Gene expression profiles during short-term heat stress in the red sea coral Stylophora pistillata

Synthesis of transcriptomic studies reveals a core response to heat stress in abalone (genus Haliotis)

BACKGROUND

As climate change causes marine heat waves to become more intense and frequent, marine species increasingly suffer from heat stress. This stress can result in reduced growth, disrupted breeding cycles, vulnerability to diseases and pathogens, and increased mortality rates. Abalone (genus Haliotis) are an ecologically significant group of marine gastropods and are among the most highly valued seafood products. However, heat stress events have had devastating impacts on both farmed and wild populations. Members of this genus are among the most susceptible marine species to climate change impacts, with over 40% of all abalone species listed as threatened with extinction. This has motivated researchers to explore the genetics linked to heat stress in abalone. A substantial portion of publicly available studies has employed transcriptomic approaches to investigate abalone genetic response to heat stress. However, to date, no meta-analysis has been conducted to determine the common response to heat stress (i.e. the core response) across the genus. This study uses a standardized bioinformatic pipeline to reanalyze and compare publicly available RNA-seq datasets from different heat stress studies on abalone.

RESULTS

Nine publicly available RNA-seq datasets from nine different heat-stress studies on abalone from seven different abalone species and three hybrids were included in the meta-analysis. We identified a core set of 74 differentially expressed genes (DEGs) in response to heat stress in at least seven out of nine studies. This core set of DEGs mainly included genes associated with alternative splicing, heat shock proteins (HSPs), Ubiquitin-Proteasome System (UPS), and other protein folding and protein processing pathways.

CONCLUSIONS

The detection of a consistent set of genes that respond to heat stress across various studies, despite differences in experimental design (e.g. stress intensity, species studied-geographical distribution, preferred temperature range, etc.), strengthens our proposal that these genes are key elements of the heat stress response in abalone. The identification of the core response to heat stress in abalone lays an important foundation for future research. Ultimately, this study will aid conservation efforts and aquaculture through the identification of resilient populations, genetic-based breeding programs, possible manipulations such as early exposure to stress, gene editing and the use of immunostimulants to enhance thermal tolerance.

Warming and polymetallic stress induce proteomic and physiological shifts in the neurotoxic Alexandrium pacificum as possible response to global changes

Harmful Algal Blooms involving the dinoflagellate Alexandrium pacificum continue to increase in ecosystems suffering the climate warming and anthropogenic pressure. Changes in the total proteome and physiological traits of the Mediterranean A. pacificum SG C10-3 strain were measured in response to increasing temperature (24 °C, 27 °C, 30 °C) and trace metal contamination (Cu2+, Pb2+, Zn2+, Cd2+). Warming reduced the cell densities and maximal growth rate (μmax), but the strain persisted at 30 °C with more large cells. The polymetallic stress increased cell sizes, reduced cell growth at 24 °C-27 °C and it increased this at 30 °C. Toxin profiles showed a predominance of GTX4 (32-38 %), then C2 (11-34 %) or GTX6 (18-24 %) among the total Paralytic Shellfish Toxins, however these were modified under warming, showing increased contents in GTX1 (among the most toxic), GTX5, C1 and NeoSTX, while dc-NeoSTX and STX (among the most toxic) only appeared at 30 °C. Under polymetallic contamination, warming also increased contents in GTX5 and NeoSTX. In contrast, polymetallic stress, or warming had harmful effects on C2 contents. Proteins were more quantitatively produced by A. pacificum SG C10-3 under warming in accordance with the high levels of up-regulated proteins found in the total proteome in this condition. Polymetallic stress, only or combined with warming, led to low proteomic modifications (1 % or 4 %), whereas warming induced strong 52 % modified proteomic response, mainly based on up-regulated proteins involved in photosynthesis (light harvesting complex protein), carbohydrate metabolism (arylsulfatase) and translation (ribosomal proteins), and with the lesser down-regulated proteins principally associated with the lipid metabolism (type I polyketide synthase). Our results show that warming triggers a strong up-regulated A. pacificum SG C10-3 proteomic response, which, coupled to modified cell sizes and toxin profiles, could help it to withstand stress conditions. This could presage the success of A. pacificum in anthropized ecosystems submitted to global warming in which this dinoflagellate also might be more toxic.

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).

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

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

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

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

Using a metabolomics approach to investigate the sensitivity of a potential Arctic-invader and its Arctic sister-species to marine heatwaves and traditional harvesting disturbances

Coastal species are threatened by fishing practices and changing environmental conditions, such as marine heatwaves (MHW). The mechanisms that confer tolerance to such stressors in marine invertebrates are poorly understood. However, differences in tolerance among different species may be attributed to their geographical distribution. To test the tolerance of species occupying different thermal ranges, we used two closely related bivalves the softshell clam Mya arenaria (Linnaeus, 1758), a cold-temperate invader with demonstrated potential for establishment in the Arctic, and the blunt gaper Mya truncata (Linnaeus, 1758), a native polar species. Clams were subjected to a thermal stress, mimicking a MHW, and harvesting stress in a controlled environment. Seven acute temperature changes (2, 7, 12, 17, 22, 27, and 32 °C) were tested at two harvesting disturbance intensities (with, without). Survival was measured after 12 days and three tissues (gills, mantle, and posterior adductor muscle) collected from surviving individuals for targeted metabolomic profiling. MHW tolerance differed significantly between species: 26.9 °C for M. arenaria and 17.8 °C for M. truncata, with a negligeable effect of harvesting. At the upper thermal limit, M. arenaria displayed a more profound metabolomic remodelling when compared to M. truncata, and this varied greatly between tissue types. Network analysis revealed differences in pathway utilization at the upper MHW limit, with M. arenaria displaying a greater reliance on multiple DNA repair and expression and cell signalling pathways, while M. truncata was limited to fewer pathways. This suggests that M. truncata is ill equipped to cope with warming environments. MHW patterning in the Northwest Atlantic may be a strong predictor of population survival and future range shifts in these two clam species. As polar environments undergo faster rates of warming compared to the global average, M. truncata may be outcompeted by M. arenaria expanding into its native range.

Environmental Concentrations of Herbicide Prometryn Render Stress-Tolerant Corals Susceptible to Ocean Warming

Global warming has caused the degradation of coral reefs around the world. While stress-tolerant corals have demonstrated the ability to acclimatize to ocean warming, it remains unclear whether they can sustain their thermal resilience when superimposed with other coastal environmental stressors. We report the combined impacts of a photosystem II (PSII) herbicide, prometryn, and ocean warming on the stress-tolerant coral Galaxea fascicularis through physiological and omics analyses. The results demonstrate that the heat-stress-induced inhibition of photosynthetic efficiency in G. fascicularis is exacerbated in the presence of prometryn. Transcriptomics and metabolomics analyses indicate that the prometryn exposure may overwhelm the photosystem repair mechanism in stress-tolerant corals, thereby compromising their capacity for thermal acclimation. Moreover, prometryn might amplify the adverse effects of heat stress on key energy and nutrient metabolism pathways and induce a stronger response to oxidative stress in stress-tolerant corals. The findings indicate that the presence of prometryn at environmentally relevant concentrations would render corals more susceptible to heat stress and exacerbate the breakdown of coral Symbiodiniaceae symbiosis. The present study provides valuable insights into the necessity of prioritizing PSII herbicide pollution reduction in coral reef protection efforts while mitigating the effects of climate change.

