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Background: Cladocopium infistulum (Symbiodiniaceae) is a dinoflagellate specialized to live in symbiosis with western Pacific giant clams (Tridacnidae). Unlike coral-associated symbionts, which reside within the host cells, C. infistulum inhabits the extracellular spaces of the clam's digestive diverticula. It is phylogenetically basal to a large species complex of stress-tolerant Cladocopium, many of which are associated with important reef-building corals in the genus Porites. This close phylogenetic relationship may explain why C. infistulum exhibits high thermotolerance relative to other tridacnid symbionts. Moreover, past analyses of microsatellite loci indicated that Cladocopium underwent whole-genome duplication prior to the adaptive radiations that led to its present diversity. Results: A draft genome assembly of C. infistulum was produced using long- and short-read sequences to explore the genomic basis for adaptations underlying thermotolerance and extracellular symbiosis among dinoflagellates and to look for evidence of genome duplication. Comparison to three other Cladocopium genomes revealed no obvious over-representation of gene groups or families whose functions would be important for maintaining C. infistulum's unique physiological and ecological properties. Preliminary analyses support the existence of partial or whole-genome duplication among Cladocopium, but additional high-quality genomes are required to substantiate these findings. Conclusion: Although this investigation of Cladocopium infistulum revealed no patterns diagnostic of heat tolerance or extracellular symbiosis in terms of overrepresentation of gene functions or genes under selection, it provided a valuable genomic resource for comparative analyses. It also indicates that ecological divergence among Cladocopium species, and potentially among other dinoflagellates, is partially governed by mechanisms other than gene content. Thus, additional high-quality, multiomic data are needed to explore the molecular basis of key phenotypes among symbiotic microalgae. [ABSTRACT FROM AUTHOR]

Corals are colonized by a plethora of microorganisms, and their diversity plays a significant role in the health and resilience of corals when they face oxidative stress leading to bleaching. In the current study, we examined 238 bacteria isolated from five different coral species (Acropora hyacinthus, Pocillopora damicornis, Podabacea crustacea, Porites lobata, and Pavona venosa) collected from the coral reef ecosystems of Kavaratti, Lakshadweep Islands, India. We found that bacteria such as Psychrobacter sp., Halomonas sp., Kushneria sp., Staphylococcus sp., Bacillus sp., Brachybacterium sp., Citrobacter sp., and Salinicola sp. were commonly present in the corals. On the other hand, Qipengyuania sp., Faucicola sp., Marihabitans sp., Azomonas sp., Atlantibacter sp., Cedecea sp., Krasalinikoviella sp., and Aidingimonas sp. were not previously reported from the corals. Among the bacterial isolates, a significant number showed high levels of biofilm formation (118), UV absorption (119), and melanin production (127). Considering these properties, we have identified a combination of seven bacteria from the genera Halomonas sp., Psychrobacter sp., Krasalinikoviella sp., and Micrococcus sp. as a potential probiotic consortium for protecting corals from oxidative stress. Overall, this study provides valuable insights into the coral microbiome and opens up possibilities for microbiome-based interventions to protect these crucial ecosystems in the face of global environmental challenges. [ABSTRACT FROM AUTHOR]

The coral-seawater interface is an important, highly dynamic microenvironment for reef-building corals. Also known as the concentration boundary layer (CBL), it is a thin layer of seawater bordering the coral surface that dictates the biochemical exchange between the coral colony and bulk seawater. The CBL is thus a key feature that modulates coral metabolism. However, CBL variation among small-polyped coral species remains largely unknown. Therefore, we recorded over 100 profiles of dissolved O2 concentration using microsensors to characterize CBL traits (thickness, surface O2 concentration, and flux) of three small-polyped branching coral species, Acropora cytherea, Pocillopora verrucosa, and Porites cylindrica. Measurements were conducted during light and darkness combined with low or moderate water flow (2 and 6 cm s−1). We found that CBL traits differed among species. CBL thickness was lowest in A. cytherea, while P. verrucosa showed the largest depletion of surface O2 in dark and highest dark flux. In addition, we found that O2 concentration gradients in the CBL occurred with three main profile shapes: diffusive, S-shaped, and complex. While diffusive profiles were the most common profile type, S-shaped and complex profiles were more frequent in P. verrucosa and P. cylindrica, respectively, and prevailed under low flow. Furthermore, profile types differed in CBL thickness and flux. Finally, low flow thickened CBLs, enhanced changes in surface O2 concentration, and reduced flux, compared to moderate flow. Overall, our findings reveal CBL variability among small-polyped branching corals and help understand CBL dynamics in response to changes in light and water flow conditions. [ABSTRACT FROM AUTHOR]

Coral skeletons are composites of aragonite and biomolecules. We report the concentrations of 11 amino acids in massive Porites spp. coral skeletons cultured at two temperatures (25 °C and 28 °C) and 3 seawater pCO2 (180, 400 and 750 µatm). Coral skeletal aspartic acid/asparagine (Asx), glutamic acid/glutamine (Glx), glycine, serine and total amino acid concentrations are significantly higher at 28 °C than at 25 °C. Skeletal Asx, Glx, Gly, Ser, Ala, L-Thr and total amino acid are significantly lower at 180 µatm seawater pCO2 compared to 400 µatm, and Ser is reduced at 180 µatm compared to 750 µatm. Concentrations of all skeletal amino acids are significantly inversely related to coral calcification rate but not to calcification media pH. Raman spectroscopy of these and additional specimens indicates that CO3 disorder in the skeletal aragonite lattice is not affected by seawater pCO2 but decreases at the higher temperature. This is contrary to observations in synthetic aragonite where disorder is positively related to the aragonite precipitation rate mediated by either increasing temperature (this study) or increasing Ω (this study and a previous report) and to the concentration of amino acid in the precipitation media (a previous report). We observe no significant relationship between structural disorder and coral calcification rate or skeletal [amino acid]. Both temperature and seawater pCO2 can significantly affect skeletal amino acid composition, and further work is required to clarify how environmental change mediates disorder. [ABSTRACT FROM AUTHOR]

Phenotypic variability is the ability of the same species to express different phenotypes under different environmental conditions. Several coral species that exist along a broad depth distribution have been shown to differ in skeletal morphology and nutrient acquisition at different depths, which has been attributed to variability in response to differing levels of light availability. This study examined the phenotypic variability of two common depth generalist corals, Montastraea cavernosa and Porites astreoides, along a gradient from 10 to 50 m in the Cayman Islands, by examining changes in skeletal morphology, photophysiology, symbiont cell density, and chlorophyll concentration. Skeletal features of M. cavernosa were found to increase in size from 10 to 30 m, but returned to smaller sizes from 30 to 50 m, while P. astreoides skeletal features continued to increase in size from 10 to 40 m. No differences were observed in either symbiont density or chlorophyll concentration across depths for either species. However, all photophysiological parameters exhibited significant depth-dependent variations in both species, revealing adaptive strategies to different light environments. These results suggest that both species have high variability in response to depth. Patterns of skeletal morphology and photophysiology, however, suggest that M. cavernosa may be more variable in regulating photosynthetic efficiency compared to P. astreoides, which likely facilitates the broader depth distribution of this species. [ABSTRACT FROM AUTHOR]

ABSTRACT 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]

The decline of coral reefs has increased interest in ecological restoration. Due to the scarcity of coral gardening projects in the Eastern Tropical Pacific, improving our understanding of such techniques is key. We report the results of coral gardening using the branching Pocillopora spp. and massive coral species (Pavona gigantea, Pavona clavus and Porites lobata) in an upwelling area in Costa Rica. We examined whether nursery type influenced Pocillopora spp. survival and growth, and how environmental conditions shaped restoration. We monitored the survival and growth of Pocillopora spp. fragments (n = 334) and microfragments of massive species (P. gigantea [n = 148], P. clavus [n = 37], P. lobata [n = 66]) over 11 months. Survival at the end of the gardening period was 51% for Pocillopora spp., 59% for P. clavus, 55% for P. gigantea, and 17% for P. lobata, with a decline after a cease in maintenance caused by the COVID-19 lockdown. Pocillopora spp. fragments in the floating nurseries exhibited higher growth (7.52 ± 1.98 and 6.64 ± 2.91 cm yr-1) than in the A-frame (4.16 ± 2.35 cm yr-1), which suggests the benefits of suspending fragments. For massive microfragments coral growth was 1.92-4.66 cm² yr-1 and were affected by pigmentation loss, causing partial tissue loss and mortality. Our results point towards acclimation to local conditions, and show the need to develop site-specific cost-efficient gardening techniques for massive species, allowing for a multi-species approach to ensure long-term ecosystem recovery. [ABSTRACT FROM AUTHOR]

