Search

ABSTRACT Coral reefs are experiencing unprecedented loss in coral cover due to increased incidence of disease and bleaching events. Thus, understanding mechanisms of disease susceptibility and resilience, which vary by species, is important. In this regard, untargeted metabolomics serves as an important hypothesis-building tool enabling the delineation of molecular factors underlying disease susceptibility or resilience. In this study, we characterize metabolomes of four species of visually healthy stony corals, including Meandrina meandrites, Orbicella faveolata, Colpophyllia natans, and Montastraea cavernosa, collected at least a year before stony coral tissue loss disease reached the Dry Tortugas, Florida, and demonstrate that both symbiont and host-derived biochemical pathways vary by species. Metabolomes of Meandrina meandrites displayed minimal intraspecies variability and the highest biological activity against coral pathogens when compared to other species in this study. The application of advanced metabolite annotation methods enabled the delineation of several pathways underlying interspecies variability. Specifically, endosymbiont-derived vitamin E family compounds, betaine lipids, and host-derived acylcarnitines were among the top predictors of interspecies variability. Since several metabolite features that contributed to inter- and intraspecies variation are synthesized by the endosymbiotic Symbiodiniaceae, which could be a major source of these compounds in corals, our data will guide further investigations into these Symbiodiniaceae-derived pathways.IMPORTANCEPrevious research profiling gene expression, proteins, and metabolites produced during thermal stress have reported the importance of endosymbiont-derived pathways in coral bleaching resistance. However, our understanding of interspecies variation in these pathways among healthy corals and their role in diseases is limited. We surveyed the metabolomes of four species of healthy corals with differing susceptibilities to the devastating stony coral tissue loss disease and applied advanced annotation approaches in untargeted metabolomics to determine the interspecies variation in host and endosymbiont-derived pathways. Using this approach, we propose the survey of immune markers such as vitamin E family compounds, acylcarnitines, and other metabolites to infer their role in resilience to coral diseases. As time-resolved multi-omics datasets are generated for disease-impacted corals, our approach and findings will be valuable in providing insight into the mechanisms of disease resistance.

The distributions of anthozoan corals are undercharacterized due to their wide bathymetric ranges, occurrences in remote locales, and difficulties of identification from morphology alone. Environmental DNA (eDNA) sequencing promises to be a noninvasive strategy to complement conventional approaches for mapping and monitoring the distribution and biodiversity of coral communities. Primers for eDNA metabarcoding have been designed to amplify nuclear and mitochondrial DNA barcodes in shallow scleractinians and mitochondrial MutS in deep-sea octocorals. However, a comprehensive method for eDNA metabarcoding of all anthozoan corals, including black corals, has not been developed. We leveraged a sequence database of global coral collections, from shallow water to the deep sea, to design new PCR primers for coral eDNA sequencing that target the 28S rRNA gene (28S rDNA). We tested the performance of these primers by amplifying and sequencing eDNA from water samples collected in the Gulf of Mexico near mesophotic and deep-sea corals that were also imaged, sampled, and sequenced. Sequencing libraries produced using the primers were highly enriched in eDNA from octocorals, black corals and scleractinians, with up to 99.9% of the reads originating from these corals. Further, the 28S barcode amplified using the primers distinguished coral genera and species in many cases, like previously developed methods that target eDNA in only octocorals or scleractinians. We recovered amplicon sequencing variants (ASVs) identical to DNA barcodes derived from Sanger sequencing and genome skimming of corals sampled at the same field sites. This new eDNA metabarcoding strategy permits targeted eDNA sequencing of black corals, octocorals, and scleractinians at sites where they co-occur and expands our current toolkit for mapping and monitoring coral communities in shallow coral reefs and the deep sea.

The morphology of stony corals (Scleractinia) remains the only means to reconstruct the most inclusive evolutionary history of the clade comprising both extant and extinct species. The definitions of morphological characters and their associated trait states are critical for assembling a dataset that could be analysed for phylogenetic reconstruction. Here, we present coral morphological data that consist of more than a hundred characters reviewed by the Corallosphere working group. These characters would eventually form the basis of a data matrix used to reconstruct the phylogeny of all extinct and extant scleractinian families. The initial results obtained by the working group comprise poorly resolved trees, which are biased by the complexity of the multiple character states and the multiplicity of researchers involved in the coding process. When the analysis is restricted to matrices consisting of families from the Triassic and Jurassic periods and coded by a single person, resolution increased, allowing for further exploration of various ingroups and outgroups. The results presented here represent analyses of (i) a data matrix with all families represented by their type genus; (ii) a data matrix with selected families represented by their solitary or phaceloid genera; (iii) a data matrix with only Triassic corals; (iv) a data matrix with only Jurassic corals; (v) a data matrix with Triassic and Jurassic corals; and (vi) data matrices with several outgroups. Well-resolved trees have been obtained in several cases. Phylogenetic rela-tionships among basal, robust and complex groups established using molecular data are discussed in the context of the morphological phylogeny obtained here.

Light is critical to coral growth through endosymbiont photosynthesis but can also act with elevated temperatures to cause coral bleaching. When more light is absorbed than can be used for photosynthesis, elevated irradiance can damage symbiont photosynthetic machinery. Hence, solar-radiation management through shading has been suggested to alleviate coral bleaching during marine heatwaves. Acropora divaricata and Acropora kenti were tested at two temperatures with 30% shading and an unshaded control to determine the relative impacts of light and temperature on coral bleaching severity. The coral bleaching response was assessed by photochemical (pulse amplitude modulated fluorometry), physiological (symbiont density, chlorophyll a concentration, catalase activity, and lipid peroxidation), and physical (mean intensity of grey or ‘percentage whiteness’) markers. Shading significantly reduced the bleaching response in A. divaricata, whilst for some parameters A. kenti responded negatively to shade. In A. divaricata, shading prevented photochemical collapse up to the experiment’s maximum 4.4 degree-heating weeks (DHW). Biomarkers of coral bleaching stress responded to shade and water temperature at 4.4 DHW; catalase activity was greatest in the shaded and ambient temperature treatment. Shading did not reduce the effects of bleaching in A. kenti; the mean intensity of grey and light saturation coefficient was greatest in the shaded treatment. Shading did, however, reduce lipid peroxidation at 3 DHW. Our results suggest shading during thermal stress may only protect some coral species, highlighting the need to consider species-specific responses when evaluating the potential efficacy of coral bleaching interventions.

Coral-dwelling gall crabs (Cryptochiridae) are common inhabitants of scleractinian corals. Several species have been described as new in recent years, including Lithoscaptus doughnut, which was described from Hong Kong based on a single female retrieved from the coral Plesiastrea peroni. Here we extend the distribution range of L. doughnut with nine additional localities throughout the Indo-West Pacific, from the Red Sea to the Coral Triangle and Japan. We describe a male specimen of L. doughnut for the first time, based on a specimen from Malaysia, and provide photographs of life and preserved material. Haplotype networks based on COI mtDNA (n = 12) and 16 rRNA sequences (n = 12) were created. We retrieved eleven COI haplotypes and six 16S haplotypes, however no clear geographic distribution pattern was discerned. Intraspecific variation in L. doughnut was 1.4% for COI and 0.2% for 16S. Lastly, the first colour photos and records of associated parasites of this species are provided.

Abstract Twelve solitary and platy, colonial coral taxa assigned to the families Microsolenidae, Misistellidae, Montlivaltiidae, Rayasmiliidae, and Thamnasteriidae are described and illustrated from the Callovian (Ifenthal Formation, Herznach Member) of the area of Andil near Liesberg, about 20 km WSW of the town of Basel, Switzerland. The platy growth forms and the presence of five species of the superfamily Cyclolitoidea suggests that these corals lived under low-level light conditions.

