Local adaptation constrains the distribution potential of heat-tolerant Symbiodinium from the Persian/Arabian Gulf

Regime shift of skeletal δ13C after 1997/1998 El Nino event in Porites coral from Green Island, Taiwan

The 1997/1998 El Niño event caused mass coral bleaching and mortality in many tropical and subtropical regions, including corals on Green Island, Taiwan, in the northwestern Pacific Ocean. This study analyzed coral carbon isotope ratios (δ13C), oxygen isotope ratios (δ18O), and Sr/Ca ratios for 29 years, including the 1997/1998 El Niño period, to examine how high water temperature events are recorded in coral geochemical indicators. Sr/Ca ratios in coral skeletons from Green Island show the lowest peak, means the highest temperature during the 1997/1998 El Niño period. However, we couldn't observe high-temperature events on δ18O. Furthermore, a negative δ13C shift was observed after El Niño events. The regime shift of δ13C might have been caused by temporal bleaching and/or a decrease in symbiotic algae due to high water temperature stress under the continuous decrease in δ13C in DIC due to the Suess effect.

The genome of a giant clam zooxanthella (Cladocopium infistulum) offers few clues to adaptation as an extracellular symbiont with high thermotolerance

BACKGROUND

Cladocopium infistulum (Symbiodiniaceae) is a dinoflagellate specialized to live in symbiosis with western Pacific giant clams (Tridacnidae). Unlike coral-associated symbionts, which reside within the host cells, C. infistulum inhabits the extracellular spaces of the clam's digestive diverticula. It is phylogenetically basal to a large species complex of stress-tolerant Cladocopium, many of which are associated with important reef-building corals in the genus Porites. This close phylogenetic relationship may explain why C. infistulum exhibits high thermotolerance relative to other tridacnid symbionts. Moreover, past analyses of microsatellite loci indicated that Cladocopium underwent whole-genome duplication prior to the adaptive radiations that led to its present diversity.

RESULTS

A draft genome assembly of C. infistulum was produced using long- and short-read sequences to explore the genomic basis for adaptations underlying thermotolerance and extracellular symbiosis among dinoflagellates and to look for evidence of genome duplication. Comparison to three other Cladocopium genomes revealed no obvious over-representation of gene groups or families whose functions would be important for maintaining C. infistulum's unique physiological and ecological properties. Preliminary analyses support the existence of partial or whole-genome duplication among Cladocopium, but additional high-quality genomes are required to substantiate these findings.

CONCLUSION

Although this investigation of Cladocopium infistulum revealed no patterns diagnostic of heat tolerance or extracellular symbiosis in terms of overrepresentation of gene functions or genes under selection, it provided a valuable genomic resource for comparative analyses. It also indicates that ecological divergence among Cladocopium species, and potentially among other dinoflagellates, is partially governed by mechanisms other than gene content. Thus, additional high-quality, multiomic data are needed to explore the molecular basis of key phenotypes among symbiotic microalgae.

Higher genotypic diversity and distinct assembly mechanism of free-living Symbiodiniaceae assemblages than sympatric coral-endosymbiotic assemblages in a tropical coral reef

While in hospite Symbiodiniaceae dinoflagellates are essential for coral health, ambient free-living counterparts are crucial for coral recruitment and resilience. Comparing free-living and in hospite Symbiodiniaceae communities can potentially provide insights into endosymbiont acquisition and recurrent recruitment in bleaching recovery. In this study, we studied coral-endosymbiotic and ambient free-living Symbiodiniaceae communities in the South China Sea. We collected samples from 183 coral and ambient plankton samples and conducted metabarcoding to investigate the diversity distribution, driving factors, and assembly mechanisms of the two groups of Symbiodiniaceae. Results revealed Cladocopium C1 and Durusdinium D1 as dominant genotypes. We detected a higher genotypic diversity in free-living than in hospite symbiodiniacean communities, but with shared dominant genotypes. This indicates a genetically diverse pool of Symbiodiniaceae available for recruitment by corals. Strikingly, we found that the cooler area had more Symbiodiniaceae thermosensitive genotypes, whereas the warmer area had more Symbiodiniaceae thermotolerant genotypes. Furthermore, in hospite and free-living Symbiodiniaceae communities were similarly affected by environmental factors, but shaped by different assembly mechanisms. The in hospite communities were controlled mainly by deterministic processes, whereas the ambient communities by stochastic processes. This study sheds light on the genetic diversity of source environmental Symbiodiniaceae and differential assembly mechanisms influencing Symbiodiniaceae inside and outside corals.IMPORTANCESymbiodiniaceae dinoflagellates play a pivotal role as key primary producers within coral reef ecosystems. Coral-endosymbiotic Symbiodiniaceae communities have been extensively studied, but relatively little work has been reported on the free-living Symbiodiniaceae community. Conducting a comparative analysis between sympatric coral-endosymbiotic and free-living Symbiodiniaceae communities can potentially enhance the understanding of how endosymbiont communities change in response to changing environments and the mechanisms driving these changes. Our findings shed light on the genetic diversity of source environmental Symbiodiniaceae and differential assembly mechanisms shaping free-living and in hospite Symbiodiniaceae communities, with implications in evaluating the adaptive and resilient capacity of corals in response to future climate change.

Can the global marine aquarium trade (MAT) be a model for sustainable coral reef fisheries?

Globally, 6 million coral reef fishers provide ~25% of emergent countries' catch, but species have low value. The marine aquarium trade (MAT) targets high-value biodiversity, but missing data amplify draconian governance and demand for international prohibition. To stimulate sustainability and reef conservation investment, we generate a fiscal baseline using the first global analysis of numbers, diversity, and biomass of MAT-traded organisms. Each year, ~55 million organisms worth US$2.15 billion at retail are traded comparable with major fisheries, e.g., tuna. A sustainable MAT also requires overexploitation assessments. We identify 25 species/genera with "Extremely High" risk ratios and place the Indonesian and Sulu-Celebes Seas in the highest exploitation category. Despite predicted hobbyist number increases, unabated reef degradation and low governance will transform the MAT into an aquaculture-dominated industry decoupled from communities (i.e., culture located in importing countries). A "MAT-positive" future requires evidence-based management/governance, consumer education, and sustainable practice incentivization but can address the biodiversity and social and economic inequality crises.

Coral Reef Population Genomics in an Age of Global Change

Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, gene flow, and hybridization have played and will continue to play an important role in the adaptation or extinction of coral reef taxa in the face of rapid environmental change, but research remains exceptionally limited compared to the urgent needs. Critical areas for future investigation include understanding evolutionary potential and the mechanisms of local adaptation, developing historical baselines, and building greater research capacity in the countries where most reef diversity is concentrated.

Degradation of starch-based bioplastic bags in the pelagic and benthic zones of the Gulf of Oman

The Gulf of Oman is becoming increasingly polluted with plastics, hence bioplastics have been considered 'a substitute', although their biodegradability in marine environments has not been well investigated. Most research has been performed on cellulose-based bioplastics, whereas starch-based bioplastics have proven to be a suitable, but less researched, alternative. This study is the first of its kind designed to investigate the degradability of two different types of starch-based bioplastic bags, available in the market and labeled as "biodegradable", in the pelagic and benthic zones of one of the warmest marine environment in the world. Fourier-Transform Infrared Spectroscopy (FTIR) showed a clear reduction in the presence of OH, CH, and CO in the bioplastic bags after 5 weeks of immersion. Thermo-Gravimetric Analysis (TGA) indicated degradation of glycerol, starch, and polyethylene. The biofouling bacterial communities on bioplastic surfaces showed distinct grouping based on the immersion zone. Candidaatus saccharibacteria, Verrucomicrobiae, Acidimicrobiia and Planctomycetia sequences were only detectable on bioplastics in the pelagic zone, whereas Actinomyces, Pseudomonas, Sphingobium and Acinetobacter related sequences were only found on bioplastics in the benthic layer. We conclude that starch-based bioplastics are more readily degradable in the Gulf of Oman than conventional plastics, hence could serve as a better environmentally friendly alternative.