The impacts of (repeat) bleaching events and the differential heat stress susceptibility of hard coral taxa are largely unknown in Malaysia, although it is part of the greater coral triangle. Here we determined bleaching trajectories of 46 hard coral taxa across- and within-reef scales based on data recorded during the first reported back-to-back coral bleaching occurrences in Malaysia between May 2019 and September 2020. Although the severity of coral bleaching in both years did not correspond to the rather small magnitude of heat stress observed, i.e., Degree Heating Weeks (DHW) of 1.05 °C-weeks and 0 °C-weeks in 2019 and 2020 respectively, we observed high levels of bleaching (55.21% and 26.63% of all surveyed colonies in 2019 and 2020, respectively). Notably, the bleaching response for both consecutive years was highly taxon-specific and significantly varied across- and within-reef scales. Mortality rates overall were low following the 2019 event, likely due to a rapid decrease in heat stress. Five of the 46 surveyed hard coral taxa exhibited more severe bleaching in 2020, despite a lower heat stress load. Interestingly, we observed low bleaching of ascribed susceptible taxa such as Acropora and Montipora, while we found taxa considered to be resilient, e.g. Heliopora and Porites, to exhibit severe bleaching, suggesting a reversal of bleaching hierarchies of taxa over time. Our findings provide a foundation for further coral bleaching studies in a region with few published records to enable more accurate regional assessments and to follow the trajectory of future coral bleaching events. [ABSTRACT FROM AUTHOR]

Anthropogenic activities increase the level of dissolved heavy metals in some tropical near‐shore environments threatening reef ecosystems. The skeleton of stony corals like Porites species potentially provides a high‐resolution geochemical archive for past heavy metal concentrations, with potentially century long records revealing baseline values before large‐scale human disturbance. However, few data exist for heavy metal partitioning into coral skeleton aragonite. To address this, culturing experiments exposing Porites lobata and Porites lichen to a mixture of dissolved Cr, Mn, Ni, Cu, Zn, Ag, Cd, Sn, Hg, and Pb over a wide concentration range have been performed. Water samples were taken frequently to monitor changes in the heavy metal concentration. Laser ablation ICP‐MS measurements of the coral aragonite revealed metal concentrations that were positively correlated with Cr, Mn, Ni, Zn, Ag, Cd, and Pb concentrations in seawater. The DTE values for most metals appear dependent on the seawater metal content, approximating a power law, and therefore stabilize at higher seawater metal/Ca ratios. The partitioning of Pb into the coral skeleton is a notable exception, with DPb being stable around 2 to 1 across a large range of "natural" to highly polluted seawater Pb concentrations. This and the general agreement with partition coefficients estimated by previous work suggests that the reconstruction of the heavy metal concentration in seawater for ecosystem monitoring is possible. However, the high variability within and between coral colonies requires further study and suggests that multiple records from multiple coral colonies should be combined to obtain robust reconstructions. Key Points: Porites corals grow normally with increased exposure to multiple metals over >1 yearSkeletal partitioning variable within and between colonies and with seawater metal contentGood agreement with previous work, especially for Pb across a large range of metal content [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]

Coral reefs worldwide are under increasing levels of pressure due to global and local stressors. Long-term monitoring of coral reefs through repeated observations at fixed survey sites allows scientists to assess temporal patterns in coral-reef communities and plays important roles in informing managers of the state of the ecosystems. Here, we describe coral assemblages in Papahānaumokuākea, the largest contiguous fully protected marine conservation area in the United States, using long-term monitoring data collected from 20 permanent (fixed) sites at three islands/atolls, Lalo, Kapou and Manawai, between 2014 and 2021. Significant temporal shifts in coral colony composition were detected at some of the monitoring sites, which were attributed to the impact of a mass coral bleaching event in 2014 and Hurricane Walaka in 2018. In particular, the bleaching affected multiple sites at Kapou and one site at Manawai where coral assemblages shifted from the Montipora dilatata/flabellata/turgescens complex to M. capitata dominance; despite being the dominant species at multiple monitoring sites prior to the bleaching, the M. dilatata/flabellata/turgescens complex has not been recorded at any of our monitoring sites in recent years. Coral conditions, such as bleaching, predation, subacute tissue loss, Porites pigmentation response and trematodiasis, did not show differences in the occurrence among the three islands/atolls once the site and temporal variabilities, as well as environmental covariates for bleaching, were considered. Coral genera, however, exhibited different sensitivities to these conditions. These findings highlight the importance of continuing coral reef monitoring at the species level, covering a broad range of coral assemblage compositions and habitat types in Papahānaumokuākea. [ABSTRACT FROM AUTHOR]

The ecological success of shallow water corals hinges on their association with photosynthetic Symbiodiniaceae algae. This is affected by environmental drivers among which sea temperature is pivotal. In 2016, a prolonged heat wave challenged New Caledonia reefs triggering a severe bleaching event. Here, we tracked 72 coral colonies comprising two species of Pocillopora and Porites from a cross-shelf gradient during the event and subsequent recovery period. Symbiodiniaceae association over time was assessed using the ITS2 marker. Bleaching prevalence and photosynthetic efficiency showed that 83% of Pocillopora and 29% of Porites colonies were affected, with corals from a mid-shelf site having been most impacted. The majority of tracked colonies recovered by December 2016, with a recorded 33% mortality of Pocillopora, while Porites showed higher resilience. Consistent with previous studies, genotyping data suggest stable, species- and site-specific associations between corals and Symbiodiniaceae. [ABSTRACT FROM AUTHOR]

Introduction: In 2023, a comprehensive survey was conducted at Qiziwan National Marine Park (QZW) to assess marine environmental variables, coral communities, and ecosystem parameters. This study aimed to evaluate the current state of coral ecosystems across different regions within the park. Methods: The survey covered 19 sampling stations distributed among four regions: Xiaojiao Park, Zhongjiao Park, Dajiao Park, and Shayutang Village. Various marine environmental parameters were measured, and coral species were identified and recorded. Results: A total of 67 species of reef-building corals belonging to 25 genera were identified. Dominant species included Porites lutea, Goniopora columna, Platygyra sinensis, Favites flexuosa, Galaxea fascicularis, and Acropora millepora. Coral coverage was found to be low at Xiaojiao Park, with high levels of turbidity and dissolved inorganic nitrogen, likely due to the nearby Changhua Port. Dajiao Park's sandy substrate made it unsuitable for coral survival. In contrast, Zhongjiao Park and Shayutang Village exhibited the best coral ecosystems. Redundancy analysis indicated that turbidity and substrate types were significant factors influencing coral distribution. Discussion: The live coral coverage at Xiaojiao Park, parts of Zhongjiao Park, and Dajiao Park declined from 14.03% in 2017 to 11.73% in 2023. This decline is potentially attributed to frequent marine construction and land use changes. Anthropogenic disturbances appear to have worsened environmental conditions, undermining coral reef survival at QZW. [ABSTRACT FROM AUTHOR]

