A global database on coral recovery following marine heatwaves.

Coral reefs support the world's most diverse marine ecosystem and provide invaluable goods and services for millions of people worldwide. They are however experiencing frequent and intensive marine heatwaves that are causing coral bleaching and mortality. Coarse-grained climate models predict that few coral reefs will survive the 3 °C sea-surface temperature rise in the coming century. Yet, field studies show localized pockets of coral survival and recovery even under high-temperature conditions. Quantifying recovery from marine heatwaves is central to making accurate predictions of coral-reef trajectories into the near future. Here we introduce the world's most comprehensive database on coral recovery following marine heatwaves and other disturbances, called Heatwaves and Coral-Recovery Database (HeatCRD) encompassing 29,205 data records spanning 44 years from 12,266 sites, 83 countries, and 160 data sources. These data provide essential information to coral-reef scientists and managers to best guide coral-reef conservation efforts at both local and regional scales.

Genome-wide analysis to uncover how Pocillopora acuta survives the challenging intertidal environment.

Characterisation of genomic variation among corals can help uncover variants underlying trait differences and contribute towards genotype prioritisation in coastal restoration projects. For example, there is growing interest in identifying resilient genotypes for transplantation, and to better understand the genetic processes that allow some individuals to survive in specific conditions better than others. The coral species Pocillopora acuta is known to survive in a wide range of habitats, from reefs artificial coastal defences, suggesting its potential use as a starter species for ecological engineering efforts involving coral transplantation onto intertidal seawalls. However, the intertidal section of coastal armour is a challenging environment for corals, with conditions during periods of emersion being particularly stressful. Here, we scanned the entire genome of P. acuta corals to identify the regions harbouring single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) that separate intertidal colonies (n = 18) from those found in subtidal areas (n = 21). Findings revealed 74,391 high quality SNPs distributed across 386 regions of the P. acuta genome. While the majority of the detected SNPs were in non-coding regions, 12% were identified in exons (i.e. coding regions). Functional SNPs that were significantly associated with intertidal colonies were found in overrepresented genomic regions linked to cellular homeostasis, metabolism, and signalling processes, which may represent local environmental adaptation in the intertidal. Interestingly, regions that exhibited CNVs were also associated with metabolic and signalling processes, suggesting P. acuta corals living in the intertidal have a high capacity to perform biological functions critical for survival in extreme environments.

Coral geochemical response to uplift in the aftermath of the 2005 Nias-Simeulue earthquake.

On 28 March 2005, the Indonesian islands of Nias and Simeulue experienced a powerful Mw 8.6 earthquake and coseismic uplift and subsidence. In areas of coastal uplift (up to ~ 2.8 m), fringing reef coral communities were killed by exposure, while deeper corals that survived were subjected to habitats with altered runoff, sediment and nutrient regimes. Here we present time-series (2000-2009) of Mn/Ca, Y/Ca and Ba/Ca variability in massive Porites corals from Nias to assess the environmental impact of a wide range of vertical displacement (+ 2.5 m to - 0.4 m). High-resolution LA-ICP-MS measurements show that skeletal Mn/Ca increased at uplifted sites, regardless of reef type, indicating a post-earthquake increase in suspended sediment delivery. Transient and/or long-term increases in skeletal Y/Ca at all uplift sites support the idea of increased sediment delivery. Coral Mn/Ca and Ba/Ca in lagoonal environments highlight the additional influences of reef bathymetry, wind-driven sediment resuspension, and phytoplankton blooms on coral geochemistry. Together, the results show that the Nias reefs adapted to fundamentally altered hydrographic conditions. We show how centuries of repeated subsidence and uplift during great-earthquake cycles along the Sunda megathrust may have shaped the modern-day predominance of massive scleractinian corals on the West Sumatran reefs.

Global warming-related response after bacterial challenge in Astroides calycularis, a Mediterranean thermophilic coral.