Gene expression of Pocillopora damicornis coral larvae in response to acidification and ocean warming

OBJECTIVES

The endosymbiosis with Symbiodiniaceae is key to the ecological success of reef-building corals. However, climate change is threatening to destabilize this symbiosis on a global scale. Most studies looking into the response of corals to heat stress and ocean acidification focus on coral colonies. As such, our knowledge of symbiotic interactions and stress response in other stages of the coral lifecycle remains limited. Establishing transcriptomic resources for coral larvae under stress can thus provide a foundation for understanding the genomic basis of symbiosis, and its susceptibility to climate change. Here, we present a gene expression dataset generated from larvae of the coral Pocillopora damicornis in response to exposure to acidification and elevated temperature conditions below the bleaching threshold of the symbiosis.

DATA DESCRIPTION

This dataset is comprised of 16 samples (30 larvae per sample) collected from four treatments (Control, High pCO2, High Temperature, and Combined pCO2 and Temperature treatments). Freshly collected larvae were exposed to treatment conditions for five days, providing valuable insights into gene expression in this vulnerable stage of the lifecycle. In combination with previously published datasets, this transcriptomic resource will facilitate the in-depth investigation of the effects of ocean acidification and elevated temperature on coral larvae and its implication for symbiosis.

Multi-omics reveals largely distinct transcript- and protein-level responses to the environment in an intertidal mussel

Organismal responses to stressful environments are influenced by numerous transcript- and protein-level mechanisms, and the relationships between expression changes at these levels are not always straightforward. Here, we used paired transcriptomic and proteomic datasets from two previous studies from gill of the California mussel, Mytilus californianus, to explore how simultaneous transcript and protein abundance patterns may diverge under different environmental scenarios. Field-acclimatized mussels were sampled from two disparate intertidal sites; individuals from one site were subjected to three further treatments (common garden, low-intertidal or high-intertidal outplant) that vary in temperature and feeding time. Assessing 1519 genes shared between the two datasets revealed that both transcript and protein expression patterns differentiated the treatments at a global level, despite numerous underlying discrepancies. There were far more instances of differential expression between treatments in transcript only (1451) or protein only (226) than of the two levels shifting expression concordantly (68 instances). Upregulated expression of cilium-associated transcripts (likely related to feeding) was associated with relatively benign field treatments. In the most stressful treatment, transcripts, but not proteins, for several molecular chaperones (including heat shock proteins and endoplasmic reticulum chaperones) were more abundant, consistent with a threshold model for induction of translation of constitutively available mRNAs. Overall, these results suggest that the relative importance of transcript- and protein-level regulation (translation and/or turnover) differs among cellular functions and across specific microhabitats or environmental contexts. Furthermore, the degree of concordance between transcript and protein expression can vary across benign versus acutely stressful environmental conditions.

Rapid shifts in thermal reaction norms and tolerance of brooded coral larvae following parental heat acclimation

Thermal priming of reef corals can enhance their heat tolerance; however, the legacy effects of heat stress during parental brooding on larval resilience remain understudied. This study investigated whether preconditioning adult coral Pocillopora damicornis to high temperatures (29°C and 32°C) could better prepare their larvae for heat stress. Results showed that heat-acclimated adults brooded larvae with reduced symbiont density and shifted thermal performance curves. Reciprocal transplant experiments demonstrated higher bleaching resistance and better photosynthetic and autotrophic performance in heat-exposed larvae from acclimated adults compared to unacclimated adults. RNA-seq revealed strong cellular stress responses in larvae from heat-acclimated adults that could have been effective in rescuing host cells from stress, as evidenced by the widespread upregulation of genes involved in cell cycle and mitosis. For symbionts, a molecular coordination between light harvesting, photoprotection and carbon fixation was detected in larvae from heat-acclimated adults, which may help optimize photosynthetic activity and yield under high temperature. Furthermore, heat acclimation led to opposing regulations of symbiont catabolic and anabolic pathways and favoured nutrient translocation to the host and thus a functional symbiosis. Notwithstanding, the improved heat tolerance was paralleled by reduced light-enhanced dark respiration, indicating metabolic depression for energy saving. Our findings suggest that adult heat acclimation can rapidly shift thermal tolerance of brooded coral larvae and provide integrated physiological and molecular evidence for this adaptive plasticity, which could increase climate resilience. However, the metabolic depression may be maladaptive for long-term organismal performance, highlighting the importance of curbing carbon emissions to better protect corals.

Coral bleaching resistance variation is linked to differential mortality and skeletal growth during recovery

The prevalence of global coral bleaching has focused much attention on the possibility of interventions to increase heat resistance. However, if high heat resistance is linked to fitness tradeoffs that may disadvantage corals in other areas, then a more holistic view of heat resilience may be beneficial. In particular, overall resilience of a species to heat stress is likely to be the product of both resistance to heat and recovery from heat stress. Here, we investigate heat resistance and recovery among individual Acropora hyacinthus colonies in Palau. We divided corals into low, moderate, and high heat resistance categories based on the number of days (4-9) needed to reach significant pigmentation loss due to experimental heat stress. Afterward, we deployed corals back onto a reef in a common garden 6-month recovery experiment that monitored chlorophyll a, mortality, and skeletal growth. Heat resistance was negatively correlated with mortality during early recovery (0-1 month) but not late recovery (4-6 months), and chlorophyll a concentration recovered in heat-stressed corals by 1-month postbleaching. However, moderate-resistance corals had significantly greater skeletal growth than high-resistance corals by 4 months of recovery. High- and low-resistance corals on average did not exhibit skeletal growth within the observed recovery period. These data suggest complex tradeoffs may exist between coral heat resistance and recovery and highlight the importance of incorporating multiple aspects of resilience into future reef management programs.

Coral larvae suppress heat stress response during the onset of symbiosis decreasing their odds of survival

The endosymbiosis between most corals and their photosynthetic dinoflagellate partners begins early in the host life history, when corals are larvae or juvenile polyps. The capacity of coral larvae to buffer climate-induced stress while in the process of symbiont acquisition could come with physiological trade-offs that alter behaviour, development, settlement and survivorship. Here we examined the joint effects of thermal stress and symbiosis onset on colonization dynamics, survival, metamorphosis and host gene expression of Acropora digitifera larvae. We found that thermal stress decreased symbiont colonization of hosts by 50% and symbiont density by 98.5% over 2 weeks. Temperature and colonization also influenced larval survival and metamorphosis in an additive manner, where colonized larvae fared worse or prematurely metamorphosed more often than noncolonized larvae under thermal stress. Transcriptomic responses to colonization and thermal stress treatments were largely independent, while the interaction of these treatments revealed contrasting expression profiles of genes that function in the stress response, immunity, inflammation and cell cycle regulation. The combined treatment either cancelled or lowered the magnitude of expression of heat-stress responsive genes in the presence of symbionts, revealing a physiological cost to acquiring symbionts at the larval stage with elevated temperatures. In addition, host immune suppression, a hallmark of symbiosis onset under ambient temperature, turned to immune activation under heat stress. Thus, by integrating the physical environment and biotic pressures that mediate presettlement event in corals, our results suggest that colonization may hinder larval survival and recruitment under projected climate scenarios.

