Search

In the face of global warming and ocean acidification, understanding the cellular mechanisms underlying coral metamorphosis and early calcification is essential, as both processes are likely to be affected by a changing environment. In this study, we used cDNA microarray expression analysis to compare transcription profiles between four distinct life stages in the 'complexa' coral Acropora millepora: 1) aposymbiotic non-calcifying planula, 2) aposymbiotic calcifying flat polyp, 3) aposymbiotic calcifying primary polyp and 4) symbiotic adult tip. Highly up-regulated genes in planulae were molecules involved in calcium signalling, lipid metabolism and development. Transcripts up-regulated in post-settlement juvenile stages regulate tissue morphogenesis, cell division and responses to oxidative stress. Transcripts with the highest expression in adult polyps are involved in responses to abiotic stimuli and asexual reproduction. Transcripts up-regulated in calcifying stages included carbonic anhydrases and organic matrix components. Additionally, our results suggest an overlap between intracellular secondary messengers following settlement and metamorphosis. A subset of fluorescent proteins were up-regulated at the planula stage but down-regulated after settlement, supporting the idea that these molecules might have a role in quenching reactive oxygen species. Altogether, our results suggest that Acropora developmental stages are transcriptionally distinct units in which transcription profiles reflect responses to different physiological and ecological conditions. [ABSTRACT FROM AUTHOR]

Ostreobium comprises endolithic algae commonly seen in conjunction with scleractinian corals. In the past, it was solely recognized as a coral skeleton bioeroder. Their relationship with corals is critical because they give photosynthetic byproducts and help the coral when it loses its primary symbionts due to stress. The variety of these algae in coral species of the genus Porites in the Tropical Eastern Pacific and western Atlantic was investigated. Ostreobium samples from seven Porites species including two from the Tropical Eastern Pacific (TEP) (P. panamensis and P. lobata) and five from the Caribbean (P. furcata, P. porites, P. colonensis, P. branneri, and P. astreoides) were extracted. Published rbcL sequences from algae found within various coral species from other parts of the world were also compared. A biogeographic analysis and two methodologies, PTP (Poisson tree process) and GMYC (general mixed Yule‐coalescent), were used to delineate the different species. The findings revealed a significant degree of genetic diversity within Ostreobium, with more than 15 groups of not more than three individuals and 40 individual lineages. Its origins date back to the Ordovician, 500 Ma, and it does not appear to preserve host specificity. The sampled locations still have a wide variety of Ostreobium. Biogeographically patterns were also confirmed, making it impossible to pinpoint the precise origins of most clades. The ancestry analyses revealed convergent events for not only the emergence of Ostreobium in a few genera of local corals, but also the phenomenon occurred in genera from far‐off places. [ABSTRACT FROM AUTHOR]

Aim: Identifying the maximum coral cover that a coral community can sustain (i.e., its 'upper limit') is important for predicting community dynamics and improving management strategies. Here, we quantify the relationship between estimated upper limits and key environmental factors on coral reefs: hard substrate availability, temperature and water clarity. Location: Great Barrier Reef (GBR), Australia (over 1400 km). Time Period: 1990 to 2022. Major Taxa Studied: Scleractinian corals. Methods: We used 32 years of data on coral cover around reef perimeters. Each reef was divided into four wave‐exposure habitats depending on prevailing wind conditions. For each site, we determined if hard coral cover had reached a plateau or upper limit. Next, we extracted existing estimates of hard substrate availability, modelled water temperature and Secchi depth. Then, we quantified the relationship between these environmental variables and the upper limits. Results: We found varying upper limits across the GBR, with a median of 33% coral cover and only 17% of the estimated upper limits exceeded 50% coral cover. Upper limits increased towards the southern reefs. Our results show that upper limits increased with increasing hard substrate availability and decreased with temperature and, to a lesser extent, with water clarity. Main Conclusions: The upper limits estimated in this study are much lower than what is commonly assumed when modelling ecological dynamics, most likely resulting in predicted recovery rates being inappropriately high. Although hard substrate ultimately restricted upper limits, there are mechanisms constraining the proportion of hard substrate that is covered by hard corals. The negative relationship between temperature and upper limits cannot be explained by changes in macroalgal abundance but may be related to changes in species composition. The quantitative relationships between the upper limits of coral cover and environmental variables will provide critical information to prioritise sites for management interventions. [ABSTRACT FROM AUTHOR]

Brazilian coral reefs are the largest and richest reefs in the Southwestern Atlantic Ocean. Despite their historical and tourist importance, coral reefs on the east coast of Brazil remained unknown until recently. This study evaluated the structure of the reef-building coral community in three tidal pools along a gradient of anthropogenic disturbance. The pool known as Dolphin Pool is the warmest and has a high abundance of stony coral Siderastrea spp. One endemic species is on the national list of threatened species. Despite the high frequency of water temperatures above the alert threshold for mass bleaching events, the tidal pools have high densities of adults and recruits of reef-building corals. The results highlight the importance of reef formations on the coastal zone of the Royal Charlotte Bank, given the uniqueness of this area, and reinforce the need for further research and adoption of adaptive conservation approaches. [ABSTRACT FROM AUTHOR]

Reproduction, embryological development, and settlement of corals are critical for survival of coral reefs through larval propagation. Yet, for many species of corals, a basic understanding of the early life‐history stages is lacking. In this study, we report our observations for ex situ reproduction in the massive reef‐building coral Porites cf. P. lobata across 2 years. Spawning occurred in April and May, on the first day after the full moon with at least 2 h of darkness between sunset and moonrise, on a rising tide. Only a small proportion of corals observed had mature gametes or spawned (14–35%). Eggs were 185–311 μm in diameter, spherical, homogenous, and provisioned with 95–155 algal cells (family Symbiodiniaceae). Males spawned before females, and ex situ fertilization rates were high for the first 2 h after egg release. Larvae were elliptical, ~300 μm long, and symbiotic. Just 2 days after fertilization, many larvae swam near the bottom of culture dishes and were competent to settle. Settlers began calcification 2 days after metamorphosis, and tentacles were developed 10 days after attachment. Our observations contrast with previous studies by suggesting an abbreviated pelagic larval period in Porites cf. P. lobata, which could lead to the isolation of some populations. The high thermal tolerance and broad geographic range of Porites cf. P. lobata suggest that this species could locally adapt to a wide range of environmental conditions, especially if larvae are locally retained. The results of this study can inform future work on reproduction, larval biology, dispersal, and recruitment in Porites cf. P. lobata, which could have an ecological advantage over less resilient coral species under future climate change. [ABSTRACT FROM AUTHOR]

