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Coral reefs are known to be one of the most diverse marine ecosystems on earth. However, these important ecosystems are heavily stressed by natural and anthropogenic activities. Environmental DNA (eDNA) metabarcoding is an innovative approach that can provide a greater diversity of taxonomic detections, non-invasive sampling, and a lower field component cost than traditional biomonitoring methods. Taiping Island (Itu Aba Island) is one of the major coral reef islands situated in the South China Sea where underwater visual surveys documented an outbreak of Crown-of-Thorns starfish (COTS) in 2021. In our study, we used eDNA metabarcoding to investigate whether there were shifts in coral communities by comparing pre- and post-COTS outbreak communities. One metabarcoding assay targeting the 18S gene and two assays targeting the ITS2 region (one of these assays specifically targeting Acroporid corals) were applied to 42 seawater samples collected in 2019 and 2021 from 12 sites around Taiping Island. Based on these three metabarcoding assays, 52 unique hard coral species were identified, corresponding to a total of 51 species in 2019 and 26 species in 2021. Our results indicated a significant decline in coral diversity but an increase in sponge diversity from the phylum porifera at Taiping Island in 2021. We suggest that these faunal shifts may be due to active feeding and disturbance of COTS at outbreak proportions that result in habitat changes. Our findings also suggest that eDNA can continue to serve as a promising tool to monitor the change in coral as well as reef-associated taxa during devastating outbreak events. [ABSTRACT FROM AUTHOR]

The capacity for natural coral reef recovery and the effectiveness of active restoration efforts are often contingent upon uncertain and understudied background variables, such as chronic predation for example. In the Maldives, small coral colonies (< 10 cm), primarily from the genera Pocillopora and Acropora (often found recolonising degraded reefs) are frequently predated on by the spiny cushion sea-star (Culcita schmideliana). Incidentally, these same corals (especially Acroporids) are often prioritised in active reef restoration practices. However, the level of risk these corallivores pose on restoration success has not yet been assessed. Here, we aimed to initially document the population densities of C. schmideliana on a degraded reef system in the Maldives (Kunfunadhoo, Baa Atoll). We then assessed their associated predatory effects on coral recruits and transplants, and explored the benefits of C. schmideliana removal on the survival of these corals. Population densities ranged between 1.2 and 3.3 individuals per 100 m2, which resulted in high predation rates on coral recruits (4 – 20%) and transplants (11 – 43%). Culcita schmideliana predation accounted for the majority of the documented mortality (85%). Where C. schmideliana were removed, a significant increase in survival for recruits (9% higher) and transplants (24% higher) was shown. Further observations linked a cessation of C. schmideliana removal to a significant rise in predation instances for previously protected corals (up to 52%). Our study therefore highlights the severe impacts of C. schmideliana predation and shows Culcita spp. population management as a viable passive solution for effective reef restoration. [ABSTRACT FROM AUTHOR]

In the face of rising global temperatures, coral reefs experience coral mass bleaching and mortality. Subtropical and mesophotic environments may represent refugia for reef corals under climate change, where they can survive and eventually recolonize degraded areas. Using a comprehensive database of fossil reefs, we empirically assess the efficacy of subtropical, deeper, and turbid mesophotic environments to restore coral reefs after past global warming events. We focus on tropical coral reefs over the last 275 million years and four rapid climate warming events, which coincided with global reef crises in the geological record. In the aftermath of such hyperthermal events, we observed an increase in the proportions of reefs occurring in deeper (blue) mesophotic environments. Additionally, we found a trend of reef distributions and coral shifting towards higher latitudes. The number of coral occurrences in turbid (brown mesophotic) environments also increased after hyperthermal events. Our results suggest that subtropical, blue, and brown mesophotic environments may have served as immediate refugia for shallow-water coral species escaping warming seawater. While the patterns of reef range shifts and the establishment of blue and brown mesophotic refugia following ancient hyperthermal events provide some hope for coral reefs under current climate change, re-establishement of background reef conditions took most times millions of years. Ante el incremento de temperatura global, los arrecifes coralinos están experimentando eventos masivos de blanqueamiento y mortalidad. Los ambientes subtropicales y mesofóticos pueden representar refugios para los corales arrecifales, en los cuales pueden escapar de los efectos del cambio climático, sobrevivir y desde allí recolonizar áreas previamente degradadas. Mediante el uso de una exhaustiva base de datos en arrecifes coralinos, en este estudio se evaluó empíricamente la eficacia de los ambientes subtropicales y mesofóticos, tanto de aguas turbias someras (marrones) como de aguas claras profundas (azules), en la recuperación de arrecifes coralinos después de eventos hipertermales en el pasado. Nuestro enfoque estuvo en los arrecifes coralinos tropicales durante los últimos 275 millones de años y cuatro eventos de calentamiento climático rápido, los cuales coinciden con crisis globales en la ocurrencia de arrecifes en el registro fósil. Como consecuencia de dichos eventos hipertermales, observamos un aumento del número de arrecifes en ambientes mesofóticos de aguas profundas (azules). Además, encontramos una tendencia en la distribución de arrecifes y corales que se desplazan hacia latitudes más altas. También se observó un aumento en el número de corales que estuvieron presentes en ambientes de aguas turbias (marrones) después de dichos eventos hipertermales. Nuestros resultados sugieren que, en el pasado, los ambientes subtropicales, mesofóticos azules y mesofóticos marrones pudieron haber servido como refugios inmediatos para las especies de coral de aguas someras, en los cuales encuentran condiciones atenuantes ante el calentamiento oceánico. Si bien los patrones de desplazamiento de los arrecifes en el rango latitudinal y el establecimiento de refugios mesofóticos de aguas marrones y azules posteriores a eventos hipertermales brindan una luz de esperanza para el futuro de los arrecifes coralinos de cara al cambio climático actual, nuestros resultados evidencian que el restablecimiento de los arrecifes puede tomar millones de años. [ABSTRACT FROM AUTHOR]

