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Scleractinian corals are capable of accumulating polycyclic aromatic hydrocarbons (PAHs) in reef environments; however, the mechanism behind their PAHs tolerance is unknown. This study investigated the occurrence and bioaccumulation of PAHs in coral reef ecosystems and examined the physiological responses induced by PAHs in coral hosts and their algal symbionts, the massive coral Galaxea fascicularis and branching coral Pocillopora damicornis. G. fascicularis had a higher PAHs accumulation capacity than P. damicornis. Both the coral hosts and algal symbionts preferentially accumulated acenaphthene, dibenzo(a,h)anthracene, and benzo(a)pyrene. The accumulated PAHs by G. fascicularis and P. damicornis hosts was accompanied by a reduction in detoxification ability. The accumulated PAHs could induce oxidative stress in P. damicorni hosts, thus G. fascicularis demonstrated a greater tolerance to PAHs compared to P. damicornis. Meanwhile, their algal symbionts had fewer physiological responses to accumulated PAHs than the coral hosts. Negative effects were not observed with benzo(a)pyrene. Taken together, these results suggest massive and branching scleractinian corals have different PAHs bioaccumulation and tolerance mechanisms, and indicate that long-term PAHs pollution could cause significant alterations of community structures in coral reef ecosystems., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The negative impacts of microplastic on reef-building corals are often attributed to the feeding responses to these particles. Although reactions to and ingestion of microplastic are frequently reported, a quantitative comparison to natural particles and of the factors influencing these responses is largely missing. Thus, this study aims to compare the feeding rates of corals to microplastic and natural particles, considering factors influencing these responses. Specifically, we I) studied the feeding responses of corals to microplastic, natural food, and non-food particles, II) examined the influence of biotic factors (i.e., biofilm on the particles and presence of natural food), III) evaluated species-specific differences in feeding responses to microplastic particles, and IV) applied a toxicodynamic model for species- and concentration-dependent risk assessments. We assessed the feeding responses of 11 coral species, spanning different life-history strategies and growth forms in experimental feeding trials. The results showed that the feeding responses of corals to microplastic differ from those to naturally occurring particles. Reactions to microplastic and natural food occurred equally often, while sand was more frequently rejected. Yet, the ingestion process was much more selective, and microplastic was ingested less frequently than natural food. The presence of a biofilm and natural food had activating effects on the feeding behavior of the corals on microplastic. Generally, coral species that exhibit a higher degree of heterotrophic feeding also reacted more often to microplastic. The species- and concentration-dependent toxicodynamic risk model built on these data reveals that most tested coral species are unlikely to be at risk under present environmental concentration levels. However, highly heterotrophic feeders, such as Blastomussa merleti, or generally vulnerable species, such as Pocillopora verrucosa, need special consideration. These findings help to better evaluate the responses of corals to microplastic and their risk in an increasingly polluted ocean., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