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.

Stylophora under stress: A review of research trends and impacts of stressors on a model coral species

Sometimes called the "lab rat" of coral research, Stylophora pistillata (Esper, 1797) has been extensively used in coral biology in studies ranging from reef ecology to coral metabolic processes, and has been used as a model for investigations into molecular and cellular biology. Previously thought to be a common species spanning a wide distribution through the Indo-Pacific region, "S. pistillata" is in fact four genetically distinct lineages (clades) with different evolutionary histories and geographical distributions. Here, we review the studies of stress responses of S. pistillatasensulato (clades 1-4) and highlight research trends and knowledge gaps. We identify 126 studies on stress responses including effects of temperature, acidification, eutrophication, pollutants and other local impacts. We find that most studies have focused on the effect of single stressors, especially increased temperature, and have neglected the combined effects of multiple stressors. Roughly 61% of studies on S. pistillata come from the northern Red Sea (clade 4), at the extreme limit of its current distribution; clades 2 and 3 are virtually unstudied. The overwhelming majority of studies were conducted in laboratory or mesocosm conditions, with field experiments constituting only 2% of studies. We also note that a variety of experimental designs and treatment conditions makes it difficult to draw general conclusions about the effects of particular stressors on S. pistillata. Given those knowledge gaps and limitations in the published research, we suggest a more standardized approach to compare responses across geographically disparate populations and more accurately anticipate responses to predicted future climate conditions.

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.

The Effects of Temperature, Light, and Feeding on the Physiology of Pocillopora damicornis, Stylophora pistillata, and Turbinaria reniformis Corals

Evidence has shown that individually feeding or reduced light can mitigate the negative effects of elevated temperature on coral physiology. We aimed to evaluate if simultaneous low light and feeding would mitigate, minimize, or exacerbate negative effects of elevated temperature on coral physiology and carbon budgets. Pocillopora damicornis, Stylophora pistillata, and Turbinaria reniformis were grown for 28 days under a fully factorial experiment including two seawater temperatures (ambient temperature of 25 °C, elevated temperature of 30 °C), two light levels (high light of 300 μmol photons m−2 s−1, low light of 150 μmol photons m−2 s−1), and either fed (Artemia nauplii) or unfed. Coral physiology was significantly affected by temperature in all species, but the way in which low light and feeding altered their physiological responses was species-specific. All three species photo-acclimated to low light by increasing chlorophyll a. Pocillopora damicornis required feeding to meet metabolic demand irrespective of temperature but was unable to maintain calcification under low light when fed. In T. reniformis, low light mitigated the negative effect of elevated temperature on total lipids, while feeding mitigated the negative effects of elevated temperature on metabolic demand. In S. pistillata, low light compounded the negative effects of elevated temperature on metabolic demand, while feeding minimized this negative effect but was not sufficient to provide 100% metabolic demand. Overall, low light and feeding did not act synergistically, nor additively, to mitigate the negative effects of elevated temperature on P. damicornis, S. pistillata, or T. reniformis. However, feeding alone was critical to the maintenance of metabolic demand at elevated temperature, suggesting that sufficient supply of heterotrophic food sources is likely essential for corals during thermal stress (bleaching) events.

New Insights From Transcriptomic Data Reveal Differential Effects of CO2 Acidification Stress on Photosynthesis of an Endosymbiotic Dinoflagellate in hospite

Ocean acidification (OA) has both detrimental as well as beneficial effects on marine life; it negatively affects calcifiers while enhancing the productivity of photosynthetic organisms. To date, many studies have focused on the impacts of OA on calcification in reef-building corals, a process particularly susceptible to acidification. However, little is known about the effects of OA on their photosynthetic algal partners, with some studies suggesting potential benefits for symbiont productivity. Here, we investigated the transcriptomic response of the endosymbiont Symbiodinium microadriaticum (CCMP2467) in the Red Sea coral Stylophora pistillata subjected to different long-term (2 years) OA treatments (pH 8.0, 7.8, 7.4, 7.2). Transcriptomic analyses revealed that symbionts from corals under lower pH treatments responded to acidification by increasing the expression of genes related to photosynthesis and carbon-concentrating mechanisms. These processes were mostly up-regulated and associated metabolic pathways were significantly enriched, suggesting an overall positive effect of OA on the expression of photosynthesis-related genes. To test this conclusion on a physiological level, we analyzed the symbiont’s photochemical performance across treatments. However, in contrast to the beneficial effects suggested by the observed gene expression changes, we found significant impairment of photosynthesis with increasing pCO₂. Collectively, our data suggest that over-expression of photosynthesis-related genes is not a beneficial effect of OA but rather an acclimation response of the holobiont to different water chemistries. Our study highlights the complex effects of ocean acidification on these symbiotic organisms and the role of the host in determining symbiont productivity and performance.

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.

Deep Neural Network Analysis for Environmental Study of Coral Reefs in the Gulf of Eilat (Aqaba)

Coral reefs are undergoing a severe decline due to ocean acidification, seawater warming and anthropogenic eutrophication. We demonstrate the applicability of Deep Learning (DL) for following these changes. We examined the distribution and frequency appearance of the eleven most common coral species at four sites in the Gulf of Eilat. We compared deep learning with conventional census methods. The methods used in this research were natural sampling units via photographing the coral reef, line transects for estimating the cover percentage at the four test sites and deep convolutional neural networks, which proved to be an efficient sparse classification for coral species using the supervised deep learning method. The main research goal was to identify the common coral species at four test sites in the Gulf of Eilat, using DL to detect differences in coral cover and species composition among the sites, and relate these to ecological characteristics, such as depth and anthropogenic disturbance. The use of this method will produce a vital database to follow changes over time in coral reefs, identify trend lines and recommend remediation measures accordingly. We outline future monitoring needs and the corresponding system developments required to meet these.