Lineage-specific symbionts mediate differential coral responses to thermal stress

BACKGROUND

Ocean warming is a leading cause of increasing episodes of coral bleaching, the dissociation between coral hosts and their dinoflagellate algal symbionts in the family Symbiodiniaceae. While the diversity and flexibility of Symbiodiniaceae is presumably responsible for variations in coral response to physical stressors such as elevated temperature, there is little data directly comparing physiological performance that accounts for symbiont identity associated with the same coral host species. Here, using Pocillopora damicornis harboring genotypically distinct Symbiodiniaceae strains, we examined the physiological responses of the coral holobiont and the dynamics of symbiont community change under thermal stress in a laboratory-controlled experiment.

RESULTS

We found that P. damicornis dominated with symbionts of metahaplotype D1-D4-D6 in the genus Durusdinium (i.e., PdD holobiont) was more robust to thermal stress than its counterpart with symbionts of metahaplotype C42-C1-C1b-C1c in the genus Cladocopium (i.e., PdC holobiont). Under ambient temperature, however, the thermally sensitive Cladocopium spp. exhibited higher photosynthetic efficiency and translocated more fixed carbon to the host, likely facilitating faster coral growth and calcification. Moreover, we observed a thermally induced increase in Durusdinium proportion in the PdC holobiont; however, this "symbiont shuffling" in the background was overwhelmed by the overall Cladocopium dominance, which coincided with faster coral bleaching and reduced calcification.

CONCLUSIONS

These findings support that lineage-specific symbiont dominance is a driver of distinct coral responses to thermal stress. In addition, we found that "symbiont shuffling" may begin with stress-forced, subtle changes in the rare biosphere to eventually trade off growth for increased resilience. Furthermore, the flexibility in corals' association with thermally tolerant symbiont lineages to adapt or acclimatize to future warming oceans should be viewed with conservative optimism as the current rate of environmental changes may outpace the evolutionary capabilities of corals. Video Abstract.

Human-induced salinity changes impact marine organisms and ecosystems

Climate change is fundamentally altering marine and coastal ecosystems on a global scale. While the effects of ocean warming and acidification on ecology and ecosystem functions and services are being comprehensively researched, less attention is directed toward understanding the impacts of human-driven ocean salinity changes. The global water cycle operates through water fluxes expressed as precipitation, evaporation, and freshwater runoff from land. Changes to these in turn modulate ocean salinity and shape the marine and coastal environment by affecting ocean currents, stratification, oxygen saturation, and sea level rise. Besides the direct impact on ocean physical processes, salinity changes impact ocean biological functions with the ecophysiological consequences are being poorly understood. This is surprising as salinity changes may impact diversity, ecosystem and habitat structure loss, and community shifts including trophic cascades. Climate model future projections (of end of the century salinity changes) indicate magnitudes that lead to modification of open ocean plankton community structure and habitat suitability of coral reef communities. Such salinity changes are also capable of affecting the diversity and metabolic capacity of coastal microorganisms and impairing the photosynthetic capacity of (coastal and open ocean) phytoplankton, macroalgae, and seagrass, with downstream ramifications on global biogeochemical cycling. The scarcity of comprehensive salinity data in dynamic coastal regions warrants additional attention. Such datasets are crucial to quantify salinity-based ecosystem function relationships and project such changes that ultimately link into carbon sequestration and freshwater as well as food availability to human populations around the globe. It is critical to integrate vigorous high-quality salinity data with interacting key environmental parameters (e.g., temperature, nutrients, oxygen) for a comprehensive understanding of anthropogenically induced marine changes and its impact on human health and the global economy.

The Evolution of Coral Reef under Changing Climate: A Scientometric Review

In this scientometric review, we employ the Web of Science Core Collection to assess current publications and research trends regarding coral reefs in relation to climate change. Thirty-seven keywords for climate change and seven keywords for coral reefs were used in the analysis of 7743 articles on coral reefs and climate change. The field entered an accelerated uptrend phase in 2016, and it is anticipated that this phase will last for the next 5 to 10 years of research publication and citation. The United States and Australia have produced the greatest number of publications in this field. A cluster (i.e., focused issue) analysis showed that coral bleaching dominated the literature from 2000 to 2010, ocean acidification from 2010 to 2020, and sea-level rise, as well as the central Red Sea (Africa/Asia), in 2021. Three different types of keywords appear in the analysis based on which are the (i) most recent (2021), (ii) most influential (highly cited), and (iii) mostly used (frequently used keywords in the article) in the field. The Great Barrier Reef, which is found in the waters of Australia, is thought to be the subject of current coral reef and climate change research. Interestingly, climate-induced temperature changes in "ocean warming" and "sea surface temperature" are the most recent significant and dominant keywords in the coral reef and climate change area.

Assessing the potential for demographic restoration and assisted evolution to build climate resilience in coral reefs

Interest is growing in developing conservation strategies to restore and maintain coral reef ecosystems in the face of mounting anthropogenic stressors, particularly climate warming and associated mass bleaching events. One such approach is to propagate coral colonies ex situ and transplant them to degraded reef areas to augment habitat for reef-dependent fauna, prevent colonization from spatial competitors, and enhance coral reproductive output. In addition to such "demographic restoration" efforts, manipulating the thermal tolerance of outplanted colonies through assisted relocation, selective breeding, or genetic engineering is being considered for enhancing rates of evolutionary adaptation to warming. Although research into such "assisted evolution" strategies has been growing, their expected performance remains unclear. We evaluated the potential outcomes of demographic restoration and assisted evolution in climate change scenarios using an eco-evolutionary simulation model. We found that supplementing reefs with pre-existing genotypes (demographic restoration) offers little climate resilience benefits unless input levels are large and maintained for centuries. Supplementation with thermally resistant colonies was successful at improving coral cover at lower input levels, but only if maintained for at least a century. Overall, we found that, although demographic restoration and assisted evolution have the potential to improve long-term coral cover, both approaches had a limited impact in preventing severe declines under climate change scenarios. Conversely, with sufficient natural genetic variance and time, corals could readily adapt to warming temperatures, suggesting that restoration approaches focused on building genetic variance may outperform those based solely on introducing heat-tolerant genotypes.