Intervention techniques to restore coral communities have become an important management tool to help recover and rehabilitate damaged reefs. The direct transplantation of healthy coral fragments is the most common method; however, there is controversy in the long-term success, as using coral clones may diminish the genetic diversity of the coral population. Genetic recombination can be achieved when the coral colony produces gametes and eventually reproduces; therefore, it is important to provide evidence that restored colonies produce gametes as their naturally recruited counterparts with similar colony size (age). Natural and restored Pocillopora coral colonies of the same size range (between 40 and 50 cm in diameter) were tagged and sampled during the rainy season to determine gamete maturation. Our results show no differences in the reproductive activity among colonies: natural and restored coral colonies matured gametes from June to October, with a peak in sexually active coral colonies in July. Also, gamete malformation was not observed. During the gamete production period, the area’s temperature ranged from 27.9 to 30.02 °C. The results’ evidence that coral colonies formed through active restoration contribute not only to the increase in live coral cover as seen in previous studies but potentially contribute in the medium term (>5 years after out-planting) to the production of larvae and local and subsidiary recruitment, since they exhibit the same reproductive patterns as their naturally formed counterparts and no differences in the reproductive activity among coral colonies. Therefore, long-term coral restoration projects contribute to maintaining the live coral cover and the genetic diversity in the region, eventually rehabilitating the coral community.

Abstract Background Mesophotic coral communities are increasingly gaining attention for the unique biological diversity they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies on corals have rarely included mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers. Results Here, we used reduced-representation genome sequencing to conduct a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed deep divergences within the two genera and undescribed diversity across the current taxonomic species. Five of the eight focal species consisted of at least two sympatric and genetically distinct lineages, which were consistently detected across different methods. Conclusions The repeated observation of genetically divergent lineages associated with mesophotic depths highlights that there may be many more mesophotic-specialist coral species than currently acknowledged and that an urgent assessment of this largely unstudied biological diversity is warranted.

Sea-level rise (SLR) is expected to elevate the depth of seawater above shallow coral reefs, reducing light availability to the benthic environment, and impacting the survival and growth of corals especially on turbid reefs. However, the extent of impact at the deepest reef zones remains unknown. Coral growth could continue to keep pace above light thresholds as sea level rises, but mortality due to light limitation could vary between localities and local conditions. Here, we examine possible outcomes of corals inhabiting Singapore's turbid reefs in the years 2050 and 2100 by characterising their depth distributions and predicting potential mortality rates based on SLR projections. Our results reveal that in 2050, under both RCP4.5 and RCP8.5 sea level projections, up to 6.24% of colonies could face mortality if their growth is not considered. In 2100, up to 7.68% mortality under RCP4.5 and up to 10.7% mortality under RCP8.5 are predicted. When coral linear extension is considered, in 2050, under both RCP4.5 and RCP8.5 sea level projections, up to 1.03% of colonies could face mortality. In 2100, up to 0.87% mortality under RCP4.5 and up to 1.84% mortality under RCP8.5 are predicted. Species-specific losses could amount to 20% of colonies primarily at the deepest zones. The most vulnerable species exhibit a depth distribution with most colonies situated at the deeper parts of their depth ranges. Our findings suggest that sea-level rise may potentially result in the loss of coral cover for some species, but overall mortality could be low.

Scleractinian corals, considered key reef ecosystem engineers, have suffered irreparable damage over the last decades, with causes widely attributed directly and indirectly to increased human pressure on coral communities. Stony coral tissue loss disease (SCTLD), first detected in Florida in 2014, by early 2023 had spread to 26 jurisdictions in the wider Caribbean, causing severe effects on coral reefs. In January 2020, monitoring efforts to detect SCTLD began on the island of Roatan in Honduras. The disease was first reported in Flowers Bay, Roatan, in September 2020. Since then, dedicated collaborative efforts have been made to assess the severity of the disease, mitigate its effects, and raise coral reef conservation awareness. To track the progression of the outbreak, presence-absence data were collected using the rover diver methodology. With at least 28 species affected, SCTLD has spread across the Bay Islands over a period of 13 months. Roatan and Utila have been the most impacted islands, with the disease encircling them rapidly at a rate of approximately 155 m/day. The spread of SCTLD was overall rapid, but geographical patterns were detected in Roatan, where it showed faster progression on the windward side than on the leeward side. Further research is required to explore whether these disparities are related to marine traffic, water quality, currents, or a combination of multiple factors. Our findings shed new knowledge on the spread of SCTLD in Honduras, which can provide insights for other Caribbean nations whose economies are also dependent on the health of their coral reefs.

Coral reefs are globally declining due to various anthropogenic stressors. Amongst those, chemical pollutants, such as pesticides from agricultural runoff, sewage or an overabundance of personal care products in coastal waters due to intense tourism, may be considered as a local stressor for reef-building corals. The extent to which such chemicals exhibit toxic effects towards corals at environmentally relevant concentrations is currently controversially discussed and existing studies are often based on varying and sometimes deficient test methods. To address this uncertainty, we adapted available methods into a reliable and comprehensive acute coral toxicity test method for the reef-building coral Montipora digitata. The toxicities of the four substances benzophenone-3 (BP-3), Diuron (DCMU), copper (Cu2+ as CuCl2, positive control) and dimethylformamide (DMF, solvent) were assessed in a 96 h semi-static test design. Endpoints such as maximum quantum yield, bleaching, tissue loss and mortality were evaluated with respect to their suitability for regulatory purposes. Overall, the endpoints bleaching and mortality yielded sensitive and robust results for the four tested substances. As the test method follows the principles of internationally standardized testing methods (ISO, OECD), it can be considered suitable for further validation and standardization. Once validated, a standardized test method will help to obtain reproducible toxicity results useful for marine hazard and risk assessment and regulatory decision making.

Abstract From the Vitznau Marl (lower Valanginian) at the locality Wart in northeastern Switzerland (Alpstein area), 18 species from 17 genera and 13 families are described, including the genera Actinaraea, Actinastrea, Adelocoenia, Aplosmilia, Axosmilia, Complexastrea, Cyathophora, Dermosmilia, Fungiastraea, Heterocoenia, Latiastrea, Montlivaltia, Placophyllia, Pleurophyllia, Stylophyllopsis, Thamnoseris, and specimens showing affinities to solitary stylophyllids. The corals from the Vitznau Marl were derived from a limestone–marl alternation that is fossiliferous and clay-rich at the base (Vitznau Marl), containing crinoids, bryozoans, and sparse reworked corals and sponges. The coral fauna is distinctly dominated by forms belonging to the category of lowest to no polyp integration (50%), followed by species of the cerioid-plocoid group (33%) and forms having the highest polyp integration (thamnasterioid; 17%). With regard to polypar size, the Wart fauna is dominated by corals having large-size (> 9 mm) polyps (= 39%), followed by corals having medium- (> 2.5‒9 mm; 33%) and small-size polyps (up to 2.5 mm; 28%). Based on morphological features, the fauna from the Vitznau Marl closely corresponds to coral assemblages that are subjected to near-chronic, moderate sediment-turbidity stress that is punctuated by high-stress events, and that are largely or entirely heterotrophic. No coral fabric was observed that would suggest a biohermal development. But in a very small number of places, structures are present which might be fragments of crusts of microbialites, pointing to the hypothesis that at least a few of the corals might have been a part of some kind of bioconstruction. At the species-level, the fauna of the Vitznau Marl shows either no or very little affinities to other Valanginian assemblages such as to the fauna of Hungary (4.3%), followed by the associations of Ukraine, Switzerland (non-Vitznau), Spain (SpII), and Bulgaria. At the genus-level, the Wart fauna shows low correspondence to the fauna of Spain (SpII) (14.5%), followed by the assemblages of Hungary, Bulgaria, and Ukraine. In addition to the Vitznau Marl corals, an account of all Valanginian coral faunas published before early 2021 is given, including their paleogeographic distribution, as well as their taxonomic and morphological characterization. For this preliminary study, a total of 206 coral species belonging to 97 genera found in the coral assemblages of the Valanginian were included. At both the genus- and the species-levels, colonial taxa are most abundant (colonial genera: 89%; colonial species 90%). The vast majority of the Valanginian genera already occurred in older strata. Only 11 genera (out of 97 = 11%) are newly recorded. The Valanginian faunas having the largest number of solitary taxa lived in both (sub-) paratropical to warm-temperate areas, and in arid regions. The coral faunas of the Valanginian are distinctly dominated by corals of well-established microstructural groups. Only 13% of the species from 24% of the genera belong to “modern” groups. Compared to the situation in the Berriasian which showed that 9% of the species and 17% of the genera belonged to modern microstructural groups, the occurrence of “modern” groups significantly increased during the Valanginian.