Global climate change is profoundly impacting coral ecosystems. Rising sea surface temperatures, in particular, disrupt coral reproductive synchrony, cause bleaching, and mortality. Oculina patagonica, a temperate scleractinian coral abundant across the Mediterranean Sea, can grow at a temperature range of 10–31 °C. Studies conducted three decades ago documented this species bleaching during the summer months, the same time as its gonads mature. However, the Eastern Mediterranean Sea is experiencing some of the fastest-warming sea surface temperatures worldwide. This study repeated the year-round in situ assessment of the reproductive cycle and gonad development and correlation to summer bleaching. In addition, thermal performance of the holobiont was assessed in an ex situ thermal stress experiment. In situ monitoring revealed no temporal changes in gonad development compared to previous studies, despite sea surface warming and concurrent bleaching. Experimental thermal performance curves indicated that photosynthetic rate peaked at 23 °C, bleached coral area was significant at 29 °C, and peaked at 34 °C. With local sea surface temperature reaching 31 °C, O. patagonica is exposed beyond its bleaching threshold during the summer months in situ. Despite this, O. patagonica maintains gonad development and physiologically recovers at the end of summer demonstrating resilience to current warming trends. [ABSTRACT FROM AUTHOR]

Corals have complex symbiotic associations that can be influenced by the environment. We compare symbiotic dinoflagellate (family: Symbiodiniaceae) associations and the microbiome of five scleractinian coral species from three different reef habitats in Palau, Micronesia. Although pH and temperature corresponded with specific host‐Symbiodiniaceae associations common to the nearshore and offshore habitats, bacterial community dissimilarity analyses indicated minimal influence of these factors on microbial community membership for the corals Coelastrea aspera, Psammocora digitata, and Pachyseris rugosa. However, coral colonies sampled close to human development exhibited greater differences in microbial community diversity compared to the nearshore habitat for the coral species Coelastrea aspera, Montipora foliosa, and Pocillopora acuta, and the offshore habitat for Coelastrea aspera, while also showing less consistency in Symbiodiniaceae associations. These findings indicate the influence that habitat location has on the bacterial and Symbiodiniaceae communities comprising the coral holobiont and provide important considerations for the conservation of coral reef communities, especially for island nations with increasing human populations and development. [ABSTRACT FROM AUTHOR]

The article discusses the spread of a sea urchin disease to the Indian Ocean, causing widespread mortalities, with evidence from Réunion Island. The disease has led to significant declines in sea urchin populations, impacting marine ecosystems. The study highlights the importance of sea urchins in maintaining ecological balance and the potential ecological consequences of large-scale sea urchin die-offs. The pathogen responsible for the disease has been identified, and its spread to other regions in the Western Indian Ocean is noted. [Extracted from the article]

Atlantic reef-building corals and coral reefs continue to experience extensive decline due to increased stressors related to climate change, disease, pollution, and numerous anthropogenic threats. To understand the impact of ocean warming and reef loss on the estimated extinction risk of shallow water Atlantic reef-building scleractinians and milleporids, all 85 valid species were reassessed under the IUCN Red List Categories and Criteria, updating the previous Red List assessment of Atlantic corals published in 2008. For the present assessment, individual species declines were estimated based on the modeled coral cover loss (1989–2019) and projected onset of annual severe bleaching events (2020–2050) across the Atlantic. Species traits were used to scale species' relative vulnerability to the modeled cover declines and forecasted bleaching events. The updated assessments place 45.88%–54.12% of Atlantic shallow water corals at an elevated extinction risk compared to the previous assessments conducted in 2008 (15.19%–40.51%). However, coral cover loss estimates indicate an improvement in reef coverage compared to the historic time-series used for the 2008 assessments. Based on this, we infer that, although remaining dangerously high, the rate of Atlantic reef coral cover decline has surprisingly slowed in recent decades. However, based on modeled projections of sea-surface temperature that predict the onset of annual severe bleaching events within the next 30 years, we listed 26 (out of 85) species as Critically Endangered in the IUCN Red List. Each of these species had previously been listed under a lower threatened category and this result alone highlights the severe threat future bleaching events pose to coral survival and the reef ecosystems they support. [ABSTRACT FROM AUTHOR]

Stony coral tissue loss disease (SCTLD) has swept through Florida reefs and caused mass mortality of numerous coral species. In the wake of these losses, efforts are underway to propagate coral species impacted by SCTLD and promote population recovery. However, numerous knowledge gaps must be addressed to effectively grow, outplant, and restore populations of the slower growing, massive species that were lost. Here, we used sexual recruits of Diploria labyrinthiformis spawned in captivity to understand how conditioning, coral size, and nutritional status at outplanting affect coral survivorship, growth, and susceptibility to predation. We found that ex situ conditioning with supplemental feeding increased coral growth rates, resulting in larger sized corals at the time of outplanting. In turn, these corals had higher growth rates in the field and a lower probability of being removed by predators than outplants that were conditioned in in situ nurseries. Additionally, we found that coral size was an important predictor of survivorship, suggesting that hastening the speed at which young corals grow and outplanting larger juveniles can improve restoration outcomes. Taken together, our results suggest that providing supplemental food to corals at ex situ facilities confers benefits that could help restore populations of massive coral species impacted by SCTLD. [ABSTRACT FROM AUTHOR]

Background: Alzheimer's disease is a neurodegenerative disease that has no cure. The drugs used to treat Alzheimer's disease are based on the inhibition of the enzyme acetylcholinesterase (AChE). In this sense, marine fungal metabolites represent an alternative source for the discovery of drugs based on AChE inhibition (IAChE). The present research carried out a bioprospecting study of marine fungi with acetylcholinesterase inhibition potential. Results: A total of 17 marine fungi were isolated from three stony corals from the Veracruz Reef System. The fungal genera identified were Geotrichum, Curvularia, Penicillium, Aspergillus, and Daldinia. The IAChE was evaluated from the broth and biomass extracts of each fungal strain. As a result, Daldinia eschscholtzii was one of the three fungi with the greatest IAChE effect (32.7%). Subsequently, a bio-directed chromatographic purification of the methanolic extract of the biomass of D. eschscholtzii was carried out. The FRL8.1 fraction was the most active with an IAChE of 41.0%, a value close to Galantamine positive control (44.0%). Furthermore, compound analysis was carried out by GC-MS. Finally, it was determined that the metabolites responsible for the inhibitory effect are probably 4,7-dihydroxycoumarin and 5-nitro-2-naphthalenamine, which was demonstrated by their interactions with the AChE enzyme receptor through molecular docking studies. Conclusions: Coral-associated marine fungi produce secondary metabolites that inhibit acetylcholinesterase. This is the first report of D. eschscholtzii isolated from the stony coral Siderastrea siderea. Finally, we consider that more studies are needed to demonstrate the IAChE potential of marine fungi associated with corals or other marine organisms. [ABSTRACT FROM AUTHOR]

