Differential gene expression during thermal stress and bleaching in the Caribbean coralMontastraea faveolata

Heat stress in symbiotic dinoflagellates: Implications on oxidative stress and cellular changes

Global warming has been shown to harmfully affect symbiosis between Symbiodiniaceae and other marine invertebrates. When symbiotic dinoflagellates (the genus Breviolum) were in vitro exposed to acute heat stress of +7 °C for a period of 5 days, the results revealed the negative impact on all physiological and other cellular parameters measured. Elevated temperatures resulted in a severe reduction in algal density of up to 9.5-fold, as well as pigment concentrations, indicating the status of the physiological stress and early signs of photo-bleaching. Reactive oxygen species (ROS) were increased in all heated dinoflagellate cells, while the antioxidant-reduced glutathione levels initially dropped on day one but increased under prolonged temperature stress. The cell viability parameters were reduced by 97 % over the heating period, with an increased proportion of apoptotic and necrotic cells. Autofluorescence (AF) for Cy5-PE 660-20 was reduced from 1.7-fold at day 1 to up to 50-fold drop at the end of heating time, indicating that the AF changes were highly sensitive to heat stress and that it could be an extremely sensitive tool for assessing the functionality of algal photosynthetic machinery. The addition of the drug 5-AZA-2'-deoxycytidine (5-AZA), which inhibits DNA methylation processes, was assessed in parallel and contributed to some alterations in algal cellular stress response. The presence of drug 5-AZA combined with the temperature stress had an additional impact on Symbiodiniaceae density and cell complexity, including the AF levels. These variations in cellular stress response under heat stress and compromised DNA methylation conditions may indicate the importance of this epigenetic mechanism for symbiotic dinoflagellate thermal tolerance adaptability over a longer period, which needs further exploration. Consequently, the increased ROS levels and changes in AF signals reported during ongoing heat stress in dinoflagellate cells could be used as early stress biomarkers in these microalgae and potentially other photosynthetic species.

Genome scans reveal signals of selection associated with pollution in fish populations of Basilichthys microlepidotus, an endemic species of Chile

The Maipo River catchment is one of Chile's most polluted basins. In recent decades, discharges of untreated sewage and organic matter have caused eutrophication and water quality degradation. We employed the indigenous silverfish species Basilichthys microlepidotus as a model organism to investigate the process of adaptation and selection on genes influenced by pollution. Using variation at single nucleotide polymorphisms (SNPs), we determined the temporal stability of the population structure patterns previously identified in this species by varying SNPs. We also examined local adaptation to pollution-selected genes. Using the genotypes of 7684 loci in 180 individuals, we identified 429 and 700 loci that may be undergoing selection. We detected these loci using the FSTHET and ARLEQUIN outlier detection software, respectively. Both software packages simultaneously identified a total of 250 loci. B. microlepidotus' population structure did not change over time at contaminated or unpolluted sites. In addition, our analysis found: (i) selection of genes associated with pollution, consistent with observations in other organisms; (ii) identification of candidate genes that are functionally linked to the same biological processes, molecular functions and/or cellular components that previously showed differential expression in the same populations; and (iii) a candidate gene with differential expression and a non-synonymous substitution.

Triggers, cascades, and endpoints: connecting the dots of coral bleaching mechanisms

The intracellular coral-dinoflagellate symbiosis is the engine that underpins the success of coral reefs, one of the most diverse ecosystems on the planet. However, the breakdown of the symbiosis and the loss of the microalgal symbiont (i.e. coral bleaching) due to environmental changes are resulting in the rapid degradation of coral reefs globally. There is an urgent need to understand the cellular physiology of coral bleaching at the mechanistic level to help develop solutions to mitigate the coral reef crisis. Here, at an unprecedented scope, we present novel models that integrate putative mechanisms of coral bleaching within a common framework according to the triggers (initiators of bleaching, e.g. heat, cold, light stress, hypoxia, hyposalinity), cascades (cellular pathways, e.g. photoinhibition, unfolded protein response, nitric oxide), and endpoints (mechanisms of symbiont loss, e.g. apoptosis, necrosis, exocytosis/vomocytosis). The models are supported by direct evidence from cnidarian systems, and indirectly through comparative evolutionary analyses from non-cnidarian systems. With this approach, new putative mechanisms have been established within and between cascades initiated by different bleaching triggers. In particular, the models provide new insights into the poorly understood connections between bleaching cascades and endpoints and highlight the role of a new mechanism of symbiont loss, i.e. 'symbiolysosomal digestion', which is different from symbiophagy. This review also increases the approachability of bleaching physiology for specialists and non-specialists by mapping the vast landscape of bleaching mechanisms in an atlas of comprehensible and detailed mechanistic models. We then discuss major knowledge gaps and how future research may improve the understanding of the connections between the diverse cascade of cellular pathways and the mechanisms of symbiont loss (endpoints).

A rapid return to normal: temporal gene expression patterns following cold exposure in the bumble bee Bombus impatiens

Bumble bees are common in cooler climates and many species likely experience periodic exposure to very cold temperatures, but little is known about the temporal dynamics of cold response mechanisms following chill exposure, especially how persistent effects of cold exposure may facilitate tolerance of future events. To investigate molecular processes involved in the temporal response by bumble bees to acute cold exposure, we compared mRNA transcript abundance in Bombus impatiens workers exposed to 0°C for 75 min (inducing chill coma) and control bees maintained at a constant ambient temperature (28°C). We sequenced the 3' end of mRNA transcripts (TagSeq) to quantify gene expression in thoracic tissue of bees at several time points (0, 10, 30, 120 and 720 min) following cold exposure. Significant differences from control bees were only detectable within 30 min after the treatment, with most occurring at the 10 min recovery time point. Genes associated with gluconeogenesis and glycolysis were most notably upregulated, while genes related to lipid and purine metabolism were downregulated. The observed patterns of expression indicate a rapid recovery after chill coma, suggesting an acute differential transcriptional response during recovery from chill coma and return to baseline expression levels within an hour, with no long-term gene expression markers of this cold exposure. Our work highlights the functions and pathways important for acute cold recovery, provides an estimated time frame for recovery from cold exposure in bumble bees, and suggests that cold hardening may be less important for these heterothermic insects.

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.

