarian-dinoflagellate symbiosis.

Genetic approaches for increasing fitness in endangered species

The global rate of wildlife extinctions is accelerating, and the persistence of many species requires conservation breeding programs. A central paradigm of these programs is to preserve the genetic diversity of the founder populations. However, this may preserve original characteristics that make them vulnerable to extinction. We introduce targeted genetic intervention (TGI) as an alternative approach that promotes traits that enable species to persist in the face of threats by changing the incidence of alleles that impact on fitness. The TGI toolkit includes methods with established efficacy in model organisms and agriculture but are largely untried for conservation, such as synthetic biology and artificial selection. We explore TGI approaches as a species-restoration tool for intractable threats including infectious disease and climate change.

Coral holobionts and biotechnology: from Blue Economy to coral reef conservation

Corals are of ecological and economic importance, providing habitat for species and contributing to coastal protection, fisheries, and tourism. Their biotechnological potential is also increasingly recognized. Particularly, the production of pharmaceutically interesting compounds by corals and their microbial associates stimulated natural product-based drug discovery. The efficient light distribution by coral skeletons for optimal photosynthesis by algal symbionts has led to 3D-printed bionic corals that may be used to upscale micro-algal cultivation for bioenergy generation. However, corals are under threat from climate change and pollution, and biotechnological approaches to increase their resilience, like 'probiotics' and 'assisted evolution', are being evaluated. In this review, we summarize the recent biotechnological developments related to corals with an emphasis on coral conservation, drug discovery and bioenergy.

Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata

Background

Corals, which form the foundation of biodiverse reef ecosystems, are under threat from warming oceans. Reefs provide essential ecological services, including food, income from tourism, nutrient cycling, waste removal, and the absorption of wave energy to mitigate erosion. Here, we studied the coral thermal stress response using network methods to analyze transcriptomic and polar metabolomic data generated from the Hawaiian rice coral Montipora capitata. Coral nubbins were exposed to ambient or thermal stress conditions over a 5-week period, coinciding with a mass spawning event of this species. The major goal of our study was to expand the inventory of thermal stress-related genes and metabolites present in M. capitata and to study gene-metabolite interactions. These interactions provide the foundation for functional or genetic analysis of key coral genes as well as provide potentially diagnostic markers of pre-bleaching stress. A secondary goal of our study was to analyze the accumulation of sex hormones prior to and during mass spawning to understand how thermal stress may impact reproductive success in M. capitata.

Methods

M. capitata was exposed to thermal stress during its spawning cycle over the course of 5 weeks, during which time transcriptomic and polar metabolomic data were collected. We analyzed these data streams individually, and then integrated both data sets using MAGI (Metabolite Annotation and Gene Integration) to investigate molecular transitions and biochemical reactions.

Results

Our results reveal the complexity of the thermal stress phenome in M. capitata, which includes many genes involved in redox regulation, biomineralization, and reproduction. The size and number of modules in the gene co-expression networks expanded from the initial stress response to the onset of bleaching. The later stages involved the suppression of metabolite transport by the coral host, including a variety of sodium-coupled transporters and a putative ammonium transporter, possibly as a response to reduction in algal productivity. The gene-metabolite integration data suggest that thermal treatment results in the activation of animal redox stress pathways involved in quenching molecular oxygen to prevent an overabundance of reactive oxygen species. Lastly, evidence that thermal stress affects reproductive activity was provided by the downregulation of CYP-like genes and the irregular production of sex hormones during the mass spawning cycle. Overall, redox regulation and metabolite transport are key components of the coral animal thermal stress phenome. Mass spawning was highly attenuated under thermal stress, suggesting that global climate change may negatively impact reproductive behavior in this species.

New developments in the field of genomic technologies and their relevance to conservation management

Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.

Large within, and between, species differences in marine cellular responses: Unpredictability in a changing environment

Predicting the impacts of altered environments on future biodiversity requires a detailed understanding of organism responses to change. To date, studies evaluating mechanisms underlying marine organism stress responses have largely concentrated on oxygen limitation and the use of heat shock proteins as biomarkers. However, whether these biomarkers represent responses that are consistent across species and different environmental stressors remains open to question. Here we show that responses to four different thermal stresses (three rates of thermal ramping (1 °C h^-1, 1 °C day^-1 or 1 °C 3 day^-1) and a three-month acclimation to warming of 2 °C) applied to three species of Antarctic marine invertebrate produced highly individual responses in gene expression profiles, both within and between species. Mapping the gene expression profiles from each treatment for each of the three species, identified considerable difference in numbers of differentially regulated transcripts ranging from 10 to 3011. When these data were correlated across the different temperature treatments, there was no evidence for a common response with only 0-2 transcripts shared between all four treatments within any one species. There were also no shared differentially expressed genes across species, even at the same thermal ramping rates. The classical cellular stress response (CSR) i.e. up-regulation of heat shock proteins, was only strongly present in two species at the fastest ramping rate of 1 °C h^-1, albeit with different sets of stress genes expressed in each species. These data demonstrate the wide variability in response to warming at the molecular level in marine species. Therefore, identification of biodiversity stress responses engendered by changing conditions will require evaluation at the species level using targeted key members of the ecosystem, strongly correlated to the local biotic and abiotic factors.

Insights into coral bleaching under heat stress from analysis of gene expression in a sea anemone model system

Loss of endosymbiotic algae ("bleaching") under heat stress has become a major problem for reef-building corals worldwide. To identify genes that might be involved in triggering or executing bleaching, or in protecting corals from it, we used RNAseq to analyze gene-expression changes during heat stress in a coral relative, the sea anemone Aiptasia. We identified >500 genes that showed rapid and extensive up-regulation upon temperature increase. These genes fell into two clusters. In both clusters, most genes showed similar expression patterns in symbiotic and aposymbiotic anemones, suggesting that this early stress response is largely independent of the symbiosis. Cluster I was highly enriched for genes involved in innate immunity and apoptosis, and most transcript levels returned to baseline many hours before bleaching was first detected, raising doubts about their possible roles in this process. Cluster II was highly enriched for genes involved in protein folding, and most transcript levels returned more slowly to baseline, so that roles in either promoting or preventing bleaching seem plausible. Many of the genes in clusters I and II appear to be targets of the transcription factors NFκB and HSF1, respectively. We also examined the behavior of 337 genes whose much higher levels of expression in symbiotic than aposymbiotic anemones in the absence of stress suggest that they are important for the symbiosis. Unexpectedly, in many cases, these expression levels declined precipitously long before bleaching itself was evident, suggesting that loss of expression of symbiosis-supporting genes may be involved in triggering bleaching.