Melanin is an essential product that plays an important role in innate immunity in a variety of organisms across the animal kingdom. Melanin synthesis is performed by many organisms using the tyrosine metabolism pathway, a general pathway that utilizes a type-three copper oxidase protein, called PO-candidates (phenoloxidase candidates). While melanin synthesis is well-characterized in organisms like arthropods and humans, it is not as well-understood in non-model organisms such as cnidarians. With the rising anthropomorphic climate change influence on marine ecosystems, cnidarians, specifically corals, are under an increased threat of bleaching and disease. Understanding innate immune pathways, such as melanin synthesis, is vital for gaining insights into how corals may be able to fight these threats. In this study, we use comparative bioinformatic approaches to provide a comprehensive analysis of genes involved in tyrosine-mediated melanin synthesis in cnidarians. Eighteen PO-candidates representing five phyla were studied to identify their evolutionary relationship. Cnidarian species were most similar to chordates due to domain presents in the amino acid sequences. From there, functionally conserved domains in coral proteins were identified in a coral disease dataset. Five stony corals exposed to stony coral tissue loss disease were leveraged to identify 18 putative tyrosine metabolism genes, genes with functionally conserved domains to their Homo sapiens counterpart. To put this pathway in the context of coral health, putative genes were correlated to melanin concentration from tissues of stony coral species in the disease exposure dataset. In this study, tyrosinase was identified in stony corals as correlated to melanin concentrations and likely plays a key role in immunity as a resistance trait. In addition, stony coral genes were assigned to all modules within the tyrosine metabolism pathway, indicating an evolutionary conservation of this pathway across phyla. Overall, this study provides a comprehensive analysis of the genes involved in tyrosine-mediated melanin synthesis in cnidarians. [ABSTRACT FROM AUTHOR]

Scleractinian corals, essential ecosystem engineers that form the base of coral reef ecosystems, have faced unprecedented mortality in recent decades due to climate change-related stressors, including disease outbreaks. Despite this emergent threat to corals, many questions still remain regarding mechanisms underlying observed variation in disease susceptibility. Recent data suggest at least some degree of variation in disease response may be linked to variability in the relationship between host corals and their algal photosymbionts (Family Symbiodiniaceae). Still, the nuances of connections between symbiosis and immunity in cnidarians, including scleractinian corals, remain poorly understood. Here, we leveraged an emergent model species, the facultatively symbiotic, temperate, scleractinian coral Astrangia poculata , to investigate associations between symbiont density and both constitutive and induced immunity. We used a combination of controlled immune challenges with heat-inactivated pathogens and transcriptomic analyses. Our results demonstrate that A. poculata mounts a robust initial response to pathogenic stimuli that is highly similar to responses documented in tropical corals. We document positive associations between symbiont density and both constitutive and induced immune responses, in agreement with recent preliminary studies in A. poculata. A suite of immune genes, including those coding for antioxidant peroxiredoxin biosynthesis, are positively associated with symbiont density in A. poculata under constitutive conditions. Furthermore, variation in symbiont density is associated with distinct patterns of immune response; low symbiont density corals induce preventative immune mechanisms, whereas high symbiont density corals mobilize energetic resources to fuel humoral immune responses. In summary, our study reveals the need for more nuanced study of symbiosis-immune interplay across diverse scleractinian corals, preferably including quantitative energy budget analysis for full disentanglement of these complex associations and their effects on host pathogen susceptibility. [ABSTRACT FROM AUTHOR]

As a part of the important species that form coral reef ecosystems, stony corals have become a potential source of pharmacologically active lead compounds for an increasing number of compounds with novel chemical structures and strong biological activity. In this study, the secondary metabolites and biological activities are reported for Aspergillus terreus C21-1, an epiphytic fungus acquired from Porites pukoensis collected from Xuwen Coral Reef Nature Reserve, China. This strain was cultured in potato dextrose broth (PDB) media and rice media with different salinities based on the OSMAC strategy. The mycelial morphology and high-performance thin layer chromatographic (HPTLC) fingerprints of the fermentation extracts together with bioautography were recorded. Furthermore, an untargeted metabolomics study was performed using principal component analysis (PCA), orthogonal projection to latent structure discriminant analysis (O-PLSDA), and feature-based molecular networking (FBMN) to analyze their secondary metabolite variations. The comprehensive results revealed that the metabolite expression in A. terreus C21-1 differed significantly between liquid and solid media. The metabolites produced in liquid medium were more diverse but less numerous compared to those in solid medium. Meanwhile, the mycelial morphology underwent significant changes with increasing salinity under PDB cultivation conditions, especially in PDB with 10% salinity. Untargeted metabolomics revealed significant differences between PDB with 10% salinity and other media, as well as between liquid and solid media. FBMN analysis indicated that alkaloids, which might be produced under high salt stress, contributed largely to the differences. The biological activities results showed that six groups of crude extracts exhibited acetylcholinesterase (AChE) inhibitory activities, along with 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging and antibacterial activities. The results of this study showed that the increase in salinity favored the production of unique alkaloid compounds by A. terreus C21-1. [ABSTRACT FROM AUTHOR]

Coral reefs, vital ecosystems supporting diverse marine life, are primarily shaped by the clonal expansion of coral colonies. Although the principles of coral clonal growth, involving polyp division for spatial extension, are well-understood, numerical modelling efforts are notably scarce in the literature. In this article, we present a parsimonious numerical model based on the cloning of polyps, using five key parameters to simulate a range of coral shapes. The model is agent-based, where each polyp represents an individual. The colony's surface expansion is dictated by the growth mode parameter (s), guiding the preferred growth direction. Varying s facilitates the emulation of diverse coral shapes, including massive, branching, cauliflower, columnar and tabular colonies. Additionally, we introduce a novel approach for self-regulatory branching, inspired by the intricate mesh-like canal system and internode regularity observed in Acropora species. Through a comprehensive sensitivity analysis, we demonstrate the robustness of our model, paving the way for future applications that incorporate environmental factors, such as light and water flow. Coral colonies are known for their high plasticity, and understanding how individual polyps interact with each other and their surroundings to create the reef structure has been a longstanding question in the field. This model offers a powerful framework for studying these interactions, enabling a future implementation of environmental factors and the possibility of identifying the key mechanisms influencing coral colonies' morphogenesis. [ABSTRACT FROM AUTHOR]

Although true coral reefs have seldom been reported from the fossil record of the Cabo Verde Archipelago, many single fossil corals and coral colonies can be found reworked in tsunami deposits and in raised marine terraces onshore on these islands. This study provides the first detailed survey of fossil corals from 7 of the 10 islands of the archipelago, sampled from Pleistocene marine terraces and tsunami deposits. A total of 168 scleractinian corals were analyzed and identified to genus and/or species level. Thirteen taxa from the families Acroporidae, Dendrophylliidae, Faviidae, Pocilloporidae, Poritidae, and Rhizangiidae were identified. The zooxanthellate fossil corals found on the Cape Verde Archipelago likely migrated from the Caribbean to the West African coast, while azooxanthellate species likely originated from the Indo-Pacific. Differences between present-day coral assemblages and fossil assemblages are assumed to result from changing environmental factors. Although reef-building taxa occur (e.g., Porites), extensive reef frameworks are absent. [ABSTRACT FROM AUTHOR]