Deciphering temporal gene expression dynamics in multiple coral species exposed to heat stress: Implications for predicting resilience

Coral reefs are facing unprecedented threats due to global climate change, particularly elevated sea surface temperatures causing coral bleaching. Understanding coral responses at the molecular level is crucial for predicting their resilience and developing effective conservation strategies. In this study, we conducted a comprehensive gene expression analysis of four coral species to investigate their long-term molecular response to heat stress. We identified distinct gene expression patterns among the coral species, with laminar corals exhibiting a stronger response compared to branching corals. Heat shock proteins (HSPs) showed an overall decreasing expression trend, indicating the high energy cost associated with sustaining elevated HSP levels during prolonged heat stress. Peroxidases and oxidoreductases involved in oxidative stress response demonstrated significant upregulation, highlighting their role in maintaining cellular redox balance. Differential expression of genes related to calcium homeostasis and bioluminescence suggested distinct mechanisms for coping with heat stress among the coral species. Furthermore, the impact of heat stress on coral biomineralization varied, with downregulation of carbonic anhydrase and skeletal organic matrix proteins indicating reduced capacity for biomineralization in the later stages of heat stress. Our findings provide insights into the molecular mechanisms underlying coral responses to heat stress and highlight the importance of considering species-specific responses in assessing coral resilience. The identified biomarkers may serve as indicators of heat stress and contribute to early detection of coral bleaching events. These findings contribute to our understanding of coral resilience and provide a basis for future research aimed at enhancing coral survival in the face of climate change.

Characterizing transcriptomic responses to sediment stress across location and morphology in reef-building corals

Anthropogenic activities increase sediment suspended in the water column and deposition on reefs can be largely dependent on colony morphology. Massive and plating corals have a high capacity to trap sediments, and active removal mechanisms can be energetically costly. Branching corals trap less sediment but are more susceptible to light limitation caused by suspended sediment. Despite deleterious effects of sediments on corals, few studies have examined the molecular response of corals with different morphological characteristics to sediment stress. To address this knowledge gap, this study assessed the transcriptomic responses of branching and massive corals in Florida and Hawai'i to varying levels of sediment exposure. Gene expression analysis revealed a molecular responsiveness to sediments across species and sites. Differential Gene Expression followed by Gene Ontology (GO) enrichment analysis identified that branching corals had the largest transcriptomic response to sediments, in developmental processes and metabolism, while significantly enriched GO terms were highly variable between massive corals, despite similar morphologies. Comparison of DEGs within orthogroups revealed that while all corals had DEGs in response to sediment, there was not a concerted gene set response by morphology or location. These findings illuminate the species specificity and genetic basis underlying coral susceptibility to sediments.

Expression analyses of stress-responsive genes in the hermatypic coral Acropora tenuis and its symbiotic dinoflagellates after exposure to the herbicide Diuron

Diuron is one of the most frequently applied herbicides in sugarcane farming in southern Japan, and Australia. In addition, it is used as a booster substance in copper-based antifouling paints. Due to these various uses, Diuron is released into the marine environment; however, little information is available on gene expression in corals and their symbiotic algae exposed to Diuron. We investigated the effects of Diuron on stress-responsive gene expression in the hermatypic coral Acropora tenuis and its symbiotic dinoflagellates. After seven days of exposure to 1 µg/L and 10 µg/L Diuron, no significant changes in the body colour of corals were observed. However, quantitative reverse transcription-polymerase chain reaction analyses revealed that the expression levels of stress-responsive genes, such as heat shock protein 90 (HSP90), HSP70, and calreticulin (CALR), were significantly downregulated in corals exposed to 10 µg/L of Diuron for seven days. Moreover, aquaglyceroporin was significantly downregulated in corals exposed to environmentally relevant concentrations of 1 µg/L Diuron. In contrast, no such effects were observed on the expression levels of other stress-responsive genes, such as oxidative stress-responsive proteins, methionine adenosyltransferase, and green/red fluorescent proteins. Diuron exposure had no significant effect on the expression levels of HSP90, HSP70, or HSP40 in the symbiotic dinoflagellates. These results suggest that stress-responsive genes, such as HSPs, respond differently to Diuron in corals and their symbiotic dinoflagellates and that A. tenuis HSPs and CALRs may be useful molecular biomarkers for predicting stress responses induced by the herbicide Diuron.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00183-0.

Similarities in biomass and energy reserves among coral colonies from contrasting reef environments

Coral reefs are declining worldwide, yet some coral populations are better adapted to withstand reductions in pH and the rising frequency of marine heatwaves. The nearshore reef habitats of Palau, Micronesia are a proxy for a future of warmer, more acidic oceans. Coral populations in these habitats can resist, and recover from, episodes of thermal stress better than offshore conspecifics. To explore the physiological basis of this tolerance, we compared tissue biomass (ash-free dry weight cm^-2), energy reserves (i.e., protein, total lipid, carbohydrate content), and several important lipid classes in six coral species living in both offshore and nearshore environments. In contrast to expectations, a trend emerged of many nearshore colonies exhibiting lower biomass and energy reserves than colonies from offshore sites, which may be explained by the increased metabolic demand of living in a warmer, acidic, environment. Despite hosting different dinoflagellate symbiont species and having access to contrasting prey abundances, total lipid and lipid class compositions were similar in colonies from each habitat. Ultimately, while the regulation of colony biomass and energy reserves may be influenced by factors, including the identity of the resident symbiont, kind of food consumed, and host genetic attributes, these independent processes converged to a similar homeostatic set point under different environmental conditions.

Transcriptomic differences between bleached and unbleached hydrozoan Millepora complanata following the 2015-2016 ENSO in the Mexican Caribbean

The 2015-2016 El Niño-southern oscillation or "ENSO" caused many M. complanata colonies that live in the Mexican Caribbean to experience extensive bleaching. The purpose of this work was to analyze the effect of bleaching on the cellular response of M. complanata, employing a transcriptomic approach with RNA-seq. As expected, bleached specimens contained a significantly lower chlorophyll content than unbleached hydrocorals. The presence of algae of the genera Durusdinium and Cladocopium was only found in tissues of unbleached M. complanata, which could be associated to the greater resistance that these colonies exhibited during bleaching. We found that 299 genes were differentially expressed in M. complanata bleached colonies following the 2015-2016 ENSO in the Mexican Caribbean. The differential expression analysis of bleached M. complanata specimens evidenced enriched terms for functional categories, such as ribosome, RNA polymerase and basal transcription factors, chaperone, oxidoreductase, among others. Our results suggest that the heat-shock response mechanisms displayed by M. complanata include: an up-regulation of endogenous antioxidant defenses; a higher expression of heat stress response genes; up-regulation of transcription-related genes, higher expression of genes associated to transport processes, inter alia. This study constitutes the first differential gene expression analysis of the molecular response of a reef-forming hydrozoan during bleaching.

Deoxygenation lowers the thermal threshold of coral bleaching

Exposure to deoxygenation from climate warming and pollution is emerging as a contributing factor of coral bleaching and mortality. However, the combined effects of heating and deoxygenation on bleaching susceptibility remain unknown. Here, we employed short-term thermal stress assays to show that deoxygenated seawater can lower the thermal limit of an Acropora coral by as much as 1 °C or 0.4 °C based on bleaching index scores or dark-acclimated photosynthetic efficiencies, respectively. Using RNA-Seq, we show similar stress responses to heat with and without deoxygenated seawater, both activating putative key genes of the hypoxia-inducible factor response system indicative of cellular hypoxia. We also detect distinct deoxygenation responses, including a disruption of O2-dependent photo-reception/-protection, redox status, and activation of an immune response prior to the onset of bleaching. Thus, corals are even more vulnerable when faced with heat stress in deoxygenated waters. This highlights the need to integrate dissolved O2 measurements into global monitoring programs of coral reefs.