Abstract The application of environmental DNA technologies is a promising new approach to rapidly audit biodiversity across large‐scale, remote regions. Here, we examine the efficacy of a dual‐assay eDNA metabarcoding approach for sessile benthic bioassessments in the turbid waters of the Lalang‐garram marine parks, Kimberley, north‐western Australia. We ask three principal questions: (1) “Is the eDNA released by sessile benthic taxa (i.e., hard and soft corals, sponges and tunicates) locally detectable?”, (2) “What level of taxonomic resolution is afforded by eDNA metabarcoding using the ITS2 region?”, and (3) “How well does eDNA metabarcoding compare to conventional benthic survey techniques?”. We report that a dual‐assay eDNA metabarcoding approach can detect approximately 70% of the local benthic taxa (i.e., at a species, genus level). It is, however, not as effective at the individual/population level, detecting only approximately 40% of unique amplicon sequence variant (ASV) signals released by an array of individual benthic organisms at the surveyed locations. In examining the efficacy and resolution of the applied ITS2 metabarcoding markers for bioassessments, we report large gaps in the variety of publicly available benthic ITS2 reference sequence data, limiting our ability to provide robust taxonomic assignments. These findings highlight the need to extend ITS2 databases for greater regional representation. Until this is adequately addressed, we recommend that investigating taxonomic assignments to a genus level is the most robust approach for benthic monitoring using eDNA. Lastly, we found eDNA metabarcoding and conventional belt transect surveys each detected numerous unique hard coral genera, indicating that a combined approach provides the most effective way to audit benthic biodiversity. This point notwithstanding, eDNA metabarcoding had the power to distinguish similar diversity trends between sites to that determined by the belt transect methodology, validating the application of eDNA metabarcoding as either a stand‐alone, or complementary technique for assessing sessile benthic taxa.

On the continental shelf off the coast of South Texas lie a series of natural hard-bottom structures (rocky outcrops and relic coral-algal reefs) known as the South Texas Banks (STB), which provide critical habitat for benthic organisms and pelagic fish. The depth of the banks, a persistent nepheloid layer, and strong currents have resulted in few studies that provide quantitative biodiversity data on the STB. Using a remotely operated vehicle (ROV), video surveys were conducted to quantitatively describe the mesophotic coral communities and assess habitat suitability of five STB: North Hospital, Hospital, Southern, Big Adam, and Mysterious Banks. Each of these STB have significantly different benthic communites, with coral communities composed primarily of antipatharians and octocorals. Big Adam Bank had the lowest biodiversity and the least coral cover. Mysterious Bank had abundant antipatharians, specifically Stichopathes spp., but low biodiversity overall. Hospital Bank had low coral diversity that was offset by high diversity in sponges and other invertebrate species. North Hospital and Southern Banks had abundant and diverse populations of coral species, including scleractinians, and other benthic invertebrates. These data indicate that the STB are crucial islands of biodiversity in an area with few suitable areas for coral reef species. In addition, predictive modelling of habitat suitability provided valuable estimates on the potential distribution of key benthic community members, such as scleractinians and antipatharians, throughout the entire areas of the five banks assessed.

Abstract Information about the distribution of alleles among marine populations is critical for determining patterns of genetic connectivity that are essential in modern conservation planning. To estimate population connectivity in Singapore's urbanized equatorial reef system, we analysed single nucleotide polymorphisms (SNPs) from two species of reef‐building corals with distinct life histories. For Porites sp., a broadcast‐spawning coral, we found cryptic lineages that were differentially distributed at inshore and central‐offshore sites that could be attributed to contemporary surface current regimes. Near panmixia was observed for Pocillopora acuta with differentiation of colonies at the farthest site from mainland Singapore, a possible consequence of the brooding nature and relatively long pelagic larval duration of the species. Furthermore, analysis of recent gene flow showed that 60–80% of colonies in each population were nonmigrants, underscoring self‐recruitment as an important demographic process in this reef system. Apart from helping to enhance the management of Singapore's coral reef ecosystems, findings here pave the way for better understanding of the evolution of marine populations in South‐East Asia.

Basic information on the reproductive biology of many scleractinian corals species is limited or entirely lacking, particularly from temperate zones, though it is essential for a better understanding of their ecology. This study describes the morphological aspects and the annual cycle of gametogenesis and biometric parameterss of the papillose cup coral Paracyathus pulchellus collected at Palinuro (Italy, Southern Tyrrhenian Sea), filling a knowledge gap about the reproductive biology of a widespread Mediterranean and Northern Atlantic coral. Samples of P. pulchellus were collected by SCUBA diving between 5- and 10-meters depth during 18 monthly collections from June 2010 to December 2011. Sexually active polyps displayed either oocytes or spermaries, indicating that P. pulchellus was gonochoric. The sex ratio of sexually active polyps was 1:1. Gametogenesis began with undifferentiated germ cells arose in the gastrodermis that migrated towards the mesoglea of the mesentery where they completed the development. During spermatogenesis, spermary diameter increased from 25 to 83 µm. Oocyte diameter ranged from 9 to 146 µm and during oogenesis the nucleus/cytoplasm ratio decreased due to the accumulation of yolk. The nucleus migrated to the periphery of the oocyte adhering closely to the cell membrane. No embryo was observed in the coelenteric cavity of the polyps, suggesting an external development of planktotrophic larvae due to the small-sized mature oocytes and a possible broadcast spawning reproductive mode. Gonadal index of both females and males increased significantly from August until November and fertilization took place from November to January. Only sexually inactive individuals were observed from February to April, suggesting a quiescence period in both males and females. Seasonal variations in water temperature and photoperiod may have a key role in regulating gametogenesis. The analysis of the main biometric parameters (polyp width, height, dry skeletal mass, volume, surface/volume ratio and bulk skeletal density) showed a negative correlation between size and skeletal density, and no sexual dimorphism.

The Persian Gulf is a thermally extreme environment in which reef corals have adapted to survive through temperature ranges that would be lethal to corals from other regions. Despite offering a unique opportunity to better understand how corals from other regions may adapt in the future, through a changing climate, much of the Gulf coral and fish communities remain to be described. In the southwestern Gulf nation of Qatar few reef sites have been described to date. We here characterize reef communities from 16 sites around the Qatar Peninsula, encompassing depths from 3 to 25m. We found the healthiest coral reef communities to be in deeper offshore reefs, with high coral and fish species richness and high coral abundance, likely a result of their occurrence below summer thermocline depths and distance from urban pressures. In contrast, we found shallow reefs, both nearshore and offshore, to have low species richness and abundance relative to deeper reefs, presumably due to impacts from recurrent bleaching events and development pressures over recent decades. The results of this work underscore the Qatar Peninsula as being at the biogeographic epicenter of the wider Gulf. However, further temperature increases may push both fishes and corals over their physiological limits. Management efforts at both the regional and global level are needed to reduce thermal stressors and preserve the rich reef ecosystems found in the waters surrounding Qatar.

A widespread and diversified mesophotic system of carbonate bioconstructions along the Southern Adriatic and Ionian Italian coasts is described, providing new data on the distribution, structure and associated megabenthic assemblages of mesophotic Mediterranean bioconstructions. The bioconstructions were detected at six different sites off the coasts of Apulia, in presence of marked morphological escarpments, developing on a basal substrate consisting of meso-Cenozoic carbonate rocks. Two biogenic structure types were observed, one mainly built by the nonsymbiotic scleractinians Phyllangia americana mouchezii and Polycyathus muellerae, at depths between approximately 35 and 55 m, and the other by the oyster Neopycnodonte cochlear, at depths from approximately 40 to 70 m. A total of 52 taxa of megabenthic invertebrates, belonging to 6 phyla, were found on the surface of the mesophotic bioconstructions, thus confirming the role of biodiversity hotspots of these carbonate structures. Megabenthic assemblages showed a remarkable heterogeneity both in pattern of species and abundance, probably depending on both the morphological differences of the seabed and the life traits of the single species. Primary bioconstructors seemed to influence the associated community pattern. This peculiar system deserves sound conservation measures in the light of the holistic ecosystem approach for the management of coastal marine areas.