Reef restoration has gained attention as it has strategic actions and powerful means in sustaining and maintaining coastal ecosystem services. This scientometric study systematically analyzes the current trends and research hotspot in coral restoration across the last five decades (1971–2022). The metadata (12,667 articles with 652,860 cited references) were obtained from the Clarivate Web of Science platform through the Core Collection database, associated with the CiteSpace and R‐software for further analysis. The results indicated that the trend of coral restoration is increasing in paper/year, with the United States, Australia, and China as major contributors to the related research. Furthermore, James Cook University, Australia had the largest number of articles, and the Consortium of Research Libraries of the United Kingdom was the most influential institution on coral restoration. The highly cited keywords are "Great Barrier Reef," "climate change," and "coral reef," while the most influential keywords are "coral," "model," and "Atlantic." A total of 23 clusters in the field with "coral reef," "phase shift," "bacterial communities," "coral restoration," "symbiotic dinoflagellate," "stony coral tissue loss disease," "bleaching event," "ocean acidification," "oyster reef," and "quantitative reconstruction" are among the top cluster size labeled. Early‐stage researcher may use both keywords and cluster analysis to find topics attractive to their future research projects. In addition, this study contributes toward evaluating recent scientific productivity about coral restoration as well as informing researchers and policymakers regarding funding, future strategic planning, and potential collaboration opportunities. [ABSTRACT FROM AUTHOR]

Zoantharia is an order among the Hexacorallia (Anthozoa: Cnidaria), and includes at least 300 species. Previously reported genomes from scleractinian corals and actiniarian sea anemones have illuminated part of the hexacorallian diversification. However, little is known about zoantharian genomes and the early evolution of hexacorals. To explore genome evolution in this group of hexacorals, here, we report de novo genome assemblies of the zoantharians Palythoa mizigama (Pmiz) and Palythoa umbrosa (Pumb), both of which are members of the family Sphenopidae, and uniquely live in comparatively dark coral reef caves without symbiotic Symbiodiniaceae dinoflagellates. Draft genomes generated from ultra-low input PacBio sequencing totaled 373 and 319 Mbp for Pmiz and Pumb, respectively. Protein-coding genes were predicted in each genome, totaling 30,394 in Pmiz and 24,800 in Pumb, with each set having ∼93% BUSCO completeness. Comparative genomic analyses identified 3,036 conserved gene families, which were found in all analyzed hexacoral genomes. Some of the genes related to toxins, chitin degradation, and prostaglandin biosynthesis were expanded in these two Palythoa genomes and many of which aligned tandemly. Extensive gene family loss was not detected in the Palythoa lineage and five of ten putatively lost gene families likely had neuronal function, suggesting biased gene loss in Palythoa. In conclusion, our comparative analyses demonstrate evolutionary conservation of gene families in the Palythoa lineage from the common ancestor of hexacorals. Restricted loss of gene families may imply that lost neuronal functions were effective for environmental adaptation in these two Palythoa species. [ABSTRACT FROM AUTHOR]

New Mesozoic (Kimmeridgian to Albian) corals from northern Mexico (Mexican states Coahuila, Durango and Sonora), that were established by Imlay and Wells between 1940 and 1946, are revised on the basis of the type material kept at the Museum of Paleontology of the University of Michigan in Ann Arbor (Mich., USA). From the six new species, only one may remain in use, and the other five species are considered to be synonyms of older taxa. [ABSTRACT FROM AUTHOR]

In warm oligotrophic waters, photosymbiotic coral can flourish across a wide depth range (0–170+ m), extending to depths where light attenuates to ~0.1% of surface values. Conventional wisdom has long assumed that mixotrophic corals must increasingly rely on heterotrophy as the ambient light available to drive photosynthesis decreases with depth. However, evidence challenging this traditional dogma has been accumulating in recent years. Although some evidence suggests that some depth-generalist coral species likely increase their reliance on heterotrophy with increasing depth, there is growing evidence that other species do not. Analysis of bulk stable isotopes (δ13C and δ15N) applied to photosymbiotic corals has been used in several ways to infer their trophic ecology and their relative dependence on symbiont photosynthesis versus heterotrophic feeding. However, metrics based on bulk tissue δ13C and δ15N values are subject to considerable uncertainty due to the multiple factors that can affect their values independent of trophic ecology. These competing factors can be quite challenging to disentangle and have led to inconsistent results and conclusions regarding trends in coral heterotrophy with depth. The evidence to date suggests no uniform trophic pattern with increasing depth or decreasing light. Different corals appear to function differently, which is not surprising given their phylogenetic diversity. [ABSTRACT FROM AUTHOR]

Molecular phylogenetics has fundamentally altered our understanding of the taxonomy, systematics and biogeography of corals. Recently developed phylogenomic techniques have started to resolve species-level relationships in the diverse and ecologically important genus Acropora , providing a path to resolve the taxonomy of this notoriously problematic group. We used a targeted capture dataset (2032 loci) to investigate systematic relationships within an Acropora clade containing the putatively widespread species Acropora tenuis and its relatives. Using maximum likelihood phylogenies and genetic clustering of single nucleotide polymorphisms from specimens, including topotypes, collected across the Indo-Pacific, we show ≥ 11 distinct lineages in the clade, only four of which correspond to currently accepted species. Based on molecular, morphological and geographical evidence, we describe two new species; Acropora rongoi n. sp. and Acropora tenuissima n. sp. and remove five additional nominal species from synonymy. Systematic relationships revealed by our molecular phylogeny are incongruent with traditional morphological taxonomy and demonstrate that characters traditionally used to delineate species boundaries and infer evolutionary history are homoplasies. Furthermore, we show that species within this clade have much smaller geographical ranges and, consequently, population sizes than currently thought, a finding with profound implications for conservation and management of reef corals. [ABSTRACT FROM AUTHOR]

Stony Coral Tissue Loss Disease (SCTLD) has caused widespread coral mortality in the Caribbean Region. However, how the disease presence alters the microbiome community, their structure, composition, and metabolic functionality is still poorly understood. In this study, we characterized the microbial communities of the tissues of apparently healthy and diseased SCTLD colonies of the species Siderastrea siderea, Orbicella faveolata, and Montastraea cavernosa to explore putative changes related to the presence of SCTLD. Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia were the best represented classes in the healthy tissues of all coral species, and alpha diversity did not show significant differences among the species. The microbial community structure between coral species was significantly different (PERMANOVA: F = 3.46, p = 0.001), and enriched genera were detected for each species: Vibrio and Photobacterium in S. siderea, Spirochaeta2 and Marivivens in O. faveolata and SAR202_clade and Nitrospira in M. cavernosa. Evidence of SCTLD in the microbial communities was more substantial in S. siderea, where differences in alpha diversity, beta diversity, and functional profiles were observed. In O. faveolata, differences were detected only in the community structure, while M. cavernosa samples showed no significant difference. Several microbial groups were found to have enriched abundances in tissue from SCTLD lesions from S. siderea and O. faveolata, but no dominant bacterial group was detected. Our results contribute to understanding microbial diversity associated with three scleractinian coral species and the shifts in their microbiomes associated with SCTLD in the Mexican Caribbean. [ABSTRACT FROM AUTHOR]