Oxidative stress, apoptosis, and transcriptional responses in Acropora microphthalma under simulated diving activities

This study simulated the effects of diving activities on the physiology, enzymatic, and transcriptional responses of Acropora microphthalma. Touching had less impact on Fv/Fm, but a few zooxanthellae were decreased and minor MDA was elevated. Caspase 3 was activated to remove damaged cells, and SOD was increased to alleviate oxidative damage. Under double or triple diving stress, we observed mass loss of zooxanthellae and Fv/Fm, a significant increase in MDA, and SOD, CAT was activated in response to oxidative stress. Transcriptome analyses showed that corals activated immune signaling pathways, anti-oxidation pathways, lysosomal, phagosomal, and cellular autophagy pathways to manage oxidation stress. Moreover, it up-regulated carbohydrate metabolisms, as well as lipopolysaccharide metabolism, glycosphingolipid biosynthesis, photorespiration, amino acid metabolism, and fatty acid beta-oxidation, but down-regulated fatty acid biosynthesis to answer energy insufficiency. This research supported that even in a short time, improper diving activities could have a serious impact on coral health.

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.

Transcriptional response of the azooxanthellate octocoral Scleronephthya gracillimum to seawater acidification and thermal stress

The stress responses to increased seawater temperature and marine acidification were investigated using a microarray to reveal transcriptional changes in S. gracillimum. For the study, corals were exposed to different stress experiments; high temperature only (26 °C, 28 °C and 30 °C), low-pH only (pH 7.5, pH 7.0 and pH 6.5) and dual stress experiments (28 °C + pH 7.8, 28 °C + pH 7.5 and 28 °C + pH 7.0), mortality and morphological changes in 24 h exposure experiments were investigated. The survival rates of each experimental group were observed. The gene expression changes in single and dual stress exposed coals were measured and the differentially expressed genes were classified with gene ontology analysis. The top three enriched gene ontology terms of DEGs in response to dual stress were metal ion binding (23.4%), extracellular region (17.2%), and calcium ion binding (12.8%). The gene showing the greatest increase in expression as a response to the dual stress was hemagglutinin/amebocyte aggregation factor, followed by interferon-inducible GTPase 5 and the gene showing the greatest decrease as a response to the dual stress was Fas-associating death domain-containing protein, followed by oxidase 2. These results represented the transcriptomic study focused on the stress responses of the temperate asymbiotic soft coral exposed to single and dual stresses. The combined effect of thermal and acidification stress on corals triggered the negative regulation of ion binding and extracellular matrix coding genes and these genes might serve as a basis for research into coral-specific adaptations to stress responses and global climate change.

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.

Metatranscriptomic Analysis of Corals Inoculated With Tolerant and Non-Tolerant Symbiont Exposed to High Temperature and Light Stress

Algal symbionts of corals can influence host stress resistance; for example, in the Pacific Ocean, whereas Cladocopium (C-type) is generally dominant in corals, Durusdinium (D-type) is found in more heat-resistant corals. Thus, the presence of D-type symbiont likely increases coral heat tolerance, and this symbiotic relationship potentially provides a hint to increase the stress tolerance of coral–algal symbioses. In this study, transcriptome profiles of Cladocopium- and Durusdinium-harboring Acropora solitaryensis (C-coral and D-coral, respectively) and algal photosystem functioning (Fv/Fm) under bleaching conditions (high temperature and light stress) were compared. Stress treatment caused algal photoinhibition that the Fv/Fm value of Symbiodiniaceae was immediately reduced. The transcriptome analysis of corals revealed that genes involved in the following processes were detected: endoplasmic reticulum (ER) stress, mitophagy, apoptosis, endocytosis, metabolic processes (acetyl-CoA, chitin metabolic processes, etc.), and the PI3K-AKT pathway were upregulated, while DNA replication and the calcium signaling pathway were downregulated in both C- and D-corals. These results suggest that unrepaired DNA and protein damages were accumulated in corals under high temperature and light stress. Additionally, some differentially expressed genes (DEGs) were specific to C- or D-corals, which includes genes involved in transient receptor potential (TRP) channels and vitamin B metabolic processes. Algal transcriptome analysis showed the increased expression of gene encoding photosystem and molecular chaperone especially in D-type symbiont. The transcriptome data imply a possible difference in the stress reactions on C-type and D-type symbionts. The results reveal the basic process of coral heat/light stress response and symbiont-type-specific coral transcriptional responses, which provides a perspective on the mechanisms that cause differences in coral stress tolerance.

Does Predation Exacerbate the Risk of Endosymbiont Loss in Heat Stressed Hermatypic Corals? Molecular Cues Provide Insights Into Species-Specific Health Outcomes in a Multi-Stressor Ocean

Ocean warming has been a major driver of coral reef bleaching and mass mortality. Coupled to other biotic pressures, corals’ ability for acclimatization and adaptation may become compromised. Here, we tested the combined effects of warming scenarios (26, 30, and 32°C) and predation (wound vs. no wound) in coral health condition (paleness, bleaching, and mortality), cellular stress responses (heat shock protein 70 kDa Hsp70, total ubiquitin Ub, and total antioxidant capacity TAC), and physiological state (integrated biomarker response index, IBR) of seven Scleractinian coral species, after being exposed for 60 days. Results show that although temperature was the main factor driving coral health condition, thermotolerant species (Galaxea fascicularis, Psammocora contigua, and Turbinaria reniformis) displayed increased paleness, bleaching, and mortality in predation treatments at high temperature, whereas thermosensitive species (Acropora tenuis, Echinopora lamellosa, and Montipora capricornis brown and green morphotypes) all died at 32°C, regardless of predation condition. At the molecular level, results show that there were significant main and interactive effects of species, temperature, and predation in the biomarkers assessed. Temperature affected Hsp70, Ub, and TAC, evidencing the role of protein folding and turnover, as well as reactive oxygen species scavenging in heat stress management. Predation increased Hsp70 and Ub, suggesting the activation of the pro-phenoloxidase system and cytokine activity, whereas the combination of both stressors mainly affected TAC during moderate stress and Ub under severe stress, suggesting that redox balance and defense of homeostasis are crucial in tissue repair at high temperature. IBR levels showed an increasing trend at 32°C in predated coral fragments (although non-significant). We conclude that coral responses to the combination of high temperature and predation pressure display high inter-species variability, but these stressors may pose a higher risk of endosymbiont loss, depending on species physiology and stress intensity.