Investigating coral recruitment is critical to better understand replenishment and resilience capacities of coral reef ecosystems and to improve their conservation. Here, we examined the spatio‐temporal patterns of coral recruitment and the influence of confamilial adult coral cover in the region of Toliara, southwest Madagascar. Terracotta tiles were immersed from October to late January over a 3‐year period (2018–2021) at 10 stations located on major reef habitats. Overall recruitment rates were relatively high compared to those of other reefs in the Southwestern Indian Ocean, ranging from 219.20 recruits.m−2 in 2018–2019 to 156.30 recruits.m−2 in 2020–2021. Recruit assemblages were dominated by Acroporidae (45.5%) and Pocilloporidae (45.0%), whereas Poritidae (1.9%) and "other" recruits (3.6%) were rarely recorded. Recruitment patterns varied among stations and habitats, with higher rates in patch reef (187.06 recruits.m−2) and outer slope stations (156.99 recruits.m−2) compared to inner slope stations (108.04 recruits.m−2). With the exception of "other" recruits, recruitment rates decreased between 2018 and 2019 and 2019 and 2020, followed by an increase in 2020–2021 that reached or even exceeded initial values at some stations. The abundance of Pocilloporidae recruits was positively correlated with the cover of confamilial adult corals, highlighting potential stock–recruitment or recruitment–limitation relationships, or an aggregative settlement of young stages near the established adult colonies, whereas no such relationships were recorded for other coral family categories. This study identified sites on the outer slope and patch reefs to consider prioritizing for protection as recruitment hotspots, as well as degraded inner slope sites that could benefit from restoration, with the important caveat that any measures should be accompanied by alternative income‐generating activities through local involvement that suits the Malagasy context, such as locally marine managed areas. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Efforts to restore coral reefs usually involve transplanting asexually propagated fast-growing corals. However, this approach can lead to outplanted populations with low genotypic diversity, composed of taxa susceptible to stressors such as marine heatwaves. Sexual coral propagation leads to greater genotypic diversity, and using slow-growing, stress-tolerant taxa may provide a longer-term return on restoration efforts due to higher outplant survival. However, there have been no reports to date detailing the full cycle of rearing stress-tolerant, slow-growing corals from eggs until sexual maturity. Here, we sexually propagated and transplanted two massive slow-growing coral species to examine long-term success as part of reef restoration efforts. Coral spat were settled on artificial substrates and reared in nurseries for approximately two years, before being outplanted and monitored for survivorship and growth for a further four years. More than half of initially settled substrates supported a living coral following nursery rearing, and survivorship was also high following outplantation with yields declining by just 10 to 14% over four years. At 6-years post-fertilisation over 90% of outplanted corals were reproductively mature, demonstrating the feasibility of restoring populations of sexually mature massive corals in under a decade. Although use of slower growing, stress tolerant corals for reef restoration may provide a longer-term return on investment due to high post-transplantation survival rates, considerable time is required to achieve even modest gains in coral cover due to their relatively slow rates of growth. This highlights the need to use a mix of species with a range of life-history traits in reef restoration and to improve survivorship of susceptible fast-growing taxa that can generate rapid increases in coral cover. [ABSTRACT FROM AUTHOR]