Alignment-Free Analysis of Whole-Genome Sequences From Symbiodiniaceae Reveals Different Phylogenetic Signals in Distinct Regions

Dinoflagellates of the family Symbiodiniaceae are predominantly essential symbionts of corals and other marine organisms. Recent research reveals extensive genome sequence divergence among Symbiodiniaceae taxa and high phylogenetic diversity hidden behind subtly different cell morphologies. Using an alignment-free phylogenetic approach based on sub-sequences of fixed length k (i.e. k-mers), we assessed the phylogenetic signal among whole-genome sequences from 16 Symbiodiniaceae taxa (including the genera of Symbiodinium, Breviolum, Cladocopium, Durusdinium and Fugacium) and two strains of Polarella glacialis as outgroup. Based on phylogenetic trees inferred from k-mers in distinct genomic regions (i.e. repeat-masked genome sequences, protein-coding sequences, introns and repeats) and in protein sequences, the phylogenetic signal associated with protein-coding DNA and the encoded amino acids is largely consistent with the Symbiodiniaceae phylogeny based on established markers, such as large subunit rRNA. The other genome sequences (introns and repeats) exhibit distinct phylogenetic signals, supporting the expected differential evolutionary pressure acting on these regions. Our analysis of conserved core k-mers revealed the prevalence of conserved k-mers (>95% core 23-mers among all 18 genomes) in annotated repeats and non-genic regions of the genomes. We observed 180 distinct repeat types that are significantly enriched in genomes of the symbiotic versus free-living Symbiodinium taxa, suggesting an enhanced activity of transposable elements linked to the symbiotic lifestyle. We provide evidence that representation of alignment-free phylogenies as dynamic networks enhances the ability to generate new hypotheses about genome evolution in Symbiodiniaceae. These results demonstrate the potential of alignment-free phylogenetic methods as a scalable approach for inferring comprehensive, unbiased whole-genome phylogenies of dinoflagellates and more broadly of microbial eukaryotes.

Effects of Temperature and Salinity on Growth, Metabolism and Digestive Enzymes Synthesis of Goniopora columna

Climate change is causing dramatic changes in global ocean temperature and salinity, threatening coral survival. Coral growth and metabolism are greatly affected by the temperature, salinity and feeding time of the environment. In order to explore the threats to coral survival caused by climate change, this study will investigate the changes in body composition, digestive enzymes and metabolism of G. columna at different temperatures and salinities. A maximum G. columna growth rate was observed at 25 °C and 30−35 psu salinity. The G. columna could survive in a wide salinity range of 25−40 psu. However, the maximum number and weight of G. columna polyps was determined at 30−35 psu. Furthermore, 30−35 psu salinity at 25 °C led to the best G. columna growth and survival, mainly because of their enhanced nutrient absorption rate, polyp expansion rate, metabolic rate and adaptability. Comparing various salinity-temperature treatment groups, all obtained values for growth, behavior and metabolism were significantly higher (p < 0.05) for 30 psu at 25 °C than other treatment groups resulting in maximum G. columna yield. In addition, the optimal timing of G. columna feeding was assessed by studying changes in body composition and digestive enzymes within 24 h of feeding. The results showed that G. columna has higher protein and protease activity between 6:00 a.m. to 12:00 noon. Therefore, at 25 °C, 30−35 psu and feeding will enhance G. columna growth and survival.

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

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

Microbiome of juvenile corals in the outer reef slope and lagoon of the South China Sea: insight into coral acclimatization to extreme thermal environments

Environmental conditions between the outer reef slope (ORS) and lagoon in tropical atolls are significantly different, but the variations of juvenile coral-microbiomes in the two environments and their relationship with coral thermal acclimatization are poorly understood. We explored this issue based on local water conditions and the microbiome of juvenile corals in the ORS and lagoon in the central South China Sea. Coral-symbiotic Symbiodiniaceae showed significant differences among coral species; Pocillopora verrucosa and Pachyseris rugosa in the ORS, and Acropora formosa in the lagoon were dominated by Durusdinium, but other corals were dominated by Cladocopium. Although A. formosa in the ORS were dominated by Cladocopium (C3u), they were dominated by Durusdinium (D1/D1a) and Cladocopium (C50) in the lagoon. Other coral species were both dominated by Cladocopium in the lagoon and ORS. The relative abundance of bacteria in the Deinococcus-Thermus was generally higher in the lagoon corals than in the ORS corals. Our study indicates that P. verrucosa, P. rugosa and Porites lutea may have high thermal tolerance based on the relatively high abundance of heat-tolerant Durusdinium and Thermus scotoductus. Likewise, A. formosa in the lagoon may acclimatize to the thermal environment based on a high relative abundance of heat-tolerant Durusdinium.

Modification of fatty acid profile and biosynthetic pathway in symbiotic corals under eutrophication

Symbiotic corals receive energy not only by ingesting food (e.g. plankton, inorganic/organic matter, i.e. heterotrophy), but also by endosymbiosis, which supplies photosynthates (dissolved inorganic carbon, i.e. autotrophy). These two sources of energy have distinct fatty acid (FA) profiles, which can be used to differentiate corals by their primary feeding mode. FA profiles have been applied as biomarkers to evaluate the quality of nutrition in the midst of environmental change. However, species-specific responses of coral FA profiles and biosynthetic pathway under cultural eutrophication are still unknown. We collected two coral species (Acropora samoensis, Platygyra carnosa) from sites with different levels of eutrophication to test for variations in FA profiles. Gas Chromatography-Mass Spectrometry (GC-MS) was performed to identify FA profiles and quantify their concentration. Our main findings are threefold: 1) chronic eutrophication inhibits corals' ability to synthesize essential FA; 2) PUFA:SFA ratio and certain FA biomarkers or their pathway can be successfully utilized to determine the relative degree of autotrophy and heterotrophy in corals; 3) under eutrophication, different FA profiles of coral host tissue are attributed to different feeding strategies. Thus, our research provides significant new insights into the roles of FA as a risk assessment tool in coral reef ecosystems under the pressure of eutrophication.

A boom-or-bust approach-The 'Glass Cannon' hypothesis in host microbiomes

In Focus: Dunphy, CM, Vollmer, SV, Gouhier, TC. (2021) Host-microbial systems as glass cannons: Explaining microbiome stability in corals exposed to extrinsic perturbations. Journal of Animal Ecology, 90, 1044-1057. The importance of symbiotic microbial communities for the functioning of animal hosts is now well-documented; however, the interactions between host microbiomes and stress are less well-understood. Dunphy et al. used a common garden experiment to show that host-microbiomes vary in their resilience across different coral species. The authors then used mathematical modelling to provide novel evidence that species with microbiomes that are regulated by host processes are robust to perturbation from stressors, but that robustness comes at a higher cost to the host. Conversely, species with microbiomes that are regulated by microbial processes are generally much more resilient and cheaper to support, but when disrupted by external stressors, the communities break down entirely-these latter species are termed 'glass cannons'. This novel hypothesis has important implications for how host microbiomes function in a rapidly changing world that exposes animal hosts to multiple biotic and abiotic perturbations.

Flexibility in Red Sea Tridacna maxima-Symbiodiniaceae associations supports environmental niche adaptation

Giant clams (Tridacninae) are important members of Indo-Pacific coral reefs and among the few bivalve groups that live in symbiosis with unicellular algae (Symbiodiniaceae). Despite the importance of these endosymbiotic dinoflagellates for clam ecology, the diversity and specificity of these associations remain relatively poorly studied, especially in the Red Sea. Here, we used the internal transcribed spacer 2 (ITS2) rDNA gene region to investigate Symbiodiniaceae communities associated with Red Sea Tridacna maxima clams. We sampled five sites spanning 1,300 km (10° of latitude, from the Gulf of Aqaba, 29°N, to the Farasan Banks, 18°N) along the Red Sea's North-South environmental gradient. We detected a diverse and structured assembly of host-associated algae with communities demonstrating region and site-specificity. Specimens from the Gulf of Aqaba harbored three genera of Symbiodiniaceae, Cladocopium, Durusdinium, and Symbiodinium, while at all other sites clams associated exclusively with algae from the Symbiodinium genus. Of these exclusively Symbiodinium-associating sites, the more northern (27° and 22°) and more southern sites (20° and 18°) formed two separate groupings despite site-specific algal genotypes being resolved at each site. These groupings were congruent with the genetic break seen across multiple marine taxa in the Red Sea at approximately 19°, and along with our documented site-specificity of algal communities, contrasted the panmictic distribution of the T. maxima host. As such, our findings indicate flexibility in T. maxima-Symbiodiniaceae associations that may explain its relatively high environmental plasticity and offers a mechanism for environmental niche adaptation.