Symbiotic dinoflagellates in the genus Symbiodiniaceae play vital roles in promoting resilience and increasing stress tolerance in their coral hosts. While much of the world's coral succumb to the stresses associated with increasingly severe and frequent thermal bleaching events, live coral cover in Papua New Guinea (PNG) remains some of the highest reported globally despite the historically warm waters surrounding the country. Yet, in spite of the high coral cover in PNG and the acknowledged roles Symbiodiniaceae play within their hosts, these communities have not been characterized in this global biodiversity hotspot. Using high-throughput sequencing of the ITS2 rDNA gene, we profiled the endosymbionts of four coral species, Diploastrea heliopora, Pachyseris speciosa, Pocillopora acuta, and Porites lutea, across six sites in PNG. Our findings reveal patterns of Cladocopium and Durusdinium dominance similar to other reefs in the Coral Triangle, albeit with much greater intra- and intergenomic variation. Host- and site-specific variations in Symbiodiniaceae type profiles were observed across collection sites, appearing to be driven by environmental conditions. Notably, the extensive intra- and intergenomic variation, coupled with many previously unreported sequences, highlight PNG as a potential hotspot of symbiont diversity. This work represents the first characterization of the coral-symbiont community structure in the PNG marine biodiversity hotspot, serving as a baseline for future studies. [ABSTRACT FROM AUTHOR]

Introduction: Several fluorescent proteins (FPs) and chromoproteins (CPs) are present in anthozoans and play possible roles in photoprotection. Coral tissues in massive corals often display discoloration accompanied by inflammation. Incidences of the pink pigmentation response (PPR) in massive Porites, described as inflammatory pink lesions of different shapes and sizes, has recently increased worldwide. FPs are reported to be present in PPR lesions, wherein a red fluorescent protein (RFP) appears to play a role in reducing reactive oxygen species. However, to date, the biochemical characterization and possible roles of the pigments involved are poorly understood. The present study aimed to identify and characterize the proteins responsible for pink discoloration in massive Porites colonies displaying PPRs, as well as to assess the differential distribution of pigments and the antioxidant properties of pigmented areas. Method: CPs were extracted from PPR lesions using gel-filtration chromatography and identified via genetic analysis using liquid chromatography-tandem mass spectrometry. The coexistence of CPs and RFP in coral tissues was assessed using microscopic observation. Photosynthetic antivity and hydrogen peroxide-scavenging activitiy were measured to assess coral stress conditions. Results: The present study revealed that the same CP (plut2.m8.16902.m1) isolated from massive Porites was present in both the pink spot and patch morphologies of the PPR. CPs were also found to coexist with RFP in coral tissues that manifested a PPR, with a differential distribution (coenosarc or tip of polyps’ tentacles). High hydrogen peroxide-scavenging rates were found in tissues affected by PPR. Discussion and Conclusion: The coexistence of CPs and RFP suggests their possible differential role in coral immunity. CPs, which are specifically expressed in PPR lesions, may serve as an antioxidant in the affected coral tissue. Overall, this study provides new knowledge to our understanding of the role of CPs in coral immunity. [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]

Sedimentation is a major cause of global near-shore coral reef decline. Although the negative impacts of sedimentation on coral reef community composition have been well-documented, the effects of sedimentation on coral metabolism in situ have received comparatively little attention. Using transcriptomics, we identified gene expression patterns changing across a previously defined sedimentation threshold that was deemed critical due to changes in coral cover and community composition. We identified genes, pathways, and molecular processes associated with this transition that may allow corals, such as Porites lobata, to tolerate chronic, severe sedimentation and persist in turbid environments. Alternative energy generation pathways may help P. lobata maintain a persistent stress response to survive when the availability of light and oxygen is diminished. We found evidence for the expression of genes linked to increased environmental sensing and cellular communication that likely allow P. lobata to efficiently respond to sedimentation stress and associated pathogen challenges. Cell damage increases under stress; consequently, we found apoptosis pathways over-represented under severe sedimentation, a likely consequence of damaged cell removal to maintain colony integrity. The results presented here provide a framework for the response of P. lobata to sedimentation stress under field conditions. Testing this framework and its related hypotheses using multi-omics approaches can deepen our understanding of the metabolic plasticity and acclimation potential of corals to sedimentation and their resilience in turbid reef systems. [ABSTRACT FROM AUTHOR]

The size structure of stony coral populations can reveal underlying demographic barriers to population growth or recovery. Recent declines in coral cover from acute disturbances are well documented, but few studies have assessed size structure and the demographic processes that determine population growth. Vital rates, such as recruitment and survival, vary spatially and temporally in response to environmental conditions, in turn influencing assemblage composition. The Southeast Florida Coral Reef Ecosystem Conservation Area (Coral ECA) is a high-latitude reef system offshore of a heavily urbanized coastline. Consecutive heat stress events, stony coral tissue loss disease (SCTLD), and Hurricane Irma caused significant declines in stony coral cover and density from 2014 to 2018. The recovery potential of stony coral assemblages is influenced by their composition, the size structure of the remnant populations, and population growth during inter-disturbance periods. To assess the viability of the remaining stony coral assemblages in the Coral ECA, we quantified variation in stony coral recruit density, abundance, size structure, and assemblage composition across depth and latitude at permanent sites over 3 years (2019-2022) when no disturbances occurred. We found spatial decoupling in recruit density, adult colony density, and cover that maintains a preponderance of small colonies and skewed size structure. At sites close to shore where recruit density was higher, there was limited evidence of survival and growth of recruits, while at sites where large colonies were sampled or cover was relatively high, there was limited recruitment. The majority (>75%) of recruits sampled were Siderastrea siderea, but size frequency distributions were positively skewed and the coefficient of variation was high, suggesting high recruit/juvenile colony mortality and little growth into larger size classes. Porites astreoides size structure was generally lognormal and mesokurtic, particularly closer to shore, suggesting a transition between size classes. Skewness decreased moving offshore in Montastraea cavernosa and S. siderea, suggesting a transition between size classes. Recruit and adult diversity also increased moving offshore, but recruits of most species were uncommon throughout the study area. We suggest that low recruitment and high mortality, particularly in small colonies and inshore, even during inter-disturbance periods, limit the population growth of stony coral assemblages in southeast Florida. [ABSTRACT FROM AUTHOR]

Endosymbiotic dinoflagellates in the family Symbiodiniaceae are physiologically and ecologically important for reef-building corals. Certain symbiotic lineages may provide adaptive functions that aid corals in coping with and surviving rapid environmental and climate changes; and thus, there is a growing interest in exploring Symbiodiniaceae communities and their associated roles. Steroid biomarkers have been proposed as a means of identifying species-specific symbionts, but their reliability has yet to be examined through comparison of different coral species that harbor known Symbiodiniaceae. Here, steroid molecular and δ13C analyses are applied to four stony corals that host identified (Porites lobata and Galaxea fascicularis) or undescribed (Goniopora tenuidens and Goniastrea minuta) Symbiodiniaceae to address this issue. The 23-Me C28Δ5,22, 23,24-Me C29Δ5,22, and dinosterol are characteristic of P. lobata; while, C29Δ5, gorgosterol, and 4α-methylgorgostanol are diagnostic for G. fascicularis, tracking the marked differences in their Symbiodiniaceae assemblages. These two steroid groups also exhibit largely similar (− 20.6 to − 17.0‰) and visibly variable (− 24.1 to − 17.3‰) δ13C signatures, following the low and high diversity of symbionts in P. lobata and G. fascicularis, respectively. Our present results, together with previous reports, clearly demonstrate the effectiveness of steroid molecular and δ13C features in depicting Symbiodiniaceae population, providing a useful complement to Symbiodiniaceae genetic analysis. A further comparison of steroid characteristics between unclear and known Symbiodiniaceae in our four corals reveals the almost identical symbiotic population between G. minuta and G. fascicularis and a restricted range of symbiotic composition in G. tenuidens that is shared with G. fascicularis (and G. minuta). Additionally, the occurrence of 5α-stanols suggestive of anaerobic conversion on Δ5-sterols implies complex steroid interactions within coral–algae–microbe holobionts. [ABSTRACT FROM AUTHOR]