Reef-building corals (Scleractinia, Anthozoa, Cnidaria) are the keystone organisms of coral reefs, which constitute the most diverse marine ecosystems. Since the first decoded coral genome reported in 2011, about 40 reference genomes are registered as of 2023. Comparative genomic analyses of coral genomes have revealed genomic characters that may underlie unique biological characteristics and coral diversification. These include existence of genes for biosynthesis of mycosporine-like amino acids, loss of an enzyme necessary for cysteine biosynthesis in family Acroporidae, and lineage-specific gene expansions of DMSP lyase-like genes in the genus Acropora. While symbiosis with endosymbiotic photosynthetic dinoflagellates is a common biological feature among reef-building corals, genes associated with the intricate symbiotic relationship encompass not only those shared by many coral species, but also genes that were uniquely duplicated in each coral lineage, suggesting diversified molecular mechanisms of coral-algal symbiosis. Coral genomic data have also enabled detection of hidden, complex population structures of corals, indicating the need for species-specific, local-scale, carefully considered conservation policies for effective maintenance of corals. Consequently, accumulating coral genomic data from a wide range of taxa and from individuals of a species not only promotes deeper understanding of coral reef biodiversity, but also promotes appropriate and effective coral reef conservation. Considering the diverse biological traits of different coral species and accurately understanding population structure and genetic diversity revealed by coral genomic analyses during coral reef restoration planning could enable us to "archive" coral reef environments that are nearly identical to natural coral reefs., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. The infection of coral-associated bacteria by bacteriophages can modify bacterial ecological interactions, yet very little is known about phage functions in the holobiont. This gap stems from methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment from coral samples. Here, we introduce a size fractionation approach that increased bacterial and viral recovery in coral metagenomes by 9-fold and 2-fold, respectively, and enabled the assembly and binning of bacterial and viral genomes at relatively low sequencing coverage. We combined these viral genomes with those derived from 677 publicly available metagenomes, viromes, and bacterial isolates from stony corals to build a global coral virus database of over 20,000 viral genomic sequences spanning four viral realms. The tailed bacteriophage families Kyanoviridae and Autographiviridae were the most abundant, replacing groups formerly referred to as Myoviridae and Podoviridae, respectively. Prophage and CRISPR spacer linkages between these viruses and 626 bacterial metagenome-assembled genomes and bacterial isolates showed that most viruses infected Alphaproteobacteria, the most abundant class, and less abundant taxa like Halanaerobiia and Bacteroidia. A host-phage-gene network identified keystone viruses with the genomic capacity to modulate bacterial metabolic pathways and direct molecular interactions with eukaryotic cells. This study reveals the genomic basis of nested symbioses between bacteriophage, bacteria, and the coral host and its endosymbiotic algae., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Calcification in photosynthetic scleractinian corals is a complicated process that involves many different biological, chemical, and physical sub-processes that happen within and around the coral tissue. Identifying and quantifying the role of separate processes in vivo or in vitro is difficult or not possible. A computational model can facilitate this research by simulating the sub-processes independently. This study presents a spatio-temporal model of the calcification physiology, which is based on processes that are considered essential for calcification: respiration, photosynthesis, Ca 2＋ -ATPase, carbonic anhydrase. The model is used to test different hypotheses considering ion transport across the calicoblastic cells and Light Enhanced Calcification (LEC). It is also used to quantify the effect of ocean acidification (OA) on the Extracellular Calcifying Medium (ECM) and ATP-consumption of Ca 2＋ -ATPase. It was able to reproduce the experimental data of three separate studies and finds that paracellular transport plays a minor role compared to transcellular transport. In the model, LEC results from increased Ca 2＋ -ATPase activity in combination with increased metabolism. Implementing OA increases the concentration of CO 2 throughout the entire tissue, thereby increasing the availability of CO 3 - in the ECM. As a result, the model finds that calcification becomes more energy-demanding and the calcification rate increases., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Coral reefs are the most diverse marine ecosystems. However, coral cover has decreased worldwide due to natural disturbances, climate change, and local anthropogenic drivers. In recent decades, various genetic methods and molecular markers have been developed to assess genetic diversity, structure, and connectivity in different coral species to determine the vulnerability of their populations. This review aims to identify population genetic studies of scleractinian corals in the last decade (2010-2020), and the techniques and molecular markers used. Bibliometric analysis was conducted to identify journals and authors working in this field. We then calculated the number of genetic studies by species and ecoregion based on data obtained from 178 studies found in Scopus and Web of Science. Coral Reefs and Molecular Ecology were the main journals published population genetics studies, and microsatellites are the most widely used molecular markers. The Caribbean, Australian Barrier Reef, and South Kuroshio in Japan are among the ecoregions with the most population genetics data. In contrast, we found limited information about the Coral Triangle, a region with the highest biodiversity and key to coral reef conservation. Notably, only 117 (out of 1500 described) scleractinian coral species have genetic studies. This review emphasizes which coral species have been studied and highlights remaining gaps and locations where such data is critical for coral conservation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Sea cucumbers are important ecological engineers in marine ecosystems. However, the fishery demand of some species, especially large-epifaunal and commercially used (LEC) sea cucumbers, has risen drastically, resulting in serious depletion of local populations for many species. Despite this problem, basic ecological data on sea cucumbers, such as population densities and preferred habitats, are often still insufficient. Here, we report on the population densities of multiple LEC sea cucumber species, and their ambient benthic communities at eight sites around Okinawa Islands. Further, we discuss the correspondence between sea cucumber densities and the surrounding coral communities. Our results show two sites within national or quasi-national parks, Aka and Manza, where stricter rules have been placed on fisheries and land reclamation compared to other areas, had the highest and third highest sea cucumber population densities among sites, respectively. Holothuria atra was observed at all survey sites and made up the majority of sea cucumber populations at all sites except for Chatan and Sesoko, where Holothuria leucospilota and Stichopus chloronotus were most abundant, respectively. Regarding the relationships between benthic composition and LEC sea cucumber species, S. chloronotus was significantly correlated with dead corals, scleractinian corals, and coralline algae. As well, H . leucospilota had significant correlations with rubble. Although there were no significant correlations between any specific scleractinian coral genus and sea cucumber densities, S. chloronotus was marginally insignificant with Platygyra and Psammocora . Notably, medium- to highly valued species were sparse in our surveys, and most of them appeared at only one site. Additionally, at one site (Odo), only three LEC sea cucumber individuals were observed. Combining these facts with relatively low population densities around the Okinawa Islands compared to densities reported in previous research from the Indo-West Pacific Ocean region, we conclude that Okinawan LEC sea cucumber populations have been and are being impacted by high levels of direct ( e.g ., overexploitation, as well as coastal development) and indirect anthropogenic pressure ( e.g ., decreasing water quality). To address the current situation, repeated monitoring and more detailed investigations to reveal the drivers that determine LEC sea cucumber species aggregations and population densities are urgently needed, along with more robust management of remaining LEC sea cucumber populations., Competing Interests: James D. Reimer is an Academic Editor for PeerJ., (© 2022 Hamamoto et al.)

Using a standardized SNP array, we identified two populations of Acropora cervicornis and one population of A. palmata in the Caribbean coast of Colombia. San Andrés was the most genetically differentiated location for both species. An average pairwise F ST value of 0.131 and 0.050 between San Andrés and neighboring collection sites was estimated, for A. cervicornis and A. palmata, respectively. Based on population patterns of both acroporid species, we inferred that Magdalena River is not a barrier of genetic connectivity among Colombian populations. Genetic comparisons between the Colombian coast of Caribbean with other Caribbean locations agree with previous studies for both species , where four populations were identified in A. cervicornis and three in A. palmata. Our results support published bio-physical model predictions and highlight the Panama-Colombia gyre as a possible isolating mechanism within the western Caribbean. However, the genetic diversity in both species was about half (mean HE per site = 0.321 in A. palmata and 0.369 in A. cervicornis ) than previous estimates in acroporid populations in the Caribbean. The lower genetic diversity as well their relative isolation and high levels of reef degradation may be of particular conservation concern that may require species-specific management coupled with science-based restoration efforts., Competing Interests: The authors declare there are no competing interests., (©2022 García-Urueña et al.)