Nematostella vectensis exhibits an enhanced molecular stress response upon co-exposure to highly weathered oil and surface UV radiation

Crude oil released into the environment undergoes weathering processes that gradually change its composition and toxicity. Co-exposure to petroleum mixtures and other stressors, including ultraviolet (UV) radiation, may lead to synergistic effects and increased toxicity. Laboratory studies should consider these factors when testing the effects of oil exposure on aquatic organisms. Here, we study transcriptomic responses of the estuarine sea anemone Nematostella vectensis to naturally weathered oil, with or without co-exposure to environmental levels of UV radiation. We find that co-exposure greatly enhances the response. We use bioinformatic analyses to identify molecular pathways implicated in this response, which suggest phototoxicity and oxidative damage as mechanisms for the enhanced stress response. Nematostella's stress response shares similarities with the vertebrate oxidative stress response, implying deep conservation of certain stress pathways in animals. We show that exposure to weathered oil along with surface-level UV exposure has substantial physiological consequences in a model cnidarian.

Larval transcriptomic responses of a stony coral, Acropora tenuis, during initial contact with the native symbiont, Symbiodinium microadriaticum

Although numerous dinoflagellate species (Family Symbiodiniaceae) are present in coral reef environments, Acropora corals tend to select a single species, Symbiodinium microadriaticum, in early life stages, even though this species is rarely found in mature colonies. In order to identify molecular mechanisms involved in initial contact with native symbionts, we analyzed transcriptomic responses of Acropora tenuis larvae at 1, 3, 6, 12, and 24 h after their first contact with S. microadriaticum, as well as with non-native symbionts, including the non-symbiotic S. natans and the occasional symbiont, S. tridacnidorum. Some gene expression changes were detected in larvae inoculated with non-native symbionts at 1 h post-inoculation, but those returned to baseline levels afterward. In contrast, when larvae were exposed to native symbionts, we found that the number of differentially expressed genes gradually increased in relation to inoculation time. As a specific response to native symbionts, upregulation of pattern recognition receptor-like and transporter genes, and suppression of cellular function genes related to immunity and apoptosis, were exclusively observed. These findings indicate that coral larvae recognize differences between symbionts, and when the appropriate symbionts infect, they coordinate gene expression to establish stable mutualism.

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.

Host-symbiont transcriptomic changes during natural bleaching and recovery in the leaf coral Pavona decussata

Coral bleaching has become a major threat to coral reefs worldwide, but for most coral species little is known about their resilience to environmental changes. We aimed to understand the gene expressional regulation underlying natural bleaching and recovery in Pavona decussata, a dominant species of scleractinian coral in the northern South China Sea. Analyzing samples collected in 2017 from the field revealed distinct zooxanthellae density, chlorophyll a concentration and transcriptomic signatures corresponding to changes in health conditions of the coral holobiont. In the host, normal-looking tissues of partially bleached colonies were frontloaded with stress responsive genes, as indicated by upregulation of immune defense, response to endoplasmic reticulum, and oxidative stress genes. Bleaching was characterized by upregulation of apoptosis-related genes which could cause a reduction in algal symbionts, and downregulation of genes involved in stress responses and metabolic processes. The transcription factors stat5b and irf1 played key roles in bleaching by regulating immune and apoptosis pathways. Recovery from bleaching was characterized by enrichment of pathways involved in mitosis, DNA replication, and recombination for tissue repairing, as well as restoration of energy and metabolism. In the symbionts, bleaching corresponded to imbalance in photosystems I and II activities which enhanced oxidative stress and limited energy production and nutrient assimilation. Overall, our study revealed distinct gene expressional profiles and regulation in the different phases of the bleaching and recovery process, and provided new insight into the molecular mechanisms underlying the holobiont's resilience that may determine the species' fate in response to global and regional environmental changes.

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.

Effects of nanostructure antifouling biocides towards a coral species in the context of global changes

Biofouling prevention is one of the biggest challenges faced by the maritime industry, but antifouling agents commonly impact marine ecosystems. Advances in antifouling technology include the use of nanomaterials. Herein we test an antifouling nano-additive based on the encapsulation of the biocide 4,5-dichloro-2-octyl-4-isothiazolin-3-one (DCOIT) in engineered silica nanocontainers (SiNC). The work aims to assess the biochemical and physiological effects on the symbiotic coral Sarcophyton cf. glaucum caused by (1) thermal stress and (2) DCOIT exposure (free or nanoencapsulated forms), in a climate change scenario. Accordingly, the following hypotheses were addressed: (H1) ocean warming can cause toxicity on S. cf. glaucum; (H2) the nanoencapsulation process decreases DCOIT toxicity towards this species; (H3) the biocide toxicity, free or encapsulated forms, can be affected by ocean warming. Coral fragments were exposed for seven days to DCOIT in both free and encapsulated forms, SiNC and negative controls, under two water temperature regimes (26 °C and 30.5 °C). Coral polyp behavior and photosynthetic efficiency were determined in the holobiont, while biochemical markers were assessed individually in the endosymbiont and coral host. Results showed transient coral polyp retraction and diminished photosynthetic efficiency in the presence of heat stress or free DCOIT, with effects being magnified in the presence of both stressors. The activity of catalase and glutathione-S-transferase were modulated by temperature in each partner of the symbiosis. The shifts in enzymatic activity were more pronounced in the presence of free DCOIT, but to a lower extent for encapsulated DCOIT. Increased levels of oxidative damage were detected under heat conditions. The findings highlight the physiological constrains elicited by the increase of seawater temperature to symbiotic corals and demonstrate that DCOIT toxicity can be minimized through encapsulation in SiNC. The presence of both stressors magnifies toxicity and confirm that ocean warming enhances the vulnerability of tropical photosynthetic corals to local stressors.

Untangling the molecular basis of coral response to sedimentation

Urbanized coral reefs are often chronically affected by sedimentation and reduced light levels, yet many species of corals appear to be able to thrive under these highly disturbed conditions. Recently, these marginal ecosystems have gained attention as potential climate change refugia due to the shading effect of suspended sediment, as well as potential reservoirs for stress-tolerant species. However, little research exists on the impact of sedimentation on coral physiology, particularly at the molecular level. Here, we investigated the transcriptomic response to sediment stress in corals of the family Merulinidae from a chronically turbid reef (one genet each of Goniastrea pectinata and Mycedium elephantotus from Singapore) and a clear-water reef (multiple genets of G. pectinata from the Gulf of Aqaba/Eilat). In two ex-situ experiments, we exposed corals to either natural sediment or artificial sediment enriched with organic matter and used whole-transcriptome sequencing (RNA sequencing) to quantify gene expression. Analysis revealed a shared basis for the coral transcriptomic response to sediment stress, which involves the expression of genes broadly related to energy metabolism and immune response. In particular, sediment exposure induced upregulation of anaerobic glycolysis and glyoxylate bypass enzymes, as well as genes involved in hydrogen sulphide metabolism and in pathogen pattern recognition. Our results point towards hypoxia as a probable driver of this transcriptomic response, providing a molecular basis to previous work that identified hypoxia as a primary cause of tissue necrosis in sediment-stressed corals. Potential metabolic and immunity trade-offs of corals living under chronic sedimentation should be considered in future studies on the ecology and conservation of turbid reefs.

Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress

As coral reefs struggle to survive under climate change, it is crucial to know whether they have the capacity to withstand changing conditions, particularly increasing seawater temperatures. Thermal tolerance requires the integrative response of the different components of the coral holobiont (coral host, algal photosymbiont, and associated microbiome). Here, using a controlled thermal stress experiment across three divergent Caribbean coral species, we attempt to dissect holobiont member metatranscriptome responses from coral taxa with different sensitivities to heat stress and use phylogenetic ANOVA to study the evolution of gene expression adaptation. We show that coral response to heat stress is a complex trait derived from multiple interactions among holobiont members. We identify host and photosymbiont genes that exhibit lineage-specific expression level adaptation and uncover potential roles for bacterial associates in supplementing the metabolic needs of the coral-photosymbiont duo during heat stress. Our results stress the importance of integrative and comparative approaches across a wide range of species to better understand coral survival under the predicted rise in sea surface temperatures.

Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance

Corals from the northern Red Sea, in particular the Gulf of Aqaba (GoA), have exceptionally high bleaching thresholds approaching >5℃ above their maximum monthly mean (MMM) temperatures. These elevated thresholds are thought to be due to historical selection, as corals passed through the warmer Southern Red Sea during recolonization from the Arabian Sea. To test this hypothesis, we determined thermal tolerance thresholds of GoA versus central Red Sea (CRS) Stylophora pistillata corals using multi-temperature acute thermal stress assays to determine thermal thresholds. Relative thermal thresholds of GoA and CRS corals were indeed similar and exceptionally high (~7℃ above MMM). However, absolute thermal thresholds of CRS corals were on average 3℃ above those of GoA corals. To explore the molecular underpinnings, we determined gene expression and microbiome response of the coral holobiont. Transcriptomic responses differed markedly, with a strong response to the thermal stress in GoA corals and their symbiotic algae versus a remarkably muted response in CRS colonies. Concomitant to this, coral and algal genes showed temperature-induced expression in GoA corals, while exhibiting fixed high expression (front-loading) in CRS corals. Bacterial community composition of GoA corals changed dramatically under heat stress, whereas CRS corals displayed stable assemblages. We interpret the response of GoA corals as that of a resilient population approaching a tipping point in contrast to a pattern of consistently elevated thermal resistance in CRS corals that cannot further attune. Such response differences suggest distinct thermal tolerance mechanisms that may affect the response of coral populations to ocean warming.

Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen

The activity of transposable elements (TEs) can be an important driver of genetic diversity with TE-mediated mutations having a wide range of fitness consequences. To avoid deleterious effects of TE activity, some fungi have evolved highly sophisticated genomic defences to reduce TE proliferation across the genome. Repeat-induced point mutation (RIP) is a fungal-specific TE defence mechanism efficiently targeting duplicated sequences. The rapid accumulation of RIPs is expected to deactivate TEs over the course of a few generations. The evolutionary dynamics of TEs at the population level in a species with highly repressive genome defences is poorly understood. Here, we analyse 366 whole-genome sequences of Parastagonospora nodorum, a fungal pathogen of wheat with efficient RIP. A global population genomics analysis revealed high levels of genetic diversity and signs of frequent sexual recombination. Contrary to expectations for a species with RIP, we identified recent TE activity in multiple populations. The TE composition and copy numbers showed little divergence among global populations regardless of the demographic history. Miniature inverted-repeat transposable elements (MITEs) and terminal repeat retrotransposons in miniature (TRIMs) were largely underlying recent intra-species TE expansions. We inferred RIP footprints in individual TE families and found that recently active, high-copy TEs have possibly evaded genomic defences. We find no evidence that recent positive selection acted on TE-mediated mutations rather that purifying selection maintained new TE insertions at low insertion frequencies in populations. Our findings highlight the complex evolutionary equilibria established by the joint action of TE activity, selection and genomic repression.

Enhancing the heat tolerance of reef-building corals to future warming

Reef-building corals thriving in extreme thermal environments may provide genetic variation that can assist the evolution of populations to rapid climate warming. However, the feasibility and scale of genetic improvements remain untested despite ongoing population declines from recurrent thermal stress events. Here, we show that corals from the hottest reefs in the world transfer sufficient heat tolerance to a naïve population sufficient to withstand end-of-century warming projections. Heat survival increased up to 84% when naïve mothers were selectively bred with fathers from the hottest reefs because of strong heritable genetic effects. We identified genomic loci associated with tolerance variation that were enriched for heat shock proteins, oxidative stress, and immune functions. Unexpectedly, several coral families exhibited survival rates and genomic associations deviating from origin predictions, including a few naïve purebreds with exceptionally high heat tolerance. Our findings highlight previously uncharacterized enhanced and intrinsic potential of coral populations to adapt to climate warming.

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.

Seascape genomics reveals candidate molecular targets of heat stress adaptation in three coral species

Anomalous heat waves are causing a major decline of hard corals around the world and threatening the persistence of coral reefs. There are, however, reefs that have been exposed to recurrent thermal stress over the years and whose corals appear to have been tolerant against heat. One of the mechanisms that could explain this phenomenon is local adaptation, but the underlying molecular mechanisms are poorly known. In this work, we applied a seascape genomics approach to study heat stress adaptation in three coral species of New Caledonia (southwestern Pacific) and to uncover the molecular actors potentially involved. We used remote sensing data to characterize the environmental trends across the reef system, and sampled corals living at the most contrasted sites. These samples underwent next generation sequencing to reveal single nucleotide polymorphisms (SNPs), frequencies of which were associated with heat stress gradients. As these SNPs might underpin an adaptive role, we characterized the functional roles of the genes located in their genomic region. In each of the studied species, we found heat stress-associated SNPs located in proximity of genes involved in pathways well known to contribute to the cellular responses against heat, such as protein folding, oxidative stress homeostasis, inflammatory and apoptotic pathways, and DNA damage-repair. In some cases, the same candidate molecular targets of heat stress adaptation recurred among species. Together, these results underline the relevance and the power of the seascape genomics approach for the discovery of adaptive traits that could allow corals to persist across wider thermal ranges.

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 proteomic analysis of skeletal tissue anomaly in the brain coral Platygyra carnosa

Coral skeletal growth anomaly (GA) is a common coral disease. It has been considered as a pathological condition comparable to abnormal tissue growth in mammals, but little is known about the molecular changes underlying coral GA. To investigate the molecular pathology of GA, we compared the proteome between normal and GA-affected tissues of the brain coral Platygyra carnosa using iTRAQ-labeling and LC-MS/MS, which quantified 818 proteins and identified 117 differentially expressed proteins (DEPs). GO analyses revealed DEPs that might be related to GA included "translational elongation", "proteasome core complex", "amine metabolic processes" and "lysosome". Several proteins implicated in calcification and fluorescence were differentially expressed at both protein and mRNA level. Protein-protein interaction network suggested possible involvement of TNF receptor signaling in GA. Overall, our results provided novel insights into the molecular pathology of coral GA, which will pave the way for determination of the causative agent(s) of this coral disease.