Abstract Identification of fossil corals is often limited due to poor preservation of external skeleton morphology, especially in the genus Acropora which is widespread across the Indo‐Pacific. Based on skeleton characteristics from thin section, we here develop a link between the internal skeleton structure and external morphology. Ten characteristics were summarized to distinguish Acropora and five related genera, including the type and differentiation of corallites, the skeleton nature of corallites (septa, columellae, dissepiments, wall), and calcification centers within septa. Acropora is distinctive for its dimorphic corallites: axial and radial. Isopora is similar to Acropora but possess more than a single axial corallites. Montipora and Astreopora (family Acroporidae) have monomorphic corallites and a synapticular ring wall, with clustered calcification center in the former and medial lines in the latter. Pocillopora and Porties are classified by distinctive dissepiments, columellae and septa. These microstructural skeleton characteristics were effective in the genus identification of fossil corals from drilled cores in the South China Sea. Eighteen detailed characteristics (ten of axial corallites, four of radial corallites, and four of coenosteum) were used in the Acropora species classification. The axial corallites size and structure (including corallite diameter, synapticular rings, and septa), the septa of radial corallites, and the arrangement of coenosteum were critical indicators for species identification. This identification guide can help paleoenvironmental and paleoecological analyses and modern coral reef conservation and restoration.

Dimethlysulfoniopropionate (DMSP) lyase is an enzyme that mediates cleavage of DMSP into dimethyl sulfide (DMS) and acrylate. DMS is an aerosol substance that may affect cloud formation, solar radiation and ocean temperatures. DMSP lyases in marine organisms, such as marine bacteria, release DMS, which might contribute to atmosphere-ocean feedback. Although DMSP lyases were first identified in marine bacteria, eukaryotic DMSP lyases or genes similar to DMSP lyase, DMSP lyase-like (DL-L) genes have been found not only in coccolithophores (Emiliania huxleyi) and symbiotic algae of the Family Symbiodiniaceae, but also in animals, including scleractinian corals (Cnidaria: Anthozoa: Hexacorallia). Comparative genomic analysis showed that gene expansion events of DL-L genes have occurred specifically in the scleractinian genus, Acropora. In the present study, we performed molecular identification of DL-L genes in Acropora digitifera. Thirteen full-length Open Reading Frames were isolated, confirming that these duplicated DL-L genes are likely expressed. A comprehensive survey of available transcriptomic databases revealed that DL-L genes have been identified not only in scleractinians (Hexacorallia), but also Octocorallia (Anthozoa) and even in a jellyfish (Cnidaria: Hydrozoa). Molecular phylogenetic analyses showed that although some sequences from cnidarian transcriptomic databases apparently originated with their symbiotic algae, cnidarian sequences from Anthozoa and Hydrozoa clustered together, indicating that these evolved from a gene in the last common ancestor of Cnidaria, dating to the Precambrian. Interestingly, cnidarian species possessing DL-L genes apparently occur only in coral reefs or shallow, warmer environments, suggesting that these genes may be essential for animals to survive in such environments. Acropora-specific duplicated DL-L genes, which originated during the past warm geological periods, may enable them to adapt to environmental changes.

In this study, the complete mitogenome sequence of the stony coral, Turbinaria bifrons Brüggemann, 1877, has been decoded for the first time by next-generation sequencing (NGS) and genome assembly. The assembled mitogenome was 18,880 bp in length, contained 13 protein coding genes, 2 transfer RNAs, and 2 ribosomal RNAs. The complete mitogenome of T. bifrons showing 97.09% identities to Tubastraea tagusensis. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for coral phylogeny.

Stony coral tissue loss disease has spread widely in the Caribbean and causes substantial changes to coral community composition because of its broad host range and high fatality rate. To reduce SCTLD impacts, intervention programs throughout the region have divers treating corals with antibiotics. We assessed the effect of antibiotic treatment in the British Virgin Islands by comparing coral communities at 13 treated sites to those at 13 untreated sites. The prevalence of white syndromes (assumed to be primarily SCTLD), the severity of white syndrome lesions, partial colony mortality and complete colony mortality all showed a qualitative pattern consistent with benefits of treatment: they were reduced at treated sites for species highly susceptible to SCTLD. In contrast, the prevalence and severity of lesions from other diseases, and other causes of tissue loss, were all unrelated to treatment. Re-ordering of rank abundance at the community-level was also consistent with a positive effect of treatment because rare, highly SCTLD-susceptible species increased slightly in relative cover at treated sites. Although there was limited statistical support for these responses individually, collectively the overall pattern of results indicates a modest beneficial effect of the intervention program for highly susceptible species. Diver-based intervention programs using antibiotics may thus be a viable part of management plans for STLD at the epidemic stage.

Reef-building corals live in symbiosis with the phototrophic dinoflagellate family Symbiodiniaceae, which comprises diverse genera such as Cladocopium and Durusdinium. Pachyseris speciosa, a widely distributed Indo-Pacific coral found in a variety of reef habitats, is known to be associated with these two Symbiodiniaceae genera, but little is known about the biogeographic variability of the endosymbiont communities across the region. In this study, the diversity and dominance patterns of Symbiodiniaceae at the western and eastern areas of the Central Indo-Pacific region were examined. We sampled Pachyseris speciosa colonies at seven and six sites in Singapore and Papua New Guinea, respectively, and genotyped their endosymbionts based on the internal transcribed spacer (ITS) markers using two distinct methods, quantitative polymerase chain reaction (qPCR) and high-throughput sequencing (HTS). Results showed 92% of all colonies in Singapore exhibiting Cladocopium dominance. There was a higher abundance of Durusdinium compared to Cladocopium in certain colonies from one site, Pulau Hantu (mean Durusdinium abundance of 90%, compared to 0–14% among all other sites). In contrast, variation in the endosymbiont communities was generally higher among sites in Papua New Guinea. Cladocopium expectedly dominated most colonies (75%), although colonies from Kimbe Bay (85%) and Kavieng (65%) showed Durusdinium dominance. Between localities, relative genus abundances based on qPCR were not significantly different, but HTS showed that the ratio of Durusdinium over Cladocopium was significantly higher in Papua New Guinea corals. Notably, 6% of colonies from Singapore and 15% from Papua New Guinea showed endosymbiont dominance patterns that were inconsistent between the two methods, underscoring the need for further validation of symbiotic algal quantification based on HTS. The richness of ITS2 type profiles was clearly lower among colonies from the impacted and turbid reefs of Singapore compared to the less urbanized reefs of Papua New Guinea. These coral intraspecific variations of Symbiodiniaceae communities within and among localities suggest that local conditions are important drivers of endosymbiosis and may ultimately influence corals’ resilience against global stressors such as ocean warming.

Quantifying recruitment of corals is important for evaluating their capacity to recover after disturbances through natural processes, yet measuring recruitment rates in situ is challenging due to the minute size of the study organism and the complexity of benthic communities. Settlement tiles are widely used in studies of coral recruitment because they can be viewed under a microscope to enhance accuracy, but methodological choices such as the rugosity of tiles used and when and how to scan tiles for recruits post-collection may cause inconsistencies in measured recruitment rates. We deployed 2,880 tiles with matching rugosity on top and bottom surfaces to 30 sites along the Florida Reef Tract for year-long saturations during a three year study. We scanned the top and bottom surfaces of the same tiles for scleractinian recruits before (live scans) and after treating tiles with sodium hypochlorite (corallite scans). Recruit counts were higher in corallite than live scans, indicating that scleractinian recruitment rates should not be directly compared between studies using live scans and those scanning tiles which have been processed to remove fouling material. Recruit counts also were higher on tile tops in general, but the proportion of settlement to the top and bottom surfaces varied significantly by scleractinian family. Thus, biases may be introduced in recruitment datasets by differences in tile rugosity or by only scanning a subset of tile surfaces. Finally, we quantified octocoral recruitment during live scans and found they preferentially settled to tile tops. We recommend that recruitment tile studies include corallite scans for scleractinian skeletons, deploy tiles with matching rugosity on top and bottom surfaces, and scan all tile surfaces.