Petrarca is an ascothoracidan endoparasite in scleratinian dendrophyllid corals. Petrarca can stimulate coral growth, forming a gall chamber to house itself inside the coral skeleton. The diversity, molecular phylogeny and feeding ecology of Petrarca are understudied. This is the first study of Petrarca to be based on light and scanning electron microscopy to document the fine-scale external and functional morphology of its trophi and other structures. A combined molecular and morphological approach revealed at least four closely related species of Petrarca , P. goanna , P. morula , Petrarca nozawai sp. nov. and Petrarca rubus sp. nov. in Turbinaria and Astreopora corals in Asia. Carapace shape and fine morphology, ultrastructure of the antennular aesthetasc, morphological characteristics of the trophi and the shape and size of the penis rami are diagnostic characters. Several morphological characters, which are all probably synapomorphies, have been proposed to distinguish the genus Petrarca from other Ascothoracida. Mouthparts morphology of Petrarca are developed for cutting and chewing, rather than for piercing and sucking as in many other Ascothoracida. The external surface of the carapace of Petrarca is ornamented with densely packed secretory papillae used putatively for the chemical dissolution of the substrate necessary for the formation of the gall chamber. [ABSTRACT FROM AUTHOR]

The invasive sun corals Tubastraea spp. were introduced to Brazil in the late 1980s. The invasion prompted rapid changes in seascapes and local biological communities by excluding native species, particularly sessile ones. However, little is known about the impact on the mobile invertebrates. Using an experimental approach this study investigated the effects of living and dead sun corals and coral cover (50 vs. 100% covered areas) on the taxonomic composition, diversity (H') and abundance of reptant and natant macro-crustaceans and tanaids at the species level. Experimental units consisted of 60 tiles measuring 400 cm2, half and fully covered with living or dead corals which were deployed between 3 and 5 m for 12 months on concrete blocks. A total of 1346 specimens of decapods were obtained (27 native and 1 invasive species). 1059 specimens of the tanaid Chondrochelia dubia were sampled. The overall taxonomic composition was neither affected by coral condition (live or dead) nor by coral cover area. The diversity of reptant and natant species responded differently to coral condition and coral cover. The combination of dead corals and full cover accounted for the highest abundance of reptants. Natant abundance was influenced by coral cover area, irrespective of coral condition. The positive relationship between body size and abundance was statistically significant. Abundance of the obligate tube builder C. dubia was favoured by the greater availability of space on blocks half covered by corals. No signs were found of invasion meltdown in the mobile crustacean fauna. [ABSTRACT FROM AUTHOR]

Middle Jurassic reefs are known and studied from a wide range of palaeolatitudes, yet southern Tethyan reefs have been relatively understudied. The high abundance of stromatoporoids in southern Tethyan reefs was suggested to indicate a tolerance to oligotrophic and overheated waters. Recent studies affirmed the longtime hypothesis of a warm equable climate in low palaeolatitudes during the Jurassic, which could account for the documented low diversities of low-latitudinal coral reefs during this time interval. We present a case study showing possible evidence for the suggested connection between heat stress, low coral diversity and the success of stromatoporoids in the southern Tethys. The study focuses on the unique erosional depression of Makhtesh Gadol, southern Israel, which preserves a continuous section of the Callovian (Middle Jurassic). It is rich in fossils of benthic macrofauna, especially patch reefs of corals and stromatoporoids. Our quantitative analysis shows, for the first time: (1) a variation between a low- and high-diversity of coral patch reefs; and (2) a major shift from coral-dominated patch reefs in the lower part of the section to dominating stromatoporoids in the upper part. The faunal assemblage is used to reconstruct the depositional environment, indicating a shallowing upwards and increasing warmer waters. Patch reef beds showing low coral diversity are correlated with isotopic reconstructions from the same section, providing evidence for elevated water temperatures. The faunal transition from corals to stromatoporoids is correlated with a similar shift in Saudi Arabia, improving the regional correlation to the Arabian Carbonate Platform. [ABSTRACT FROM AUTHOR]

Sexually produced juvenile scleractinian corals play a key role in the adaptation process of coral reefs, as they are considered to possess an innate plasticity and thus can adjust to changing environmental parameters within a certain range. In this study we investigated in detail the early life stages of the brooding species Leptastrea purpurea to identify, categorize and visualize the critical steps of the complex transformation process from a swimming coral larva to a sessile coral recruit and later to a coral colony. For that, we performed settlement experiments using previously known cues: cycloprodigiosin (CYPRO) and crustose coralline algae (CCA) as well as novel cues: crude extracts of Pseudoalteromonas espejiana and P. piscicida to identify a general, cue-independent settlement pathway. We monitored the development of L. purpurea over 12 months using bright field and fluorescence microscopy. Also we identified the fluorescence signals of L. purpurea with confocal microscopy at four crucial development steps: (A) swimming larva, (B) metamorphosing larva, (C) coral recruit and (D) adult coral. Our methodological approach allowed us to observe an ontogenetic shift of fluorescence signals which provokes the hypothesis that certain fluorescence patterns might be connected to distinct sequential functions in the early life cycle of scleractinian corals. Our observations showed great similarities to the early development of other brooding and spawning corals, making L. purpurea a prospective candidate to be used as a model organism for coral research. Furthermore, our in-depth picture series provides a robust monitoring reference for coral nurseries or field applications and demonstrates the potential of fluorescence as an indicator to instantly determine the growth stage of a developing coral recruit.