Divergent expression of hypoxia response systems under deoxygenation in reef-forming corals aligns with bleaching susceptibility

Exposure of marine life to low oxygen is accelerating worldwide via climate change and localized pollution. Mass coral bleaching and mortality have recently occurred where reefs have experienced chronic low oxygen events. However, the mechanistic basis of tolerance to oxygen levels inadequate to sustain normal functioning (i.e. hypoxia) and whether it contributes to bleaching susceptibility, remain unknown. We therefore experimentally exposed colonies of the environmentally resilient Acropora tenuis, a common reef-building coral from the Great Barrier Reef, to deoxygenation-reoxygenation stress that was aligned to their natural night-day light cycle. Specifically, the treatment involved removing the 'night-time O₂ buffer' to challenge the inherent hypoxia thresholds. RNA-Seq analysis revealed that coral possess a complete and active hypoxia-inducible factor (HIF)-mediated hypoxia response system (HRS) homologous to other metazoans. As expected, A. tenuis exhibited bleaching resistance and showed a strong inducibility of HIF target genes in response to deoxygenation stress. We applied this same approach in parallel to a colony of Acropora selago, known to be environmnetally susceptible, which conversely exhibited a bleaching phenotype response. This phenotypic divergence of A. selago was accompanied by contrasting gene expression profiles indicative of varied effectiveness of their HIF-HRS. Based on our RNA-Seq analysis, we propose (a) that the HIF-HRS is central for corals to manage deoxygenation stress and (b) that key genes of this system (and the wider gene network) may contribute to variation in coral bleaching susceptibility. Our analysis suggests that heat shock protein (hsp) 70 and 90 are important for low oxygen stress tolerance and further highlights how hsp90 expression might also affect the inducibility of coral HIF-HRS in overcoming a metabolic crisis under deoxygenation stress. We propose that differences in coral HIF-HRS could be central in regulating sensitivity to other climate change stressors-notably thermal stress-that commonly drive bleaching.

Coral gasdermin triggers pyroptosis

Gasdermins are executioners of the inflammatory cell death pathway pyroptosis that has so far been studied exclusively in vertebrates. In this study, we identified gasdermin E (GSDME) homologs in several invertebrate species including corals. We report that coral GSDME was cleaved by caspase 3 at two sites, yielding two active isoforms of GSDME N-terminal domain that were capable of inducing pyroptosis. Ectopic coexpression of coral GSDME and caspase 3 in human cells promoted pyroptosis. Corals infected with Vibrio coralliilyticus, a bacterial pathogen causing rapid tissue necrosis of corals worldwide, exhibited necrotic death with elevated caspase 3 activity and GSDME cleavage, whereas inhibition of caspase 3 blocked GSDME cleavage and protected corals from necrotic death. These results indicate that functional gasdermin exists in invertebrates and that coral gasdermin is involved in pathogen-induced coral death. Furthermore, our studies also suggest that mediation of pyroptosis is an evolutionarily conserved function of gasdermins.

Transcriptome Analyses of Immune System Behaviors in Primary Polyp of Coral Acropora digitifera Exposed to the Bacterial Pathogen Vibrio coralliilyticus under Thermal Loading

Elevated sea surface temperature associated with global warming is a serious threat to coral reefs. Elevated temperatures directly or indirectly alter the distribution of coral-pathogen interactions and thereby exacerbate infectious coral diseases. The pathogenic bacterium Vibrio coralliilyticus is well-known as a causative agent of infectious coral disease. Rising sea surface temperature promotes the infection of corals by this bacterium, which causes several coral pathologies, such as bacterial bleaching, tissue lysis, and white syndrome. However, the effects of thermal stress on coral immune responses to the pathogen are poorly understood. To delineate the effects of thermal stress on coral immunity, we performed transcriptome analysis of aposymbiotic primary polyps of the reef-building coral Acropora digitifera exposed to V. coralliilyticus under thermal stress conditions. V. coralliilyticus infection of coral that was under thermal stress had negative effects on various molecular processes, including suppression of gene expression related to the innate immune response. In response to the pathogen, the coral mounted various responses including changes in protein metabolism, exosome release delivering signal molecules, extracellular matrix remodeling, and mitochondrial metabolism changes. Based on these results, we provide new insights into innate immunity of A. digitifera against pathogen infection under thermal stress conditions.

Maternal effects in gene expression of interspecific coral hybrids

Maternal effects have been well documented for offspring morphology and life history traits in plants and terrestrial animals, yet little is known about maternal effects in corals. Further, few studies have explored maternal effects in gene expression. In a previous study, F1 interspecific hybrid and purebred larvae of the coral species Acropora tenuis and Acropora loripes were settled and exposed to ambient or elevated temperature and pCO₂ conditions for 7 months. At this stage, the hybrid coral recruits from both ocean conditions exhibited strong maternal effects in several fitness traits. We conducted RNA-sequencing on these corals and showed that gene expression of the hybrid Acropora also exhibited clear maternal effects. Only 40 genes were differentially expressed between hybrids and their maternal progenitor. In contrast, ~2000 differentially expressed genes were observed between hybrids and their paternal progenitors, and between the reciprocal F1 hybrids. These results indicate that maternal effects in coral gene expression can be long-lasting. Unlike findings from most short-term stress experiments in corals, no genes were differentially expressed in the hybrid nor purebred offspring after seven months of exposure to elevated temperature and pCO₂ conditions.

Impact of Ocean Warming and Acidification on Symbiosis Establishment and Gene Expression Profiles in Recruits of Reef Coral Acropora intermedia

The onset of symbiosis and the early development of most broadcast spawning corals play pivotal roles in recruitment success, yet these critical early stages are threatened by multiple stressors. However, molecular mechanisms governing these critical processes under ocean warming and acidification are still poorly understood. The present study investigated the interactive impact of elevated temperature (∼28.0°C and ∼30.5°C) and partial pressure of carbon dioxide (pCO₂) (∼600 and ∼1,200 μatm) on early development and the gene expression patterns in juvenile Acropora intermedia over 33 days. The results showed that coral survival was >89% and was unaffected by high temperature, pCO₂, or the combined treatment. Notably, high temperature completely arrested successful symbiosis establishment and the budding process, whereas acidification had a negligible effect. Moreover, there was a positive exponential relationship between symbiosis establishment and budding rates (y = 0.0004e^6.43x, R = 0.72, P < 0.0001), which indicated the importance of symbiosis in fueling asexual budding. Compared with corals at the control temperature (28°C), those under elevated temperature preferentially harbored Durusdinium spp., despite unsuccessful symbiosis establishment. In addition, compared to the control, 351 and 153 differentially expressed genes were detected in the symbiont and coral host in response to experimental conditions, respectively. In coral host, some genes involved in nutrient transportation and tissue fluorescence were affected by high temperature. In the symbionts, a suite of genes related to cell growth, ribosomal proteins, photosynthesis, and energy production was downregulated under high temperatures, which may have severely hampered successful cell proliferation of the endosymbionts and explains the failure of symbiosis establishment. Therefore, our results suggest that the responses of symbionts to future ocean conditions could play a vital role in shaping successful symbiosis in juvenile coral.

Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee

Global temperature changes have emphasized the need to understand how species adapt to thermal stress across their ranges. Genetic mechanisms may contribute to variation in thermal tolerance, providing evidence for how organisms adapt to local environments. We determine physiological thermal limits and characterize genome-wide transcriptional changes at these limits in bumble bees using laboratory-reared Bombus vosnesenskii workers. We analyze bees reared from latitudinal (35.7-45.7°N) and altitudinal (7-2154 m) extremes of the species' range to correlate thermal tolerance and gene expression among populations from different climates. We find that critical thermal minima (CTMIN) exhibit strong associations with local minimums at the location of queen origin, while critical thermal maximum (CTMAX) was invariant among populations. Concordant patterns are apparent in gene expression data, with regional differentiation following cold exposure, and expression shifts invariant among populations under high temperatures. Furthermore, we identify several modules of co-expressed genes that tightly correlate with critical thermal limits and temperature at the region of origin. Our results reveal that local adaptation in thermal limits and gene expression may facilitate cold tolerance across a species range, whereas high temperature responses are likely constrained, both of which may have implications for climate change responses of bumble bees.

Transcriptomic signatures of cold adaptation and heat stress in the winter ant (Prenolepis imparis)

Climate change is a serious threat to biodiversity; it is therefore important to understand how animals will react to this stress. Ectotherms, such as ants, are especially sensitive to the climate as the environmental temperature influences myriad aspects of their biology, from optimal foraging time to developmental rate. In this study, we conducted an RNA-seq analysis to identify stress-induced genes in the winter ant (Prenolepis imparis). We quantified gene expression during heat and cold stress relative to a control temperature. From each of our conditions, we sequenced the transcriptome of three individuals. Our de novo assembly included 13,324 contigs that were annotated against the nr and SwissProt databases. We performed gene ontology and enrichment analyses to gain insight into the physiological processes involved in the stress response. We identified a total of 643 differentially expressed genes across both treatments. Of these, only seven genes were differentially expressed in the cold-stressed ants, which could indicate that the temperature we chose for trials did not induce a strong stress response, perhaps due to the cold adaptations of this species. Conversely, we found a strong response to heat: 426 upregulated genes and 210 downregulated genes. Of these, ten were expressed at a greater than ten-fold change relative to the control. The transcripts we could identify included those encoding for protein folding genes, heat shock proteins, histones, and Ca2+ ion transport. One of these transcripts, hsc70-4L was found to be under positive selection. We also characterized the functional categories of differentially expressed genes. These candidate genes may be functionally conserved and relevant for related species that will deal with rapid climate change.

Coral evolutionary responses to microbial symbioses

This review explores how microbial symbioses may have influenced and continue to influence the evolution of reef-building corals (Cnidaria; Scleractinia). The coral holobiont comprises a diverse microbiome including dinoflagellate algae (Dinophyceae; Symbiodiniaceae), bacteria, archaea, fungi and viruses, but here we focus on the Symbiodiniaceae as knowledge of the impact of other microbial symbionts on coral evolution is scant. Symbiosis with Symbiodiniaceae has extended the coral's metabolic capacity through metabolic handoffs and horizontal gene transfer (HGT) and has contributed to the ecological success of these iconic organisms. It necessitated the prior existence or the evolution of a series of adaptations of the host to attract and select the right symbionts, to provide them with a suitable environment and to remove disfunctional symbionts. Signatures of microbial symbiosis in the coral genome include HGT from Symbiodiniaceae and bacteria, gene family expansions, and a broad repertoire of oxidative stress response and innate immunity genes. Symbiosis with Symbiodiniaceae has permitted corals to occupy oligotrophic waters as the algae provide most corals with the majority of their nutrition. However, the coral-Symbiodiniaceae symbiosis is sensitive to climate warming, which disrupts this intimate relationship, causing coral bleaching, mortality and a worldwide decline of coral reefs. This article is part of the theme issue 'The role of the microbiome in host evolution'.

Global gene expression patterns in Porites white patch syndrome: Disentangling symbiont loss from the thermal stress response in reef-building coral

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

Cnidarian Immunity and the Repertoire of Defense Mechanisms in Anthozoans

Anthozoa is the most specious class of the phylum Cnidaria that is phylogenetically basal within the Metazoa. It is an interesting group for studying the evolution of mutualisms and immunity, for despite their morphological simplicity, Anthozoans are unexpectedly immunologically complex, with large genomes and gene families similar to those of the Bilateria. Evidence indicates that the Anthozoan innate immune system is not only involved in the disruption of harmful microorganisms, but is also crucial in structuring tissue-associated microbial communities that are essential components of the cnidarian holobiont and useful to the animal's health for several functions including metabolism, immune defense, development, and behavior. Here, we report on the current state of the art of Anthozoan immunity. Like other invertebrates, Anthozoans possess immune mechanisms based on self/non-self-recognition. Although lacking adaptive immunity, they use a diverse repertoire of immune receptor signaling pathways (PRRs) to recognize a broad array of conserved microorganism-associated molecular patterns (MAMP). The intracellular signaling cascades lead to gene transcription up to endpoints of release of molecules that kill the pathogens, defend the self by maintaining homeostasis, and modulate the wound repair process. The cells play a fundamental role in immunity, as they display phagocytic activities and secrete mucus, which acts as a physicochemical barrier preventing or slowing down the proliferation of potential invaders. Finally, we describe the current state of knowledge of some immune effectors in Anthozoan species, including the potential role of toxins and the inflammatory response in the Mediterranean Anthozoan Anemonia viridis following injection of various foreign particles differing in type and dimensions, including pathogenetic bacteria.

Experimental investigation of tidal and freshwater influence on Symbiodiniaceae abundance in Anthopleura elegantissima

The San Francisco Bay outflow creates a tidally influenced low-salinity plume that affects adjacent coastal sites. In the study region, Anthopleura elegantissima (Cnidaria; Anthozoa) hosts a single symbiont, the dinoflagellate Breviolum muscatinei. Salinity, temperature, and aerial stress induce a bleaching response similar to corals where symbionts are expelled, causing further energetic stress. Using field observations of environmental conditions and symbiont abundance at sites on a gradient of exposure to estuarine outflow, along with a fully crossed multifactorial lab experiment, we tested for changes in symbiont abundance in response to various combinations of three stressors. Lab experiments were designed to mimic short term outflow events with low salinity, high temperature, and aerial exposure treatments. The lab aerial exposure treatment was a statistically significant factor in suppressing symbiont repopulation (ANOVA, p = .017). In the field, symbiont density decreased with increasing tidal height at the site closest to freshwater outflow (ANOVA, p = .007), suggesting that aerial exposure may affect symbiont density more than sea surface temperature and salinity. Unanticipated documentation of survival in 9 months of sand burial and subsequent repopulation of symbionts is reported as a six-month extension to past observations, exemplifying strong tolerance to environmental insult in this Cnidarian mutualism. The study of this symbiosis is useful in examining predicted changes in ocean conditions in tidepool communities and considering relative sources of stress.