Coral reefs, the most biodiverse habitats in the ocean, are formed by anthozoan cnidarians, the scleractinian corals. Recently, however, ongoing climate change has imperiled scleractinian corals and coral reef environments are changing drastically. Thus, convenient, high-density monitoring of scleractinian corals is essential to understand changes in coral reef communities. Environmental DNA (eDNA) metabarcoding is potentially one of the most effective means of achieving it. Using publicly available scleractinian mitochondrial genomes, we developed high-specificity primers to amplify mitochondrial 12S ribosomal RNA (12S) and cytochrome oxidase-1 (CO1) genes of diverse scleractinian corals, which could be used for genus-level metabarcoding analyses, using next-generation sequencing technologies. To confirm the effectiveness of these primers, PCR amplicon sequencing was performed using eDNA isolated along the seashore of Okinawa, Japan. We successfully amplified all eDNA samples using PCR. Approximately 93 and 72% of PCR amplicon sequences of 12S and CO1 primers originated from scleractinian 12S and CO1 genes, respectively, confirming higher specificities for coral mitochondrial genes than primers previously used for coral eDNA metabarcoding. We also found that hierarchical clustering, based on the percentage of mapped reads to each scleractinian genus, discriminates between sampling locations, suggesting that eDNA surveys are sufficiently powerful to reveal differences between coral communities separated by

Reefal limestones of the Štramberk Carbonate Platform are preserved as olistoliths and pebbles in deep-water flysch of the Outer Carpathians (Czech Republic, Poland). They contain the richest coral assemblages of the Jurassic/Cretaceous transition (Tithonian–Berriasian). Symbiotic associations between corals and tube-dwelling macroorganisms were recognized only in the branching scleractinian corals Calamophylliopsis flabellum and Calamophylliopsis sp. One to seven calcareous tubes were recognized either in coral calyces, embedded in the wall, or attached to it. Two types of tubes were recognized: Type 1: tubes with a diameter of 0.3–0.6 mm and a very thin wall (ca. 0.05 mm), mostly occurring inside corallites, and nearly exclusively in the Štramberk-type limestone of Poland; Type 2: tubes with an outer diameter of 0.8–2.0 mm and a thick wall (ca. 0.1 mm, some even up to 0.2 mm), mostly found in the Štramberk Limestone of the Czech Republic. Growth lamellae were observed in some thick walls. Most tubes are almost straight, some are curved. The tubes were probably produced by serpulids or by embedment of organic-walled sabellid polychaete worms. It is likely the oldest record of a sabellid–coral association. Modification of the coral skeleton in contact with tubes indicates that the worms were associated with live corals. For many modern and fossil worm–coral associations, this symbiotic association is interpreted as mutualistic or commensal.

The Oligocene, well known as the apex of Cenozoic reef growth, is a crucial period of time to investigate the mutual relationship between coral reef construction and coral diversity and their link with palaeoclimate and palaeoenvironmental changes. Here we provide a complete characterization of the Upper Oligocene reef complex of the Castro Limestone (Salento Peninsula, S Italy), which is one of the best-preserved Oligocene coral reefs of the Mediterranean region. By combining facies analysis with the first detailed characterization of its coral fauna, we show that the Castro Limestone has both a rich scleractinian coral fauna (25 genera and 41 species) and a large reef volume, and it represents a luxuriant fringing reef formed within the euphotic zone in clear water conditions facing the open sea. The coral fauna differs both in its composition and in its proportions among reef palaeoenvironments, ranging from the shallow back reef to the fore reef slope, and its stratigraphic and palaeogeographic distribution testifies to the persistence of a cosmopolitan Tethyan fauna in Oligocene time, with the Mediterranean and Indo-Pacific provinces being more closely connected than the Mediterranean and the Caribbean. The age of the Castro Limestone is here reassigned to the middle-late Chattian, which coincides with the Late Oligocene Warming Event (LOWE) when atmospheric CO2 values declined. We suggest that the strong reef-building capacity of the Castro Limestone, coupled with high coral diversity, was not hampered by warming conditions but most probably promoted by the reduced pCO2 and a suitable local/regional physiographic setting.

The Oligocene, well known as the apex of Cenozoic reef growth, is a crucial period of time to investigate the mutual relationship between coral reef construction and coral diversity and their link with palaeoclimate and palaeoenvironmental changes. Here we provide a complete characterization of the Upper Oligocene reef complex of the Castro Limestone (Salento Peninsula, S Italy), which is one of the best-preserved Oligocene coral reefs of the Mediterranean region. By combining facies analysis with the first detailed characterization of its coral fauna, we show that the Castro Limestone has both a rich scleractinian coral fauna (25 genera and 41 species) and a large reef volume, and it represents a luxuriant fringing reef formed within the euphotic zone in clear water conditions facing the open sea. The coral fauna differs both in its composition and in its proportions among reef palaeoenvironments, ranging from the shallow back reef to the fore reef slope, and its stratigraphic and palaeogeographic distribution testifies to the persistence of a cosmopolitan Tethyan fauna in Oligocene time, with the Mediterranean and Indo-Pacific provinces being more closely connected than the Mediterranean and the Caribbean. The age of the Castro Limestone is here reassigned to the middle-late Chattian, which coincides with the Late Oligocene Warming Event (LOWE) when atmospheric CO2 values declined. We suggest that the strong reef-building capacity of the Castro Limestone, coupled with high coral diversity, was not hampered by warming conditions but most probably promoted by the reduced pCO2 and a suitable local/regional physiographic setting.

Coral research is being ushered into the genomic era. To fully capitalize on the potential discoveries from this genomic revolution, the rapidly increasing number of high-quality genomes requires effective pairing with rigorous taxonomic characterizations of specimens and the contextualization of their ecological relevance. However, to date there is no formal framework that genomicists, taxonomists, and coral scientists can collectively use to systematically acquire and link these data. Spurred by the recently announced “Coral symbiosis sensitivity to environmental change hub” under the “Aquatic Symbiosis Genomics Project” - a collaboration between the Wellcome Sanger Institute and the Gordon and Betty Moore Foundation to generate gold-standard genome sequences for coral animal hosts and their associated Symbiodiniaceae microalgae (among the sequencing of many other symbiotic aquatic species) - we outline consensus guidelines to reconcile different types of data. The metaorganism nature of the coral holobiont provides a particular challenge in this context and is a key factor to consider for developing a framework to consolidate genomic, taxonomic, and ecological (meta)data. Ideally, genomic data should be accompanied by taxonomic references, i.e., skeletal vouchers as formal morphological references for corals and strain specimens in the case of microalgal and bacterial symbionts (cultured isolates). However, exhaustive taxonomic characterization of all coral holobiont member species is currently not feasible simply because we do not have a comprehensive understanding of all the organisms that constitute the coral holobiont. Nevertheless, guidelines on minimal, recommended, and ideal-case descriptions for the major coral holobiont constituents (coral animal, Symbiodiniaceae microalgae, and prokaryotes) will undoubtedly help in future referencing and will facilitate comparative studies. We hope that the guidelines outlined here, which we will adhere to as part of the Aquatic Symbiosis Genomics Project sub-hub focused on coral symbioses, will be useful to a broader community and their implementation will facilitate cross- and meta-data comparisons and analyses.

Abstract Background Scleractinian corals are important reef builders, but around the world they are under the threat of global climate change as well as local stressors. Molecular resources are critical for understanding a species’ stress responses and resilience to the changing environment, but such resources are unavailable for most scleractinian corals, especially those distributed in the South China Sea. We therefore aimed to provide transcriptome resources for 14 common species, including a few structure forming species, in the South China Sea. Description We sequenced the transcriptome of 14 species of scleractinian corals using high-throughput RNA-seq and conducted de novo assembly. For each species, we produced 7.4 to 12.0 gigabases of reads, and assembled them into 271 to 762 thousand contigs with a N50 value of 629 to 1427 bp. These contigs included 66 to 114 thousand unigenes with a predicted open reading frame, and 74.3 to 80.5% of the unigenes were functionally annotated. In the azooxanthelate species Tubastraea coccinea, 41.5% of the unigenes had at least a best-hit sequence from corals. In the other thirteen species, 20.2 to 48.9% of the annotated unigenes had best-hit sequences from corals, and 28.3 to 51.6% from symbiotic algae belonging to the family Symbiodinaceae. With these resources, we developed a transcriptome database (CoralTBase) which features online BLAST and keyword search for unigenes/functional terms through a user friendly Internet interface. Short conclusion We developed comprehensive transcriptome resources for 14 species of scleractinian corals and constructed a publicly accessible database (www.comp.hkbu.edu.hk/~db/CoralTBase). CoralTBase will facilitate not only functional studies using these corals to understand the molecular basis of stress responses and adaptation, but also comparative transcriptomic studies with other species of corals and more distantly related cnidarians.