Genotype by environment interactions in coral bleaching

Climate-driven reef decline has prompted the development of next-generation coral conservation strategies, many of which hinge on the movement of adaptive variation across genetic and environmental gradients. This process is limited by our understanding of how genetic and genotypic drivers of coral bleaching will manifest in different environmental conditions. We reciprocally transplanted 10 genotypes of Acropora cervicornis across eight sites along a 60 km span of the Florida Reef Tract and documented significant genotype × environment interactions in bleaching response during the severe 2015 bleaching event. Performance relative to site mean was significantly different between genotypes and can be mostly explained by ensemble models of correlations with genetic markers. The high explanatory power was driven by significant enrichment of loci associated DNA repair, cell signalling and apoptosis. No genotypes performed above (or below) bleaching average at all sites, so genomic predictors can provide practitioners with 'confidence intervals' about the chance of success in novel habitats. These data have important implications for assisted gene flow and managed relocation, and their integration with traditional active restoration.

Longevity strategies in response to light in the reef coral Stylophora pistillata

Aging is a multifactorial process that results in progressive loss of regenerative capacity and tissue function while simultaneously favoring the development of a large array of age-related diseases. Evidence suggests that the accumulation of senescent cells in tissue promotes both normal and pathological aging. Oxic stress is a key driver of cellular senescence. Because symbiotic long-lived reef corals experience daily hyperoxic and hypoxic transitions, we hypothesized that these long-lived animals have developed specific longevity strategies in response to light. We analyzed transcriptome variation in the reef coral Stylophora pistillata during the day-night cycle and revealed a signature of the FoxO longevity pathway. We confirmed this pathway by immunofluorescence using antibodies against coral FoxO to demonstrate its nuclear translocation. Through qPCR analysis of nycthemeral variations of candidate genes under different light regimens, we found that, among genes that were specifically up- or downregulated upon exposure to light, human orthologs of two "light-up" genes (HEY1 and LONF3) exhibited anti-senescence properties in primary human fibroblasts. Therefore, these genes are interesting candidates for counteracting skin aging. We propose a large screen for other light-up genes and an investigation of the biological response of reef corals to light (e.g., metabolic switching) to elucidate these processes and identify effective interventions for promoting healthy aging in humans.

Deep neural network recognition of shallow water corals in the Gulf of Eilat (Aqaba)

We describe the application of the computerized deep learning methodology to the recognition of corals in a shallow reef in the Gulf of Eilat, Red Sea. This project is aimed at applying deep neural network analysis, based on thousands of underwater images, to the automatic recognition of some common species among the 100 species reported to be found in the Eilat coral reefs. This is a challenging task, since even in the same colony, corals exhibit significant within-species morphological variability, in terms of age, depth, current, light, geographic location, and inter-specific competition. Since deep learning procedures are based on photographic images, the task is further challenged by image quality, distance from the object, angle of view, and light conditions. We produced a large dataset of over 5,000 coral images that were classified into 11 species in the present automated deep learning classification scheme. We demonstrate the efficiency and reliability of the method, as compared to painstaking manual classification. Specifically, we demonstrated that this method is readily adaptable to include additional species, thereby providing an excellent tool for future studies in the region, that would allow for real time monitoring the detrimental effects of global climate change and anthropogenic impacts on the coral reefs of the Gulf of Eilat and elsewhere, and that would help assess the success of various bioremediation efforts.

Meta-analysis of the coral environmental stress response: Acropora corals show opposing responses depending on stress intensity

As climate change progresses, reef-building corals must contend more often with suboptimal conditions, motivating a need to understand coral stress response. Here, we test the hypothesis that there is a stereotyped transcriptional response that corals enact under all stressful conditions, functionally characterized by downregulation of growth, and activation of cell death, response to reactive oxygen species, immunity, and protein folding and degradation. We analyse RNA-seq and Tag-Seq data from 14 previously published studies and supplement them with four new experiments involving different stressors, totaling over 600 gene expression profiles from the genus Acropora. Contrary to expectations, we found not one, but two distinct types of response. The type A response was observed under all kinds of high-intensity stress, was correlated between independent projects and was functionally consistent with the hypothesized stereotyped response. The consistent correlation between projects, irrespective of stress type, supports the type A response as the general coral environmental stress response (ESR), a blanket solution to severely stressful conditions. The distinct type B response was observed under lower intensity stress and was more variable among studies. Unexpectedly, at the level of individual genes and functional categories, the type B response was broadly opposite the type A response. Finally, taking advantage of the breadth of the data set, we present contextual annotations for previously unannotated genes based on consistent stress-induced differences across independent projects.

Atmospheric Forcing of the High and Low Extremes in the Sea Surface Temperature over the Red Sea and Associated Chlorophyll-a Concentration

Taking advantage of 37-year-long (1982–2018) of high-quality satellite datasets, we examined the role of direct atmospheric forcing on the high and low sea surface temperature (SST) extremes over the Red Sea (RS). Considering the importance of SST in regulating ocean physics and biology, the associated impacts on chlorophyll (Chl-a) concentration were also explored, since a small change in SST can cause a significant impact in the ocean. After describing the climate features, we classified the top 5% of SST values (≥31.5 °C) as extreme high events (EHEs) during the boreal summer period and the lowest SST values (≤22.8 °C) as extreme low events (ELEs) during the boreal winter period. The spatiotemporal analysis showed that the EHEs (ELEs) were observed over the southern (northern) basin, with a significant warming trend of 0.027 (0.021) °C year−1, respectively. The EHEs were observed when there was widespread less than average sea level pressure (SLP) over southern Europe, northeast Africa, and Middle East, including in the RS, leading to the cold wind stress from Europe being relatively less than usual and the intrusion of stronger than usual relatively warm air mass from central Sudan throughout the Tokar Gap. Conversely, EHEs were observed when above average SLP prevailed over southern Europe and the Mediterranean Sea as a result of the Azores high and westward extension of the Siberian anticyclone, which led to above average transfer of cold and dry wind stress from higher latitudes. At the same time, notably less wind stress due to southerlies that transfer warm and humid air masses northward was observed. Furthermore, physical and biological responses related to extreme stress showed distinct ocean patterns associated with each event. It was found that the Chl-a concentration anomalies over the northern basin caused by vertical nutrient transport through deep upwelling processes are the manifestation of the superimposition of ELEs. The situation was the opposite for EHEs due to the stably stratified ocean boundary layer, which is a well-known consequence of global warming.

Tissue-specific effects of temperature on proteasome function

Variation in ambient growth temperature can cause changes in normal animal physiology and cellular functions such as control of protein homeostasis. A key mechanism for maintaining proteostasis is the selective degradation of polyubiquitinated proteins, mediated by the ubiquitin-proteasome system (UPS). It is still largely unsolved how temperature changes affect the UPS at the organismal level. Caenorhabditis elegans nematodes are normally bred at 20 °C, but for some experimental conditions, 25 °C is often used. We studied the effect of 25 °C on C. elegans UPS by measuring proteasome activity and polyubiquitinated proteins both in vitro in whole animal lysates and in vivo in tissue-specific transgenic reporter strains. Our results show that an ambient temperature shift from 20 to 25 °C increases the UPS activity in the intestine, but not in the body wall muscle tissue, where a concomitant accumulation of polyubiquitinated proteins occurs. These changes in the UPS activity and levels of polyubiquitinated proteins were not detectable in whole animal lysates. The exposure of transgenic animals to 25 °C also induced ER stress reporter fluorescence, but not the fluorescence of a heat shock responsive reporter, albeit detection of a mild induction in hsp-16.2 mRNA levels. In conclusion, C. elegans exhibits tissue-specific responses of the UPS as an organismal strategy to cope with a rise in ambient temperature.