Physiological plasticity of corals to temperature stress in marginal coral communities

Adaptation and/or acclimatization through various mechanisms have been suggested to help some tropical coral species to overcome temperature-induced bleaching that is intensifying with climate change; however, while much research has been done on the physiological responses of tropical and subtropical corals to stress, little is known about these responses in corals in marginal environments-e.g., high-latitude and non-reefal communities. In this study, we examined the thermal-tolerant physiology of the flowerpot coral, Alveopora japonica, endemic to the high-latitude Jeju Island (33.39°N), South Korea and Oulastrea crispata and Coelastrea aspera from the subtropical non-reefal coral community on the Penghu Islands (23.34°N), Taiwan. Analysis of physiological parameters; photochemical efficiency, Chlorophyll pigment, Symbiodiniaceae cell number and host soluble proteins - showed that A. japonica can survive through a wide range of temperature stresses (10-32 °C) over a period of 8 days without showing signs of bleaching. In addition, corals O. crispata and C. aspera withstood temperature stresses of up to 33 °C and repeated temperature fluctuations without bleaching. Our results indicate that, under large seasonal variations and asymmetrical daily fluctuations in temperature, corals currently living in marginal environments could have thermal plasticity, allowing them to survive in the future climate change scenarios. This study reiterates the importance of studying the eco-physiology of corals that are generally ignored because of their neutral or positive responses to stress.

Long-term ecological changes in fishes and macro-invertebrates in the world's warmest coral reefs

The Arabian Gulf is a natural laboratory for examining the consequences of large-scale disturbances due to global warming on coral reef ecosystems because of its extreme temperature regime. Using a coral reef monitoring time series extending from 1985 to 2015, we examined the long-term ecological changes in fish and macro-invertebrate communities as these habitats suffered heat shocks. We used a GLMM modelling framework to obtain clean annual signals in community indicators from noisy data. We also visualized temporal change in the taxonomic composition of fishes and macro-invertebrates. A phase shift from predominantly reef-building corals to barren grounds occurred between 1996 and 2000. Macro-invertebrates responded rapidly, and most of associated indicators recovered to pre-shift levels in 15 years. Fishes generally had lagged responses to the phase shift and had shifted to a new state with lower abundance, as well as different species composition. Increased levels of herbivory first by macro-invertebrates, mostly sea urchins, and then fishes, could have suppressed macro-algae expansion and consequently led to the dominance of barren ground. When the phase shift occurred, most of the 14 fish families declined in abundance while macro-invertebrate groups increased. Fish families able to utilize non-coral habitats appeared more resilient to the disturbances and subsequent coral degradation. Unlike other regions, we observed high resilience of the coral-dependent butterflyfishes to coral loss, possibly due to local migration from other less-impacted coral reefs. We hypothesized a top-down control mechanism mediated by predation by fishes has contributed to shaping the temporal and spatial patterns of the macro-invertebrates. Our results also revealed differences in spatial preferences among fishes and macro-invertebrate groups, which could be used to set priorities and develop effective conservation and management strategies.

The World Coral Conservatory (WCC): A Noah's ark for corals to support survival of reef ecosystems

Global change causes widespread decline of coral reefs. In order to counter the anticipated disappearance of coral reefs by the end of this century, many initiatives are emerging, including creation of marine protected areas (MPAs), reef restoration projects, and assisted evolution initiatives. Such efforts, although critically important, are locally constrained. We propose to build a “Noah's Ark” biological repository for corals that taps into the network of the world’s public aquaria and coral reef scientists. Public aquaria will serve not only as a reservoir for the purpose of conservation, restoration, and research of reef-building corals but also as a laboratory for the implementation of operations for the selection of stress-resilient and resistant genotypes. The proposed project will provide a global dimension to coral reef education and protection as a result of the involvement of a network of public and private aquaria.

Global change is causing a widespread decline in coral reefs. This Community Page article proposes to build the World Coral Conservatory, a “Noah's Ark” biological repository that taps into the network of the world’s public aquaria and coral reef scientists, in order to preserve the fast-disappearing biodiversity of coral reefs.

Homogenization of Endosymbiont Communities Hosted by Equatorial Corals during the 2016 Mass Bleaching Event

Thermal stress drives the bleaching of reef corals, during which the endosymbiotic relationship between Symbiodiniaceae microalgae and the host breaks down. The endosymbiont communities are known to shift in response to environmental disturbances, but how they respond within and between colonies during and following bleaching events remains unclear. In 2016, a major global-scale bleaching event hit countless tropical reefs. Here, we investigate the relative abundances of Cladocopium LaJeunesse & H.J.Jeong, 2018 and Durusdinium LaJeunesse, 2018 within and among Pachyseris speciosa colonies in equatorial Singapore that are known to host both these Symbiodiniaceae clades. Bleached and unbleached tissues from bleaching colonies, as well as healthy colonies, during and following the bleaching event were sampled and analyzed for comparison. The nuclear ribosomal internal transcribed spacer (ITS) regions were separately amplified and quantified using a SYBR Green-based quantitative polymerase chain reaction (qPCR) method and Illumina high-throughput sequencing. We found Cladocopium to be highly abundant relative to Durusdinium. The relative abundance of Durusdinium, known to be thermally tolerant, was highest in post-bleaching healthy colonies, while bleached and unbleached tissues from bleaching colonies as well as tissue from healthy colonies during the event had depressed proportions of Durusdinium. Given the importance of Durusdinium for thermal tolerance and stress response, it is surprising that bleached tissue showed limited change over healthy tissue during the bleaching event. Moreover, colonies were invariably dominated by Cladocopium during bleaching, but a minority of colonies were Durusdinium-dominant during non-bleaching times. The detailed characterization of Symbiodiniaceae in specific colonies during stress and recovery will provide insights into this crucial symbiosis, with implications for their responses during major bleaching events.

Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

BACKGROUND

The capacity of reef-building corals to tolerate (or adapt to) heat stress is a key factor determining their resilience to future climate change. Changes in coral microbiome composition (particularly for microalgal endosymbionts and bacteria) is a potential mechanism that may assist corals to thrive in warm waters. The northern Red Sea experiences extreme temperatures anomalies, yet corals in this area rarely bleach suggesting possible refugia to climate change. However, the coral microbiome composition, and how it relates to the capacity to thrive in warm waters in this region, is entirely unknown.

RESULTS

We investigated microbiomes for six coral species (Porites nodifera, Favia favus, Pocillopora damicornis, Seriatopora hystrix, Xenia umbellata, and Sarcophyton trocheliophorum) from five sites in the northern Red Sea spanning 4° of latitude and summer mean temperature ranges from 26.6 °C to 29.3 °C. A total of 19 distinct dinoflagellate endosymbionts were identified as belonging to three genera in the family Symbiodiniaceae (Symbiodinium, Cladocopium, and Durusdinium). Of these, 86% belonged to the genus Cladocopium, with notably five novel types (19%). The endosymbiont community showed a high degree of host-specificity despite the latitudinal gradient. In contrast, the diversity and composition of bacterial communities of the surface mucus layer (SML)-a compartment particularly sensitive to environmental change-varied significantly between sites, however for any given coral was species-specific.