Introduction: One of the main bottlenecks in restoration projects based on sexual reproduction is post-settlement survival, mainly due to competition for substrate with fleshy algae and predation. Therefore, substrates of different shapes and materials have been created and tested, seeking to optimize these processes with attractive surfaces for the larvae and structures where the recruits are protected from predation, and competition is reduced. Objective: To improve settlement and post-settlement survival of two important Caribbean reef-building corals, using different coatings on substrates. Methods: To determine whether substrate coatings properties are favourable to larval settlement in Orbicella annularis, and O. faveolata, collected in Puerto Morelos, Mexican Caribbean, we evaluated their settlement for three weeks on six coatings with a combination of properties. Each coating was designed to provide a combination of two out of three properties: 1) water repellence (hydrophobicity), 2) phosphorescence-based colour, and 3) mineral-enriched surface chemistry. In a separate experiment larvae settlement was tested using coatings with a single property. Finally, we determined the post-settlement survival of O. annularis and O. faveolata on the different coatings for seven weeks. Results: The combination of high hydrophobicity and light blue phosphorescent microparticles and high hydrophobicity and red-orange phosphorescent microparticles resulted in a higher settlement of O. annularis and O. faveolata when compared with other coatings (30.8 - 66.7 % higher). No significant differences were found in the number of larval settled when the water-repellence and the phosphorescence-based were evaluated independently. Post-settlement survival time on substrates was low, with a maximum of 34 days after settlement for O. annularis and 42 days for O. faveolata. Conclusions: In terms of the larval settlement, the combination of the coatings properties appears to play an essential role in the choice of microhabitat for both O. annularis and O. faveolata. But individually these properties did not generate an advantage in the larval settlement. Moreover, some chemical components associated with the coatings may be counterproductive to the survival of the polyps over time. [ABSTRACT FROM AUTHOR]

Accurate identification of scleractinian coral species is fundamental for proper biodiversity estimates, for aiding in efforts of reef monitoring, conservation, restoration, and for the management of coral reefs. Here, we provide the first DNA barcoding reference library for coral species in Eilat, Red Sea, based on the mitochondrial gene cytochrome c oxidase subunit I (COI), targeting the identification of stony coral species from shallow (0–12 m) reefs. A total of 191 specimens were collected, depicting 14 families, 39 genera, and 94 species (all are new full species records to the BOLD system). Three species (Sclerophyllia margariticola, Cyphastrea magna, and Psammocora profundacella) are first records for Eilat's coral reef. The results presented here strengthen the claim that COI is not universally informative for delimitation of stony coral species, a notion reinforced by the constructed maximum likelihood phylogenetic tree. This library is the first step in a long journey towards elucidating coral biodiversity in the coral reef at Eilat and for improving future management and monitoring efforts. [ABSTRACT FROM AUTHOR]

The abundance and health of scleractinian coral communities of Hormuz Island were investigated. For this purpose, we employed 20 m line intercept transects—12 in the intertidal zone and 15 subtidally to evaluate coral cover and community composition. The estimated dead coral coverage was 6.21%±0.81%, while live coral coverage was 16.93%±1.81%, considered as very poor. Totally, 12 genera were recorded, of which Porites with 11.9%±1.4% live cover was the dominant, while Goniopora had the least cover (0.07%±0.08%). Based on Mann-Whitney U-test, live coral coverage, dead coral coverage, algal coverage, cover of other benthic organisms and abiotic components showed significant univariate differences between zones (p<0.05). The Spearman correlation test between the abundance of biotic and abiotic components indicated significant negative correlation of live coral and sand with zoantharian and significant positive correlation of algae and other benthic organisms with rubble. The reef health indices used for the corals indicated that, in general, the environmental conditions were not suitable, which could be attributed to both natural and anthropogenic factors, the most important of which was zoantharian' overgrowth on the scleractinian corals in this region. [ABSTRACT FROM AUTHOR]