The geochemistry of tropical coral skeletons is widely used in paleoclimate reconstructions. However, sub‐aerially exposed corals may be affected by diagenesis, altering the aragonite skeleton through partial dissolution, or infilling of secondary minerals like calcite. We analyzed the impact of intra‐skeletal calcite on the geochemistry (δ18O, Sr/Ca, Mg/Ca, Li/Mg, Li/Ca, U/Ca, B/Ca, Ba/Ca, and Mn/Ca) of a sub‐aerially exposed Porites sp. coral. Each micro‐milled coral sample was split into two aliquots for geochemistry and X‐ray diffraction (XRD) analysis to quantify the direct impact of calcite on geochemistry. We modified the sample loading technique for XRD to detect low calcite levels (1%–2%; total uncertainty = 0.33%, 2σ) in small samples (∼7.5 mg). Calcite content ranged from 0% to 12.5%, with higher percentages coinciding with larger geochemical offsets. Sr/Ca, Li/Mg, Li/Ca, and δ18O‐derived sea‐surface temperature (SST) anomalies per 1% calcite were +0.43°C, +0.24°C, +0.11°C, and +0.008°C, respectively. A 3.6% calcite produces a Sr/Ca‐SST signal commensurate with local SST seasonality (∼1.5°C), which we propose as the cut‐off level for screening calcite diagenesis in paleo‐temperature reconstructions. Inclusion of intra‐skeletal calcite decreases B/Ca, Ba/Ca, and U/Ca values, and increases Mg/Ca values, and can therefore impact reconstructions of paleoclimate and the carbonate chemistry of the semi‐isolated calcifying fluid in corals. This study emphasizes the importance of quantifying fine‐scale calcite diagenesis to identify coral preservation levels and assure robust paleoclimate reconstructions. Key Points: The modified sample loading technique adopted for X‐ray diffraction significantly reduced the uncertainty of calcite measurement down to 0.33%Temperature reconstructions based on Sr/Ca, Li/Mg, and Li/Ca are significantly affected by low levels of intra‐skeletal calcite (1%–2%)Impact of low levels of intra‐skeletal calcite on δ18O, Ba/Ca, Mn/Ca, and U/Ca is not significant [ABSTRACT FROM AUTHOR]

Tropical cyclones (TCs) lead to huge economic losses and casualties in coastal regions, but multi‐decadal variation of TC remains poorly understood due to the limited length of observational records and low‐resolution reconstructions. Porites corals provide continuous and monthly resolved records that allow for the determination of weather‐timescale (weekly to monthly) extreme events, including TC, to overcome the above limitations. Here we synthesize five coral Δδ18O records from the South China Sea (SCS) and develop a coral TC frequency index, in good agreement with post‐1980 instrumental records and sediment‐based TC reconstructions over the past century. Our results indicate that TC frequency in the SCS exhibits pronounced decadal variations, with active TCs corresponding to the negative phase of the Pacific Decadal Oscillation. Our findings here provide novel evidence for past TC changes in the SCS and a constraint for predicting future TC changes. Plain Language Summary: The impact of tropical cyclones (TCs) on coastal regions results in significant economic losses and casualties. Due to the relatively short observations or low‐resolution records, assessing long‐term changes of TCs has suffered from large uncertainties. Porites corals are sensitive to environmental changes and can provide century‐long, monthly resolved records, which could serve as a potential archive for reconstructing past TCs. Here we present five coral Δδ18O records from the South China Sea (SCS) and develop two TC frequency indexes. Both the TCs generated in the SCS and those entering the SCS from the Western North Pacific are reflected in our coral‐based TCs reconstruction. In addition, our reconstruction suggests that the TCs in the SCS were increased in 1878–1888, 1894–1904, 1934–1952, 1971–1978, and 1995–2004, which corresponded to the negative phase of the Pacific Decadal Oscillation over the past century. Our findings provide new evidence for historical changes in TCs in the SCS and a valuable constraint for predicting future TC variations. Key Points: The low residual oxygen isotope values of coral strongly respond to tropical cyclones in the South China SeaExcluding temperature, we reconstruct tropical cyclone activities in the South China Sea over the past century using coral oxygen isotopesPacific Decadal Oscillation modulates tropical cyclones in the South China Sea over the past century [ABSTRACT FROM AUTHOR]

Variously shaped corals, such as branching and massive corals, exhibit divergent environmental susceptibility properties. The susceptibility potential of these corals may be regulated by specific symbiotic Symbiodiniaceae and bacteria. In this study, we investigated seawater characteristics between the north and south zones at the Wuzhizhou Island (WZZ), sampled branching coral Acropora hyacinthus, lamellar coral Montipora informis, and massive coral (Galaxea fascicularis and Porites lutea). Physiological characteristics were measured, and amplicon sequencing was performed to Symbiodiniaceae and bacterial community structure analysis. Corals experienced severe anthropogenic disturbance, with more than 1.4-fold increase in DIN, including NH 4 + , NO 3 - , and NO 2 - in the north of the WZZ Island compared to the southern region. However, massive corals (G. fascicularis and P. lutea) showed relatively less disruption in both their symbiont composition and physiological responses. Notably, M. informis displayed distinct variations, with disturbances in the northern region resulted in a decline in the density of symbiotic micro-algae associated with Cladocopium sp. C26 due to elevated concentrations of ammonium and nitrate. The four coral species hosted different symbionts within the same area. P. lutea hosted Cladocopium sp. C15 with the lowest density of symbiotic micro-algae, along with the lowest Fv/Fm and YII values compared to other corals in the southern zone. G. fascicularis exhibited high abundance of Durusdinium sp. D1 and D4, which showed strong correlation with Fv/Fm. In southern M. informis, Cladocopium sp. C26 was identified as the predominant symbiotic micro-algae that displayed a significant positive correlation with YII. The bacterial community composition and metabolism functional attribution predicted by PICRUSt differed between A. hyacinthus, M. informis, and massive corals (G. fascicularis, P. lutea). Comprehensive analysis revealed different susceptibility properties among branching, lamellar, and massive corals under anthropogenic disturbance associated with changes in Symbiodiniaceae and bacterial community. [ABSTRACT FROM AUTHOR]

The growing threat of global warming on coral reefs underscores the urgency of identifying heat‐tolerant corals and discovering their adaptation mechanisms to high temperatures. Corals growing in intertidal rock pools that vary markedly in daily temperature may have improved heat tolerance. In this study, heat stress experiments were performed on scleractinian coral Porites lutea from subtidal habitat and intertidal rock pool of Weizhou Island in the northern South China Sea. Thermotolerance differences in corals from the two habitats and their mechanisms were explored through phenotype, physiological indicators, ITS2, 16S rRNA, and RNA sequencing. At the extremely high temperature of 34°C, rock pool P. lutea had a stronger heat tolerance than those in the subtidal habitat. The strong antioxidant capacity of the coral host and its microbial partners was important in the resistance of rock pool corals to high temperatures. The host of rock pool corals at 34°C had stronger immune and apoptotic regulation, downregulated host metabolism and disease‐infection‐related pathways compared to the subtidal habitat. P. lutea, in this habitat, upregulated Cladocopium C15 (Symbiodiniaceae) photosynthetic efficiency and photoprotection, and significantly increased bacterial diversity and coral probiotics, including ABY1, Ruegeria, and Alteromonas. These findings indicate that rock pool corals can tolerate high temperatures through the integrated response of coral holobionts. These corals may be 'touchstones' for future warming. Our research provides new insights into the complex mechanisms by which corals resist global warming and the theoretical basis for coral reef ecosystem restoration and selection of stress‐resistant coral populations. [ABSTRACT FROM AUTHOR]

The implications of ocean acidification are acute for calcifying organisms, notably tropical reef corals, for which accretion generally is depressed and dissolution enhanced at reduced seawater pH. We describe year‐long experiments in which back reef and fore reef (17‐m depth) communities from Moorea, French Polynesia, were incubated outdoors under pCO2 regimes reflecting endpoints of representative concentration pathways (RCPs) expected by the end the century. Incubations were completed in three to four flumes (5.0 × 0.3 m, 500 L) in which seawater was refreshed and circulated at 0.1 m s−1, and the response of the communities was evaluated monthly by measurements of net community calcification (NCC) and net community productivity (NCP). For both communities, NCC (but not NCP) was affected by treatments and time, with NCC declining with increasing pCO2, and for the fore reef, becoming negative (i.e., dissolution was occurring) at the highest pCO2 (1067–1433 μatm, RCP8.5). There was scant evidence of community adjustment to reduce the negative effects of ocean acidification, and inhibition of NCC intensified in the back reef as the abundance of massive Porites spp. declined. These results highlight the risks of dissolution under ocean acidification for coral reefs and suggest these effects will be most acute in fore reef habitats. Without signs of amelioration of the negative effects of ocean acidification during year‐long experiments, it is reasonable to expect that the future of coral reefs in acidic seas can be predicted from their current known susceptibility to ocean acidification. [ABSTRACT FROM AUTHOR]