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.

Ion transporter gene expression is linked to the thermal sensitivity of calcification in the reef coral Stylophora pistillata

Coral calcification underpins biodiverse reef ecosystems, but the physiology underlying the thermal sensitivity of corals to changing seawater temperatures remains unclear. Furthermore, light is also a key factor in modulating calcification rates, but a mechanistic understanding of how light interacts with temperature to affect coral calcification is lacking. Here, we characterized the thermal performance curve (TPC) of calcification of the wide-spread, model coral species Stylophora pistillata, and used gene expression analysis to investigate the role of ion transport mechanisms in thermally-driven declines in day and nighttime calcification. Focusing on genes linked to transport of dissolved inorganic carbon (DIC), calcium and H+, our study reveals a high degree of coherence between physiological responses (e.g. calcification and respiration) with distinct gene expression patterns to the different temperatures in day and night conditions. At low temperatures, calcification and gene expression linked to DIC transport processes were downregulated, but showed little response to light. By contrast, at elevated temperature, light had a positive effect on calcification and stimulated a more functionally diverse gene expression response of ion transporters. Overall, our findings highlight the role of mechanisms linked to DIC, calcium and H+ transport in the thermal sensitivity of coral calcification and how this sensitivity is influenced by light.

The Algal Symbiont Modifies the Transcriptome of the Scleractinian Coral Euphyllia paradivisa During Heat Stress

The profound mutualistic symbiosis between corals and their endosymbiotic counterparts, Symbiodiniaceae algae, has been threatened by the increase in seawater temperatures, leading to breakdown of the symbiotic relationship-coral bleaching. To characterize the heat-stress response of the holobiont, we generated vital apo-symbiotic Euphyllia paradivisa corals that lacked the endosymbiotic algae. Using RNA sequencing, we analyzed the gene expression of these apo-symbionts vs. symbiotic ones, to test the effect of the algal presence on the tolerance of the coral. We utilized literature-derived lists of "symbiosis differentially expressed genes" and "coral heat-stress genes" in order to compare between the treatments. The symbiotic and apo-symbiotic samples were segregated into two separate groups with several different enriched gene ontologies. Our findings suggest that the presence of endosymbionts has a greater negative impact on the host than the environmental temperature conditions experienced by the holobiont. The peak of the stress reaction was identified as 28 °C, with the highest number of differentially expressed genes. We suggest that the algal symbionts increase coral holobiont susceptibility to elevated temperatures. Currently, we can only speculate whether coral species, such as E. paradivisa, with the plasticity to also flourish as apo-symbionts, may have a greater chance to withstand the upcoming global climate change challenge.

The role of chromatin dynamics under global warming response in the symbiotic coral model Aiptasia

Extreme weather events frequency and scale are altered due to climate change. Symbiosis between corals and their endosymbiotic-dinoflagellates (Symbiodinium) is susceptible to these events and can lead to what is known as bleaching. However, there is evidence for coral adaptive plasticity in the role of epigenetic that have acclimated to high-temperature environments. We have implemented ATAC-seq and RNA-seq to study the cnidarian-dinoflagellate model Exaptasia pallida (Aiptasia) and expose the role of chromatin-dynamics in response to thermal-stress. We have identified 1309 genomic sites that change their accessibility in response to thermal changes. Moreover, apo-symbiotic Aiptasia accessible sites were enriched with NFAT, ATF4, GATA3, SOX14, and PAX3 motifs and expressed genes related to immunological pathways. Symbiotic Aiptasia accessible sites were enriched with NKx3-1, HNF4A, IRF4 motifs and expressed genes related to oxidative-stress pathways. Our work opens a new path towards understanding thermal-stress gene regulation in association with gene activity and chromatin-dynamics.

Comparative Analysis of the Soluble Proteome and the Cytolytic Activity of Unbleached and Bleached Millepora complanata ("Fire Coral") from the Mexican Caribbean

Coral bleaching caused by global warming has resulted in massive damage to coral reefs worldwide. Studies addressing the consequences of elevated temperature have focused on organisms of the class Anthozoa, and up to now, there is little information regarding the mechanisms by which reef forming Hydrozoans face thermal stress. In this study, we carried out a comparative analysis of the soluble proteome and the cytolytic activity of unbleached and bleached Millepora complanata ("fire coral") that inhabited reef colonies exposed to the 2015-2016 El Niño-Southern Oscillation in the Mexican Caribbean. A differential proteomic response involving proteins implicated in key cellular processes, such as glycolysis, DNA repair, stress response, calcium homeostasis, exocytosis, and cytoskeleton organization was found in bleached hydrocorals. Four of the proteins, whose levels increased in bleached specimens, displayed sequence similarity to a phospholipase A2, an astacin-like metalloprotease, and two pore forming toxins. However, a protein, which displayed sequence similarity to a calcium-independent phospholipase A2, showed lower levels in bleached cnidarians. Accordingly, the hemolytic effect of the soluble proteome of bleached hydrocorals was significantly higher, whereas the phospholipase A2 activity was significantly reduced. Our results suggest that bleached M. complanata is capable of increasing its toxins production in order to balance the lack of nutrients supplied by its symbionts.

Molecular convergence and positive selection associated with the evolution of symbiont transmission mode in stony corals

Heritable symbioses have been critical for the evolution of life. The genetic consequences of evolving a heritable symbiosis from the perspective of the symbiont are well established, but concomitant changes in the host remain unresolved. In stony corals, heritable, vertical transmission has evolved repeatedly, providing a unique opportunity to investigate the genomic basis of this complex trait. We conducted a comparative analysis of 25 coral transcriptomes to identify orthologous genes exhibiting signatures of positive selection and convergent amino acid substitutions in vertically transmitting lineages. The frequency of convergence events tends to be higher among vertically transmitting lineages, consistent with the proposed role of selection in driving the evolution of convergent transmission mode phenotypes. Of 10 774 orthologous genes, 403 exhibited at least one molecular convergence event and evidence of positive selection in at least one vertically transmitting lineage. Functional enrichments among these top candidate genes include processes previously implicated in symbiosis including endocytosis, immune response, cytoskeletal protein binding and cytoplasmic membrane-bounded vesicles. Finally, several novel candidates were identified among 100 genes showing evidence of positive selection at the particular convergence event, highlighting the value of our approach for generating new insight into host mechanisms associated with the evolution of heritable symbioses.