Azooxanthellate scleractinian corals, a group of species that lack a symbiotic relationship with dinoflagellates, are influenced by environmental variables at various scales. As the global commitment to sustainably manage ocean ecosystems and resources rises, there is a growing need to describe biodiversity trends in previously unsampled areas. Benthic invertebrate research in South Africa is a developing field, and many taxa in deep water environments remain inadequately characterized. Recently, the South African azooxanthellate scleractinian fauna was taxonomically reviewed, but their distributional correlations with physical parameters have not been studied. Here we aim to understand the biodiversity gradients of the South African azooxanthellate coral fauna by analysing the environmental correlates of museum samples. The associated coordinate data were georeferenced and depth obtained from a national bathymetric dataset, prior to undertaking a multivariate analysis. This analysis encompassed several steps, including the grouping of the longitude and depth data (environmental data), identifying families characteristic of the group variability, and examining the correlation of the associated data with the biological data. Additionally, the analysis involved quantifying diversity patterns along the environmental gradients. Overall, our results confirmed two longitudinal groups (eastern margin [Group A] vs southern and western margin [Group B]) and 11 depth categories represented within two bathymetric zones (shallow [50–200 m] and deep [300–1000 m]). Caryophylliids, flabellids, and dendrophylliids contributed the most towards distinguishing longitudinal and depth gradients. Both abiotic variable (longitudinal and depth) partially explained coral distribution patterns, with depth being highly correlated to the species variation observed. Data limitations within our data set resulted to unexplained variance, however, despite these limitations, the study demonstrates that historical museum samples provide a valuable data source that can fill research sampling gaps and help improve the understanding of biodiversity patterns of the coral fauna in under sampled marine ecosystems. [ABSTRACT FROM AUTHOR]

Biome degradation characterizes the Anthropocene Epoch, and modern ecology is deeply involved with describing the changes underway. Most research has focused on the role of acute disturbances in causing conspicuous changes in ecosystem structure, which leads to an underappreciation of the chronic effects causing large changes through the cumulative effects of small perturbations over decades. Coral reefs epitomize this trend, because the changes in community structure are profound, yet the data to quantify these effects are usually insufficient to evaluate the relative roles of different disturbance types. Here, four decades of surveys from two coral reefs (9 and 14 m depth) off St. John, US Virgin Islands, are used to quantify the associations of acute and chronic events with the changes in benthic community structure. These reefs profoundly changed over 36 years, with coral death altering species assemblages to depress abundances of the ecologically important coral Orbicella spp. and elevating the coverage of macroalgae and crustose coralline algae/turf/bare space (CTB). Linear mixed models revealed the prominent role of chronic variation in temperature in accounting for changes in coverage of corals, macroalgae, and CTB, with rising temperature associated with increases in coral cover on the deep reef, and declines on the shallow reef. Hurricanes were also associated with declines in coral cover on the shallow reef, and increases on the deep reef. Multivariate analyses revealed strong associations between community structure and temperature, but weaker associations with hurricanes, bleaching, and diseases. These results highlight the overwhelming importance of chronically increasing temperature in altering the benthic community structure of Caribbean reefs. [ABSTRACT FROM AUTHOR]

In contrast to tropical and subtropical regions, where coral abundance is declining due to elevated summer seawater temperatures, expansions of coral ranges have been reported in temperate Japanese regions due to an increase in seawater temperature. However, the vulnerability of corals in temperate Japanese regions to elevated summer seawater temperatures is not well known. In this study, we assessed the bleaching state of corals with elevated seawater temperatures during summer in a temperate Japanese coastal sea around Takashima Island, using an underwear color reference card (Coral Health Chart). This study showed that the color of temperate corals turned pale with increasing seawater temperature during summer. However, the corals did not reach a bleached state. Approaching a typhoon may contribute to maintenance of coral health at Takashima Beach by mitigating high seawater temperatures during summer and preventing the accumulation of thermal stress in corals. [ABSTRACT FROM AUTHOR]

Aim: Predicting and acting on the future of ecosystems requires understanding species distribution shifts due to climate change. We investigated which corals are more likely to shift their distribution in the Southwestern Atlantic under a warming scenario. Location: Southwestern Atlantic (SWA; 1° N–28° S). Methods: We used spatial distribution models with a Bayesian approach to predict the current and future (2050 and 2100) coral occurrence probabilities of 12 zooxanthellate corals and hydrocorals under an intermediate scenario of increasing greenhouse gas emissions (RCP6.0) projected by the Intergovernmental Panel on Climate Change (IPCC). Results: We found a decline in the occurrence probabilities of all 12 taxa within the tropics (1° N–20° S) and an increase towards subtropical sites (20–28° S) as early as 2050. The most significant declines are projected to occur between 9° S and 20° S, a region that currently hosts the richest reef complex in the South Atlantic, the Abrolhos bank. The imminent loss of suitable habitat in the tropics mostly threatens the Brazilian endemics and range restricted corals Mussismilia braziliensis and Mussismilia harttii, while more widely distributed taxa such as Siderastrea spp., Millepora spp. and Porites spp. are expected to expand their ranges southwards. Main Conclusions: The projected declines in the tropical region are likely to reduce structural complexity causing biodiversity loss. The overall increase in occurrence probabilities in subtropical areas indicates tropicalisation of SWA reefs, which may benefit species already established in these areas and potentially enrich coral assemblages through the range expansion of taxa that currently do not occur in the region. These findings emphasise the need to support ecological corridors that could aid coral migration towards more suitable habitats under climate change. [ABSTRACT FROM AUTHOR]

The growth properties and environmental adaptability of different corals and symbionts vary. Therefore, insights from the adaptive mechanisms of Symbiodiniaceae in corals are very meaningful. In this study, we surveyed the seawater characteristics at three sites on Luhuitou fringing reef, Hainan Island (China), sampling three native corals Pocillopora damicornis, Acropora hyacinthus, and Galaxea fascicularis on 27 September 2021. The photo-physiological (Fv/Fm, Y(II), α, and rETR) were measured, and high-throughput sequencing of Symbiodiniaceae ITS was performed. The Luhuitou site had the lowest temperature (28.845 °C ± 0.01), salinity (33.967 ± 0.03), and pH (8.468 ± 0.05) among the three sites. The Sanya site contained significantly the highest ammonium (7.406 μmol/L ± 1, P < 0.05). The nitrate of the Xiaozhou site was 1.5 times significantly higher than the other two sites. Three corals and their Symbiodiniaceae were adapted differently. P. damicornis showed more plasticity and was dominant by Cladocopium sp. C1d at high-ammonium habitat. A. hyacinthus was dominated by Cladocopium (C3 and C1232) and they had the lowest Fv/Fm (0.595 ± 0.02) in poor integrated water quality environments (the Xiaozhou site) among three corals, suggesting that the less adaptation. G. fascicularis established a stable symbiotic relationship with Durusidinium sp. D1, and they had a more stable symbiotic system and were better suited for long-term reef restoration. Our results provide a deeper understanding of the environmental adaptations of three corals at the Luhuitou fringing reef. Meanwhile, it provides a perspective application for coral transplantation species selection in restoring local reef ecology in the future. [ABSTRACT FROM AUTHOR]

Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and affected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available metagenomic sequencing samples of SCTLD lesions and healthy tissues from 4 stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. These reads were then used as a reference to which we matched and removed reads from diseased lesion tissue samples, and the remaining reads associated only with disease lesions were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. To assess the utility of our pipeline, a species-level analysis of a candidate genus, Vibrio , was used to demonstrate the pipeline's effectiveness. Our approach revealed both complementary and unique coral microbiome members compared with a prior metagenome analysis of the same dataset. [ABSTRACT FROM AUTHOR]