CONCLUSION

The conserved endosymbiotic community suggests high physiological plasticity to support holobiont productivity across the different latitudinal regimes. Further, the presence of five novel algal endosymbionts suggests selection of certain genotypes (or genetic adaptation) within the semi-isolated Red Sea. In contrast, the dynamic composition of bacteria associated with the SML across sites may contribute to holobiont function and broaden the ecological niche. In doing so, SML bacterial communities may aid holobiont local acclimatization (or adaptation) by readily responding to changes in the host environment. Our study provides novel insight about the selective and endemic nature of coral microbiomes along the northern Red Sea refugia.

High levels of floridoside at high salinity link osmoadaptation with bleaching susceptibility in the cnidarian-algal endosymbiosis

Coral reefs are in global decline mainly due to increasing sea surface temperatures triggering coral bleaching. Recently, high salinity has been linked to increased thermotolerance and decreased bleaching in the sea anemone coral model Aiptasia. However, the underlying processes remain elusive. Using two Aiptasia host­–endosymbiont pairings, we induced bleaching at different salinities and show reduced reactive oxygen species (ROS) release at high salinities, suggesting a role of osmoadaptation in increased thermotolerance. A subsequent screening of osmolytes revealed that this effect was only observed in algal endosymbionts that produce 2-O-glycerol-α-D-galactopyranoside (floridoside), an osmolyte capable of scavenging ROS. This result argues for a mechanistic link between osmoadaptation and thermotolerance, mediated by ROS-scavenging osmolytes (e.g., floridoside). This sheds new light on the putative mechanisms underlying the remarkable thermotolerance of corals from water bodies with high salinity such as the Red Sea or Persian/Arabian Gulf and holds implications for coral thermotolerance under climate change.

This article has an associated First Person interview with the first author of the paper.

Summary: Using the coral model Aiptasia, we show increased thermotolerance at high salinities, concomitant with a reduced reactive oxygen species (ROS) release by algal endosymbionts. This suggests a mechanistic link between osmoadaptation and thermotolerance, mediated by ROS-scavenging osmolytes.

Intraspecific variation in the response of the estuarine European isopod Cyathura carinata (Krøyer, 1847) to ocean acidification

In the present study the model isopod, Cyathura carinata were exposed to four pH_NIST treatments (control: 7.9; 7.5, 7, 6.5) in order to determine the tolerance and pH threshold value this estuarine species withstand under future acidification scenarios. Seawater acidification significantly affected the lifespan of C. carinata, where population density was remarkably reduced at the lowest pH treatment. The longevity, survivorship and swimming activity (related to the acquisition of energy) of these isopods decreased with decreasing pH. Furthermore, to determine the possible metabolic plasticity of this species, the swimming activity, the Na+/K + -ATPase activity (relevant for osmoregulation process), and the RNA:DNA ratio (an indicator of fitness) were measure from two populations of C. carinata, one inhabiting a stable environment (pH_NIST 7.5-8.0) and one inhabiting a fluctuating pCO₂ regimes (pH 3.3-8.5) subjected to three pH treatments (7.9, 7.0 and 6.5). The population from high fluctuating pCO₂ conditions showed capacity to withstand to pH 6.5, as well as higher longevity and metabolic plasticity, when compared with the population from the habitat with slight pCO₂ variation. These results indicate that Cyathura population from stable environments could be vulnerable to ocean acidification because it could trigger detrimental effects on its survival energy budget, and growth. However, ocean acidification has limited effect on the energy budget and survival of C. carinata population from highly variable habitats, suggesting that they are able to cope with the elevated energy demand. The difference showed between populations is likely an indication of genetic differentiation in tolerance to ocean acidification, possibly attributable to local adaptations, which could provide the raw material necessary for adaptation to future conditions. In addition, our results suggest that when assessing marine crustacean responses to changing environments on a global scale, variability in population and metabolic responses need to be considered.

Host-symbiont combinations dictate the photo-physiological response of reef-building corals to thermal stress

High sea surface temperatures often lead to coral bleaching wherein reef-building corals lose significant numbers of their endosymbiotic dinoflagellates (Symbiodiniaceae). These increasingly frequent bleaching events often result in large scale coral mortality, thereby devasting reef systems throughout the world. The reef habitats surrounding Palau are ideal for investigating coral responses to climate perturbation, where many inshore bays are subject to higher water temperature as compared with offshore barrier reefs. We examined fourteen physiological traits in response to high temperature across various symbiotic dinoflagellates in four common Pacific coral species, Acropora muricata, Coelastrea aspera, Cyphastrea chalcidicum and Pachyseris rugosa found in both offshore and inshore habitats. Inshore corals were dominated by a single homogenous population of the stress tolerant symbiont Durusdinium trenchii, yet symbiont thermal response and physiology differed significantly across coral species. In contrast, offshore corals harbored specific species of Cladocopium spp. (ITS2 rDNA type-C) yet all experienced similar patterns of photoinactivation and symbiont loss when heated. Additionally, cell volume and light absorption properties increased in heated Cladocopium spp., leading to a greater loss in photo-regulation. While inshore coral temperature response was consistently muted relative to their offshore counterparts, high physiological variability in D. trenchii across inshore corals suggests that bleaching resilience among even the most stress tolerant symbionts is still heavily influenced by their host environment.

Marine heatwaves reveal coral reef zones susceptible to bleaching in the Red Sea

As the Earth's temperature continues to rise, coral bleaching events become more frequent. Some of the most affected reef ecosystems are located in poorly monitored waters, and thus, the extent of the damage is unknown. We propose the use of marine heatwaves (MHWs) as a new approach for detecting coral reef zones susceptible to bleaching, using the Red Sea as a model system. Red Sea corals are exceptionally heat-resistant, yet bleaching events have increased in frequency. By applying a strict definition of MHWs on >30 year satellite-derived sea surface temperature observations (1985-2015), we provide an atlas of MHW hotspots over the Red Sea coral reef zones, which includes all MHWs that caused major coral bleaching. We found that: (a) if tuned to a specific set of conditions, MHWs identify all areas where coral bleaching has previously been reported; (b) those conditions extended farther and occurred more often than bleaching was reported; and (c) an emergent pattern of extreme warming events is evident in the northern Red Sea (since 1998), a region until now thought to be a thermal refuge for corals. We argue that bleaching in the Red Sea may be vastly underrepresented. Additionally, although northern Red Sea corals exhibit remarkably high thermal resistance, the rapidly rising incidence of MHWs of high intensity indicates this region may not remain a thermal refuge much longer. As our regionally tuned MHW algorithm was capable of isolating all extreme warming events that have led to documented coral bleaching in the Red Sea, we propose that this approach could be used to reveal bleaching-prone regions in other data-limited tropical regions. It may thus prove a highly valuable tool for policymakers to optimize the sustainable management of coastal economic zones.