Microbes play a key role in reef dynamics, mediating the competition between scleractinian corals and benthic algae; however, major shifts in bacterial communities among coral species in response to increases in the abundance of algae are not well understood. We investigated the taxonomic composition of coral-associated microbial communities under algae-overgrowth conditions using 16S rRNA gene sequencing. The results showed that non-algal (i.e., healthy) tissue (HH) had lower bacterial abundance and diversity than tissue collected from the coral–algae interface boundary (HA) and areas of algae growth (AA). Specifically, the HA and AA samples had higher relative abundances of Saprospiraceae, Rhodobacteraceae, and Alteromonadaceae. Compared with Platygyra sp. and Montipora sp., the physiological response of Pocillopora sp. was more intense under algae-induced stress based on microbial gene function prediction. Our results indicate that algal pressure can significantly alter the microbial community structure and function of coral ecosystems. Our data thus provide new insight into the relationship between corals and their microbiome under environmental stress. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 FST 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 siteD0.321 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. [ABSTRACT FROM AUTHOR]

Members of the ammonium transporter family occur in all domains of life. However, they have been characterized, at the molecular level, mainly in bacteria and plants, whereas in animals their molecular characterization is limited to a few species. In marine invertebrates, recent studies have reported a multitude of physiological functions in which ammonium could take part. Among them, calcification is one for which very few data are available. In scleractinian corals, it has been reported that external sources of ammonium and/or ammonium containing compounds enhance calcification. However, despite these physiological insights, the underlying transport mechanisms are still unknown at the molecular level. In this study, we performed a first molecular characterization of ammonium transporters in the scleractinian coral Stylophora pistillata. By performing differential gene expression analysis, through quantitative real-time PCR, we show that S. pistillata ammonium transporters possess different tissue specificities. Most notably, one ammonium transporter, spiAMT1d, is specifically expressed in the coral tissue containing the calcifying cells. Furthermore, we determined spiAMT1d subcellular localization by immunostaining S. pistillata histological cross-sections and show that it localizes on the apical side of the calcifying cells and in their intracellular compartments. Taken together our results strongly suggest a role of ammonium transporters in coral calcification and lay the groundwork for many future studies aiming to better elucidate the potential role of ammonium in calcification. [ABSTRACT FROM AUTHOR]

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 FST 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.

Ocean acidification (OA) poses a major threat to calcifying organisms such as reef-building corals, typically leading to reduced calcification rates. Mechanisms to compensate the effects of OA on coral growth may, however, involve processes other than calcification. Yet, the physiological patterns mediating coral growth under OA are not fully understood, despite an extensive body of literature characterizing physiological changes in corals under OA. Therefore, we conducted a three-month laboratory experiment with six scleractinian coral species (Acropora humilis, Acropora millepora, Pocillopora damicornis, Pocillopora verrucosa, Porites cylindrica, and Porites lutea) to assess physiological parameters that potentially characterize growth (calcification, volume, and surface area), maintenance (tissue biomass, and lipid and protein content), and cellular stress (apoptotic activity) response under ambient (pH 7.9) and low pH (pH 7.7). We identified genus- and species-specific physiological parameters potentially mediating the observed growth responses to low pH. We found no significant changes in calcification but species showed decreasing growth in volume and surface area, which occurred alongside changes in maintenance and cellular stress parameters that differed between genera and species. Acropora spp. showed elevated cellular stress and Pocillopora spp. showed changes in maintenance-associated parameters, while both genera largely maintained growth under low pH. Conversely, Porites spp. experienced the largest decreases in volume growth but showed no major changes in parameters related to maintenance or cellular stress. Our findings indicate that growth- and calcification-related responses alone may not fully reflect coral susceptibility to OA. They may also contribute to a better understanding of the complex physiological processes leading to differential growth changes of reef-building corals in response to low pH conditions.

The article presents data indicating the relationship of the bathymetric distribution of solitary endemic scleractinian corals inhabiting the Antarctic continental shelf and upper continental slope with the vertical density of the Antarctic Circumpolar Current. The study is based on materials collected by expeditions of the Shirshov Institute of Oceanology (IO RAS) and the literature data. The results show that endemic species that appeared in the Late Neogene and Pleistocene were unable to propagate across other oceans due to the existing horizontal and vertical density of the Arctic Circumpolar Current during that period. [ABSTRACT FROM AUTHOR]