Coral microbiomes differ in the mucus, soft tissue and skeleton of a coral colony, but whether variations exist in different tissues of a single polyp is unknown. In the stony coral, Fimbriaphyllia ancora, we identified 8,994 amplicon sequencing variants (ASVs) in functionally differentiated polyp tissues, i.e., tentacles, body wall, mouth and pharynx, mesenterial filaments, and gonads (testes and ovaries), with a large proportion of ASVs specific to individual tissues. However, shared ASVs comprised the majority of microbiomes from all tissues in terms of relative abundance. No tissue‐specific ASVs were found, except in testes, for which there were only two samples. At the generic level, Endozoicomonas was significantly less abundant in the body wall, where calicoblastic cells reside. On the other hand, several bacterial taxa presented significantly higher abundances in the mouth. Interestingly, although without statistical confirmation, gonadal tissues showed lower ASV richness and relatively high abundances of Endozoicomonas (in ovaries) and Pseudomonas (in testes). These findings provide evidence for microbiome heterogeneity between tissues within coral polyps, suggesting a promising field for future studies of functional interactions between corals and their bacterial symbionts. [ABSTRACT FROM AUTHOR]

Here, we provide the first in situ observations of foraging habitats of Chaetodon daedalma, which is endemic to the subtropical north‐west Pacific. Overall, 62.4% of bites were from the substratum, 30.7% from scleractinian corals, 3.3% from crustose coralline algae, 2.1% from macroalgae, and 1.2% from hydroids. The range in the percentage of bites taken from scleractinian corals among individuals was 0%–76%, and no fish fed exclusively on coral. Our in situ feeding observations confirm that the species is a facultative corallivore. [ABSTRACT FROM AUTHOR]

Background: Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions. Results: The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation. Conclusion: Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community. [ABSTRACT FROM AUTHOR]

Understanding the dispersal potential of different species is essential for predicting recovery trajectories following local disturbances and the potential for adaptive loci to spread to populations facing extreme environmental changes. However, dispersal distances have been notoriously difficult to estimate for scleractinian corals, where sexually (as gametes or larvae) or asexually (as fragments or larvae) derived propagules disperse through vast oceans. Here, we demonstrate that generational dispersal distances for sexually produced propagules can be indirectly inferred for corals using individual-based isolation-by-distance (IbD) analyses by combining reduced-representation genomic sequencing with photogrammetric spatial mapping. Colonies from the genus Agaricia were densely sampled across plots at four locations and three depths in Curaçao. Seven cryptic taxa were found among the three nominal species (Agaricia agaricites, Agaricia humilis and Agaricia lamarcki), with four taxa showing generational dispersal distances within metres (two taxa within A. agaricites and two within A. humilis). However, no signals of IbD were found in A. lamarcki taxa and thus these taxa probably disperse relatively longer distances. The short distances estimated here imply that A. agaricites and A. humilis populations are reliant on highly localized replenishment and demonstrate the need to estimate dispersal distances quantitatively for more coral species. [ABSTRACT FROM AUTHOR]

Recent studies have predominantly spotlighted bacterial diversity within coral microbiomes, leaving coral-associated fungi in the shadows of scientific inquiry. This study endeavors to fill this knowledge gap by delving into the biodiversity, distribution and functional differences of fungi associated with soft corals Cladiella krempfi and Sarcophyton tortuosum, gorgonian coral Dichotella gemmacea and stony coral Favia speciosa from the South China Sea. Leveraging high-throughput sequencing of fungal internal transcribed spacer-1 (ITS1) region of the rRNA gene, a total of 431 fungal amplicon sequence variants (ASVs) were identified in this study, which indicated that a large number of fungal communities were harbored in the South China Sea corals. Noteworthy among our findings is that 10 fungal genera are reported for the first time in corals, with Candolleomyces, Exophiala, Fomitopsis, Inaequalispora, Kneiffiella, Paraphaeosphaeria, and Yamadazyma belonging to the Ascomycota, and Cystobasidium, Psathyrella, and Solicoccozyma to the Basidiomycota. Moreover, significant differences (p < 0.05) of fungal communities were observed among the various coral species. In particular, the gorgonian coral D. gemmacea emerged as a veritable haven for fungal diversity, boasting 307 unique ASVs. Contrastingly, soft corals S. tortuosum and C. krempfi exhibited modest fungal diversity, with 36 and 21 unique ASVs, respectively, while the stony coral F. speciosa hosted a comparatively sparse fungal community, with merely 10 unique ASVs in total. These findings not only provide basic data on fungal diversity and function in the South China Sea corals, but also underscore the imperative of nuanced conservation and management strategies for coral reef ecosystems worldwide. [ABSTRACT FROM AUTHOR]

Once considered the most speciose mostly azooxanthellate scleractinian group, the family Caryophylliidae is found to be highly polyphyletic based on molecular data and is undergoing a process of systematic revision. High‐throughput sequencing methods coupled with morphological analyses have facilitated revision of several scleractinian lineages, including the aforementioned family. In previous studies that relied on few mitochondrial and nuclear markers, the caryophylliid genera Stephanocyathus and Vaughanella were phylogenetically recovered in separate clades from the lineage that includes the type genus of the family, Caryophyllia, which is considered the 'true' Caryophylliidae. To help untangle the relationship among taxa of this family, here a new deep‐sea scleractinian family (Stephanocyathidae Vaga, Cairns & Kitahara fam. nov.) is proposed based on phylogenomic reconstructions coupled with molecular features, specifically gene order, of the complete mitochondrial genome. Evolutionary reconstructions were based on both mitochondrial and nuclear ultraconserved elements (UCEs) and exon loci data sets and confirmed the divergent position of the genera Stephanocyathus and Vaughanella. The new family shows a specific gene transposition in the mitochondrial genome, not present in the 'true' caryophylliid lineage, but instead already observed for the species Paraconotrochus antarcticus, recovered as sister taxon of the here proposed new family. Although its phylogenetic position is unknown, the genus Ericiocyathus is also added to the new family, based on macromorphological similarities. This study represents a step forward in our understanding of deep‐sea corals relationships and provide further information (e.g., mitochondrial gene order) that will aid in future efforts of assessing the systematic of caryophylliid lineages. [ABSTRACT FROM AUTHOR]

The coral reef microbiome plays a vital role in the health and resilience of reefs. Previous studies have examined phage therapy for coral pathogens and for modifying the coral reef microbiome, but defence systems against coral‐associated bacteria have received limited attention. Phage defence systems play a crucial role in helping bacteria fight phage infections. In this study, we characterized a new defence system, Hma (HmaA‐HmaB‐HmaC), in the coral‐associated Halomonas meridiana derived from the scleractinian coral Galaxea fascicularis. The Swi2/Snf2 helicase HmaA with a C‐terminal nuclease domain exhibits antiviral activity against Escherichia phage T4. Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence. Additionally, HmaA homologues are present in ~1000 bacterial and archaeal genomes. The high frequency of HmaA helicase in Halomonas strains indicates the widespread presence of these phage defence systems, while the insertion of defence genes in the hma region confirms the existence of a defence gene insertion hotspot. These findings offer insights into the diversity of phage defence systems in coral‐associated bacteria and these diverse defence systems can be further applied into designing probiotics with high‐phage resistance. [ABSTRACT FROM AUTHOR]