The microplastic pollution has become a worldwide ecological concerns and imposed negative impacts on the coral reef ecosystems. In the present study, the distribution and characteristics of microplastics in the seawater, marine sediment and three scleractinian coral species (Pocillopora damicornis, Galaxea fascicularis, and Porites lutea) at five representative atolls in the Xisha Islands were investigated. The average microplastic abundances in the seawater and marine sediment were 9.5 ± 3.7 particles L -1 and 280.9 ± 231.9 particles kg -1 (dry weight), and the average contents of microplastics in P. damicornis, G. fascicularis and P. lutea were 0.9 ± 0.5 particles cm -2 , 1.2 ± 0.6 particles cm -2 , and 2.5 ± 1.6 particles cm -2 , respectively. There were no significant correlations for the microplastic concentration between the reef environment and the corals. These results infer that the microplastic pollution is severe in the coral reef ecosystem in the Xisha Islands, and scleractinian corals could enrich microplastics from the reef environment. In addition, more than 80% of the microplastics in the seawater, marine sediment and corals were smaller than 2 mm, and the most common types of microplastics were cellophane (61.13%) and polyethylene terephthalate (33.49%). Black and fibers were the most common color and shape of the microplastics in the seawater and marine sediment, respectively. The microplastics in transparent color, film shape and small size (<2 mm) were highly accumulated in corals. Besides, cluster analysis showed that significant difference of microplastic characteristics existed between the corals and the reef environment, and the features of enriched microplastics among three coral species were also different. Moreover, P. lutea exhibited a stronger ability in enriching microplastics than G. fascicularis and P. damicornis. These results suggest that the microplastic-enriching capacities of scleractinian corals are species-specific, and species acclimated to microplastic pollution might become predominant in future coral community., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The distribution and functions of neurons in scleractinian corals remain largely unknown. This study focused on the Arg-Phe amide family of neuropeptides (RFamides), which have been shown to be involved in a variety of biological processes in animals, and performed molecular identification and characterization in the adult scleractinian coral Euphyllia ancora. The deduced amino acid sequence of the identified RFamide preprohormone was predicted to contain 20 potential neuropeptides, including 1 Pro-Gly-Arg-Phe (PGRF) amide and 15 Gln-Gly-Arg-Phe (QGRF) amide peptides. Tissue distribution analysis showed that the level of transcripts in the tentacles was significantly higher than that in other polyp tissues. Immunohistochemical analysis with the FMRFamide antibody showed that RFamide neurons were mainly distributed in the epidermis of the tentacles and mouth with pharynx. Treatment of E. ancora polyps with synthetic QGRFamide peptides induced polyp contraction. The induction of polyp contraction by QGRFamide peptide treatment was also observed in another scleractinian coral, Stylophora pistillata. These results strongly suggested that RFamides play a role in the regulation of polyp contraction in adult scleractinians., (Copyright © 2021. Published by Elsevier Inc.)

With coral reefs declining globally, resilience of these ecosystems hinges on successful coral recruitment. However, knowledge of the acclimatory and/or adaptive potential in response to environmental challenges such as ocean acidification (OA) in earliest life stages is limited. Our combination of physiological measurements, microscopy, computed tomography techniques and gene expression analysis allowed us to thoroughly elucidate the mechanisms underlying the response of early-life stages of corals, together with their algal partners, to the projected decline in oceanic pH. We observed extensive physiological, morphological and transcriptional changes in surviving recruits, and the transition to a less-skeleton/more-tissue phenotype. We found that decreased pH conditions stimulate photosynthesis and endosymbiont growth, and gene expression potentially linked to photosynthates translocation. Our unique holistic study discloses the previously unseen intricate net of interacting mechanisms that regulate the performance of these organisms in response to OA.

β-Glucosidase is a microbial cellulose multienzyme that plays an important role in the regulation of the entire cellulose hydrolysis process, which is the rate-limiting step in bacterial carbon cycling in marine environments. Despite its importance in coral reefs, the diversity of β-glucosidase-producing bacteria, their genes, and enzymatic characteristics are poorly understood. In this study, 87 β-glucosidase-producing cultivable bacteria were screened from 6 genera of corals. The isolates were assigned to 21 genera, distributed among three groups: Proteobacteria, Firmicutes, and Actinobacteria. In addition, metagenomics was used to explore the genetic diversity of bacterial β-glucosidase enzymes associated with scleractinian corals, which revealed that these enzymes mainly belong to the glycosidase hydrolase family 3 (GH3). Finally, a novel recombinant β-glucosidase, referred to as Mg9373, encompassing 670 amino acids and a molecular mass of 75.2 kDa, was classified as a member of the GH3 family and successfully expressed and characterized. Mg9373 exhibited excellent tolerance to ethanol, NaCl, and glucose. Collectively, these results suggest that the diversity of β-glucosidase-producing bacteria and genes associated with scleractinian corals is high and novel, indicating great potential for applications in the food industry and agriculture.