Relatively high-latitude coral reefs could be potential "refuges" for corals under climate change. One of the most important aspects limiting their availability as refuges is low-temperature stress. However, the mechanisms underlying the response of coral holobionts to low-temperature stress is unclear. In this study, we aimed to explore the underlying mechanisms by recording the maximum quantumyields of photosystemII (Fv/Fm) and transcriptome responses of Porites lutea under acute (1--2 weeks) and chronic (6--12 weeks) low-temperature stress at 20°C and 14°C. The P. lutea samples were collected from a relatively high- latitude coral reef in the South China Sea (109°00'--109°15'E and 21°00'--21°10' N). The study suggested that: (1) Under acute low-temperature stress, the Fv/Fm of Symbiodiniaceae dropped by 64%, which was significantly higher than the 49% observed under chronic stress. Low-temperature stress inhibited photosystem II (PSII) functioning, with greater inhibition under acute stress. (2) Downregulation of sugar metabolism-related genes under low-temperature stress implied that the decrease in energy was due to obstruction of PSII. (3) Under low-temperature stress, calcification-related genes were downregulated in coral hosts, possibly because of energy deprivation caused by inhibited photosynthesis, Symbiodiniaceae expulsion, and oxidative phosphorylation uncoupling in mitochondria. (4) Acute low-temperature stress induced the upregulation of genes related to the TNF signaling pathway and endoplasmic reticulum stress, promoting apoptosis and coral bleaching. However, these phenomena were not observed during chronic stress, suggesting acclimation to chronic low- temperature stress and a greater survival pressure of acute low-temperature stress on coral holobionts. In conclusion, low-temperature stress inhibits Symbiodiniaceae PSII functioning, reducing energy production and affecting calcification in coral holobionts. Acute low-temperature stress is more threatening to coral holobionts than chronic stress. [ABSTRACT FROM AUTHOR]

Although biogenic carbonates, such as foraminifera and coccolithophorids, are valuable tools for reconstructing past environments, scleractinian corals also offer environmental data from tropical to subtropical regions with a higher time resolution. For example, oxygen isotopes (δ18O) and strontium-calcium (Sr/Ca) ratios have been utilized to reconstruct sea surface temperatures and salinity, primarily through the use of massive-type Porites sp. from the Pacific, as well as corals like Diploria and Montastrea from the Atlantic. While a few types of corals other than Porites have been utilized in paleoclimate studies, comprehensive evaluations of their geochemical tracers as temperature proxies have not been thoroughly conducted. Therefore, in this study, we focused on branching-type Acropora, which are found worldwide and are often present in fossil corals. We conducted a comparison of the chemical compositions (δ18O, δ13C, Sr/Ca, U/Ca, Mg/Ca, and Ba/Ca) of Acropora digitifera and Porites australiensis through temperature-controlled culture experiments. The validity of using the chemical components of A. digitifera as temperature proxies was then evaluated. Three colonies of A. digitifera and P. australiensis were collected for culture experiments on Sesoko Island, Okinawa, Japan. We reared coral samples in seawater with five different temperature settings (18, 21, 24, 27, 30°). The calcification rate and photosynthesis efficiency (Fv/Fm) of each nubbin were measured during the experimental period. After the culture experiment for 77 days, chemical components in skeletal parts grown during the experiment were then measured. Consequently, the mean growth rates and Fv/Fm throughout the experiment were higher for A. digitifera (0.22%/d and 0.63 for growth rate and Fv/Fm) compared to those for P. australiensis (0.11%/d and 0.38 for growth rate and Fv/Fm). This suggests that the higher efficiency of photosynthesis in A. digitifera would promote greater calcification compared to P. australiensis. Regarding the potential use as temperature proxies, A. digitifera exhibited a strong negative correlation, on average, between δ18O and the water temperature (r = 0.95, p< 0.001). The temperature dependency was found to be comparable to that reported in Porites corals (-0.11 and -0.17 ?/°C for P. australiensis and A. digitifera, respectively). Thus, the δ18O of A. digitifera appeared to be a useful temperature proxy, although it was also slightly influenced by skeletal growth rate at the same temperature. A strong negative correlation was also observed between the mean Sr/Ca ratio and temperature in A. digitifera (r = 0.61, p< 0.001) as well as P. australiensis (r = 0.56, p< 0.001), without a clear influence from the skeletal growth rate. Therefore, the skeletal Sr/Ca ratio in corals may have been primarily influenced by water temperature, although large deviations in Sr/Ca were observed in A. digitifera, even at the same temperature settings. This deviation can be reduced by subsampling an apical part of a polyp including the axis of skeletal growth. The U/Ca ratio of A. digitifera appeared to be affected by internal pH variation within the corals, especially at 30°C. Similar to U/Ca ratios, metabolic and kinetic effects on corals were observed in δ13C of A. digitifera at 18 and 30°C. In addition, considering the variation pattern of both U/Ca and δ13C of A. digitifera at 30°C, it has been suggested that respirations may overwhelm photosynthesis for coral samples at 30°C. Therefore, the U/Ca and δ13C of A. digitifera could potentially be used as proxies of biomineralization processes, whereas the δ18O and Sr/Ca displayed a high possibility of acting as temperature proxies. [ABSTRACT FROM AUTHOR]

Coral reefs are the most diverse ecosystem on the planet based on the abundance and diversity of phyla and higher taxa. However, it is still difficult to assess the diversity of lower taxa, especially at the species level. One tool for improving the identification of lower taxa are genetic markers that can distinguish cryptic species and assess species boundaries. Here, we present one such approach for an important and challenging group of reef-building corals. Porites corals are the main reef-builders of many coral reefs in the Indo-Pacific, owing to the massive growth forms of some species. The current number of valid Porites species is controversial, inflated with many synonymies, and often based on gross colony morphology although several morphospecies believed to be widespread and common can only be distinguished based on detailed microstructure analyses by taxonomic experts. Here, we test the suitability of multiple regions of mtDNA as genetic barcodes to identify suitable markers for species differentiation and unambiguous identification. Resulting sequencing data was further used for the first phylogenetic analysis of Guam's Porites species. We tested eight different mitochondrial markers and analyzed four in detail for 135 Porites specimens: mtDNA markers were amplified for 67 Porites specimens from Guam, representing 12 nominal Porites species, and combined with 69 mitochondrial genomes, mostly from Hawaii. The combination of all 4 markers distinguished 10 common and 7 uncommon Central-West Pacific Porites species. Most clades separate species along taxonomic boundaries, which is uncommon for Porites corals and testifies to the suitability of our multi-marker approach, and a combination of the two most promising barcodes distinguished 8/10 common species. These barcodes are thus suitable to distinguish virtually cryptic species in one of the most important and challenging coral genera. They offer a cheap, fast and reliable way to identify Porites species for species-level research, monitoring and conservation. [ABSTRACT FROM AUTHOR]

As coral reefs continue to decline due to anthropogenic stressors, community characterizations will reveal both historical selection processes and adaptive potential to environmental change. To address the potential role of color in the distribution and resilience of massive Porites corals, we surveyed the distributions of two dominant color morphs (brown and purple), and a unique intermediate state, across a depth gradient in Guam, Micronesia. We found that brown colonies dominated populations across all depths, and larger colonies had higher rates of partial tissue mortality and active disease lesions. Despite the dominance of brown colonies, both brown and purple color morphs showed a high similarity in susceptibility, as indicated by the colony sizes, the severity of partial tissue mortality, and the prevalence of active disease lesions. This is a non‐intuitive result given the presence of phenotypic plasticity between color morphs, evident by an intermediate, transitionary stage between brown and purple colonies that suggests a functional divergence between one color over the other. The study also revealed the dominance of small colonies at depth, which provides some insight into the ecological impacts that may have shaped Guam's current massive Porites population size structure over the past several decades. With this, we provide foundational insight into the adaptive strategies and historical pressures that have shaped the modern massive Porites population. [ABSTRACT FROM AUTHOR]