Latitudinal Variation in the Molecular Diversity and Community Composition of Symbiodiniaceae in Coral From the South China Sea

Coral reefs are continuing to decline worldwide due to anthropogenic climate change. The study of the molecular diversity and biogeographical patterns of Symbiodiniaceae, is essential to understand the adaptive potential and resilience of coral–algal symbiosis. Next generation sequencing was used to analyze the Symbiodiniaceae rDNA internal transcribed spacer 2 marker genes from 178 reef-building coral samples in eight coral habitats across approximately 13° of latitude in the South China Sea (SCS). A total of three Symbiodiniaceae genera, Cladocopium, Durusdinium, and Gerakladium, as well as 31 dominant Symbiodiniaceae types, were identified. Symbiodiniaceae richness, diversity, and community composition varied according to latitude; intermediate and low latitude coral reefs (IR and LR) have higher Symbiodiniaceae richness and diversity than high latitude coral habitats (HC and HR). A PERMANOVA analysis found significant differences in the Symbiodiniaceae community composition in the SCS (F = 14.75, R² = 0.20, p = 0.001 < 0.01). The major dominant Symbiodiniaceae types were C1 in the HC and the HR, C1/Cspc/C50/C15 and D1 in the IR, and C3u and C15 in the LR. Canonical correspondence analysis showed that the relative abundance of different Symbiodiniaceae types is affected by multiple environmental factors. Phylogenetic analysis indicated that the Symbiodiniaceae type Cladocopium, which shared common ancestors, shows similar environmental adaptability. Based on these results, we suggest that coral host species played a relatively small role in the identity of the dominant Symbiodiniaceae type. Therefore, the biogeographical patterns of Symbiodiniaceae may be mainly affected by environmental factors. Our research provides a comprehensive overview of the biogeography of Symbiodiniaceae in the SCS, where coral communities and reefs are widely distributed across different latitude regions and have variable environmental conditions. Our data will provide support for further study of the regional diversification of Symbiodiniaceae and the ecological resilience of the coral-Symbiodiniaceae symbioses.

SymPortal: A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling

We present SymPortal (SymPortal.org), a novel analytical framework and platform for genetically resolving the algal symbionts of reef corals using next‐generation sequencing (NGS) data of the ITS2 rDNA. Although the ITS2 marker is widely used to genetically characterize taxa within the family Symbiodiniaceae (formerly the genus Symbiodinium), the multicopy nature of the marker complicates its use. Commonly, the intragenomic diversity resultant from this multicopy nature is collapsed by analytical approaches, thereby focusing on only the most abundant sequences. In contrast, SymPortal employs logic to identify within‐sample informative intragenomic sequences, which we have termed ‘defining intragenomic variants' (DIVs), to identify ITS2‐type profiles representative of putative Symbiodiniaceae taxa. By making use of this intragenomic ITS2 diversity, SymPortal is able to resolve genetic delineations using the ITS2 marker at a level that was previously only possible by using additional genetic markers. We demonstrate this by comparing this novel approach to the most commonly used alternative approach for NGS ITS2 data, the 97% similarity clustering to operational taxonomic units (OTUs). The SymPortal platform accepts NGS raw sequencing data as input to provide an easy‐to‐use, standardization‐enforced, and community‐driven framework that integrates with a database to gain resolving power with increased use. We consider that SymPortal, in conjunction with ongoing large‐scale sampling and sequencing efforts, should play an instrumental role in making future sampling efforts more comparable and in maximizing their efficacy in working towards the classification of the global Symbiodiniaceae diversity.

Flexible Symbiotic Associations of Symbiodinium With Five Typical Coral Species in Tropical and Subtropical Reef Regions of the Northern South China Sea

The coral symbiont Symbiodinium plays important roles in the adaptation of coral to environmental changes. However, coral-Symbiodinium symbiotic associations are not well-understood in the South China Sea (SCS) whilst considering environmental factors and host taxa. In this study, next-generation sequencing of the internal transcribed spacer region 2 (ITS2) marker gene was used to explore the symbiotic associations between Symbiodinium and five typical coral species across tropical and subtropical reef regions of the SCS. The results showed that Acropora sp., Galaxea fascicularis, Platygyra lamellina, and Sarcophyton glaucum exhibited distinct Symbiodinium compositions between tropical and subtropical reef regions, whereas Porites lutea had stable Symbiodinium compositions. More heterogeneous Symbiodinium compositions among different coral species were observed in the tropical region, but there were no statistically significant differences in Symbiodinium compositions among different coral species in subtropical reef regions. There was a correlation between the Symbiodinium compositions and environmental factors, except for the composition of P. lutea. Symbiodinium subclades D1, D2, C71, C71a, C21, C3b, and C161 were primarily explained by the seawater temperature, nitrate, ammonia, and phosphate. Several host-specific Symbiodinium subclades (e.g., C15, C15.6, and C91) were observed in P. lutea as well. The findings of this study demonstrate the relationship of Symbiodinium diversity with coral hosts and the environment are helpful for elucidating the adaptation of corals to global climate change and anthropogenic disturbance.

Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot

For tropical marine species, hotspots of endemism occur in peripheral areas furthest from the center of diversity, but the evolutionary processes that lead to their origin remain elusive. We test several hypotheses related to the evolution of peripheral endemics by sequencing ultraconserved element (UCE) loci to produce a genome-scale phylogeny of 47 butterflyfish species (family Chaetodontidae) that includes all shallow water butterflyfish from the coastal waters of the Arabian Peninsula (i.e., Red Sea to Arabian Gulf) and their close relatives. Bayesian tree building methods produced a well-resolved phylogeny that elucidated the origins of butterflyfishes in this hotspots of endemism. We show that UCEs, often used to resolve deep evolutionary relationships, represent an important tool to assess the mechanisms underlying recently diverged taxa. Our analyses indicate that unique environmental conditions in the coastal waters of the Arabian Peninsula probably contributed to the formation of endemic butterflyfishes. Older endemic species are also associated with narrow versus broad depth ranges, suggesting that adaptation to deeper coral reefs in this region occurred only recently (<1.75 Ma). Even though deep reef environments were drastically reduced during the extreme low sea level stands of glacial ages, shallow reefs persisted, and as such there was no evidence supporting mass extirpation of fauna in this region.

Validation of the binary designation Symbiodinium thermophilum (Dinophyceae)

The binary designation Symbiodinium thermophilum was invalid due to the absence of an illustration as required by Article 44.2 of the ICN. Herein, it is validated. This species is the most common symbiont in reef corals in the southern Persian/Arabian Gulf, the world's hottest body of water sustaining reef coral growth.

Population collapse dynamics in Acropora downingi, an Arabian/Persian Gulf ecosystem-engineering coral, linked to rising temperature

As in the tropical Atlantic, Acropora populations in the southern Persian/Arabian Gulf plummeted within two decades after having been ecosystem engineers on most wave-exposed reefs since the Pleistocene. Since 1996/1998 live coral cover in the Gulf declined by over 90% in many areas, primarily due to bleaching and diseases caused by rising temperatures. In the formerly dominant table-coral species A. downingi, population dynamics corresponding to disturbance regimes was quantified in three transition matrices (lower disturbance pre-1996; moderate disturbance from 1998 to 2010 and 2013 to 2017, disturbed in 1996/1998, 2010/11/12, 2017). Increased disturbance frequency and severity caused progressive reduction in coral size, cover, and population fecundity. Small size-classes were bolstered more by partial colony mortality than sexual recruitment. Some large corals had a size refuge and resisted die-back but were also lost with increasing disturbance. Matrix and biophysical larval flow models suggested one metapopulation. Southern, Arabian, populations could be connected to northern, Iranian, populations but this connectivity was lost under assumptions of pelagic larval duration at rising temperatures shortened to a third. Then, the metapopulation disintegrated into isolated populations. Connectivity required to avoid extinctions increased exponentially with disturbance frequency and correlation of disturbances across the metapopulation. Populations became unsustainable at eight disturbances in 15 years, when even highest theoretical recruitment no longer compensated mortality. This lethal disturbance frequency was 3-fold that of the moderately disturbed monitoring period and 4-fold of the preceding low-disturbance period-suggesting ongoing shortening of the disturbance-free period. Observed population collapse and environmental changes in the Gulf suggest that A. downingi is heading toward at least functional extinction mainly due to increasingly frequent temperature-induced mortality events, clearly linked to climate change.