The high diversity and biomass of organisms associated with coral communities depend directly on the maintenance or changes in the benthic composition. Over a decade, we evaluated the spatiotemporal variation in the benthic structure and composition of an insular coral community in the Northeastern Tropical Pacific. Our results show that local conditions drive spatiotemporal differences, and benthic organisms such as sponges, crustose coralline algae, octocorals, and hydrocorals all increased in abundance (cover) in response to negative thermal anomalies caused by the 2010–2011 La Niña event. In contrast, abnormally high temperatures, such as those recorded during the 2015–2016 El Niño Southern Oscillation (ENSO) event, explain the loss of scleractinian corals and crustose coralline algae coverage, which reduced the benthic groups' richness (BGR), diversity (H'BG), and evenness (J'BG), with evidence of a consequent decrease in ecosystem function recorded the following year. Our analysis also showed that sites with high habitat heterogeneity harbored higher average BRG and H'BG values and were less affected by environmental fluctuations than sites with high live scleractinian coral cover and lower BRG and H'BG values. Therefore, the benthic structure was impacted differently by the same perturbation, and changes in the benthic community composition affected the groups associated with the community and ecological functions. More importantly, regional stressors such as the ENSO event caused only temporary changes in the benthic community structure, demonstrating the high resilience of the community to annual and interannual stressors. [ABSTRACT FROM AUTHOR]

Geochemical proxies of sea surface temperature (SST) and seawater pH (pHsw) in scleractinian coral skeletons are valuable tools for reconstructing tropical climate variability. However, most coral skeletal SST and pHsw proxies are univariate methods that are limited in their capacity to circumvent non-climate-related variability. Here we present a novel multivariate method for reconstructing SST and pHsw from the geochemistry of coral skeletons. Our Scleractinian Multivariate Isotope and Trace Element (SMITE) method optimizes reconstruction skill by leveraging the covariance across an array of coral elemental and isotopic data with SST and pHsw. First, using a synthetic proxy experiment, we find that SMITE SST reconstruction statistics (correlation, accuracy, and precision) are insensitive to noise and variable calibration period lengths relative to Sr/Ca. While SMITE pHsw reconstruction statistics remain relative to δ11B throughout the same synthetic experiment, the magnitude of the long-term trend in pHsw is progressively lost under conditions of moderate-to-high analytical uncertainty. Next, we apply the SMITE method to an array of seven coral-based geochemical variables (B/Ca, δ11B, Li/Ca, Mg/Ca, Sr/Ca, U/Ca & Li/Mg) measured from two Bermudan Porites astreoides corals. Despite a <3.5 year calibration period, SMITE SST and pHsw estimates exhibit significantly better accuracy, precision, and correlation with their respective climate targets than the best single- and dual-proxy estimators. Furthermore, SMITE model parameters are highly reproducible between the two coral cores, indicating great potential for fossil applications (when preservation is high). The results shown here indicate that the SMITE method can outperform the most common coral-based SST and pHsw reconstructions methods to date, particularly in datasets with a large variety of geochemical variables. We therefore provide a list of recommendations and procedures for users to begin implementing the SMITE method as well as an open-source software package to facilitate dissemination of the SMITE method. [ABSTRACT FROM AUTHOR]

Fluorescence is a widespread phenomenon found in animals, bacteria, fungi, and plants. In marine environments fluorescence has been proposed to play a role in physiological and behavioral responses. Many fluorescent proteins and other molecules have been described in jellyfish, corals, and fish. Here we describe fluorescence in marine species, which we observed and photographed during night dives in the Banda Sea, Indonesia, and in the Red Sea, Egypt. Among various phyla we found fluorescence in sponges, molluscs, tunicates, and fish. Our study extends the knowledge on how many different organisms fluoresce in marine environments. We describe the occurrence of fluorescence in 27 species, in which fluorescence has not been described yet in peer-reviewed literature. It especially extends the knowledge beyond Scleractinia, the so far best described taxon regarding diversity in fluorescent proteins. [ABSTRACT FROM AUTHOR]

Climate change poses an existential threat to coral reefs. A warmer and more acidic ocean weakens coral ecosystems and increases the intensity of hurricanes. The wind–wave–current interactions during a hurricane deeply change the ocean circulation patterns and hence potentially affect the dispersal of coral larvae and coral disease agents. Here, we modeled the impact of major hurricane Irma (September 2017) on coral larval and stony coral tissue loss disease (SCTLD) connectivity in Florida's Coral Reef. We coupled high‐resolution coastal ocean circulation and wave models to simulate the dispersal of virtual coral larvae and disease agents between thousands of reefs. While being a brief event, our results suggest the passage of hurricane Irma strongly increased the probability of long‐distance exchanges while reducing larval supply. It created new connections that could promote coral resilience but also probably accelerated the spread of SCTLD by about a month. As they become more intense, hurricanes' double‐edged effect will become increasingly pronounced, contributing to increased variability in transport patterns and an accelerated rate of change within coral reef ecosystems. [ABSTRACT FROM AUTHOR]

This article is a response to a previous paper about coral reefs in the Jaffna Peninsula in Northern Sri Lanka. The authors of the response agree that identifying coral species can be challenging and used morphological characteristics, with molecular methods to confirm doubtful species. They found 38 new coral species in Sri Lanka and acknowledge the limitations of their methods, emphasizing the need for further research. The document provides a table listing various coral species, their scientific names, and geographical distribution. [Extracted from the article]

Endozoicomonas is globally the most prevalent and consistently found bacterial genus associated with Cnidaria; strains of Endozoicomonas are known to codiversify with their coral hosts, and they are widely presumed to be key mutualists. A high abundance of Endozoicomonas in corals is associated with a decreased capacity to adjust to environmental change as well as with life history trade-offs. In other marine host–microbe systems, such as clams and fish, Endozoicomonas is a known parasite and pathogen. Genomic characteristics – such as genome size and structure, and the presence of eukaryote-like proteins and effectors – do not support the view that Endozoicomonas is an obligate and exclusive coral mutualist but may suggest a diverse and potentially intracellular lifestyle, including commensalism, parasitism, or pathogenicity. Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral– Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum. [ABSTRACT FROM AUTHOR]

Scleractinian corals are the main modern builders of coral reefs, which are major hot spots of marine biodiversity. Southern Atlantic reef corals are understudied compared to their Caribbean and Indo‐Pacific counterparts and many hypotheses about their population dynamics demand further testing. We employed thousands of single nucleotide polymorphisms (SNPs) recovered via ezRAD to characterize genetic population structuring and species boundaries in the amphi‐Atlantic hard coral genus Favia. Coalescent‐based species delimitation (BFD* – Bayes Factor Delimitation) recovered F. fragum and F. gravida as separate species. Although our results agree with depth‐related genetic structuring in F. fragum, they did not support incipient speciation of the 'tall' and 'short' morphotypes. The preferred scenario also revealed a split between two main lineages of F. gravida, one from Ascension Island and the other from Brazil. The Brazilian lineage is further divided into a species that occurs throughout the Northeastern coast and another that ranges from the Abrolhos Archipelago to the state of Espírito Santo. BFD* scenarios were corroborated by analyses of SNP matrices with varying levels of missing data and by a speciation‐based delimitation approach (DELINEATE). Our results challenge current notions about Atlantic reef corals because they uncovered surprising genetic diversity in Favia and rejected the long‐standing hypothesis that Abrolhos Archipelago may have served as a Pleistocenic refuge during the last glaciations. [ABSTRACT FROM AUTHOR]