Recent research suggests that nitrogen (N) cycling microbes are important for coral holobiont functioning. In particular, coral holobionts may acquire bioavailable N via prokaryotic dinitrogen (N2) fixation or remove excess N via denitrification activity. However, our understanding of environmental drivers on these processes in hospite remains limited. Employing the strong seasonality of the central Red Sea, this study assessed the effects of environmental parameters on the proportional abundances of N cycling microbes associated with the hard corals Acropora hemprichii and Stylophora pistillata. Specifically, we quantified changes in the relative ratio between nirS and nifH gene copy numbers, as a proxy for seasonal shifts in denitrification and N2 fixation potential in corals, respectively. In addition, we assessed coral tissue-associated Symbiodiniaceae cell densities and monitored environmental parameters to provide a holobiont and environmental context, respectively. While ratios of nirS to nifH gene copy numbers varied between seasons, they revealed similar seasonal patterns in both coral species, with ratios closely following patterns in environmental nitrate availability. Symbiodiniaceae cell densities aligned with environmental nitrate availability, suggesting that the seasonal shifts in nirS to nifH gene abundance ratios were probably driven by nitrate availability in the coral holobiont. Thereby, our results suggest that N cycling in coral holobionts probably adjusts to environmental conditions by increasing and/or decreasing denitrification and N2 fixation potential according to environmental nitrate availability. Microbial N cycling may, thus, extenuate the effects of changes in environmental nitrate availability on coral holobionts to support the maintenance of the coral–Symbiodiniaceae symbiosis.

The Florida Keys reef tract (FKRT) has a unique geological history wherein Holocene sea-level rise and bathymetry interacted, resulting in a reef-building system with notable spatial differences in reef development. Overprinted on this geologic history, recent global and local stressors have led to degraded reefs dominated by fleshy algae, soft corals, and sponges. Here, we assessed how coral physiology (calcification rate, tissue thickness, reproduction, symbiosis, and bleaching) varies seasonally (winter vs. summer) and geographically using 40 colonies of the mustard hill coral Porites astreoides from four sites across 350 km along the FKRT from 2015 to 2017. The study coincided with a high-temperature event in late summer 2015 that caused heterogeneous levels of coral bleaching across sites. Bleaching severity differed by site, with bleaching response more aligned with heat stress retroactively calculated from local degree heating weeks than those predicted by satellites. Despite differences in temperature profiles and bleaching severity, all colonies hosted Symbiodiniaceae of the same genus (formerly Clade A and subtypes). Overall, P. astreoides at Dry Tortugas National Park, the consistently coolest site, had the highest calcification rates, symbiont cell densities, and reproductive potential (all colonies were reproductive, with most planula larvae per polyp). Corals at Dry Tortugas and Fowey Rocks Light demonstrated strong seasonality in net calcification (higher in summer) and did not express visual or partial-mortality responses from the bleaching event; in contrast, colonies in the middle and southern part of the upper keys, Sombrero Key and Crocker Reef, demonstrated similar reduced fitness from bleaching, but differential recovery trajectories following the heat stress. Identifying reefs, such as Dry Tortugas and possibly Fowey Rocks Light that may serve as heat-stress refugia, is important in selecting candidate sites for adaptive reef-management strategies, such as selective propagation and assisted gene flow, to increase coral-species adaptation to ocean warming.

Acropora pruinosa is a threatened zooxanthellate scleractinian coral that is distributed in the temperate areas along the coastline of Japan and the northern area of the South China Sea. Since A. pruinosa propagates both asexually and sexually, assessing clonal diversity and genetic connectivity among populations is important for conservation. In addition, high morphological variations in the field create confusion during species identification. To examine the existence of hidden genetic lineages, clonality, and genetic connectivity of A. pruinosa for conservation, we applied microsatellite analysis. Clustering analysis indicated two distinct geographically separated genetic lineages: one is distributed in the west, and the other is distributed in the east. The two lineages co-existed in Nishidomari, Kochi. There was no obvious difference in morphological characteristics between the two lineages. Although the factors influencing the observed distribution patterns remain unknown, there is a possibility that the two lineages might have diverged somewhere in the north-western Kyushu and north-eastern Pacific coast habitats in the past, and then periodically colonized the current habitats. A low clonal diversity was observed in most of the populations, indicating a high rate of asexual reproduction associated with their branching morphologies. In addition, there are strong genetic structuring in this species, indicating weak connectivity among populations. These results indicated a low larval dispersal potential among populations and that populations are basically sustained by a high rate of clone propagation and self-seeding. The existence of cryptic lineages and genetically isolated populations with high clonality emphasized the importance of conservation of A. pruinosa.

Abstract The biological world is rapidly changing following decades of anthropogenic disturbances. Under these conditions, species with stable or increasing abundances have been described as winners with the potential for future success, but this assertion is unreliable without knowledge of the selective basis of winning. The incentive to find winners is acute for reef corals, for which large declines in abundance have motivated restoration efforts targeting winning corals. On Caribbean reefs, Porites astreoides has emerged as a potential winner, but the demographic basis of this categorization is poorly known. Here we test for demographic benchmarks of winning in this species by quantifying abundances and sizes of colonies over 28 yr on the south coast of St. John, US Virgin Islands. From 1992 to 2001, the density of colonies of P. astreoides showed little variation while colonies increased in size by 58%, but from 2002 to 2019, population density increased 2.7‐fold, and colony size declined by 41%; accompanying these trends, the mean absolute cover of Porites spp. declined by 46% from 2010 to 2019. Low recruitment and rising abundances of colonies ≤4 cm diameter suggest that partial mortality and fission depressed colony sizes. The reversal over three decades of a positive demographic trend for a ubiquitous coral underscores the challenges of identifying winners from short‐term population performance. Without a mechanistic understanding of fitness, the search for winners based on demographic trends may be futile.

During the Carnian, oligotrophic shallow-water regions of the western Tethys were occupied by small, coral-rich patch reefs. Scleractinian corals, which already contributed to the formation of the reef structure, owed their position most probably to the symbiosis with dinoflagellate algae (zooxanthellae). Using microstructural (regularity of growth increments) and geochemical (oxygen and carbon stable isotopes) criteria of zooxanthellae symbiosis, we investigated whether this partnership was widespread among Carnian scleractinians from the Italian Dolomites (locality Alpe di Specie). Although corals from this locality are renowned from excellent mineralogical preservation (aragonite), their skeletons were rigorously tested against traces of diagenesis Irrespective of their growth forms, well preserved skeletons of corals from the Dolomites, most frequently revealed regular growth bands (low values of coefficient of variation) typical of modern zooxanthellate corals. Paradoxically, some Carnian taxa (Thamnasteriomorpha frechi and Thamnasteriomorphasp.)with highly integrated thamnasterioid colonies which today are formed exclusively by zooxanthellate corals, showed irregular fine-scale growth bands (coefficient of variation of 40% and 41% respectively) that could suggest their asymbiotic status. However, similar irregular skeletal banding is known also in some modern agariciids (Leptoseris fragilis) which are symbiotic with zooxanthellae. This may point to a similar ecological adaptation of Triassic taxa with thamnasterioid colonies. Contrary to occasionally ambiguous interpretation of growth banding, all examined Carnian corals exhibited lack of distinct correlation between carbon (δ13C range between 0.81‰ and 5.81‰) and oxygen (δ18O values range between −4.21‰ and −1.06‰) isotope composition of the skeleton which is consistent with similar pattern in modern zooxanthellates. It is therefore highly likely, that Carnian scleractinian corals exhibited analogous ecological adaptations as modern symbiotic corals and that coral-algal symbiosis that spread across various clades of Scleractinia preceded the reef bloom at the end of the Triassic.

In the Caribbean Basin the distribution and diversity patterns of deep-sea scleractinian corals and stylasterid hydrocorals are poorly known compared to their shallow-water relatives. In this study, we examined species distribution and community assembly patterns of scleractinian and stylasterid corals on three high-profile seamounts within the Anegada Passage, a deep-water throughway linking the Caribbean Sea and western North Atlantic. Using remotely operated vehicle surveys conducted on the E/V Nautilus by the ROV Hercules in 2014, we characterized coral assemblages and seawater environmental variables between 162 and 2,157 m on Dog Seamount, Conrad Seamount, and Noroît Seamount. In all, 13 morphospecies of scleractinian and stylasterid corals were identified from video with stylasterids being numerically more abundant than both colonial and solitary scleractinians. Cosmopolitan framework-forming species including Madrepora oculata and Solenosmilia variabilis were present but occurred in patchy distributions among the three seamounts. Framework-forming species occurred at or above the depth of the aragonite saturation horizon with stylasterid hydrocorals being the only coral taxon observed below Ωarag values of 1. Coral assemblage variation was found to be strongly associated with depth and aragonite saturation state, while other environmental variables exerted less influence. This study enhances our understanding of the factors that regulate scleractinian and stylasterid coral distribution in an underreported marginal sea and establishes a baseline for monitoring future environmental changes due to ocean acidification and deoxygenation in the tropical western Atlantic.