Gene Expression and Photophysiological Changes in Pocillopora acuta Coral Holobiont Following Heat Stress and Recovery

The ability of corals to withstand changes in their surroundings is a critical survival mechanism for coping with environmental stress. While many studies have examined responses of the coral holobiont to stressful conditions, its capacity to reverse responses and recover when the stressor is removed is not well-understood. In this study, we investigated among-colony responses of Pocillopora acuta from two sites with differing distance to the mainland (Kusu (closer to the mainland) and Raffles Lighthouse (further from the mainland)) to heat stress through differential expression analysis of target genes and quantification of photophysiological metrics. We then examined how these attributes were regulated after the stressor was removed to assess the recovery potential of P. acuta. The fragments that were subjected to heat stress (2 °C above ambient levels) generally exhibited significant reduction in their endosymbiont densities, but the extent of recovery following stress removal varied depending on natal site and colony. There were minimal changes in chl a concentration and maximum quantum yield (Fv/Fm, the proportion of variable fluorescence (Fv) to maximum fluorescence (Fm)) in heat-stressed corals, suggesting that the algal endosymbionts’ Photosystem II was not severely compromised. Significant changes in gene expression levels of selected genes of interest (GOI) were observed following heat exposure and stress removal among sites and colonies, including Actin, calcium/calmodulin-dependent protein kinase type IV (Camk4), kinesin-like protein (KIF9), and small heat shock protein 16.1 (Hsp16.1). The most responsive GOIs were Actin, a major component of the cytoskeleton, and the adaptive immune-related Camk4 which both showed significant reduction following heat exposure and subsequent upregulation during the recovery phase. Our findings clearly demonstrate specific responses of P. acuta in both photophysiological attributes and gene expression levels, suggesting differential capacity of P. acuta corals to tolerate heat stress depending on the colony, so that certain colonies may be more resilient than others.

Coral Bleaching: A Colorful Struggle for Survival

An optical feedback loop involving the coral host and its photosynthetic microalgal symbionts is responsible for the extreme coloration of corals during certain bleaching events. Colorful bleaching occurs after brief or mild exposure to heat or nutrient stress. Importantly, it can indicate good recovery prospects for the affected corals.

Gene regulation underpinning increased thermal tolerance in a laboratory-evolved coral photosymbiont

Small increases in ocean temperature can disrupt the obligate symbiosis between corals and dinoflagellate microalgae, resulting in coral bleaching. Little is known about the genes that drive the physiological and bleaching response of algal symbionts to elevated temperature. Moreover, many studies to-date have compared highly divergent strains, making it challenging to accredit specific genes to contrasting traits. Here, we compare transcriptional responses at ambient (27°C) and bleaching-relevant (31°C) temperatures in a monoclonal, wild-type (WT) strain of Symbiodiniaceae to those of a selected-strain (SS), derived from the same monoclonal culture and experimentally evolved to elevated temperature over 80 generations (2.5 years). Thousands of genes were differentially expressed at a log fold-change of >8 between the WT and SS over a 35 days temperature treatment period. At 31°C, WT cells exhibited a temporally unstable transcriptomic response upregulating genes involved in the universal stress response such as molecular chaperoning, protein repair, protein degradation and DNA repair. Comparatively, SS cells exhibited a temporally stable transcriptomic response and downregulated many stress response genes that were upregulated by the WT. Among the most highly upregulated genes in the SS at 31°C were algal transcription factors and a gene probably of bacterial origin that encodes a type II secretion system protein, suggesting interactions with bacteria may contribute to the increased thermal tolerance of the SS. Genes and functional pathways conferring thermal tolerance in the SS could be targeted in future genetic engineering experiments designed to develop thermally resilient algal symbionts for use in coral restoration and conservation.

Responding to Threats Both Foreign and Domestic: NOD-Like Receptors in Corals

Historically mechanisms with which basal animals such as reef-building corals use to respond to changing and increasingly stressful environments have remained elusive. However, the increasing availability of genomic and transcriptomic data from these organisms has provided fundamental insights into the biology of these critically important ecosystem engineers. Notably, insights into cnidarians gained in the post-genomics age have revealed a surprisingly complex immune system which bears a surprising level of similarity with the vertebrate innate immune system. This system has been critically linked to how corals respond to the two most prominent threats on a global scale, emerging coral diseases and increasing water temperature, which are recognized cellularly as either foreign or domestic threats, respectively. These threats can arise from pathogenic microbes or internal cellular dysfunction, underscoring the need to further understand mechanisms corals use to sense and respond to threats to their cellular integrity. In this investigation and meta-analysis, we utilize resources only recently available in the post-genomic era to identify and characterize members of an underexplored class of molecules known as NOD-like receptors in the endangered Caribbean coral Orbicella faveolata. We then leverage these data to identify pathways possibly mediated by NLRs in both O. faveolata and the ecologically important branching coral Acropora digitifera. Overall, we find support that this class of proteins may provide a mechanistic link to how reef-building corals respond to threats both foreign and domestic.

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.

Warm temperatures, cool sponges: the effect of increased temperatures on the Antarctic sponge Isodictya sp

Although the cellular and molecular responses to exposure to relatively high temperatures (acute thermal stress or heat shock) have been studied previously, only sparse empirical evidence of how it affects cold-water species is available. As climate change becomes more pronounced in areas such as the Western Antarctic Peninsula, both long-term and occasional acute temperature rises will impact species found there, and it has become crucial to understand the capacity of these species to respond to such thermal stress. Here, we use the Antarctic sponge Isodictya sp. to investigate how sessile organisms (particularly Porifera) can adjust to acute short-term heat stress, by exposing this species to 3 and 5 °C for 4 h, corresponding to predicted temperatures under high-end 2080 IPCC-SRES scenarios. Assembling a de novo reference transcriptome (90,188 contigs, >93.7% metazoan BUSCO genes) we have begun to discern the molecular response employed by Isodictya to adjust to heat exposure. Our initial analyses suggest that TGF-β, ubiquitin and hedgehog cascades are involved, alongside other genes. However, the degree and type of response changed little from 3 to 5 °C in the time frame examined, suggesting that even moderate rises in temperature could cause stress at the limits of this organism’s capacity. Given the importance of sponges to Antarctic ecosystems, our findings are vital for discerning the consequences of short-term increases in Antarctic ocean temperature on these and other species.