A worldwide increase in the prevalence of coral diseases and mortality has been linked to ocean warming due to changes in coral-associated bacterial communities, pathogen virulence, and immune system function. In the Mediterranean basin, the worrying upward temperature trend has already caused recurrent mass mortality events in recent decades. To evaluate how elevated seawater temperatures affect the immune response of a thermophilic coral species, colonies of Astroides calycularis were exposed to environmental (23 °C) or elevated (28 °C) temperatures, and subsequently challenged with bacterial lipopolysaccharides (LPS). Using immunolabeling with specific antibodies, we detected the production of Toll-like receptor 4 (TLR4) and nuclear factor kappa B (NF-kB), molecules involved in coral immune responses, and heat shock protein 70 (HSP70) activity, involved in general responses to thermal stress. A histological approach allowed us to characterize the tissue sites of activation (epithelium and/or gastroderm) under different experimental conditions. The activity patterns of the examined markers after 6 h of LPS stimulation revealed an up-modulation at environmental temperature. Under warmer conditions plus LPS-challenge, TLR4-NF-kB activation was almost completely suppressed, while constituent elevated values were recorded under thermal stress only. An HSP70 up-regulation appeared in both treatments at elevated temperature, with a significantly higher activation in LPS-challenge colonies. Such an approach is useful for further understanding the molecular pathogen-defense mechanisms in corals in order to disentangle the complex interactive effects on the health of these ecologically relevant organisms related to global climate change.

Combining environmental DNA and visual surveys can inform conservation planning for coral reefs.

Environmental DNA (eDNA) metabarcoding has the potential to revolutionize conservation planning by providing spatially and taxonomically comprehensive data on biodiversity and ecosystem conditions, but its utility to inform the design of protected areas remains untested. Here, we quantify whether and how identifying conservation priority areas within coral reef ecosystems differs when biodiversity information is collected via eDNA analyses or traditional visual census records. We focus on 147 coral reefs in Indonesia's hyper-diverse Wallacea region and show large discrepancies in the allocation and spatial design of conservation priority areas when coral reef species were surveyed with underwater visual techniques (fishes, corals, and algae) or eDNA metabarcoding (eukaryotes and metazoans). Specifically, incidental protection occurred for 55% of eDNA species when targets were set for species detected by visual surveys and 71% vice versa. This finding is supported by generally low overlap in detection between visual census and eDNA methods at species level, with more overlap at higher taxonomic ranks. Incomplete taxonomic reference databases for the highly diverse Wallacea reefs, and the complementary detection of species by the two methods, underscore the current need to combine different biodiversity data sources to maximize species representation in conservation planning.

A large non-parasitic population of Savalia savaglia (Bertoloni, 1819) in the Boka Kotorska Bay (Montenegro).

The golden coral Savalia savaglia is a long-living ecosystem engineer of Mediterranean circalittoral assemblages, able to induce necrosis of gorgonians' and black corals' coenenchyme and grow on their cleaned organic skeleton. Despite its rarity, in Boka Kotorska Bay (Montenegro) a shallow population of more than 1000 colonies was recorded close to underwater freshwater springs, which create very peculiar environmental conditions. In this context, the species was extremely abundant at two sites, while gorgonians were rare. The abundance and size of S. savaglia colonies and the diversity of the entire benthic assemblage were investigated by photographic sampling in a depth range of 0-35 m. Several living fragments of S. savaglia spread on the sea floor and small settled colonies (< 5 cm high) suggested a high incidence of asexual reproduction and a non-parasitic behaviour of this population. This was confirmed by studying thin sections of the basal portion of the trunk where the central core, generally represented by the remains of the gorgonian host skeleton, was lacking. The S. savaglia population of Boka Kotorska Bay forms the unique Mediterranean assemblage of the species deserving the definition of animal forest. Recently, temporary mitigation measures for anthropogenic impact were issued by the Government of Montenegro. Nevertheless, due to the importance of the sites the establishment of a permanent Marine Protected Area is strongly recommended.

Interplay of management and environmental drivers shifts size structure of reef fish communities.

Countries are expanding marine protected area (MPA) networks to mitigate fisheries declines and support marine biodiversity. However, MPA impact evaluations typically assess total fish biomass. Here, we examine how fish biomass disaggregated by adult and juvenile life stages responds to environmental drivers, including sea surface temperature (SST) anomalies and human footprint, and multiple management types at 139 reef sites in the Mesoamerican Reef (MAR) region. We found that total fish biomass generally appears stable across the region from 2006 to 2018, with limited rebuilding of fish stocks in MPAs. However, the metric of total fish biomass masked changes in fish community structure, with lower adult than juvenile fish biomass at northern sites, and adult:juvenile ratios closer to 1:1 at southern sites. These shifts were associated with different responses of juvenile and adult fish to environmental drivers and management. Juvenile fish biomass increased at sites with high larval connectivity and coral cover, whereas adult fish biomass decreased at sites with greater human footprint and SST anomalies. Adult fish biomass decreased primarily in Honduran general use zones, which suggests insufficient protection for adult fish in the southern MAR. There was a north-south gradient in management and environmental drivers, with lower coverage of fully protected areas and higher SST anomalies and coastal development in the south that together may undermine the maintenance of adult fish biomass in the southern MAR. Accounting for the interplay between environmental drivers and management in the design of MPAs is critical for increasing fish biomass across life history stages.