One of the most conserved traits in the evolution of biomineralizing organisms is the taxon-specific selection of skeletal minerals. All modern scleractinian corals are thought to produce skeletons exclusively of the calcium-carbonate polymorph aragonite. Despite strong fluctuations in ocean chemistry (notably the Mg/Ca ratio), this feature is believed to be conserved throughout the coral fossil record, spanning more than 240 million years. Only one example, the Cretaceous scleractinian coral Coelosmilia (ca. 70 to 65 Ma), is thought to have produced a calcitic skeleton. Here, we report that the modern asymbiotic scleractinian coral Paraconotrochus antarcticus living in the Southern Ocean forms a two-component carbonate skeleton, with an inner structure made of high-Mg calcite and an outer structure composed of aragonite. P. antarcticus and Cretaceous Coelosmilia skeletons share a unique microstructure indicating a close phylogenetic relationship, consistent with the early divergence of P. antarcticus within the Vacatina (i.e., Robusta) clade, estimated to have occurred in the Mesozoic (ca. 116 Mya). Scleractinian corals thus join the group of marine organisms capable of forming bimineralic structures, which requires a highly controlled biomineralization mechanism; this capability dates back at least 100 My. Due to its relatively prolonged isolation, the Southern Ocean stands out as a repository for extant marine organisms with ancient traits., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

The genus Acropora comprises the most diverse and abundant scleractinian corals (Anthozoa, Cnidaria) in coral reefs, the most diverse marine ecosystems on Earth. However, the genetic basis for the success and wide distribution of Acropora are unknown. Here, we sequenced complete genomes of 15 Acropora species and 3 other acroporid taxa belonging to the genera Montipora and Astreopora to examine genomic novelties that explain their evolutionary success. We successfully obtained reasonable draft genomes of all 18 species. Molecular dating indicates that the Acropora ancestor survived warm periods without sea ice from the mid or late Cretaceous to the Early Eocene and that diversification of Acropora may have been enhanced by subsequent cooling periods. In general, the scleractinian gene repertoire is highly conserved; however, coral- or cnidarian-specific possible stress response genes are tandemly duplicated in Acropora. Enzymes that cleave dimethlysulfonioproprionate into dimethyl sulfide, which promotes cloud formation and combats greenhouse gasses, are the most duplicated genes in the Acropora ancestor. These may have been acquired by horizontal gene transfer from algal symbionts belonging to the family Symbiodiniaceae, or from coccolithophores, suggesting that although functions of this enzyme in Acropora are unclear, Acropora may have survived warmer marine environments in the past by enhancing cloud formation. In addition, possible antimicrobial peptides and symbiosis-related genes are under positive selection in Acropora, perhaps enabling adaptation to diverse environments. Our results suggest unique Acropora adaptations to ancient, warm marine environments and provide insights into its capacity to adjust to rising seawater temperatures., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Background: Sexual reproduction of scleractinians has captured the attention of researchers and the general public for decades. Although extensive ecological data has been acquired, underlying molecular and cellular mechanisms remain largely unknown. In this study, to better understand mechanisms underlying gametogenesis, we isolated ovaries and testes at different developmental phases from a gonochoric coral, Euphyllia ancora, and adopted a transcriptomic approach to reveal sex- and phase-specific gene expression profiles. In particular, we explored genes associated with oocyte development and maturation, spermiogenesis, sperm motility / capacitation, and fertilization., Results: 1.6 billion raw reads were obtained from 24 gonadal samples. De novo assembly of trimmed reads, and elimination of contigs derived from symbiotic dinoflagellates (Symbiodiniaceae) and other organisms yielded a reference E. ancora gonadal transcriptome of 35,802 contigs. Analysis of 4 developmental phases identified 2023 genes that were differentially expressed during oogenesis and 678 during spermatogenesis. In premature/mature ovaries, 631 genes were specifically upregulated, with 538 in mature testes. Upregulated genes included those involved in gametogenesis, gamete maturation, sperm motility / capacitation, and fertilization in other metazoans, including humans. Meanwhile, a large number of genes without homology to sequences in the SWISS-PROT database were also observed among upregulated genes in premature / mature ovaries and mature testes., Conclusions: Our findings show that scleractinian gametogenesis shares many molecular characteristics with that of other metazoans, but it also possesses unique characteristics developed during cnidarian and/or scleractinian evolution. To the best of our knowledge, this study is the first to create a gonadal transcriptome assembly from any scleractinian. This study and associated datasets provide a foundation for future studies regarding gametogenesis and differences between male and female colonies from molecular and cellular perspectives. Furthermore, our transcriptome assembly will be a useful reference for future development of sex-specific and/or stage-specific germ cell markers that can be used in coral aquaculture and ecological studies.

Metal pollution is nowadays a serious threat worldwide for ecosystem and human health. Despite that, there is still a paucity of data on metal impact on coral reef ecosystems. Herein, the levels of eleven metals (Mn, Zn, Cu, Cr, Co, Ni, V, As, Cd, Hg, Pb) were assessed in surface sediments, seawater samples, Scleractinian corals (tissue and skeleton) and their algal symbionts collected from Kharg and Lark coral reefs in the Persian Gulf, Iran. At Kharg, surface sediments and seawater showed higher concentrations of metals than Lark, attributable to the higher metal loads and petrochemical activities in the area. Sediment quality guidelines indicated Hg as a serious threat to biota both at Kharg and Lark. Accordingly, metals bioaccumulation and bioconcentration was higher in corals from Kharg relatively to Lark Island. Interestingly, as supported by values of BCFs and BSAFs, metal accumulation was higher in coral tissues in respect to skeletons, and in zooxanthellae relatively to coral tissues at both coral reefs. Differential metal bioaccumulation was found among Scleractinian species, indicating that corals have distinct selectivity for assimilating metals from ambient sediments and seawater. Overall, metal accumulation in corals and zooxanthellae is an appropriate tool for environmental monitoring studies in coral reefs. Noteworthy, the use of Porites lutea, among Scleractinian corals, seems to be as a good bioindicator in monitoring studies of metal pollution., (Copyright © 2018. Published by Elsevier B.V.)