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

The "coral gardening" approach has been effective in facilitating the recovery of degraded reefs but methodological variations can influence survivorship and growth of the coral material. In addition, the disproportionate use of certain corals, such as acroporids and pocilloporids, has contributed to a general lack of information on growth patterns and restoration strategies for species that are less common. To investigate how the yield of other species may be increased to support reef restoration efforts in Singapore, we assessed the effects of (1) environment (nursery, reef, and seawall) and (2) transplant orientation (horizontal and vertical) on the performance of Echinopora horrida (Dana, 1846) fragments. Fragments secured in the coral nursery grew significantly faster and survived better than those transplanted on the reef and seawall, highlighting the importance of a nursery‐rearing phase in optimizing the yield of this species. Additionally, survivorship and growth rates were not significantly different between vertically and horizontally transplanted corals, suggesting that modifying transplant orientation was less crucial toward enhancing coral yield. Our findings highlighted the need to optimize the propagation techniques of a wider range of understudied coral species in order to preserve their genetic diversity in the face of anthropogenic and climatic impacts. [ABSTRACT FROM AUTHOR]

Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low‐coverage genome sequencing) is a promising method to not only extract high‐copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome‐skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target‐capture baitsets, we bioinformatically obtained UCEs and exons from the genome‐skimming data and incorporated them with data from previously published target‐capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from >95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low‐cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens. [ABSTRACT FROM AUTHOR]

Tropical marine lakes are small land-locked marine waterbodies occurring in karstic coastal areas. During biodiversity surveys in 12 marine lakes in Raja Ampat, Southwest Papua province, Indonesia, we recorded at least 37 species belonging to 29 genera of hard corals. Their observed associated symbiont fauna consisted of bivalve molluscs and polychaete worms. Marine lake temperature ranged from 30.0 to 32.5 °C, acidity from pH 7.6 to 8.1, and salinity from 26.4 to 33.2 ppt. This study provides the first inventory of the marginal coral communities in the extreme habitat of marine lakes, under chronic extreme environmental conditions of higher temperatures, land-based nutrient loads, and sedimentation. [ABSTRACT FROM AUTHOR]

The recent rise in ocean temperatures, accompanied by other environmental changes, has notably increased the occurrence and spread of diseases in Octocorallia, many species of which are integral to shallow tropical and subtropical coral reef ecosystems. This study focuses on the understanding of these diseases, which has been largely limited to symptomatic descriptions, with clear etiological factors identified in only a fraction of cases. A key example is the multifocal purple spots syndrome (MFPS) affecting the common Caribbean octocoral sea fan Gorgonia ventalina, linked to the gall-forming copepods of the genus Sphaerippe, a member of the widespread family, Lamippidae. The specialized nature of these copepods as endoparasites in octocorals suggests the potential for the discovery of similar diseases across this host spectrum. Our investigation employed four molecular markers to study disease hotspots in Saint Eustatius, Curaçao, northwest and southwest Cuba, and Bonaire. This led to the discovery of a group of copepod species in these varied Caribbean locations. Importantly, these species are morphologically indistinguishable through traditional methods, challenging established taxonomic approaches. The observed diversity of symbionts, despite the host species' genetic uniformity, is likely due to variations in larval dispersal mechanisms. Our phylogenetic analyses confirmed that the Lamippidae copepods belong to the order, Poecilostomatoida (Copepoda), and revealed their sister group relationship with the Anchimolgidae, Rhynchomolgidae, and Xarifiidae clades, known for their symbiotic relationships with scleractinian corals. These results add to our understanding of the evolutionary and ecological interactions of copepods and their hosts, and the diseases that they cause, and are important data in a changing climate. [ABSTRACT FROM AUTHOR]

Cryptofaunal nematodes, those living on the hard substrate of the coral reefs, are largely unknown in terms of diversity and assemblage structure. We described nematode assemblages at seven sites spanning about 200 km along Jardines de La Reina, a well-preserved reef system in the Greater Antilles. We identified about 3000 nematodes, mostly of the families Desmodoridae and Chromadoridae; the most abundant species were Croconema cinctum, Desmodora communis, and Euchromadora vulgaris. The regional richness was moderate with 70 observed species (0.95 confidence interval: 65–75 species) and 75 extrapolated species (0.95 CI: 68–83 species). This richness was lower than in other reef biotopes, maybe reflecting evolutionary constraints due to interactions with stony corals. The local expected richness at 100 individuals was similar among sites, with a median of 26 species (0.95 CI: 20–34 species), and likely caused by diversification rate and evolutionary time acting at the same pace on populations. The taxonomic β-diversity was high and without differences among sites (median: 0.85; 0.95 CI: 0.33–1), probably due to significant substrate heterogeneity at 10-cm scale. The prevalence of replacement over richness difference suggests that local processes (e.g., environmental filtering and competition) contribute more to β-diversity than niche availability, which would be largely similar across the reef terraces. Contrary to our expectations, no gradient of assemblage structure occurred, nor significant effect of benthic cover on nematodes. However, nematode functional structure showed a conservative set of biological traits reflecting adaptations to hydrodynamic regime: armed oral cavity/intermediate colonizing capability/ornamented cuticles/conical tail. Our results provide insights about the taxonomic and functional diversity of nematodes and highlight the vast knowledge gaps about the processes ruling the meiofauna community structure in coral reefs. [ABSTRACT FROM AUTHOR]

Mutualism profoundly affects the morphology and ecological evolution of both hosts and symbionts involved. Heterocyathus is a solitary scleractinian coral that lives on soft substrata, and sipunculan worms live symbiotically in the tube-like cavities (orifice) inside the coral skeletons. This habitat provides protection to the sipunculan worms against predators and—owing to the mobility of the worms—prevents the coral from being buried with sediments. The orifice growth is closely related to the symbiont sipunculan worms; however, this has not been previously elucidated. Here, we clarified the growth process of scleractinian coral orifices and the influence of sipunculan activity on this. The orifices were originally formed by rapid accretion deposits. The coral soft tissue enveloping the growth edge of the orifice repeatedly retreated to the outer side due to direct damage to the soft part and/or excessive stress caused by the rubbing of the sipunculan through locomotion, excretion, and feeding behaviour. This resulted in a toppled-domino microskeletal structure appearance and maintenance of the orifice growth. These outcomes demonstrate the first example of the direct influence of symbionts on the skeletal morphogenesis of scleractinian corals. The mutualism between the two organisms is maintained by the beneficial confrontation in forming orifices. [ABSTRACT FROM AUTHOR]