The Kuroshio intrusion (KI) is a northwestward‐flowing branch of the Kuroshio Current, which enters the South China Sea (SCS) and regulates its temperature, salinity, and water mass exchanges. However, limited direct observations hinder our understanding of KI's mechanisms and responses to climate change. Here, we present a 60‐year bi‐monthly resolved coral oxygen isotope (δ18Oc) record from Dongsha Atoll, the northern SCS. The dry‐season (December–March) δ18Oc record reveals interannual to decadal variabilities of the KI. The impact of the East Asian winter monsoon (EAWM) on Dongsha δ18Oc was more pronounced during the 1970s and 1980s and after the early 2000s, while the influence of the El Niño‐Southern Oscillation (ENSO) on Dongsha δ18Oc was higher between the 1980s and 1990s. The Pacific Decadal Oscillation (PDO) may have a relatively minor effect on KI strength or may indirectly modulate KI strength through its influence on ENSO activities. Our Dongsha δ18Oc record highlight the importance of the EAWM, ENSO, and PDO in predicting future KI changes. Plain Language Summary: The Kuroshio intrusion is a branch of the Kuroshio Current. It flows into the South China Sea and affects its temperature, salinity, and water movement. We however know very little how the Kuroshio intrusion responds to climate changes. Here we present a study on the chemical composition of a coral core from Dongsha Atoll in the northern South China Sea. Our study shows that the intrusion varies markedly over the past 60 years and is connected to changes in sea surface salinity. Stronger intrusions align with stronger East Asian winter monsoon intensity and El Niño events. Understanding how the Kuroshio intrusion reacts to climate change is important for effectively managing the potential impacts of global warming on the marine ecosystem. Key Points: A 60‐year‐long coral oxygen isotope record from Dongsha Atoll, South China Sea reveals interannual to decadal variations in the Kuroshio intrusionStrong Kuroshio intrusion, corresponding to high sea surface salinity, is identifiable over the past 60 yearsThe Kuroshio intrusion variations are primarily driven by East Asian winter monsoon changes and also influenced by El Niño‐Southern Oscillation [ABSTRACT FROM AUTHOR]

Coral reefs are in decline worldwide, making it increasingly important to promote coral recruitment in new or degraded habitat. Coral reef morphology--the structural form of reef substrate--affects many aspects of reef function, yet the effect of reef morphology on coral recruitment is not well understood. We used structure-from-motion photogrammetry and airborne remote sensing to measure reef morphology (rugosity, curvature, slope, and fractal dimension) across a broad continuum of spatial scales and evaluated the effect of morphology on coral recruitment in three broadcast-spawning genera. We also measured the effect of other environmental and biotic factors such as fish density, adult coral cover, hydrodynamic larval import, and depth on coral recruitment. All variables combined explained 72% of coral recruitment in the study region. Coarse reef rugosity and curvature mapped at ≥2 m spatial resolution--such as large colonies, knolls, and boulders--were positively correlated with coral recruitment, explaining 22% of variation in recruitment. Morphology mapped at finer scales (≤32 cm resolution) was not significant. Hydrodynamic larval import was also positively related to coral recruitment in Porites and Montipora spp., and grazer fish density was linked to significantly lower recruitment in all genera. In addition, grazer density, reef morphology, and hydrodynamic import had differential effects on coral genera, reflecting genus-specific life history traits, and model performance was lower in gonochoric species. Overall, coral reef morphology is a key indicator of recruitment potential that can be detected by remote sensing, allowing potential larval sinks to be identified and factored into restoration actions. [ABSTRACT FROM AUTHOR]

Coral capacity to tolerate low pH affects coral community composition and, ultimately, reef ecosystem function. Low pH submarine discharges ('Ojo'; Yucatán, México) represent a natural laboratory to study plasticity and acclimatization to low pH in relation to ocean acidification. A previous >2‐year coral transplant experiment to ambient and low pH common garden sites revealed differential survivorship across species and sites, providing a framework to compare mechanistic responses to differential pH exposures. Here, we examined gene expression responses of transplants of three species of reef‐building corals (Porites astreoides, Porites porites and Siderastrea siderea) and their algal endosymbiont communities (Symbiodiniaceae) originating from low pH (Ojo) and ambient pH native origins (Lagoon or Reef). Transplant pH environment had the greatest effect on gene expression of Porites astreoides hosts and symbionts and P. porites hosts. Host P. astreoides Ojo natives transplanted to ambient pH showed a similar gene expression profile to Lagoon natives remaining in ambient pH, providing evidence of plasticity in response to ambient pH conditions. Although origin had a larger effect on host S. siderea gene expression due to differences in symbiont genera within Reef and Lagoon/Ojo natives, subtle effects of low pH on all origins demonstrated acclimatization potential. All corals responded to low pH by differentially expressing genes related to pH regulation, ion transport, calcification, cell adhesion and stress/immune response. This study demonstrates that the magnitude of coral gene expression responses to pH varies considerably among populations, species and holobionts, which could differentially affect acclimatization to and impacts of ocean acidification. [ABSTRACT FROM AUTHOR]

Background: Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However, the coral holobiont contains both dead and living bacteria. The former can be the result of corals feeding on bacteria, rapid swings from hyper- to hypoxic conditions in the coral tissue, the presence of antimicrobial compounds in coral mucus, and an abundance of lytic bacteriophages. Results: By combining propidium monoazide (PMA) treatment with high-throughput sequencing on six coral species (Acropora loripes, A. millepora, A. kenti, Platygyra daedalea, Pocillopora acuta, and Porites lutea) we were able to obtain information on bacterial communities with little noise from non-viable microbial DNA. Metabarcoding of the 16S rRNA gene showed significantly higher community evenness (85%) and species diversity (31%) in untreated compared with PMA-treated tissue for A. loripes only. While PMA-treated coral did not differ significantly from untreated samples in terms of observed number of ASVs, > 30% of ASVs were identified in untreated samples only, suggesting that they originated from cell-free/non-viable DNA. Further, the bacterial community structure was significantly different between PMA-treated and untreated samples for A. loripes and P. acuta indicating that DNA from non-viable microbes can bias community composition data in coral species with low bacterial diversity. Conclusions: Our study is highly relevant to microbiome studies on coral and other host organisms as it delivers a solution to excluding non-viable DNA in a complex community. These results provide novel insights into the dynamic nature of host-associated microbiomes and underline the importance of applying versatile tools in the analysis of metabarcoding or next-generation sequencing data sets. [ABSTRACT FROM AUTHOR]

Pink pigmentation on massive corals is quite commonly observed in the global reefs, but its function on the surface area of corals is less understood. In the present study, the coral video transect method was employed to document the incidence of pink pigmentation on Porites colonies from 21 islands under the Gulf of Mannar Marine Biosphere Reserve (GoMMBR), India. Results revealed that 19% (n = 77 out of 517) of Porites sp. colonies displayed pink pigmentation as a stress indicator in response to the colonization of epibionts. Porites colonies exhibited pink pigmentation when infected with epibionts like a vermetid snail, Ceraesignum sp. (12%; n = 49), a rhodolith, Hydrolithon sp. (5%; n = 21), or both (2%; n = 7). This study indicates that Porites pink pigment deposition aids in minimizing surface tissue area damage by preventing further progression of infesting agents such as vermitid snails and rhodoliths on the surface areas of corals. [ABSTRACT FROM AUTHOR]

Photoacclimation is a key homeostatic process that enables photosymbiotic reef corals to flourish within highly variable light environments. However, the temporal dynamics of photoacclimation remain poorly characterized. We studied photoacclimation at several time points over 24 d in two scleractinian coral taxa (mounding Porites spp. and branching Acropora muricata). Coral specimens preacclimated at 24°C and 171 μmol quanta m−2 s−1 were exposed to three light levels (−32%, +27%, and +65% relative to that of the acclimation period) at two temperatures (control, 24°C; mildly stressful, 29°C). Intra‐tissue light environment—specifically, photon pressure per symbiont—increased dramatically with each additional light dose and again with increasing temperature in Porites spp.; net photosynthesis (Pnet) rates continued to change for at least 2 weeks following light increase but not light reduction, and vice versa for symbiont densities. Intra‐tissue light environments were substantially dimmer and more homogeneous among all light treatments in A. muricata, which continued to increase its light‐use efficiency and Pnet through time in most or all treatments. Consequently, prolonged change in Fv/Fm at elevated temperature in Porites spp. but not A. muricata may have been caused by differing photodamage loads. Moderation of light levels by conditions within the coral tissue seems to affect the temporal dynamics of the photoacclimation response, and this finding emphasizes new avenues for photoacclimation research. [ABSTRACT FROM AUTHOR]