Symbiosis and coloniality are ecologically important traits for corals of the order Scleractinia. Symbiotic (zooxanthellate) species are highly successful in shallow waters of tropical and subtropical seas and most of them are colonial. On the other hand, azooxanthellate species present wide distribution ranges and expand to the deep-sea at more than 6,000 m depth. These are mostly solitary, with only few species colonial that form extensive deep reefs. Each ecologically distinctive group encompasses half of the biodiversity of the order and they are not grouped into differentiated monophyletic clades. Paleontologists and evolutionary biologists have debated for decades whether modern scleractinian corals have evolved from symbiotic or colonial ancestors and how these traits have evolved and being involved in the diversification process in corals. Previous comparative analyses throw evidence in favor of coevolution of these characters and toward repetitive loss of symbiosis and coloniality. Nevertheless, the discovery of the origin of the group deep in the Paleozoic, with a deep divergent clade composed of only azooxanthellate corals has questioned these findings. With this work, we disentangle the patterns in the evolution of symbiosis and coloniality, testing if they are correlated and if they follow a gradual or episodic mode of evolution. To this end, we first produce the most complete time-calibrated phylogenetic tree for the order Scleractinia, including new sequences of never-before sampled species and genera. These novel sequences contribute to alleviate the current molecular under sampling of azooxanthellate species. Incorporating phylogenetic uncertainty, we obtained strong evidence in favor of a correlated and episodic model of evolution. This model led to the inference of an azooxanthellate and solitary most recent ancestor of scleractinians. Transition rates between the four different combinations of the two traits showed that while coloniality is gained and lost multiple times, symbiosis first appears around 282 Ma and is never lost. Also, coloniality seems to have appeared before symbiosis in azooxanthellate lineages. Thus, azooxanthellate corals, and especially colonial lineages, have been acting as a source of biodiversity for shallow zooxanthellate coral communities, highlighting the uniqueness of shallow and deep species and the need to preserve them.

The present study deals with a detailed taxonomic study Of the Scleractinia from the middle and upper parts of the Calcare di Zu (Zu Limestone), a formation outcropping in the Central Lombardy and dated as Rhaetian (Late Triassic). The specimens examined belong to the Collections of the Natural History of the Cities of Bergamo and Milano. Some specimens deposited at the Museum in Milano belong to the original collection of Stoppani (figured by this author in 1857 to 1865 papers). According the present revision, the genus Stylophyllopsis Frech, 1890 is a junior synonym of the genus Lepiconus Stoppani, 1857 and Retiophyllia paraclathrata Roniewicz, 1974 is a junior synonym of Retiophyllia langobardica (Stoppani, 1857). The fauna consists of 11 species, belonging to the genera: Cyathocoenia, Astraeomorpha, Pamiroseris, Palaeastraea, Lepiconus, Stylophyllum, Retiophyllia and «Thecosmilia». Some of the identified species are known only from Stoppani Collection. Someothers, instead, have a larger distribution and are recorded from the northern Side of the Alps, from the Tatra Mountains, Iran, Pamir, and from Northern America.

The presence of associated endofauna can have an impact on the health of corals. During fieldwork on the southern Caribbean island of Curaçao in 2021, the presence of an unknown coral-dwelling worm snail was discovered, which appeared to cause damage to its hosts. A study of photo archives revealed that the species was already present during earlier surveys at Curaçao since 2014 and also in the southern Caribbean island of Bonaire in 2019. It was not found in St. Eustatius, an island in the eastern Caribbean, during an expedition in 2015. The vermetid snail was preliminarily identified as Petaloconchus sp. Its habitat choice resembles that of P. keenae, a West Pacific coral symbiont. The Caribbean species was observed in 21 host coral species, more than reported for any other vermetid. Because Petaloconchus sp. is a habitat generalist, it is possible that it was introduced from an area with another host-coral fauna. The unknown vermetid is considered to be cryptogenic until future studies reveal its actual identity and its native range.

Abstract Background Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there are two major clades, Complexa and Robusta, but the genomic bases of significant differences between them remain unclear. Results Draft genome assemblies and annotations were generated for three coral species: Galaxea fascicularis (Complexa), Fungia sp., and Goniastrea aspera (Robusta). Whilst phylogenetic analyses strongly support a deep split between Complexa and Robusta, synteny analyses reveal a high level of gene order conservation between all corals, but not between corals and sea anemones or between sea anemones. HOX-related gene clusters are, however, well preserved across all of these combinations. Differences between species are apparent in the distribution and numbers of protein domains and an apparent correlation between number of HSP20 proteins and stress tolerance. Uniquely amongst animals, a complete histidine biosynthesis pathway is present in robust corals but not in complex corals or sea anemones. This pathway appears to be ancestral, and its retention in the robust coral lineage has important implications for coral nutrition and symbiosis. Conclusions The availability of three new coral genomes enabled recognition of a de novo histidine biosynthesis pathway in robust corals which is only the second identified biosynthetic difference between corals. These datasets provide a platform for understanding many aspects of coral biology, particularly the interactions of corals with their endosymbionts.

A limestone deposit with an unusual fauna is reported from the late Miocene of northern Italy (Ca’ Fornace site). The petrography of the carbonate and its distinct carbon isotope signature (with δ13C values as low as -57.6‰) clearly identify this limestone as an ancient methane-seep deposit. The dominant faunal elements are serpulid tubes belonging to Protis, and extremely inflated, medium-sized shells of the lucinid bivalve Anodontia mioinflata sp. nov. Also common is the small bathymodiolin Idas aff. tauroparva, plus some large specimens of the lucinid Lucinoma, and poorly preserved, medium-sized specimens of a possible vesicomyid bivalve, an arcid bivalve, small gastropods of the genera Laeviphitus (Elachisinidae), Anatoma (Scissurellidae), as well as desmophyliid and caryophyllid scleractinian corals. This faunal assemblage is quite distinct from the typical Miocene seep faunas in northern Italy, which are dominated by large bivalves of the Lucinidae (Meganodontia), Vesicomyidae (Archivesica), and Bathymodiolinae, possibly due to a shallower depositional depth of the Ca’ Fornace site.

Coral–zooxanthellae holobionts are one of the most productive ecosystems in the ocean. With global warming and ocean acidification, coral ecosystems are facing unprecedented challenges. To save the coral ecosystems, we need to understand the symbiosis of coral–zooxanthellae. Although some Scleractinia (stony corals) transcriptomes have been sequenced, the reliable full-length transcriptome is still lacking due to the short-read length of second-generation sequencing and the uncertainty of the assembly results. Herein, PacBio Sequel II sequencing technology polished with the Illumina RNA-seq platform was used to obtain relatively complete scleractinian coral M. foliosa transcriptome data and to quantify M. foliosa gene expression. A total of 38,365 consensus sequences and 20,751 unique genes were identified. Seven databases were used for the gene function annotation, and 19,972 genes were annotated in at least one database. We found 131 zooxanthellae transcripts and 18,829 M. foliosa transcripts. A total of 6328 lncRNAs, 847 M. foliosa transcription factors (TFs), and 2 zooxanthellae TF were identified. In zooxanthellae we found pathways related to symbiosis, such as photosynthesis and nitrogen metabolism. Pathways related to symbiosis in M. foliosa include oxidative phosphorylation and nitrogen metabolism, etc. We summarized the isoforms and expression level of the symbiont recognition genes. Among the membrane proteins, we found three pathways of glycan biosynthesis, which may be involved in the organic matter storage and monosaccharide stabilization in M. foliosa. Our results provide better material for studying coral symbiosis.