Skeletons of contemporary reef‐building scleractinian corals are formed of aragonite, a polymorph of the calcium carbonate (CaCO3), notwithstanding calcite being a more stable phase under the condition of coral habitats. Circumstances developing aragonite in coral calcification have been addressed currently. Considering that the symbiotic relationship between the coral host and dinoflagellate algae (zooxanthellae) is perhaps relevant to coral calcification, we studied the impact of these symbiotic relationships on CaCO3 polymorph selection. Juvenile scleractinian corals (Acropora tenuis and Acropora digitifera) absent symbionts were cultured in seawaters with varied Mg/Ca molar ratios (mMg/Ca), and the mineral phases of the skeletons were detected employing X‐ray diffraction. The findings revealed that diminutive quantities of calcite precipitated as coral skeleton in Acropora digitifera surprisingly in pseudo‐present seawater (mMg/Ca∼5). Additionally, coral developed skeletons from only calcite in seawater with an mMg/Ca < 1. The evidence gathered in this investigation suggests that the symbiotic relationship affects the establishment of aragonite skeletons in the course of coral calcification. Plain Language Summary: Skeletons of contemporary reef‐building corals are made of calcium carbonate. The calcium carbonates have polymorphs: calcite, aragonite, and vaterite. Aragonite is a component of coral skeletons, but calcite can thermodynamically precipitate more easily than aragonite in the living conditions of corals. Circumstances resulting in aragonite precipitation in coral calcification have been addressed recently. Considering that the symbiotic relationship between the coral host and dinoflagellate algae is perhaps relevant to coral calcification, we studied the impact of these symbiotic relationships on aragonite precipitation. Juvenile scleractinian corals without symbionts were cultured in seawater with varied Mg/Ca molar ratios to evaluate the effects of mineral component differences resulting from Mg/Ca molar ratio on calcium carbonate polymorphs. The mineral phases of the skeletons were identified using an X‐ray diffraction. The findings revealed that small quantities of calcite precipitated as coral skeleton in pseudo‐present seawater (Mg/Ca molar ratio of ∼5). Additionally, coral developed skeletons from only calcite in seawater with an Mg/Ca molar ratio of <1. The evidence gathered in this investigation suggests that the symbiotic relationship affects the establishment of aragonite skeletons in the course of coral calcification. Key Points: Reef‐building corals build their skeletons using calcium carbonate in aragonite form, which is thermodynamically less stable than calciteCorals build entirely calcitc skeletons in artificial seawater with low Mg/Ca ratio without a symbiotic relationship with zooxthantellaeA symbiotic relationship involves CaCO3 polymorph selection in coral calcification [ABSTRACT FROM AUTHOR]

This study reports the first attempt to quantitatively describe a Dendrophyllia ramea population on the Apollo bank (Ionian Sea), revealed in summer 2021 through a remotely operated vehicle (ROV) survey. The habitat description, bathymetric distribution, population density, and structure of the species were assessed by image analysis. A well-developed population of D. ramea, located on boulders on a sedimentary plateau at 70–80 m depth, was observed. The density ranged on average between 0.17 ± 0.04 and 0.8 ± 2.4 colonies m–2 with dense patches up to 8 colonies m–2. The population consisted primarily of many isolated single corallites and colonies of various sizes, some of which reached a maximum height of more than 40 cm. Deepwater fishing activities, primarily longline fishing, negatively affected this species. The newly collected data add knowledge about this vulnerable scleractinian coral. The documented negative effect of fishing activities on vulnerable marine ecosystem (VME) species further highlights the need for urgent conservation measures.

Accurate identification of scleractinian coral species is fundamental for proper biodiversity estimates, for aiding in efforts of reef monitoring, conservation, restoration, and for the management of coral reefs. Here, we provide the first DNA barcoding reference library for coral species in Eilat, Red Sea, based on the mitochondrial gene cytochrome c oxidase subunit I (COI), targeting the identification of stony coral species from shallow (0–12 m) reefs. A total of 191 specimens were collected, depicting 14 families, 39 genera, and 94 species (all are new full species records to the BOLD system). Three species (Sclerophyllia margariticola, Cyphastrea magna, and Psammocora profundacella) are first records for Eilat’s coral reef. The results presented here strengthen the claim that COI is not universally informative for delimitation of stony coral species, a notion reinforced by the constructed maximum likelihood phylogenetic tree. This library is the first step in a long journey towards elucidating coral biodiversity in the coral reef at Eilat and for improving future management and monitoring efforts.

Microbes play a key role in reef dynamics, mediating the competition between scleractinian corals and benthic algae; however, major shifts in bacterial communities among coral species in response to increases in the abundance of algae are not well understood. We investigated the taxonomic composition of coral-associated microbial communities under algae-overgrowth conditions using 16S rRNA gene sequencing. The results showed that non-algal (i.e., healthy) tissue (HH) had lower bacterial abundance and diversity than tissue collected from the coral–algae interface boundary (HA) and areas of algae growth (AA). Specifically, the HA and AA samples had higher relative abundances of Saprospiraceae, Rhodobacteraceae, and Alteromonadaceae. Compared with Platygyra sp. and Montipora sp., the physiological response of Pocillopora sp. was more intense under algae-induced stress based on microbial gene function prediction. Our results indicate that algal pressure can significantly alter the microbial community structure and function of coral ecosystems. Our data thus provide new insight into the relationship between corals and their microbiome under environmental stress.