Background: Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still a matter of debate. Indeed, the relative contribution of host and environment and especially thermal regime in shaping the microbial communities should be examined carefully to evaluate the potential role of symbionts for holobiont adaptation in the context of global changes. We used the sessile, long-lived, symbiotic and environmentally sensitive reef-building coral Pocillopora damicornis to address these issues., Results: We sampled Pocillopora damicornis colonies corresponding to two different mitochondrial lineages in different geographic areas displaying different thermal regimes: Djibouti, French Polynesia, New Caledonia, and Taiwan. The community composition of bacteria and the algal endosymbiont Symbiodinium were characterized using high-throughput sequencing of 16S rRNA gene and internal transcribed spacer, ITS2, respectively. Bacterial microbiota was very diverse with high prevalence of Endozoicomonas, Arcobacter, and Acinetobacter in all samples. While Symbiodinium sub-clade C1 was dominant in Taiwan and New Caledonia, D1 was dominant in Djibouti and French Polynesia. Moreover, we also identified a high background diversity (i.e., with proportions < 1%) of A1, C3, C15, and G Symbiodinum sub-clades. Using redundancy analyses, we found that the effect of geography was very low for both communities and that host genotypes and temperatures differently influenced Symbiodinium and bacterial microbiota. Indeed, while the constraint of host haplotype was higher than temperatures on bacterial composition, we showed for the first time a strong relationship between the composition of Symbiodinium communities and minimal sea surface temperatures., Conclusion: Because Symbiodinium assemblages are more constrained by the thermal regime than bacterial communities, we propose that their contribution to adaptive capacities of the holobiont to temperature changes might be higher than the influence of bacterial microbiota. Moreover, the link between Symbiodinium community composition and minimal temperatures suggests low relative fitness of clade D at lower temperatures. This observation is particularly relevant in the context of climate change, since corals will face increasing temperatures as well as much frequent abnormal cold episodes in some areas of the world.

Coral reef ecosystems are among the most biodiverse habitats in the marine realm. They not only contribute with a plethora of ecosystem services, but they also are beneficial to humankind via nurturing marine fisheries and sustaining recreational activities. We will discuss the biology of coral reefs and their ecophysiology including the complex bacterial microbiota associated with them.

The future of coral reefs under increasing CO 2 depends on their capacity to recover from disturbances. To predict the recovery potential of coral communities that are fully acclimatized to elevated CO 2 , we compared the relative success of coral recruitment and later life stages at two volcanic CO 2 seeps and adjacent control sites in Papua New Guinea. Our field experiments showed that the effects of ocean acidification (OA) on coral recruitment rates were up to an order of magnitude greater than the effects on the survival and growth of established corals. Settlement rates, recruit and juvenile densities were best predicted by the presence of crustose coralline algae, as opposed to the direct effects of seawater CO 2 Offspring from high CO 2 acclimatized parents had similarly impaired settlement rates as offspring from control parents. For most coral taxa, field data showed no evidence of cumulative and compounding detrimental effects of high CO 2 on successive life stages, and three taxa showed improved adult performance at high CO 2 that compensated for their low recruitment rates. Our data suggest that severely declining capacity for reefs to recover, due to altered settlement substrata and reduced coral recruitment, is likely to become a dominant mechanism of how OA will alter coral reefs., (© 2017 The Author(s).)

Critical to determining vulnerability or resilience of reef corals to Ocean Acidification (OA) is a clearer understanding of the extent to which corals can control carbonate chemistry in their Extracellular Calcifying Medium (ECM) where the CaCO 3 skeleton is produced. Here, we employ a mathematical framework to calculate ECM aragonite saturation state (Ω arag.(ECM) ) and carbonate system ion concentration using measurements of calcification rate, seawater characteristics (temperature, salinity and pH) and ECM pH (pH (ECM) ). Our calculations of ECM carbonate chemistry at current-day seawater pH, indicate that Ω arag.(ECM) ranges from ∼10 to 38 (mean 20.41), i.e. about 5 to 6-fold higher than seawater. Accordingly, Dissolved Inorganic Carbon (DIC) and Total Alkalinity (TA) were calculated to be around 3 times higher in the ECM than in seawater. We also assessed the effects of acidification on ECM chemical properties of the coral Stylophora pistillata. At reduced seawater pH our calculations indicate that Ω arag.(ECM) remains almost constant. DIC (ECM) and TA (ECM) gradually increase as seawater pH declines, reaching values about 5 to 6-fold higher than in seawater, respectively for DIC and TA. We propose that these ECM characteristics buffer the effect of acidification and explain why certain corals continue to produce CaCO 3 even when seawater chemistry is less favourable., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Marked shifts in the composition of coral assemblages are occurring at many locations, but it is unknown whether these are permanent shifts reinforced by patterns of population replenishment. This study examined the composition of juvenile coral assemblages across the United Arab Emirates (UAE). Densities of juvenile corals varied significantly among locations, but were highest where coral cover was highest. Juvenile coral assemblages within the Persian Gulf were dominated by Porites, while no Acropora were recorded. We expect therefore, continued declines in Acropora abundance, while observed dominance of Porites is likely to persist. In the Oman Sea, Pocillopora was the dominant juvenile coral, with Acropora and Stylophora also recorded. This study shows that taxonomic differences in replenishment are reinforcing temporal shifts in coral composition within the southern Persian Gulf, but not in the Oman Sea. Differences in environmental conditions and disturbance regimes likely explain the divergent responses between regions., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Roughly 240 million years ago (Ma), scleractinian corals rapidly expanded and diversified across shallow marine environments. The main driver behind this evolution is uncertain, but the ecological success of modern reef-building corals is attributed to their nutritional symbiosis with photosynthesizing dinoflagellate algae. We show that a suite of exceptionally preserved Late Triassic (ca. 212 Ma) coral skeletons from Antalya (Turkey) have microstructures, carbonate 13 C/ 12 C and 18 O/ 16 O, and intracrystalline skeletal organic matter 15 N/ 14 N all indicating symbiosis. This includes species with growth forms conventionally considered asymbiotic. The nitrogen isotopes further suggest that their Tethys Sea habitat was a nutrient-poor, low-productivity marine environment in which photosymbiosis would be highly advantageous. Thus, coral-dinoflagellate symbiosis was likely a key driver in the evolution and expansion of shallow-water scleractinians.