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

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

Heat stress compromises epithelial integrity in the coral, Acropora hyacinthus

It is well understood that heat stress causes bleaching in corals. Much work has focused on the way heat stress disrupts corals’ symbiotic relationship with endosymbiotic algal dinoflagellate, Symbiodiniaceae, a process called bleaching. However, the damage to the coral tissue that occurs during the bleaching process and, importantly, the factors that contribute to subsequent recovery, are not well understood. I hypothesize that the host tissue damage created by heat stress initiates cascades of wound healing factors that maintain epithelial integrity. These factors may be found to contribute to the coral’s potential capacity to recover. In this study, I present evidence that heat stress causes damage to the coral host tissue and that collagen is present in the gastrodermis of heat-stressed corals. I found that, during the early stages of bleaching, an important transcription factor for wound healing, Grainyhead, is expressed throughout the gastrodermis, where the cellular and tissue rearrangements occur. Lastly, using phylogenetics, I found that cnidarian Grainyhead proteins evolved three distinct groups and that evolution of this protein family likely happened within each taxonomic group. These findings have important implications for our study of coral resiliency in the face of climate change.

Transcriptomic analysis reveals protein homeostasis breakdown in the coral Acropora millepora during hypo-saline stress

Background

Coral reefs can experience salinity fluctuations due to rainfall and runoff; these events can have major impacts on the corals and lead to bleaching and mortality. On the Great Barrier Reef (GBR), low salinity events, which occur during summer seasons and can involve salinity dropping ~ 10 PSU correlate with declines in coral cover, and these events are predicted to increase in frequency and severity under future climate change scenarios. In other marine invertebrates, exposure to low salinity causes increased expression of genes involved in proteolysis, responses to oxidative stress, and membrane transport, but the effects that changes in salinity have on corals have so far received only limited attention. To better understand the coral response to hypo-osmotic stress, here we investigated the transcriptomic response of the coral Acropora millepora in both adult and juvenile life stages to acute (1 h) and more prolonged (24 h) exposure to low salinity.

Results

Differential gene expression analysis revealed the involvement of both common and specific response mechanisms in Acropora. The general response to environmental stressors included up-regulation of genes involved in the mitigation of macromolecular and oxidative damage, while up-regulation of genes involved in amino acid metabolism and transport represent specific responses to salinity stress.

Conclusions

This study is the first comprehensive transcriptomic analysis of the coral response to low salinity stress and provides important insights into the likely consequences of heavy rainfall and runoff events on coral reefs.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5527-2) contains supplementary material, which is available to authorized users.

Rapid microevolution during recent range expansion to harsh environments

BACKGROUND

Adaptive evolution is one of the crucial mechanisms for organisms to survive and thrive in new environments. Recent studies suggest that adaptive evolution could rapidly occur in species to respond to novel environments or environmental challenges during range expansion. However, for environmental adaptation, many studies successfully detected phenotypic features associated with local environments, but did not provide ample genetic evidence on microevolutionary dynamics. It is therefore crucial to thoroughly investigate the genetic basis of rapid microevolution in response to environmental changes, in particular on what genes and associated variation are responsible for environmental challenges. Here, we genotyped genome-wide gene-associated microsatellites to detect genetic signatures of rapid microevolution of a marine tunicate invader, Ciona robusta, during recent range expansion to the harsh environment in the Red Sea.

RESULTS

The Red Sea population was significantly differentiated from the other global populations. The genome-wide scan, as well as multiple analytical methods, successfully identified a set of adaptive genes. Interestingly, the allele frequency largely varied at several adaptive loci in the Red Sea population, and we found significant correlations between allele frequency and local environmental factors at these adaptive loci. Furthermore, a set of genes were annotated to get involved in local temperature and salinity adaptation, and the identified adaptive genes may largely contribute to the invasion success to harsh environments.

CONCLUSIONS

All the evidence obtained in this study clearly showed that environment-driven selection had left detectable signatures in the genome of Ciona robusta within a few generations. Such a rapid microevolutionary process is largely responsible for the harsh environmental adaptation and therefore contributes to invasion success in different aquatic ecosystems with largely varied environmental factors.

Transcriptional response of the heat shock gene hsp70 aligns with differences in stress susceptibility of shallow-water corals from the Mediterranean Sea

Shallow-water corals of the Mediterranean Sea are facing a dramatic increase in water temperature due to climate change, predicted to increase the frequency of bleaching and mass mortality events. However, supposedly not all corals are affected equally, as they show differences in stress susceptibility, as suggested by physiological outputs of corals along temperature gradients and under controlled conditions in terms of reproduction, demography, growth, calcification, and photosynthetic efficiency. In this study, gene expression and induction of a 70-kDa heat shock protein (HSP70) was analyzed in five common shallow-water hard corals in the Mediterranean Sea, namely Astroides calycularis, Balanophyllia europaea, Caryophyllia inornata, Cladocora caespitosa, and Leptopsammia pruvoti. The main aim was to assess the contribution of this evolutionary conserved cytoprotective mechanism to the physiological plasticity of these species that possess different growth modes (solitary vs colonial) and trophic strategies (zooxanthellate vs azooxanthellate). Using quantitative real-time PCR, in situ hsp70 baseline levels and expression profiles after a heat-shock exposure were assessed. Levels of hsp70 and heat stress induction were higher in zooxanthellate than in azooxanthellate species, and different heat stress transcriptional profiles were observed between colonial and solitary zooxanthellate corals. On the whole, the hsp70 transcriptional response to heat stress aligns with stress susceptibility of the species and suggests a contribution of trophic strategy and morphology in shaping coral resilience to stress. Understanding these molecular processes may contribute to assess the potential effects and relative resilience of Mediterranean corals under climate change.

Antimicrobial and stress responses to increased temperature and bacterial pathogen challenge in the holobiont of a reef-building coral

Global increases in coral disease prevalence have been linked to ocean warming through changes in coral-associated bacterial communities, pathogen virulence and immune system function. However, the interactive effects of temperature and pathogens on the coral holobiont are poorly understood. Here, we assessed three compartments of the holobiont (host, Symbiodinium and bacterial community) of the coral Montipora aequituberculata challenged with the pathogen Vibrio coralliilyticus and the commensal bacterium Oceanospirillales sp. under ambient (27°C) and elevated (29.5 and 32°C) seawater temperatures. Few visual signs of bleaching and disease development were apparent in any of the treatments, but responses were detected in the holobiont compartments. V. coralliilyticus acted synergistically and negatively impacted the photochemical efficiency of Symbiodinium at 32°C, while Oceanospirillales had no significant effect on photosynthetic efficiency. The coral, however, exhibited a minor response to the bacterial challenges, with the response towards V. coralliilyticus being significantly more pronounced, and involving the prophenoloxidase-activating system and multiple immune system-related genes. Elevated seawater temperatures did not induce shifts in the coral-associated bacterial community, but caused significant gene expression modulation in both Symbiodinium and the coral host. While Symbiodinium exhibited an antiviral response and upregulated stress response genes, M. aequituberculata showed regulation of genes involved in stress and innate immune response processes, including immune and cytokine receptor signalling, the complement system, immune cell activation and phagocytosis, as well as molecular chaperones. These observations show that M. aequituberculata is capable of maintaining a stable bacterial community under elevated seawater temperatures and thereby contributes to preventing disease development.