Los países están ampliando las redes de áreas marinas protegidas (AMP) para mitigar la disminución de las pesquerías y apoyar la biodiversidad marina. Sin embargo, las evaluaciones de impacto de las AMP típicamente estudian la biomasa total de peces. Aquí, examinamos cómo la biomasa de peces desagregada por etapas de vida adultas y juveniles responde a factores ambientales como anomalías de la temperatura superficial del mar (SST) e impacto humano, y múltiples tipos de manejo en 139 sitios de arrecifes en el sistema arrecifal mesoamericano (SAM). Encontramos que la biomasa total de peces en general parece estable en toda la región entre 2006 y 2018, con una recuperación limitada de las poblaciones de peces en las AMP. Sin embargo, la métrica de biomasa total de peces enmascaró los cambios en la estructura de la comunidad de peces, con una biomasa de peces adultos más baja que juveniles en los sitios del norte, y proporciones adulto:juvenil más cercana a 1:1 en los sitios del sur. Estos cambios fueron asociados con diferentes respuestas de peces juveniles y adultos a variables ambientales y de manejo. La biomasa de peces juveniles aumentó en sitios con alta conectividad larvaria y cobertura coralina, mientras que la biomasa de peces adultos disminuyó en sitios con mayor impacto humano y anomalías en la SST. La biomasa de peces adultos disminuyó principalmente en las zonas de uso general (GUZ) hondureñas, lo cual sugiere una protección insuficiente para peces adultos en el sur del SAM. Hubo un gradiente norte­sur en el manejo y los factores ambientales, con menor cobertura de áreas totalmente protegidas y mayores anomalías de SST y desarrollo costero en el sur. En conjunto esto puede degradar el mantenimiento de la biomasa de peces adultos en el sur del SAM. La interacción entre factores ambientales y el manejo en el diseño de las AMP es fundamental para aumentar la biomasa de peces en todas las etapas del ciclo de vida.

Rubellicoccus peritrichatus gen. nov., sp. nov., isolated from crustose coralline algae in a coral aquarium.

A Gram-stain-negative, motile, aerobic, non-spore-forming coccus, designated strain CR14T, was isolated from crustose coralline algae. Cells grew at 20-30 °C (optimum, 25 °C), at pH 6-9 (optimum, pH 7.6) and with NaCl concentrations of 0.5-9 % (w/v; optimum, 2-4 %). Global alignment based on 16S rRNA gene sequences indicated strain CR14T is closest to Ruficoccus amylovorans JCM 31066T with an identity of 92 %. The average nucleotide identity and average amino acid identity values between CR14T and R. amylovorans JCM 31066T were 68.4 and 59.9 %, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CR14T forms an independent branch within the family Cerasicoccaeae, which was consistent with the phylogenomic results. The sole isoprenoid quinone was MK-7. The major fatty acids were C14 : 0, C18 : 1 ω9c, C19 : 0 cyc 9,10 DMA, C16 : 0, and C18 : 2 ω6c. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and two unidentified lipids. The genome DNA G+C content was 48.7 mol%. Based on morphological, physiological and chemotaxonomic characteristics, strain CR14T is suggested to represent a novel species in a new genus, for which the name Rubellicoccus peritrichatus gen. nov., sp. nov. is proposed. The type strain is CR14T (=MCCC 1K03845T=KCTC 72139T).

Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment.

Beneficial microorganisms for corals (BMCs), or probiotics, can enhance coral resilience against stressors in laboratory trials. However, the ability of probiotics to restructure the coral microbiome in situ is yet to be determined. As a first step to elucidate this, we inoculated putative probiotic bacteria (pBMCs) on healthy colonies of Pocillopora verrucosa in situ in the Red Sea, three times per week, during 3 months. pBMCs significantly influenced the coral microbiome, while bacteria of the surrounding seawater and sediment remained unchanged. The inoculated genera Halomonas, Pseudoalteromonas, and Bacillus were significantly enriched in probiotic-treated corals. Furthermore, the probiotic treatment also correlated with an increase in other beneficial groups (e.g., Ruegeria and Limosilactobacillus), and a decrease in potential coral pathogens, such as Vibrio. As all corals (treated and non-treated) remained healthy throughout the experiment, we could not track health improvements or protection against stress. Our data indicate that healthy, and therefore stable, coral microbiomes can be restructured in situ, although repeated and continuous inoculations may be required in these cases. Further, our study provides supporting evidence that, at the studied scale, pBMCs have no detectable off-target effects on the surrounding microbiomes of seawater and sediment near inoculated corals.