Coral reefs maintain extraordinary biodiversity and provide protection from tsunamis and storm surge, but inshore coral reef health is degrading in many regions due to deteriorating water quality. Deconvolving natural and anthropogenic changes to water quality is hampered by the lack of long term, dated water quality data but such records are required for forward modelling of reef health to aid their management. Reef corals provide an excellent archive of high resolution geochemical (trace element) proxies that can span hundreds of years and potentially provide records used through the Holocene. Hence, geochemical proxies in corals hold great promise for understanding changes in ancient water quality that can inform broader oceanographic and climatic changes in a given region. This article reviews and highlights the use of coral-based trace metal archives, including metal transported from rivers to the ocean, incorporation of trace metals into coral skeletons and the current 'state of the art' in utilizing coral trace metal proxies as tools for monitoring various types of local and regional source-specific pollution (river discharge, land use changes, dredging and dumping, mining, oil spills, antifouling paints, atmospheric sources, sewage). The three most commonly used coral trace element proxies (i.e., Ba/Ca, Mn/Ca, and Y/Ca) are closely associated with river runoff in the Great Barrier Reef, but considerable uncertainty remains regarding their complex biogeochemical cycling and controlling mechanisms. However, coral-based water quality reconstructions have suffered from a lack of understanding of so-called vital effects and early marine diagenesis. The main challenge is to identify and eliminate the influence of extraneous local factors in order to allow accurate water quality reconstructions and to develop alternate proxies to monitor water pollution. Rare earth elements have great potential as they are self-referencing and reflect basic terrestrial input., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Corals are mixotrophs: they are able to fix inorganic carbon through the activity of their symbiotic dinoflagellates and to gain nitrogen from predation on plankton and uptake of dissolved organic and inorganic nutrients. They also live in close association with diverse diazotrophic communities, inhabiting their skeleton, tissue and mucus layer, which are able to fix dinitrogen (N2). The quantity of fixed N2 transferred to the corals and its distribution within coral compartments as well as the quantity of nitrogen assimilated through the ingestion of planktonic diazotrophs are still unknown. Here, we quantified nitrogen assimilation via (i) N2 fixation by symbiont diazotrophs, (ii) ingestion of cultured unicellular diazotrophs and (iii) ingestion of natural planktonic diazotrophs. We estimate that the ingestion of diazotrophs provides 0.76±0.15 µg N cm(-2) h(-1), suggesting that diazotrophs represent a non-negligible source of nitrogen for scleractinian corals., (© 2016. Published by The Company of Biologists Ltd.)

We report here an interannual survey (2006-2012) of coral cover in the northwestern lagoon of New Caledonia, to assess the impact of an important dredging operation (August 2008-February 2010) associated with the construction of the largest nickel mining site in the Pacific. A BACI (Before-After Control-Impact) analysis failed to detect any significant interaction between period (before, during, and after dredging) and the category of the stations (impact vs. control). Among the 31 stations surveyed, only seven showed decreasing coral cover during the study period, mainly due to a decline in Acroporidae. However, the relationship between the dredging and this decrease was highly plausible only for one station, situated 0.9km from the dredging site. High hydrodynamism in the study area, the abundance of resistant corals and efficient protective measures during the dredging operation might explain these localised and limited impacts., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Transcription factors encoded by the Dmrt gene family regulate multiple aspects of animal reproduction. Most studies investigating the Dmrt gene family were conducted in model organisms from bilateral species, with a particular emphasis on gene function in male sex determination. It is still unclear whether the E. ancora Dmrt (EaDmrt) genes found in basal metazoans such as cnidarians share similar characteristics with orthologs in other metazoans. In this study, seven full Dmrt gene transcript sequences for a gonochoric coral, Euphyllia ancora (phylum: Cnidaria; class: Anthozoa), were obtained through transcriptome data mining, RT-PCR analysis, rapid amplification of cDNA ends, and sequencing. These EaDmrts were subjected to quantitative assays measuring temporal and tissue-specific expression. Results demonstrated a unique gene expression pattern for EaDmrtE, which is enriched in female germ cells during the spawning season. Based on the phylogenetic analyses performed across the homologous Dmrt genes in metazoans, we found that the female-specific EaDmrtE gene is not related to the DM1 gene of Acropora spp. coral nor to Dmrt1 of vertebrates, which are involved in sexual reproduction, especially in sex determination (vertebrate Dmrt1). Additionally, high levels of EaDmrtE transcripts detected in unfertilized mature eggs are retained in newly formed zygotes but decrease during embryonic development. We suggest that the newly discovered gene may play a role in oogenesis and early embryogenesis as a maternal factor in corals. Therefore, the sexual reproduction-associated Dmrt gene(s) should have arisen in cnidarians and might have evolved multiple times in metazoans., (© 2016 by the Society for the Study of Reproduction, Inc.)