The Intergovernmental Panel on Climate Change (IPCC) predicted that ocean surface temperature will rise of 0.6–2.0°C by 2100. Ocean warming is expected to produce strong impacts on marine ecosystems such as coral reefs, affecting their physiological events including reproductive processes. To date, relatively few studies have examined the effects of climate change on the reproductive success of temperate corals and even less in the azooxanthellate ones. This study examined the reproductive output of the azooxanthellate Mediterranean coral Caryophyllia inornata along a wide latitudinal gradient of seawater temperature and solar radiation. A total of 260 samples, collected from five populations along the Western Italian coast, have been analyzed through histological techniques. The intriguing aspects characterizing all populations of C. inornata along the latitudinal gradient are a strong male-biased sex ratio and the presence of embryos in all stages of development throughout the year in females, males, and sexually inactive individuals. This peculiarity could suggest a mixed strategy of sexual and asexual reproduction in this species as has been observed for some anemones of the genus Actinia. Fecundity and spermary abundance (i.e., the number of reproductive elements per body volume unit), gonadal index (i.e., the percentage of body volume occupied by the germ cells) and fertility (i.e., the number of embryos per body volume unit) in females, males and sexually inactive individuals were unrelated to solar radiation and temperature along the latitudinal gradient. These results suggest that the reproduction in C. inornata is not affected by increasing solar radiation and temperature. The lack of zooxanthellae could make this species less dependent on these environmental parameters, as previously hypothesized for another azooxanthellate species, Leptopsammia pruvoti, investigated along the same gradient.

Over the past few decades, modern coral taxonomy, combining morphology and molecular sequence data, has resolved many long-standing questions about scleractinian corals. In this study, we sequenced the complete mitochondrial genomes of three Merulinidae corals (Dipsastraea rotumana, Favites pentagona, and Hydnophora exesa) for the first time using next-generation sequencing. The obtained mitogenome sequences ranged from 16,466 bp (D. rotumana) to 18,006 bp (F. pentagona) in length, and included 13 unique protein-coding genes (PCGs), two transfer RNA genes, and two ribosomal RNA genes . Gene arrangement, nucleotide composition, and nucleotide bias of the three Merulinidae corals were canonically identical to each other and consistent with other scleractinian corals. We performed a Bayesian phylogenetic reconstruction based on 13 protein-coding sequences of 86 Scleractinia species. The results showed that the family Merulinidae was conventionally nested within the robust branch, with H. exesa clustered closely with F. pentagona and D. rotumana clustered closely with Favites abdita. This study provides novel insight into the phylogenetics of species within the family Merulinidae and the evolutionary relationships among different Scleractinia genera.

Abstract On most tropical coral reefs, decades of disturbances have ratcheted down coral cover to create low abundance communities. In such a state, the reefs of St. John, US Virgin Islands, were hit by two Category 5 hurricanes in September 2017, yet the effects on two sites dominated by Orbicella annularis were minor in terms of coral cover. To explore the implications of this outcome, the fates of O. annularis colonies were determined from photoquadrats and used to prepare size‐based matrix models for the year preceding the storms and the four months bracketing the storms. The populations displayed contrasting dynamics from 1988 to July 2017, with coral cover declining from 43% to 5% at Yawzi Point but remaining at ~30% at Tektite. Over this period, colony sizes declined, with ≥82% having planar areas ≤50 cm2 (i.e., the smallest size class) by July 2017, and while densities declined from 47 to 8 colonies/m2 at Yawzi Point, they increased from 36 to 51 colonies/m2 at Tektite. Hurricanes Irma and Maria depressed coral cover by 1–4%, transitioned colonies into the smallest size class (>87% by November), killed 27% and 5% of the colonies in the smallest size class at Yawzi Point and Tektite, respectively, and depressed the 5‐yr intrinsic rate of population growth (λ) to 0.53–0.87. Twenty‐year projections suggested these demographic effects will not have ecologically meaningful impacts on population size, at least compared to projections initiated assuming Hurricanes Irma and Maria had not occurred. With low cover of O. annularis distributed among many small colonies, future disturbances may play more important roles in winnowing the few remaining host genotypes rather than further depressing coral cover.

Over half of all extant stony corals (Cnidaria: Anthozoa: Scleractinia) harbour endosymbiotic dinoflagellates of the family Symbiodiniaceae, forming the foundational species of modern shallow reefs. However, whether these associations are conserved on the coral phylogeny remains unknown. Here we aim to characterise Symbiodiniaceae communities in eight closely-related species in the genera Merulina, Goniastrea and Scapophyllia, and determine if the variation in endosymbiont community structure can be explained by the phylogenetic relatedness among hosts. We perform DNA metabarcoding of the nuclear internal transcribed spacer 2 using Symbiodiniaceae-specific primers on 30 coral colonies to recover three major endosymbiont clades represented by 23 distinct types. In agreement with previous studies on Southeast Asian corals, we find an abundance of Cladocopium and Durusdinium, but also detect Symbiodinium types in three of the eight coral host species. Interestingly, differences in endosymbiont community structure are dominated by host variation at the intraspecific level, rather than interspecific, intergeneric or among-clade levels, indicating a lack of phylogenetic constraint in the coral-endosymbiont association among host species. Furthermore, the limited geographic sampling of four localities spanning the Western and Central Indo-Pacific preliminarily hints at large-scale spatial structuring of Symbiodiniaceae communities. More extensive collections of corals from various regions and environments will help us better understand the specificity of the coral-endosymbiont relationship.

Background The coral genus Acropora contains more than 150 species with very high morphological diversity. This high diversity may have been caused by repeated hybridization via mass spawning. However, we have little information whether hybrids are formed in these corals. Identifying morphological differences between hybrids and their parental species would provide an opportunity to find wild hybrids in the field and to understand how colony shapes of Acropora have become highly diversified throughout evolutionary history. In the two morphologically distinctive coral species Acropora florida and A. intermedia in the Indo-Pacific, their gametes show high rates of bi-directional intercrossing in vitro, and thus these two species are ideal species to investigate the morphological traits of the hybrids. Methods We examined morphological characters of F1 hybrids from A. florida to A. intermedia, which were produced from in vitro crossing experiments. To compare morphological differences, we grew juveniles and mature colonies of reciprocal F1 hybrids (FLOint: A. florida eggs × A. intermedia sperm, and INTflo: A. intermedia eggs × A. florida sperm) and of the parental species (purebreds of A. intermedia and A. florida). We analyzed skeletal morphology such as colony size, branch length, and branching number, and compared them with those of a putative F1 hybrid between A. florida and A. intermedia found in the field. We also confirmed the molecular phylogenetic position of F1 hybrids, parental species, and a putative F1 hybrid using the mitochondrial non-coding region. Results Our morphological analysis revealed that branching number of the F1 hybrids was intermediate relative to the parental species. Moreover, the FLOint hybrids were morphologically more closely related to the maternal species A. florida, and the INTflo hybrids were to A. intermedia. Molecular data showed that A. florida and A. intermedia were clearly divided into two clades, and that F1 hybrids grouped in the clade based on their maternal parent. A very similar pattern to the INTflo hybrids was obtained for the putative F1 hybrid in nature. Discussion Our results revealed that F1 hybrids between two Indo-Pacific species A. florida and A. intermedia had intermediate morphology relative to their parent species but reflected the maternal parent more. Similarity to maternal species in hybrids is opposite to the Caribbean Acropora species that had more paternal morphological characters in hybrids. These results further suggest that some genetic factor in eggs is likely to affect determination of colony shape in the Indo-Pacific. At present, we have considered colonies with intermediate morphs between different species to be intra-specific morphological variation, but they may be real F1 hybrids. Indeed, a putative F1 hybrid represented similar morphological and molecular features to the F1 hybrids, and thus it is plausible to be attributed as a “real” F1 hybrid in nature.

Marine organisms and their associated microbes are rich in diverse chemical leads. With the development of marine biotechnology, a considerable number of research activities are focused on marine bacteria and fungi-derived bioactive compounds. Marine bacteria and fungi are ranked on the top of the hierarchy of all organisms, as they are responsible for producing a wide range of bioactive secondary metabolites with possible pharmaceutical applications. Thus, they have the potential to provide future drugs against challenging diseases, such as cancer, a range of viral diseases, malaria, and inflammation. This review aims at describing the literature on secondary metabolites that have been obtained from Scleractinian-associated organisms including bacteria, fungi, and zooxanthellae, with full coverage of the period from 1982 to 2020, as well as illustrating their biological activities and structure activity relationship (SAR). Moreover, all these compounds were filtered based on ADME analysis to determine their physicochemical properties, and 15 compounds were selected. The selected compounds were virtually investigated for potential inhibition for SARS-CoV-2 targets using molecular docking studies. Promising potential results against SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and methyltransferase (nsp16) are presented.

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.