Impact of human disturbance on biogeochemical fluxes in tropical seascapes.

Tropical seascapes rely on the feedback relationships among mangrove forests, seagrass meadows, and coral reefs, as they mutually facilitate and enhance each other's functionality. Biogeochemical fluxes link tropical coastal habitats by exchanging material flows and energy through various natural processes that determine the conditions for life and ecosystem functioning. However, little is known about the seascape-scale implications of anthropogenic disruptions to these linkages. Despite the limited number of integrated empirical studies available (with only 11 out of 81 selected studies focusing on the integrated dynamics of mangroves, seagrass, and corals), this review emphasizes the importance of biogeochemical fluxes for ecosystem connectivity in tropical seascapes. It identifies four primary anthropogenic influences that can disturb these fluxes-nutrient enrichment, chemical pollution, microbial pollution, and solid waste accumulation-resulting in eutrophication, increased disease incidence, toxicity, and disruptions to water carbonate chemistry. This review also highlights significant knowledge gaps in our understanding of biogeochemical fluxes and ecosystem responses to perturbations in tropical seascapes. Addressing these knowledge gaps is crucial for developing practical strategies to conserve and manage connected seascapes effectively. Integrated research is needed to shed light on the complex interactions and feedback mechanisms within these ecosystems, providing valuable insights for conservation and management practices.

Climate change impacts on mesophotic regions of the Great Barrier Reef.

Climate change projections for coral reefs are founded exclusively on sea surface temperatures (SST). While SST projections are relevant for the shallowest reefs, neglecting ocean stratification overlooks the striking differences in temperature experienced by deeper reefs for all or part of the year. Density stratification creates a buoyancy barrier partitioning the upper and lower parts of the water column. Here, we mechanistically downscale climate models and quantify patterns of thermal stratification above mesophotic corals (depth 30 to 50 m) of the Great Barrier Reef (GBR). Stratification insulates many offshore regions of the GBR from heatwaves at the surface. However, this protection is lost once global average temperatures exceed ~3 °C above preindustrial, after which mesophotic temperatures surpass a recognized threshold of 30 °C for coral mortality. Bottom temperatures on the GBR (30 to 50 m) from 2050 to 2060 are estimated to increase by ~0.5 to 1 °C under lower climate emissions (SSP1-1.9) and ~1.2 to 1.7 °C under higher climate emissions (SSP5-8.5). In short, mesophotic coral reefs are also threatened by climate change and research might prioritize the sensitivity of such corals to stress.

ReScape: transforming coral-reefscape images for quantitative analysis.

Ever since the first image of a coral reef was captured in 1885, people worldwide have been accumulating images of coral reefscapes that document the historic conditions of reefs. However, these innumerable reefscape images suffer from perspective distortion, which reduces the apparent size of distant taxa, rendering the images unusable for quantitative analysis of reef conditions. Here we solve this century-long distortion problem by developing a novel computer-vision algorithm, ReScape, which removes the perspective distortion from reefscape images by transforming them into top-down views, making them usable for quantitative analysis of reef conditions. In doing so, we demonstrate the first-ever ecological application and extension of inverse-perspective mapping-a foundational technique used in the autonomous-driving industry. The ReScape algorithm is composed of seven functions that (1) calibrate the camera lens, (2) remove the inherent lens-induced image distortions, (3) detect the scene's horizon line, (4) remove the camera-roll angle, (5) detect the transformable reef area, (6) detect the scene's perspective geometry, and (7) apply brute-force inverse-perspective mapping. The performance of the ReScape algorithm was evaluated by transforming the perspective of 125 reefscape images. Eighty-five percent of the images had no processing errors and of those, 95% were successfully transformed into top-down views. ReScape was validated by demonstrating that same-length transects, placed increasingly further from the camera, became the same length after transformation. The mission of the ReScape algorithm is to (i) unlock historical information about coral-reef conditions from previously unquantified periods and localities, (ii) enable citizen scientists and recreational photographers to contribute reefscape images to the scientific process, and (iii) provide a new survey technique that can rigorously assess relatively large areas of coral reefs, and other marine and even terrestrial ecosystems, worldwide. To facilitate this mission, we compiled the ReScape algorithm into a free, user-friendly App that does not require any coding experience. Equipped with the ReScape App, scientists can improve the management and prediction of the future of coral reefs by uncovering historical information from reefscape-image archives and by using reefscape images as a new, rapid survey method, opening a new era of coral-reef monitoring.