The symbiosis between corals and dinoflagellates promotes the rapid growth of corals in shallow tropical oceans, and the high overall productivity of coral reefs. The aim of this study was to quantify and understand variation in carbon acquisition and allocation among coral species. We measured multiple physiological traits (including symbiont density, calcification, photosynthesis and tissue composition) for the same coral fragments to facilitate direct comparisons between species (Stylophora pistillata, Pocillopora damicornis, Galaxea fascicularis, Turbinaria reniformis and Acropora sp.). Tissue protein content was highly sensitive to the availability of particulate food, increasing in fed colonies of all species. Despite among-species variation in physiology, and consistent effects of feeding on some traits, overall energy allocation to tissue compared with skeleton growth did not depend on food availability. Extrapolating from our results, estimated whole-assemblage carbon uptake varied >20-fold across different coral assemblages, but this variation was largely driven by differences in the tissue surface area of different colony morphologies, rather than by differences in surface-area-specific physiological rates. Our results caution against drawing conclusions about reef productivity based solely on physiological rates measured per unit tissue surface area. Understanding the causes and consequences of among-species variation in physiological energetics provides insight into the mechanisms that underlie the fluxes of organic matter within reefs, and between reefs and the open ocean., (© 2015. Published by The Company of Biologists Ltd.)

We report variation in the size-structure of three coral taxa in the Society Islands (French Polynesia) using a hierarchical sampling design that integrates the regional (among three islands: Moorea, Raiatea, Tahiti), island (among three locations around each island), and local levels (among three depths: 6, 12, 18 m, at each location). All coral taxa exhibited strong heterogeneity in their size-structure, with marked variation among depths, locations, and islands. Porites spp. and Acropora globiceps populations at 6 m depth were dominated by smaller size classes compared to other depths. Regional-scale variation was particularly evident for Pocillopora meandrina and A. globiceps, with a higher proportion of smaller colonies found at Raiatea, probably as a result of recent cyclones followed by higher recruitment rates. Porites spp. populations were characterized by a preponderance of larger colonies, and greater size ranges compared to the other two taxa., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

As anthropogenic climate change is an ongoing concern, scientific investigations on its impacts on coral reefs are increasing. Although impacts of combined ocean acidification (OA) and temperature stress (T) on reef-building scleractinian corals have been studied at the genus, species and population levels, there are little data available on how individual corals respond to combined OA and anomalous temperatures. In this study, we exposed individual colonies of Acropora digitifera, Montipora digitata and Porites cylindrica to four pCO2-temperature treatments including 400 μatm-28 °C, 400 μatm-31 °C, 1000 μatm-28 °C and 1000 μatm-31 °C for 26 days. Physiological parameters including calcification, protein content, maximum photosynthetic efficiency, Symbiodinium density, and chlorophyll content along with Symbiodinium type of each colony were examined. Along with intercolonial responses, responses of individual colonies versus pooled data to the treatments were investigated. The main results were: 1) responses to either OA or T or their combination were different between individual colonies when considering physiological functions; 2) tolerance to either OA or T was not synonymous with tolerance to the other parameter; 3) tolerance to both OA and T did not necessarily lead to tolerance of OA and T combined (OAT) at the same time; 4) OAT had negative, positive or no impacts on physiological functions of coral colonies; and 5) pooled data were not representative of responses of all individual colonies. Indeed, the pooled data obscured actual responses of individual colonies or presented a response that was not observed in any individual. From the results of this study we recommend improving experimental designs of studies investigating physiological responses of corals to climate change by complementing them with colony-specific examinations., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Pollution by heavy metals remains today an important threat to the health of humans and ecosystems, but there is still a paucity of data on the response of early life stages of key organisms. In this context, the present work assessed the fertilization success rate of two Acropora species (A. cytherea and A. pulchra) from the French Polynesia reefs exposed to six increasing copper concentrations in seawater. The two species showed a relatively high tolerance to copper (4h30-EC50 was 69.4 ± 4.8 μg L(-1) and 75.4 ± 6.4 μg L(-1) for A. cytherea and A. pulchra, respectively). As Cu concentration increases, an increasing proportion of deformed embryos was recorded (67.6% and 58.5% for A. cytherea and A. pulchra, respectively, at 220 μg Cu L(-1)). These results demonstrated thus, that high levels of copper could negatively impair the normal fertilization process of coral gametes and therefore alter the renewal of coral populations. Since the two Acropora species investigated in this study displayed a high resistance to copper, these results should be considered in the context of multiple stressors associated with climate change, where rising temperature or ocean acidification may significantly exacerbate copper toxicity., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Zooxanthellate cnidarians are trophically complex, relying on both autotrophy and heterotrophy. Although several aspects of heterotrophy have been studied in these organisms, information linking prey capture with digestion is still missing. We used prey-specific PCR-based tools to assess feeding and prey digestion of two zooxanthellate cnidarians - the tropical sea anemone Aiptasia sp. and the scleractinian coral Oculina arbuscula. Prey DNA disappeared rapidly for the initial 1-3 days, whereas complete digestion of prey DNA required up to 10 days in O. arbuscula and 5 or 6 days in Aiptasia sp. depending on prey species. These digestion times are considerably longer than previously reported from microscopy-based examination of zooxanthellate cnidarians and prey DNA breakdown in other marine invertebrates, but similar to prey DNA breakdown reported from terrestrial invertebrates such as heteroptera and spiders. Deprivation of external prey induced increased digestion rates during the first days after feeding in O. arbuscula, but after 6 days of digestion, there were no differences in the remaining prey levels in fed and unfed corals. This study indicates that prey digestion by symbiotic corals may be slower than previously reported and varies with the type of prey, the cnidarian species and its feeding history. These observations have important implications for bioenergetic and trophodynamic studies on zooxanthellate cnidarians., (© 2013 John Wiley & Sons Ltd.)