Species identification for spawning corals relies heavily on morphology. Recent molecular phylogenetic approaches have demonstrated the limits of traditional coral taxonomy based solely on skeletal morphology. Merulinidae is considered a complex taxonomic group, containing 24 genera and 149 species. This family is one of the most taxonomically challenging and its taxonomy has largely improved in recent studies. However, studies of the phylogeny of Merulinidae are constrained by limited geographic scales. In Taiwan, merulinid corals are dominant in non-reefal communities on northeast coasts and they consistently spawn between summer and fall. This study is a first attempt to establish a molecular database of merulinid corals in this new area, including a volcanic island (Kueishan Island), and provide information about sexual reproduction. We analyzed 65 specimens, including 9 genera and 28 species collected from Taiwan using one mitochondrial marker (COI: cytochrome c oxidase subunit 1 gene) and three nuclear markers (ITS: nuclear ribosomal internal transcribed spacer, 28S rDNA D1 and D2, and histone H3) to re-examine phylogenetic relationships and search for new species. Overall, 58 COI sequences, 59 for ITS, 63 for 28S, and 62 histone sequences were newly obtained from the collected specimens. The reconstructed molecular tree demonstrates that all the specimens and reference sequences we examined are clustered within Merulinidae. Subclades A, B, C, D/E, F, G, H, and I are congruent with previous studies. However, Astrea curta is separated from the other congeneric species, Astrea annuligera (XVII-B), which is a sister to Favites and defined as a new subclade K. In addition, two new species (Paragoniastrea deformis and Paragoniastrea australensis) were discovered for the first time in Taiwan, and we defined them as a new subclade J. In addition, A. curta, P. auastralensis, and P. deformis are all hermaphroditic spawners and released bundles in July. This study greatly improves the accuracy of biodiversity estimates, systematic taxonomy, and reproduction for Taiwan’s coral ecosystem.

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.)

Although cold-water coral (CWC) biology, physiology, and connectivity, have been extensively studied, few studies have so far focused on their reproductive biology. The reproductive biology of colonies of the reef-building Lophelia pertusa (Linnaeus 1758), now synonymised as Desmophyllum pertusum , and Madrepora oculata (Linnaeus 1758) from the Mediterranean Sea, an area particularly exposed to the effects of anthropogenic pressures, was investigated for the first time using histological techniques. Samples were collected from the Lacaze-Duthiers canyon in the Gulf of Lion, northwestern Mediterranean Sea, where the corals are living at 13 °C, close to their upper limit of thermal tolerance. The gametogenic cycle suggests a seasonal spawning of D. pertusum in autumn to early winter, similarly to population from the Gulf of Mexico. This period corresponds to the formation of storm-induced deep-sea water plumes, likely acting as a time giver for coral spawning and facilitates larval dispersal. Madrepora oculata shows continuous reproduction as already identified in eastern and western North Atlantic, with reproductive features of a species less opportunistic than D. pertusum , consistent with its other biological characteristics. This difference between the two species is of paramount importance to define strategies of conservation. • First data on the reproduction of two cold-water corals in the Mediterranean Sea. • Potential spawning date in autumn and/or early winter for Desmophyllum pertusum. • Role of deep-sea currents in timing of spawning for this species. • Madrepora oculata harbor different strategy, with a continuous reproduction. [ABSTRACT FROM AUTHOR]

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, Ca2＋-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 Ca2＋-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 Ca2＋-ATPase activity in combination with increased metabolism. Implementing OA increases the concentration of CO 2 throughout the entire tissue, thereby increasing the availability of C O 3 − in the ECM. As a result, the model finds that calcification becomes more energy-demanding and the calcification rate increases. • Several hypotheses on coral calcification are tested using a computational model. • The model is able to reproduce the experimental data of three separate studies. • The model finds that paracellular ion transport into the ECM plays a minor role. • Implementing OA in the model increased the calcification rate and ATP consumption. • In the model, LEC is the result of increased metabolism and Ca 2 + -ATPase activity. [ABSTRACT FROM AUTHOR]

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. • Microsatellites are the most widely used markers in the study of genetic populations in scleractinian corals. • In spite of 1500 species of scleractinian corals, only 117 species have been studied for population genetics. • The two most studied ecoregions are those included in the Caribbean Sea and the Great Barrier Reef. • The most studied species are those of the genus Acropora and Pocillopora. [ABSTRACT FROM AUTHOR]