RADReef: A global Holocene Reef Rate of Accretion Dataset.

Reef cores are a powerful tool for investigating temporal changes in reef communities. Radiometric dating facilitates the determination of vertical accretion rates, which has allowed for examination of local-regional controlling factors, such as subsidence and sea level changes. Coral reefs must grow at sufficient rates to keep up with sea level rise, or risk 'drowning.' As sea level is expected to rise significantly in the next 100 years and beyond, it is important to understand whether reefs will be able to survive. Historical records of reef accretion rates extracted from cores provide valuable insights into extrinsic controlling factors of reef growth and are instrumental in helping predict if future reefs can accrete at rates needed to overcome predicted sea level changes. While extensive research exists at local and regional scales, limited attention has been given to identifying global patterns and drivers. To address this, we present "RADReef": A global dataset of dated Holocene reef cores. RADReef serves as a foundation for further research on past, present and future reef accretion.

Corals survive severe bleaching event in refuges related to taxa, colony size, and water depth.

Marine heatwaves are increasing in frequency and duration, threatening tropical reef ecosystems through intensified coral bleaching events. We examined a strikingly variable spatial pattern of bleaching in Moorea, French Polynesia following a heatwave that lasted from November 2018 to July 2019. In July 2019, four months after the onset of bleaching, we surveyed > 5000 individual colonies of the two dominant coral genera, Pocillopora and Acropora, at 10 m and 17 m water depths, at six forereef sites around the island where temperature was measured. We found severe bleaching increased with colony size for both coral genera, but Acropora bleached more severely than Pocillopora overall. Acropora bleached more at 10 m than 17 m, likely due to higher light availability at 10 m compared to 17 m, or greater daily temperature fluctuation at depth. Bleaching in Pocillopora corals did not differ with depth but instead varied with the interaction of colony size and Accumulated Heat Stress (AHS), in that larger colonies (> 30 cm) were more sensitive to AHS than mid-size (10-29 cm) or small colonies (5-9 cm). Our findings provide insight into complex interactions among coral taxa, colony size, and water depth that produce high spatial variation in bleaching and related coral mortality.

Linking cell biology and ecology to understand coral symbiosis evolution.

Understanding the evolution of coral endosymbiosis requires a predictive framework that integrates life-history theory and ecology with cell biology. The time has come to bridge disciplines and use a model systems approach to achieve this aim.

Decline of a distinct coral reef holobiont community under ocean acidification.

BACKGROUND: Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH - an important global coral reef stressor - can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome. RESULTS: We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO2 seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation. CONCLUSIONS: We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem changed. Video Abstract.

Life goes on: Spatial heterogeneity promotes biodiversity in an urbanized coastal marine ecosystem.

Both human populations and marine biodiversity are concentrated along coastlines, with growing conservation interest in how these ecosystems can survive intense anthropogenic impacts. Tropical urban centres provide valuable research opportunities because these megacities are often adjacent to mega-diverse coral reef systems. The Pearl River Delta is a prime exemplar, as it encompasses one of the most densely populated and impacted regions in the world and is located just northwest of the Coral Triangle. However, the spatial and taxonomic complexity of this biodiversity, most of which is small, cryptic in habitat and poorly known, make comparative analyses challenging. We deployed standardized settlement structures at seven sites differing in the intensity of human impacts and used COI metabarcoding to characterize benthic biodiversity, with a focus on metazoans. We found a total of 7184 OTUs, with an average of 665 OTUs per sampling unit; these numbers exceed those observed in many previous studies using comparable methods, despite the location of our study in an urbanized environment. Beta diversity was also high, with 52% of the OTUs found at just one site. As expected, we found that the sites close to point sources of pollution had substantially lower diversity (44% less) relative to sites bathed in less polluted oceanic waters. However, the polluted sites contributed substantially to the total animal diversity of the region, with 25% of all OTUs occurring only within polluted sites. Further analysis of Arthropoda, Annelida and Mollusca showed that phylogenetic clustering within a site was common, suggesting that environmental filtering reduced biodiversity to a subset of lineages present within the region, a pattern that was most pronounced in polluted sites and for the Arthropoda. The water quality gradients surrounding the PRD highlight the unique role of in situ studies for understanding the impacts of complex urbanization pressures on biodiversity.