Abstract The Kuroshio intrusion (KI) is a northwestward‐flowing branch of the Kuroshio Current, which enters the South China Sea (SCS) and regulates its temperature, salinity, and water mass exchanges. However, limited direct observations hinder our understanding of KI's mechanisms and responses to climate change. Here, we present a 60‐year bi‐monthly resolved coral oxygen isotope (δ18Oc) record from Dongsha Atoll, the northern SCS. The dry‐season (December–March) δ18Oc record reveals interannual to decadal variabilities of the KI. The impact of the East Asian winter monsoon (EAWM) on Dongsha δ18Oc was more pronounced during the 1970s and 1980s and after the early 2000s, while the influence of the El Niño‐Southern Oscillation (ENSO) on Dongsha δ18Oc was higher between the 1980s and 1990s. The Pacific Decadal Oscillation (PDO) may have a relatively minor effect on KI strength or may indirectly modulate KI strength through its influence on ENSO activities. Our Dongsha δ18Oc record highlight the importance of the EAWM, ENSO, and PDO in predicting future KI changes.

Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria, (2) enriched tightly attached and potential intracellular bacteria, and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include known nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs, and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives. [ABSTRACT FROM AUTHOR]

Coral reefs in southeast Florida have experienced severe losses in coral cover and diversity in recent decades, primarily due to disease outbreaks and bleaching events exacerbated by anthropogenic impacts. Subsequent increases in "weedy" coral species like Agaricia spp. and Porites spp. have been observed on many reefs in this region. At the northernmost boundary of the Florida's Coral Reef, St. Lucie Reef in Martin County has experienced a particularly notable increase in the abundance of Porites astreoides. To identify potential larval sources and P. astreoides population dynamics that may be contributing to observed coral community shifts, we sampled P. astreoides across five locations in southeast Florida from St. Lucie Reef to Fort Lauderdale and assessed population genetic structure using 2bRAD sequencing to generate single-nucleotide polymorphism (SNP) data. We identified high rates of clonality within and among the sample populations. Despite the brooding reproductive strategy of P. astreoides, there were relatively high levels of connectivity among populations and varying levels of genetic structure which correlated with geographic gradients. The genetic diversity and connectivity data reported here for P. astreoides populations in southeast Florida suggest that recent increases in abundance may be driven by high fecundity and long-range dispersal of a few successful genotypes. [ABSTRACT FROM AUTHOR]

The coral reef ecosystem on Seureudong Island, Sawang Bau Village, Sawang District, South Aceh is very important for the surrounding ecosystem, with the fringing reef type, namely the shape of its growth around the island. This study aims to determine the current condition of coral cover and the types available on Seureudong Island. The Point Intercept Transect (PIT) Method was used. The results showed that the coral forms found at the study site were branching, digitate, encrusting, foliose, massive, mushroom, plates, and submassive. The percentage of the bottom substrate is dominated by hard coral (hard coral) at 45.33%, Dead Coral with Algae/DCA (37.11%), sand (9.89%), rubble of 3.56%, rock (1.56%), algae turf (1.44%), macroalgae (1%) and dead coral (0.11%). At the study site, 25 genera were identified, with Porites (36%) being the most common genus. At the research location, there were also genera with a total presence of less than 1%. These genera were Acanthastrea, Ctenactis, Favia, Favites, Fungia, Gardineroseris, Goniopora, Halimeda, Heliopora, Hydnophora, Leptastrea, Montastrea, Pavona, and Seriatopora. The water quality at the research location still complies with the standards of coral life. The results of these observations must be carried out periodically so that they can always update the condition of coral reefs on Seureudong Island. [ABSTRACT FROM AUTHOR]

In this study, the bacterial microbiota associated with apparently healthy corals of Acropora palmata, Orbicella faveolata, and Porites porites and the surrounding seawater and sediment were evaluated via the MiSeq Illumina sequencing of the V4 region of 16S rRNA at three reef sites in the Mexican Caribbean. Bacterial assemblages associated with apparently healthy corals and sediments showed no significant differences between sites. The colonies of A. palmata showed a dominance of families Amoebophilaceae, Spirochaetaceae, Myxococcaceae, and Cyclobacteriaceae. Meanwhile, the colonies of O. faveolata and P. porites revealed a high prevalence of the Rhodobacteraceae and Kiloniellaceae families. The families Rhodobacteraceae, Cryomorphaceae, Cyanobiaceae, and Flavobacteriaceae were predominant in seawater samples, while Pirellulaceae, Nitrosococcaceae, and Woeseiaceae were predominant in sediments. Variations in A. palmata bacterial assemblages were correlated with salinity, sea surface temperature, and depth. These variables, along with nitrate, phosphate, and ammonium concentrations, were also correlated with changes in the bacterial composition of P. porites, seawater, and sediments. However, none of the environmental variables were related to the bacterial taxa of O. faveolata. Aerobic chemoheterotrophy and fermentation, followed by nitrate reduction and ureolysis, were the metabolic functions with the highest occurrence in the bacterial assemblages associated with all substrates. [ABSTRACT FROM AUTHOR]

Purpose: Coral degradation is a worldwide ecological problem. Bacterial diseases are a great danger to coral health. The pathogenic bacterium Vibrio alginolyticus XSBZ14 isolated from diseased coral had been identified as the pathogenic bacterium of Porites andrewsi White syndrome (PAWS) in Xisha Archipelago on transmission experiment. To date, the molecular mechanism by which this pathogen causes disease is unknown, and molecular diagnostics for diseases caused by this bacterium have not been developed. In an effort to restore damaged coral ecosystems in the South China Sea, efforts are underway to transplant flat-branch shore corals. There is therefore an urgent need to further develop specific and rapid detection methods for V. alginolyticus XSBZ14 in order to prevent this epidemic and ensure the successful implementation of compilation transplants. Methods: At first, a low sequence identity single-copy sequence S2 was selected from the genome by in-house Perl script. Using the designed specific primers, four different types of standard curves were subsequently plotted for the accurate quantification of the strain XSBZ14 in four different samples (DNA, bacterial suspension, coral tissue, seawater). Then, use the strain to infect the Galaxea fascicularis and test the strain in the coral culture water during the week. Results: The rapid detection method of pathogenic bacteria by RT-PCR was established. The limit of detection (LOD) of the RT-PCR was 0.88 pg/reaction (0.44 pg/μL) in DNA, 2 CFU/reaction (1000 CFU/mL) in bacterial suspension, 2 CFU/reaction in coral tissue, and 20 CFU/reaction in seawater for the strain XSBZ14, respectively. In addition, according to the detection results of the RT-PCR, the strain XSBZ14 could survive in Galaxea fascicularis for a week, and the strain could also be detected from its reared seawater. Conclusion: These results indicated that the RT-PCR detection method of a coral pathogenic strain XSBZ14 was established. The method is a robust tool for the rapid detection and quantification of the coral pathogen, XSBZ14, and is very useful for PAWS epidemiological survey and specific pathogen-free coral transplantation in the South China Sea. And other coral species and their habitats might act as an important reservoir for the strain XSBZ14 and mediated its horizontal transmission in coral reefs. [ABSTRACT FROM AUTHOR]