Decadal trends in Red Sea maximum surface temperature

Ocean warming is a major consequence of climate change, with the surface of the ocean having warmed by 0.11 °C decade^-1 over the last 50 years and is estimated to continue to warm by an additional 0.6 - 2.0 °C before the end of the century¹. However, there is considerable variability in the rates experienced by different ocean regions, so understanding regional trends is important to inform on possible stresses for marine organisms, particularly in warm seas where organisms may be already operating in the high end of their thermal tolerance. Although the Red Sea is one of the warmest ecosystems on earth, its historical warming trends and thermal evolution remain largely understudied. We characterized the Red Sea's thermal regimes at the basin scale, with a focus on the spatial distribution and changes over time of sea surface temperature maxima, using remotely sensed sea surface temperature data from 1982 - 2015. The overall rate of warming for the Red Sea is 0.17 ± 0.07 °C decade^-1, while the northern Red Sea is warming between 0.40 and 0.45 °C decade^-1, all exceeding the global rate. Our findings show that the Red Sea is fast warming, which may in the future challenge its organisms and communities.

Influencing Mechanism of Ocean Acidification on Byssus Performance in the Pearl Oyster Pinctada fucata

The byssus is an important adhesive structure by which bivalves robustly adhere to underwater substrates. It is susceptible to carbon dioxide-driven ocean acidification (OA). Previous investigations have documented significant adverse effects of OA on the performance of byssal threads, but the mechanisms remain largely unknown. In this study, multiple approaches were employed to reveal the underlying mechanisms for the effects of OA on byssus production and mechanical properties in the pearl oyster Pinctada fucata. The results showed that OA altered the abundance and secondary structure of byssal proteins and affected the contents of metal ions in distal threads, which together reduced the byssus diameter and amplified byssus nanocavity, causing reductions in mechanical properties (strength and extensibility). Expression analysis of key foot protein genes further confirmed changes in byssal protein abundance. Moreover, comparative transcriptome analysis revealed enrichment of ion transportation- and apoptosis-related categories, up-regulation of apoptosis-related pathways, and down-regulation of the "extracellular matrix-receptor interaction" pathway, which may influence foot locomotion physiology, leading to a decrease in byssus production. This study provides mechanistic insight into the effects of OA on pearl oyster byssus, which should broaden our overall understanding of the impacts of OA on marine ecosystem.

Epipodial Tentacle Gene Expression and Predetermined Resilience to Summer Mortality in the Commercially Important Greenlip Abalone, Haliotis laevigata

"Summer mortality" is a phenomenon that occurs during warm water temperature spikes that results in the mass mortality of many ecologically and economically important mollusks such as abalone. This study aimed to determine whether the baseline gene expression of abalone before a laboratory-induced summer mortality event was associated with resilience to summer mortality. Tentacle transcriptomes of 35 greenlip abalone (Haliotis laevigata) were sequenced prior to the animals being exposed to an increase in water temperature-simulating conditions which have previously resulted in summer mortality. Abalone derived from three source locations with different environmental conditions were categorized as susceptible or resistant to summer mortality depending on whether they died or survived after the water temperature was increased. We detected two genes showing significantly higher expression in resilient abalone relative to susceptible abalone prior to the laboratory-induced summer mortality event. One of these genes was annotated through the NCBI non-redundant protein database using BLASTX to an anemone (Exaiptasia pallida) Transposon Ty3-G Gag Pol polyprotein. Distinct gene expression signatures were also found between resilient and susceptible abalone depending on the population origin, which may suggest divergence in local adaptation mechanisms for resilience. Many of these genes have been suggested to be involved in antioxidant and immune-related functions. The identification of these genes and their functional roles have enhanced our understanding of processes that may contribute to summer mortality in abalone. Our study supports the hypothesis that prestress gene expression signatures are indicative of the likelihood of summer mortality.

Physiological plasticity related to zonation affects hsp70 expression in the reef-building coral Pocillopora verrucosa

This study investigates for the first time the transcriptional regulation of a stress-inducible 70-kDa heat shock protein (hsp70) in the scleractinian coral Pocillopora verrucosa sampled at three locations and two depths (3 m and 12 m) in Bangka Island waters (North Sulawesi, Indonesia). Percentage of coral cover indicated reduced habitat suitability with depth and at the Tanjung Husi (TA) site, which also displayed relatively higher seawater temperatures. Expression of the P. verrucosa hsp70 transcript evaluated under field conditions followed a depth-related profile, with relatively higher expression levels in 3-m collected nubbins compared to the 12-m ones. Expression levels of metabolism-related transcripts ATP synthase and NADH dehydrogenase indicated metabolic activation of nubbins to cope with habitat conditions of the TA site at 3 m. After a 14-day acclimatization to common and fixed temperature conditions in the laboratory, corals were subjected for 7 days to an altered thermal regime, where temperature was elevated at 31°C during the light phase and returned to 28°C during the dark phase. Nubbins collected at 12 m were relatively more sensitive to thermal stress, as they significantly over-expressed the selected transcripts. Corals collected at 3 m appeared more resilient, as they showed unaffected mRNA expressions. The results indicated that local habitat conditions may influence transcription of stress-related genes in P. verrucosa. Corals exhibiting higher basal hsp70 levels may display enhanced tolerance towards environmental stressors.

Mediterranean versus Red sea corals facing climate change, a transcriptome analysis

The anthropogenic increase in atmospheric CO₂ that drives global warming and ocean acidification raises serious concerns regarding the future of corals, the main carbonate biomineralizers. Here we used transcriptome analysis to study the effect of long-term gradual temperature increase (annual rate), combined with lowered pH values, on a sub-tropical Red Sea coral, Stylophora pistillata, and on a temperate Mediterranean symbiotic coral Balanophyllia europaea. The gene expression profiles revealed a strong effect of both temperature increase and pH decrease implying for synergism response. The temperate coral, exposed to a twice as high range of seasonal temperature fluctuations than the Red Sea species, faced stress more effectively. The compensatory strategy for coping apparently involves deviating cellular resources into a massive up-regulation of genes in general, and specifically of genes involved in the generation of metabolic energy. Our results imply that sub-lethal, prolonged exposure to stress can stimulate evolutionary increase in stress resilience.