Season structures prokaryotic partners but not algal symbionts in subtropical hard corals

Coral reef ecosystems have great economic, social, and ecological value. The ecological success of coral reef ecosystems critically depends on coral-algal symbiosis and coral-prokaryotic partnership. However, seasonal changes underlying these relationships in subtropical hard corals of Hong Kong are poorly studied. Here, we compared the community changes of algal symbionts and prokaryotic partners in Platygyra carnosa and Galaxea fascicularis from Hong Kong collected at two seasonal time points of winter and summer via massively parallel sequencing of genetic markers and multivariate analysis. The results indicated that algal symbionts showed no significant changes between the two seasonal time points but prokaryotic partners changed substantially. Prokaryotic partners putatively involved in photosynthesis, nitrogen fixation, and sulfur oxidation increased significantly from winter to summer, while prokaryotic partners potentially associated with chemosynthesis, ammonia oxidation, and nitrite oxidation decreased significantly from winter to summer. Dissolved oxygen and pH served as the main contributors influencing prokaryotic partners in winter, while temperature, turbidity, and salinity played a dominant role in shaping prokaryotic partners in summer. The findings of the present study suggest that season structures prokaryotic partners but not algal symbionts in subtropical hard corals.

Thermal refugia against coral bleaching throughout the northern Red Sea

Tropical reefs have been impacted by thermal anomalies caused by global warming that induced coral bleaching and mortality events globally. However, there have only been very few recordings of bleaching within the Red Sea despite covering a latitudinal range of 15° and consequently it has been considered a region that is less sensitive to thermal anomalies. We therefore examined historical patterns of sea surface temperature (SST) and associated anomalies (1982-2012) and compared warming trends with a unique compilation of corresponding coral bleaching records from throughout the region. These data indicated that the northern Red Sea has not experienced mass bleaching despite intensive Degree Heating Weeks (DHW) of >15°C-weeks. Severe bleaching was restricted to the central and southern Red Sea where DHWs have been more frequent, but far less intense (DHWs <4°C-weeks). A similar pattern was observed during the 2015-2016 El Niño event during which time corals in the northern Red Sea did not bleach despite high thermal stress (i.e. DHWs >8°C-weeks), and bleaching was restricted to the central and southern Red Sea despite the lower thermal stress (DHWs < 8°C-weeks). Heat stress assays carried out in the northern (Hurghada) and central (Thuwal) Red Sea on four key reef-building species confirmed different regional thermal susceptibility, and that central Red Sea corals are more sensitive to thermal anomalies as compared to those from the north. Together, our data demonstrate that corals in the northern Red Sea have a much higher heat tolerance than their prevailing temperature regime would suggest. In contrast, corals from the central Red Sea are close to their thermal limits, which closely match the maximum annual water temperatures. The northern Red Sea harbours reef-building corals that live well below their bleaching thresholds and thus we propose that the region represents a thermal refuge of global importance.

High-frequency temperature variability mirrors fixed differences in thermal limits of the massive coral Porites lobata (Dana, 1846)

Spatial heterogeneity in environmental characteristics can drive adaptive differentiation when contrasting environments exert divergent selection pressures. This environmental and genetic heterogeneity can substantially influence population and community resilience to disturbance events. Here, we investigated corals from the highly variable back reef habitats of Ofu Island in American Samoa that thrive in thermal conditions known to elicit widespread bleaching and mortality elsewhere. To investigate the relative importance of acclimation vs. site of origin in shaping previously observed differences in coral tolerance limits in Ofu, specimens of the common Indo-Pacific coral Porites lobata (Dana, 1846) from locations with differing levels of thermal variability were acclimated to low and high thermal variation in controlled common garden aquaria. Overall, there were minimal effects of the acclimation exposure. Corals native to the site with the highest level of daily variability grew fastest, regardless of acclimation treatment. When exposed to lethal thermal stress, corals native to both variable sites contained elevated levels of heat shock proteins and maintained photosynthetic performance for 1-2 days longer than corals from the stable environment. Despite being separated by&lt;5 km, there was significant genetic differentiation among coral colonies (FST=0.206, p&lt;0.0001; nuclear ribosomal DNA), while Symbiodiniaceae were all Cladocopium sp. (ITS-type C15). Our study demonstrates consistent signatures of adaptation in growth and stress resistance in corals from naturally thermally variable habitats, suggesting that differences in the amount of thermal variability may be an important contributor to adaptive differentiation in reef building corals.

High salinity conveys thermotolerance in the coral model Aiptasia

The endosymbiosis between dinoflagellate algae of the genus Symbiodinium and stony corals provides the foundation of coral reef ecosystems. Coral bleaching, the expulsion of endosymbionts from the coral host tissue as a consequence of heat or light stress, poses a threat to reef ecosystem functioning on a global scale. Hence, a better understanding of the factors contributing to heat stress susceptibility and tolerance is needed. In this regard, some of the most thermotolerant corals live in particularly saline habitats, but possible effects of high salinity on thermotolerance in corals are anecdotal. Here we test the hypothesis that high salinity may lead to increased thermotolerance. We conducted a heat stress experiment at low, intermediate, and high salinities using a set of host-endosymbiont combinations of the coral model Aiptasia. As expected, all host-endosymbiont combinations showed reduced photosynthetic efficiency and endosymbiont loss during heat stress, but the severity of bleaching was significantly reduced with increasing salinities for one of the host-endosymbiont combinations. Our results show that higher salinities can convey increased thermotolerance in Aiptasia, although this effect seems to be dependent on the particular host strain and/or associated symbiont type. This finding may help explain the extraordinarily high thermotolerance of corals in high salinity environments, such as the Red Sea and the Persian/Arabian Gulf, and provides novel insight regarding factors that contribute to thermotolerance. Since our results are based on a salinity effect in symbiotic sea anemones, it remains to be determined whether this salinity effect can also be observed in stony corals.

Summary: High salinity can be a factor contributing to increased cnidarian thermal tolerance, as indicated by reduced algal endosymbiont loss and reduced photosynthetic impairment in the sea anemone Aiptasia.