High response diversity and conspecific density-dependence, not species interactions, drive dynamics of coral reef fish communities.

Species-to-species and species-to-environment interactions are key drivers of community dynamics. Disentangling these drivers in species-rich assemblages is challenging due to the high number of potentially interacting species (the 'curse of dimensionality'). We develop a process-based model that quantifies how intraspecific and interspecific interactions, and species' covarying responses to environmental fluctuations, jointly drive community dynamics. We fit the model to reef fish abundance time series from 41 reefs of Australia's Great Barrier Reef. We found that fluctuating relative abundances are driven by species' heterogenous responses to environmental fluctuations, whereas interspecific interactions are negligible. Species differences in long-term average abundances are driven by interspecific variation in the magnitudes of both conspecific density-dependence and density-independent growth rates. This study introduces a novel approach to overcoming the curse of dimensionality, which reveals highly individualistic dynamics in coral reef fish communities that imply a high level of niche structure.

Responses of the coral reef cryptobiome to environmental gradients in the Red Sea.

An essential component of the coral reef animal diversity is the species hidden in crevices within the reef matrix, referred to as the cryptobiome. These organisms play an important role in nutrient cycling and provide an abundant food source for higher trophic levels, yet they have been largely overlooked. Here, we analyzed the distribution patterns of the mobile cryptobiome (>2000 µm) along the latitudinal gradient of the Saudi Arabian coast of the Red Sea. Analysis was conducted based on 54 Autonomous Reef Monitoring Structures. We retrieved a total of 5273 organisms, from which 2583 DNA sequences from the mitochondrially encoded cytochrome c oxidase I were generated through sanger sequencing. We found that the cryptobiome community is variable over short geographical distances within the basin. Regression tree models identified sea surface temperature (SST), percentage cover of hard coral and turf algae as determinant for the number of operational taxonomic units present per Autonomous Reef Monitoring Structures (ARMS). Our results also show that the community structure of the cryptobiome is associated with the energy available (measured as photosynthetic active radiation), sea surface temperature, and nearby reef habitat characteristics (namely hard corals, turf and macroalgae). Given that temperature and reef benthic characteristics affect the cryptobiome, current scenarios of intensive climate change are likely to modify this fundamental biological component of coral reef functioning. However, the trajectory of change is unknow and can be site specific, as for example, diversity is expected to increase above SST of 28.5°C, and with decreasing hard coral and turf cover. This study provides a baseline of the cryptobenthic community prior to major coastal developments in the Red Sea to be used for future biodiversity studies and monitoring projects. It can also contribute to better understand patterns of reef biodiversity in a period where Marine Protected Areas are being discussed in the region.

Gene expression plasticity facilitates acclimatization of a long-lived Caribbean coral across divergent reef environments.

Local adaptation can increase fitness under stable environmental conditions. However, in rapidly changing environments, compensatory mechanisms enabled through plasticity may better promote fitness. Climate change is causing devastating impacts on coral reefs globally and understanding the potential for adaptive and plastic responses is critical for reef management. We conducted a four-year, three-way reciprocal transplant of the Caribbean coral Siderastrea siderea across forereef, backreef, and nearshore populations in Belize to investigate the potential for environmental specialization versus plasticity in this species. Corals maintained high survival within forereef and backreef environments, but transplantation to nearshore environments resulted in high mortality, suggesting that nearshore environments present strong environmental selection. Only forereef-sourced corals demonstrated evidence of environmental specialization, exhibiting the highest growth in the forereef. Gene expression profiling 3.5 years post-transplantation revealed that transplanted coral hosts exhibited profiles more similar to other corals in the same reef environment, regardless of their source location, suggesting that transcriptome plasticity facilitates acclimatization to environmental change in S. siderea. In contrast, algal symbiont (Cladocopium goreaui) gene expression showcased functional variation between source locations that was maintained post-transplantation. Our findings suggest limited acclimatory capacity of some S. siderea populations under strong environmental selection and highlight the potential limits of coral physiological plasticity in reef restoration.