Molecular assessment of the effect of light and heterotrophy in the scleractinian coral Stylophora pistillata

Corals acquire nutrients via the transfer of photosynthates by their endosymbionts (autotrophy), or via zooplankton predation by the animal (heterotrophy). During stress events, corals lose their endosymbionts, and undergo starvation, unless they increase their heterotrophic capacities. Molecular mechanisms by which heterotrophy sustains metabolism in stressed corals remain elusive. Here for the first time, to the best of our knowledge, we identified specific genes expressed in heterotrophically fed and unfed colonies of the scleractinian coral Stylophora pistillata, maintained under normal and light-stress conditions. Physiological parameters and gene expression profiling demonstrated that fed corals better resisted stress than unfed ones by exhibiting less oxidative damage and protein degradation. Processes affected in light-stressed unfed corals (HLU), were related to energy and metabolite supply, carbohydrate biosynthesis, ion and nutrient transport, oxidative stress, Ca(2+) homeostasis, metabolism and calcification (carbonic anhydrases, calcium-transporting ATPase, bone morphogenetic proteins). Two genes (cp2u1 and cp1a2), which belong to the cytochrome P450 superfamily, were also upregulated 249 and 10 times, respectively, in HLU corals. In contrast, few of these processes were affected in light-stressed fed corals (HLF) because feeding supplied antioxidants and energetic molecules, which help repair oxidative damage. Altogether, these results show that heterotrophy helps prevent the cascade of metabolic problems downstream of oxidative stress.

RNA-Seq revealed the impairment of immune defence of tilapia against the infection of Streptococcus agalactiae with simulated climate warming

Global warming is one of the causes of disease outbreaks in fishes. Understanding its mechanisms is critical in aquaculture and fisheries. We used tilapia to study the effects of a high temperature on the infection of a bacterial pathogen Streptococcus agalactiae using RNA-Seq. We found that the dissolved oxygen level in water at 32 °C is lower than at 22 °C, and tilapia infected with the pathogen died more rapidly at 32 °C. The gene expression profiles showed significant differences in fish raised under different conditions. We identified 126 and 576 differentially expressed genes (DEGs) at 4 and 24 h post infection at 22 °C, respectively, whereas at 32 °C, the data were 312 and 1670, respectively. Almost all responding pathways at 22 °C were involved in the immune responses, whereas at 32 °C, the enriched pathways were not only involved in immune responses but also involved in oxygen and energy metabolisms. We identified significant signals of immunosuppression of immune responses at 32 °C. In addition, many of the enriched transcription factors and DEGs under positive selection were involved in immune responses, oxygen and/or energy metabolisms. Our results suggest that global warming could reduce the oxygen level in water and impair the defence of tilapia against bacterial infection.

Coral Carbonic Anhydrases: Regulation by Ocean Acidification

Global change is a major threat to the oceans, as it implies temperature increase and acidification. Ocean acidification (OA) involving decreasing pH and changes in seawater carbonate chemistry challenges the capacity of corals to form their skeletons. Despite the large number of studies that have investigated how rates of calcification respond to ocean acidification scenarios, comparatively few studies tackle how ocean acidification impacts the physiological mechanisms that drive calcification itself. The aim of our paper was to determine how the carbonic anhydrases, which play a major role in calcification, are potentially regulated by ocean acidification. For this we measured the effect of pH on enzyme activity of two carbonic anhydrase isoforms that have been previously characterized in the scleractinian coral Stylophora pistillata. In addition we looked at gene expression of these enzymes in vivo. For both isoforms, our results show (1) a change in gene expression under OA (2) an effect of OA and temperature on carbonic anhydrase activity. We suggest that temperature increase could counterbalance the effect of OA on enzyme activity. Finally we point out that caution must, thus, be taken when interpreting transcriptomic data on carbonic anhydrases in ocean acidification and temperature stress experiments, as the effect of these stressors on the physiological function of CA will depend both on gene expression and enzyme activity.

Evolutionary Consequences of DNA Methylation in a Basal Metazoan

Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein-coding sequences is particularly puzzling, because methylation causes cytosine hypermutability and hence is likely to produce deleterious amino acid substitutions. We investigate this enigma using an evolutionarily basal group of Metazoa, the stony corals (order Scleractinia, class Anthozoa, phylum Cnidaria). We show that patterns of coral gbM are similar to other invertebrate species, predicting wide and active transcription and slower sequence evolution. We also find a strong correlation between gbM and codon bias, resulting from systematic replacement of CpG bearing codons. We conclude that gbM has strong effects on codon evolution and speculate that this may influence establishment of optimal codons.

Gene expression profiles during short-term heat stress; branching vs. massive Scleractinian corals of the Red Sea

It is well-established that there is a hierarchy of susceptibilities amongst coral genera during heat-stress. However, molecular mechanisms governing these differences are still poorly understood. Here we explored if specific corals possessing different morphologies and different susceptibilities to heat stress may manifest varied gene expression patterns. We examined expression patterns of seven genes in the branching corals Stylophora pistillata and Acropora eurystoma and additionally in the massive robust coral, Porites sp. The tested genes are representatives of key cellular processes occurring during heat-stress in Cnidaria: oxidative stress, ER stress, energy metabolism, DNA repair and apoptosis. Varied response to the heat-stress, in terms of visual coral paling, algal maximum quantum yield and host gene expression was evident in the different growth forms. The two branching corals exhibited similar overall responses that differed from that of the massive coral. A. eurystoma that is considered as a susceptible species did not bleach in our experiment, but tissue sloughing was evident at 34 °C. Interestingly, in this species redox regulation genes were up-regulated at the very onset of the thermal challenge. In S. pistillata, bleaching was evident at 34 °C and most of the stress markers were already up-regulated at 32 °C, either remaining highly expressed or decreasing when temperatures reached 34 °C. The massive Porites species displayed severe bleaching at 32 °C but stress marker genes were only significantly elevated at 34 °C. We postulate that by expelling the algal symbionts from Porites tissues, oxidation damages are reduced and stress genes are activated only at a progressed stage. The differential gene expression responses exhibited here can be correlated with the literature well-documented hierarchy of susceptibilities amongst coral morphologies and genera in Eilat’s coral reef.

Interactive Effects of Seawater Acidification and Elevated Temperature on the Transcriptome and Biomineralization in the Pearl Oyster Pinctada fucata

Interactive effects of ocean acidification and ocean warming on marine calcifiers vary among species, but little is known about the underlying mechanisms. The present study investigated the combined effects of seawater acidification and elevated temperature (ambient condition: pH 8.1 × 23 °C, stress conditions: pH 7.8 × 23 °C, pH 8.1 × 28 °C, and pH 7.8 × 28 °C, exposure time: two months) on the transcriptome and biomineralization of the pearl oyster Pinctada fucata, which is an important marine calcifier. Transcriptome analyses indicated that P. fucata implemented a compensatory acid-base mechanism, metabolic depression and positive physiological responses to mitigate the effects of seawater acidification alone. These responses were energy-expensive processes, leading to decreases in the net calcification rate, shell surface calcium and carbon content, and changes in the shell ultrastructure. Elevated temperature (28 °C) within the thermal window of P. fucata did not induce significant enrichment of the sequenced genes and conversely facilitated calcification, which was detected to alleviate the negative effects of seawater acidification on biomineralization and the shell ultrastructure. Overall, this study will help elucidate the mechanisms by which pearl oysters respond to changing seawater conditions and predict the effects of global climate change on pearl aquaculture.