Scleractinian corals vary in response to rapid shifts in the marine environment and changes in reef community structure post-disturbance reveal a clear relationship between coral performance and morphology. With exceptions, massive corals are thought to be more tolerant and branching corals more vulnerable to changing environmental conditions, notably thermal stress. The typical responses of massive and branching coral taxa, respectively, are well documented; however, the biological and functional characteristics that underpin this variation are not well understood. We address this gap by comparing multiple biological attributes that are correlated with skeletal architecture in two perforate (having porous skeletal matrices with intercalating tissues) and two imperforate coral species (Montipora aequituberculata, Porites lobata, Pocillopora damicornis, and Seriatopora hystrix) representing three morphotypes. Our results reveal inherent biological heterogeneity among corals and the potential for perforate skeletons to create complex, three-dimensional internal habitats that impact the dynamics of the symbiosis. Patterns of tissue thickness are correlated with the concentration of symbionts within narrow regions of tissue in imperforate corals versus broad distribution throughout the larger tissue area in perforate corals. Attributes of the perforate and environmentally tolerant P. lobata were notable, with tissues ∼5 times thicker than in the sensitive, imperforate species P. damicornis and S. hystrix. Additionally, P. lobata had the lowest baseline levels of superoxide and Symbiodinium that provisioned high levels of energy. Given our observations, we hypothesize that the complexity of the visually obscured internal environment has an impact on host-symbiont dynamics and ultimately on survival, warranting further scientific investigation., (Copyright © 2013 Elsevier GmbH. All rights reserved.)

Osmotic stress represents a limiting physical parameter for marine organisms and especially for sessile scleractinian corals which are known to be basically stenohaline and osmoconformers. The salinity changes may cause important cellular damage since corals lack any developed physiological regulatory system. One mechanism of reaction to deleterious conditions is the rapid increase of the induction of heat shock proteins. This study highlights the modulation of the expression of a mitochondrial heat shock protein, such as the chaperonin Hsp60, in the animal tissues of the scleractinian coral Seriatopora caliendrum under three salinity scenarios (hypersalinity of 45 ppt, hyposalinity of 25 ppt and extreme hyposalinity of 15 ppt). The study was performed during the time course of a 2-day period and accompanied also by the assessment of the coral health condition. For each salinity stress S. caliendrum responds differently at the morphological and cellular levels, since the Hsp60 exhibited specific patterns of expression and the coral showed different tissue appearance. Furthermore, the response reflects the severity and exposure length of the disturbance. However, the results indicate that S. caliendrum seems able to tolerates high salinity better than low salinity. In particular, in extreme hyposalinity conditions, a considerable gradual down-regulation of Hsp60 was detected accompanied by necrosis and degradation of the coral tissues. The study suggests that Hsp60 may be involved in the mechanisms of cellular response to stress caused by exposure to adverse salinity., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

The functional composition of reef fish assemblages is highly conserved across large biogeographic areas, but it is unknown whether assembly rules hold at biogeographical and environmental extremes for coral reefs. This study examined the functional composition of butterflyfishes in the Persian Gulf, Musandam Peninsula, and Gulf of Oman. Only five species of butterflyfishes were recorded during this study, and mostly just in the Gulf of Oman. Unlike most locations in the Indo-Pacific where butterflyfish assemblages are dominated by obligate corallivores, the only obligate corallivore recorded, Chaetodon melapterus, was rare or absent at all locations. The most common and widespread species was Chaetodon nigropunctatus, which is shown to be a facultative corallivore. The diversity of butterflyfishes in the Persian Gulf is likely to have been constrained by its' biogeographical history and isolation, but functional composition appears to be further affected by limited abundance of prey corals and harsh environmental conditions., (Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.)

Three species of cryptochirid crabs, obligatory symbionts of scleractinian corals, have so far been recorded from Brazil:Troglocarcinus corallicola,Opecarcinus hypostegusandKroppcarcinus siderastreicola. All three genera are monospecific. Individuals belonging to an undescribed species ofTroglocarcinus, here described asT. hirsutussp. nov., were found associated with colonies ofMussismiliafrom Bahia State, northeastern region of Brazil. The new species is distinguished from its congener mainly by a carapace with several large spines delimiting the protogastric and mesogastric regions, sternite of first pereopod with setae and third pleopod of female being uniramous or biramous. An emendation to the diagnosis of the monospecificTroglocarcinusis proposed. http://zoobank.org/urn:lsid:zoobank.org:pub:0FA03021-69A6-4F93-AA0A-6451BC6D2DE4 [ABSTRACT FROM AUTHOR]

Spatial aggregation among strong competitors has been identified as a putative mechanism promoting the coexistence of weak competitors in intensely competitive communities. With notable exceptions in plant communities, few investigators have tested this hypothesis experimentally. In this study, we manipulated the spatial arrangement of corals to test whether within-patch aggregation of a strong coral competitor enhances the success of a weaker coral competitor. Corals grown in simple aggregated arrangements, where the number and type of competitors were held constant, grew almost twice as much as those in non aggregated arrangements. These growth results suggest that species coexistence is promoted by aggregation within competitive neighborhoods. Thus spatial aggregation may be one of several important mechanisms contributing to the persistence of weak competitors and species coexistence on coral reefs. [ABSTRACT FROM AUTHOR]