The Berriasian carbonate successions cropping out in the shallow-water platform of the easternmost Prebetic Domain (SE Spain) involve reef-associated environments including a diverse epibiota with diceratid representatives unreported so far. Interpretation of different sub-environments suggests a proximal-distal shallow platform transect. In the shallowest nearshore environment, high energy conditions are recorded, with fine-grained bioclasts interbedded with episodes with black pebbles. Subsequently, a more restricted intra-platform environment is represented by oncoidal rudstones with benthic foraminifera, photophilic microencrusters, microbial-type coatings, mud mounds and a rich record of epibenthic biota preserved in life position (diceratid patches, stromatoporoids, and a diverse coral assemblage). This association points to relatively stable and restrictive low-energy conditions in a proximal shallow-water subtidal environment below the fair-weather wave base. Distally, a deeper, opener setting is established. Here, phaceloid and thin-laminated corals are preserved in life position in a calpionellid-rich matrix typifying a mesophotic reefal complex with clear open marine influence. Biostratigraphical analysis performed mainly on benthic foraminifera, algae, diceratids, and coral representatives allows to specify a Berriasian age for these facies. New occurrence data are also reported, such as the oldest record of the coral genus Floriastrea worldwide. The highly diverse coral assemblages reveal a species-level taxonomic divergence in relation with taxa from the same biochore and palaeogeographical domain, supporting the endemic condition for this fauna. The first report of diceratids in the Eastern Prebetic around the J/C transition evokes Heterodiceras as possible precursor of the Cretaceous rudist build-ups developed in the Urgonian platforms in the Prebetic Domain. [Display omitted] • Berriasian reefal habitats from the Betic Range are described for the first time. • Epibenthic biota reveals a deepening transect (nearshore to open sea environments). • Berriasian diceratids are recorded for the first time in the South-Iberian margins. • Earliest occurrence data of the genus Floriastrea worldwide is settled. • The biogeographical endemic condition is inferred from the coral and rudist faunas. [ABSTRACT FROM AUTHOR]

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.)

Species identification for spawning corals relies heavily on morphology. Recent molecular phylogenetic approaches have demonstrated the limits of traditional coral taxonomy based solely on skeletal morphology. Merulinidae is considered a complex taxonomic group, containing 24 genera and 149 species. This family is one of the most taxonomically challenging and its taxonomy has largely improved in recent studies. However, studies of the phylogeny of Merulinidae are constrained by limited geographic scales. In Taiwan, merulinid corals are dominant in non-reefal communities on northeast coasts and they consistently spawn between summer and fall. This study is a first attempt to establish a molecular database of merulinid corals in this new area, including a volcanic island (Kueishan Island), and provide information about sexual reproduction. We analyzed 65 specimens, including 9 genera and 28 species collected from Taiwan using one mitochondrial marker (COI: cytochrome c oxidase subunit 1 gene) and three nuclear markers (ITS: nuclear ribosomal internal transcribed spacer, 28S rDNA D1 and D2, and histone H3) to re-examine phylogenetic relationships and search for new species. Overall, 58 COI sequences, 59 for ITS, 63 for 28S, and 62 histone sequences were newly obtained from the collected specimens. The reconstructed molecular tree demonstrates that all the specimens and reference sequences we examined are clustered within Merulinidae. Subclades A, B, C, D/E, F, G, H, and I are congruent with previous studies. However, Astrea curta is separated from the other congeneric species, Astrea annuligera (XVII-B), which is a sister to Favites and defined as a new subclade K. In addition, two new species (Paragoniastrea deformis and Paragoniastrea australensis) were discovered for the first time in Taiwan, and we defined them as a new subclade J. In addition, A. curta, P. auastralensis, and P. deformis are all hermaphroditic spawners and released bundles in July. This study greatly improves the accuracy of biodiversity estimates, systematic taxonomy, and reproduction for Taiwan's coral ecosystem. [ABSTRACT FROM AUTHOR]

Coral endosymbionts act as a bio-indicator of coral ecosystem under extreme environmental conditions. The health of the coral ecosystem depends on the endosymbiont cell density of the coral hosts. Therefore, it is of interest to analyze ten coral fragments found to be under the genera Acropora, Favites, Favia, and Porites collected at various locations from Veedhalai to Mandapam, southeast coast of India during January 2019 to March 2019. The zooxanthellae cell count ranged between 4.08 (Porites sp.9) and 13.75x105 cells cm2 -1 (Favites sp.3). This indicates the health of the corals in the region. The genus (clade) level identification of endosymbionts was detected using the host excluding primers of small subunit DNA (nssrDNA). Bidirectional sequencing of 18S nrDNA gene (SSU) of all ten coral fragments show that the Veedhalai corals is associated with the genus Durusdinium (Clade D) but the corals of Mandapam is associated with the genera, Cladocopium (Clade C) and Durusdinium (Clade D). It is known that the thermal stress has negative impact on coral reef ecosystem of the world. The dominance of the genus Durusdinium in the scleractinian corals of Palk Bay may be due to frequent exposure to thermal stress. This thermotolerant endosymbionts is opportunistic. Thus, the corals of Veedhalai and Mandapam coasts, Palk Bay, India are necessarily packed with thermotolerant endosymbionts enabling conservation., Competing Interests: The authors declare no conflict of Interest, (© 2022 Biomedical Informatics.)