The role of floridoside in osmoadaptation of coral-associated algal endosymbionts to high-salinity conditions

The endosymbiosis between Symbiodinium dinoflagellates and stony corals provides the foundation of coral reef ecosystems. The survival of these ecosystems is under threat at a global scale, and better knowledge is needed to conceive strategies for mitigating future reef loss. Environmental disturbance imposing temperature, salinity, and nutrient stress can lead to the loss of the Symbiodinium partner, causing so-called coral bleaching. Some of the most thermotolerant coral-Symbiodinium associations occur in the Persian/Arabian Gulf and the Red Sea, which also represent the most saline coral habitats. We studied whether Symbiodinium alter their metabolite content in response to high-salinity environments. We found that Symbiodinium cells exposed to high salinity produced high levels of the osmolyte 2-O-glycerol-α-d-galactopyranoside (floridoside), both in vitro and in their coral host animals, thereby increasing their capacity and, putatively, the capacity of the holobiont to cope with the effects of osmotic stress in extreme environments. Given that floridoside has been previously shown to also act as an antioxidant, this osmolyte may serve a dual function: first, to serve as a compatible organic osmolyte accumulated by Symbiodinium in response to elevated salinities and, second, to counter reactive oxygen species produced as a consequence of potential salinity and heat stress.

Acclimatization of symbiotic corals to mesophotic light environments through wavelength transformation by fluorescent protein pigments

The depth distribution of reef-building corals exposes their photosynthetic symbionts of the genus Symbiodinium to extreme gradients in the intensity and spectral quality of the ambient light environment. Characterizing the mechanisms used by the coral holobiont to respond to the low intensity and reduced spectral composition of the light environment in deeper reefs (greater than 20 m) is fundamental to our understanding of the functioning and structure of reefs across depth gradients. Here, we demonstrate that host pigments, specifically photoconvertible red fluorescent proteins (pcRFPs), can promote coral adaptation/acclimatization to deeper-water light environments by transforming the prevalent blue light into orange-red light, which can penetrate deeper within zooxanthellae-containing tissues; this facilitates a more homogeneous distribution of photons across symbiont communities. The ecological importance of pcRFPs in deeper reefs is supported by the increasing proportion of red fluorescent corals with depth (measured down to 45 m) and increased survival of colour morphs with strong expression of pcRFPs in long-term light manipulation experiments. In addition to screening by host pigments from high light intensities in shallow water, the spectral transformation observed in deeper-water corals highlights the importance of GFP-like protein expression as an ecological mechanism to support the functioning of the coral-Symbiodinium association across steep environmental gradients.

Genetic structure of coral-Symbiodinium symbioses on the world's warmest reefs

Corals in the Arabian/Persian Gulf (PAG) survive extreme sea temperatures (summer mean: >34°C), and it is unclear whether these corals have genetically adapted or physiologically acclimated to these conditions. In order to elucidate the processes involved in the thermal tolerance of PAG corals, it is essential to understand the connectivity between reefs within and outside of the PAG. To this end, this study set out to investigate the genetic structure of the coral, Platygyra daedalea, and its symbiotic algae in the PAG and neighbouring Gulf of Oman. Using nuclear markers (the ITS region and an intron of the Pax-C gene), this study demonstrates genetic divergence of P. daedalea on reefs within the thermally extreme PAG compared with those in the neighbouring Gulf of Oman. Isolation by distance of P. daedalea was supported by the ITS dataset but not the Pax-C intron. In addition, the symbiont community within the PAG was dominated by C3 symbionts, while the purportedly thermotolerant clade D was extremely rare and was common only at sites outside of the PAG. Analysis of the psbA^ncr indicates that the C3 variant hosted by P. daedalea in the PAG belongs to the newly described species, Symbiodinium thermophilum. The structuring of the coral and symbiont populations suggests that both partners of the symbiosis may contribute to the high bleaching thresholds of PAG corals. While limited gene flow has likely played a role in local adaptation within the PAG, it also indicates limited potential for natural export of thermal tolerance traits to reefs elsewhere in the Indian Ocean threatened by climate change.

Symbiont community stability through severe coral bleaching in a thermally extreme lagoon

Coral reefs are threatened by climate change as coral-algal symbioses are currently living close to their upper thermal limits. The resilience of the algal partner plays a key role in determining the thermal tolerance of the coral holobiont and therefore, understanding the acclimatory limits of present day coral-algal symbioses is fundamental to forecasting corals' responses to climate change. This study characterised the symbiont community in a highly variable and thermally extreme (Max = 37.5 °C, Min = 16.8 °C) lagoon located in the southern Persian/Arabian Gulf using next generation sequencing of ITS2 amplicons. Despite experiencing extreme temperatures, severe bleaching and many factors that would be expected to promote the presence of, or transition to clade D dominance, the symbiont communities of the lagoon remain dominated by the C3 variant, Symbiodinium thermophilum. The stability of this symbiosis across multiple genera with different means of symbiont transmission highlights the importance of Symbiodinium thermophilum for corals living at the acclimatory limits of modern day corals. Corals in this extreme environment did not undergo adaptive bleaching, suggesting they are living at the edge of their acclimatory potential and that this valuable source of thermally tolerant genotypes may be lost in the near future under climate change.

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

AIM

Coral reefs rely on the symbiosis between scleractinian corals and intracellular, photosynthetic dinoflagellates of the genus Symbiodinium making the assessment of symbiont diversity critical to our understanding of ecological resilience of these ecosystems. This study characterizes Symbiodinium diversity around the Arabian Peninsula, which contains some of the most thermally diverse and understudied reefs on Earth.

LOCATION

Shallow water coral reefs throughout the Red Sea (RS), Sea of Oman (SO), and Persian/Arabian Gulf (PAG).

METHODS

Next-generation sequencing of the ITS2 marker gene was used to assess Symbiodinium community composition and diversity comprising 892 samples from 46 hard and soft coral genera.

RESULTS

Corals were associated with a large diversity of Symbiodinium, which usually consisted of one or two prevalent symbiont types and many types at low abundance. Symbiodinium communities were strongly structured according to geographical region and to a lesser extent by coral host identity. Overall symbiont communities were composed primarily of species from clade A and C in the RS, clade A, C, and D in the SO, and clade C and D in the PAG, representing a gradual shift from C- to D-dominated coral hosts. The analysis of symbiont diversity in an Operational Taxonomic Unit (OTU)-based framework allowed the identification of differences in symbiont taxon richness over geographical regions and host genera.

MAIN CONCLUSIONS

Our study represents a comprehensive overview over biogeography and molecular diversity of Symbiodinium in the Arabian Seas, where coral reefs thrive in one of the most extreme environmental settings on the planet. As such our data will serve as a baseline for further exploration into the effects of environmental change on host-symbiont pairings and the identification and ecological significance of Symbiodinium types from regions already experiencing 'Future Ocean' conditions.

Temperature shapes coral-algal symbiosis in the South China Sea

With the increase in sea surface temperature (SST), scleractinian corals are exposed to bleaching threats but may possess certain flexibilities in terms of their associations with symbiotic algae. Previous studies have shown a close symbiosis between coral the and Symbiodinium; however, the spatial variation of the symbiosis and the attribution underlying are not well understood. In the present study, we examined coral-algal symbiosis in Galaxea fascicularis and Montipora spp. from three biogeographic regions across ~10° of latitude in the South China Sea. Analysis of similarities (ANOSIM) indicated a highly flexible coral-algal symbiosis in both G. fascicularis and Montipora spp. and canonical correspondence analysis (CCA) showed that temperature explained 83.2% and 60.1% of the explanatory subclade variations in G. fascicularis and Montipora spp., respectively, which suggested that temperature was the main environmental factor contributing to the diversity of Symbiodinium across the three regions. The geographic specificity of the Symbiodinium phylogeny was identified, revealing possible environmental selection across the three regions. These results suggest that scleractinian corals may have the ability to regulate Symbiodinium community structures under different temperatures and thus be able to adapt to gradual climate change.