Coral reefs in Sanya Bay have been degrading in recent decades under climate change and human activities. To identify physiological changes of scleractinian corals and corresponding influencing factors, aquatic environmental factors and physiological parameters of Pocillopora damicornis, Porites pukoensis and their symbiotic zooxanthellae were examined in four Sanya Bay coral reef areas in December 2020 (winter) and July 2021 (summer). The density and chlorophyll a+c2 content of the symbiotic zooxanthellae were significantly high in winter and low in summer. Superoxide dismutase and caspase3 activities of corals and zooxanthellae were high in summer and low in winter, whereas catalase activity showed the opposite pattern. The variations were consistent for both coral symbionts. Water temperature and salinity were the main factors affecting the physiological variations of corals. Compared with winter, the high temperature/low salinity aquatic environment in summer reduced the density and chlorophyll a+c2 content of zooxanthellae, resulting in high superoxide dismutase and caspase3 activities in the corals and zooxanthellae. In addition, turbidity was an important factor affecting the physiological characteristics of coral–zooxanthellae symbionts among the four coral reef areas. Our results have important implications for understanding the changes in coral reef communities in Sanya Bay and coral reef protection. [ABSTRACT FROM AUTHOR]

Coral reefs are one of the most biodiverse marine ecosystems. Diverse microbes are associated with corals, including zooxanthellae, protists, prokaryotes, and viruses. This study aimed to investigate the genetic diversity of the culturable fungi associated with scleractinian corals in the Gulf of Thailand. Ribosomal DNA sequence analysis and morphological analysis of 130 fungal isolates revealed a high diversity of fungal phylotypes from three coral species: Pavona decussata, Pocillopora damicornis and Porites lutea. Ascomycota was the most abundant fungal phylum. The predominant orders included Eurotiales, Cladosporiales, Hypocreales, Mycosphaerellales, and Diaporthales. There were eight orders of the Basidiomycota dominated by Polyporales, Hymenochaetales, Agaricales, and Wallemiales. A principal component analysis was performed to compare abundance and correlation between the fungal communities, sampling locations and coral species. The results showed that the dissimilarity of fungal communities corresponded to geographic localities. On the other hand, there was a considerable overlap between the fungal communities of different coral species. The results from this research provide information on the diversity and ecology of the fungal communities associated with scleractinian corals in the Gulf of Thailand. [ABSTRACT FROM AUTHOR]

The coral skeleton harbours a diverse community of bacteria and microeukaryotes exposed to light, O2 and pH gradients, but how such physicochemical gradients affect the coral skeleton microbiome remains unclear. In this study, we employed chemical imaging of O2 and pH, hyperspectral reflectance imaging and spatially resolved taxonomic and inferred functional microbiome characterization to explore links between the skeleton microenvironment and microbiome in the reef‐building corals Porites lutea and Paragoniastrea benhami. The physicochemical environment was more stable in the deep skeleton, and the diversity and evenness of the bacterial community increased with skeletal depth, suggesting that the microbiome was stratified along the physicochemical gradients. The bulk of the coral skeleton was in a low O2 habitat, whereas pH varied from pH 6–9 with depth. Physicochemical gradients of O2 and pH of the coral skeleton explained the β‐diversity of the bacterial communities, and skeletal layers that showed O2 peaks had a higher relative abundance of endolithic algae, reflecting a link between the abiotic environment and the microbiome composition. Our study links the physicochemical, microbial and functional landscapes of the coral skeleton and provides new insights into the involvement of skeletal microbes in the coral holobiont metabolism. [ABSTRACT FROM AUTHOR]

Crude oil extraction is a hot topic concerning industrial applications. The extracted oil emulsions treatment with demulsifier is demanded for markets. Herein, we prepared a naturally based demulsifier comprising calcium phosphates from coralline materials. The XRD verifies successful formation of the intended calcium phosphate with characteristic peaks where the most intense peak at 30º for (211) plane matched well with card and former research. The SEM reveals the formation of the spherical, flowery shape. Zeta potential reaches −10 mV indicating reasonable stability of the demulsifier. For examining the separation efficiency using the bottle test, few drops of the demulsifer (~100 ppm) are enough for the separation at 55°C for 40 min in the water bath. Inherently, the separation initiates within few seconds. The extended results for the demulsifier are applied onto the ASH field (Borg Alarab, Egypt) and compared to other companies reports. The optimum separation efficiency for salt and water contents from crude oil reaches 9 PTB and 0.1%vol, respectively, after treatment by heating unit (Sigma package). The recommended values for these factors are 30 PTB and 2%vol. The efficiency of separation exceeds 99% for water and salt. This direction is significantly important for oil production and industry. [ABSTRACT FROM AUTHOR]

Modern scleractinian corals can display high phenotypic plasticity, which reflects an interplay among various environmental controls, such as sediment input, water hydrodynamics or light intensity. In particular, the latter can strongly influence the morphology of coral species living across broad depth gradients. Light intensity was also a factor shaping the colonies of extinct Palaeozoic tabulate corals (Anthozoa: Tabulata). Based on gradual transitions in morphology observed in corals from the Middle Devonian (Givetian stage, ~ 385 Ma) mesophotic coral ecosystems (MCE) of the Aferdou el Mrakib reef (Anti-Atlas mountains, Morocco) and comparative material originating from different palaeobathymetric and biogeographical settings, we show that Devonian tabulate corals, such as Roseoporella and Alveolites, were characterised by high phenotypic plasticity and the ability to dramatically change their morphology depending on the inferred light conditions. Such a mechanism is similar to that observed in modern scleractinians, e.g. Porites sillimaniana. This recurring morphological theme suggests that Palaeozoic tabulate corals shared many functional characteristics of modern scleractinians. [ABSTRACT FROM AUTHOR]

The Philippine archipelago's complex bathymetry, hydrology, and geologic history indicate the likely development of unique coral communities. However, there are few studies on coral community structure in the Philippines. Adult coral composition was analyzed through classification and ordination of data from 206 sampling stations, covering all Philippine marine biogeographic regions, on upper slopes of mostly well-developed fringing reefs. Seven coral community types are distinguished: I—moderately wave-exposed, mostly southwest-facing slopes with abundant massive Porites and branching Acropora; II—highly wave-exposed, mostly northeast-facing slopes, dominated by encrusting Isopora; III—low-exposure slopes with high hard coral cover (HCC), dominated by branching Porites; IV—wave-sheltered communities with abundant Galaxea; V—low-HCC communities with stress-tolerant corals; VI—Heliopora-dominated communities; VII—communities with low HCC and high macroalgal cover. Coral composition in these types is influenced by broad-scale hydrologic regimes (i.e., wave exposure and monsoon forcing) and local stressors. Applications of the typology are proposed for the spatial management of protected seascapes. [ABSTRACT FROM AUTHOR]

Anthropogenic stressors threaten reefs worldwide and natural in situ coral reproduction may be inadequate to meet this challenge. Land-based culture can provide increased coral growth, especially with microfragments. Wetested whether culture methods using different algal fouling communities could improve the growth and health metrics of microfragments of the Hawaiian coral, Porites compressa. Culture method fouling communities were: (1) similar to a reef environment (Mini Reef); (2) clean tanks managed to promote crustose coralline algae (Clean Start); and (3) tanks curated beforehand with poorly-competing algae (Green Film) assessed in winter and summer months. The Green Film method during the winter produced the fastest microfragment mean growth at 28 days until the first row of new polyps developed, and also the highest tank and plate metric health scores. Time efficient, standardized methods for land-based culture designed to maximize growth and production of coral fragments will contribute considerably to the success of large-scale restoration efforts. [ABSTRACT FROM AUTHOR]

Spherulites are radial distributions of acicular crystals, common in biogenic, geologic, and synthetic systems, yet exactly how spherulitic crystals nucleate and grow is still poorly understood. To investigate these processes in more detail, we chose scleractinian corals as a model system, because they are well known to form their skeletons from aragonite (CaCO3) spherulites, and because a comparative study of crystal structures across coral species has not been performed previously. We observed that all 12 diverse coral species analyzed here exhibit plumose spherulites in their skeletons, with well-defined centers of calcification (CoCs), and crystalline fibers radiating from them. In 7 of the 12 species, we observed a skeletal structural motif not observed previously: randomly oriented, equant crystals, which we termed "sprinkles". In Acropora pharaonis, these sprinkles are localized at the CoCs, while in 6 other species, sprinkles are either layered at the growth front (GF) of the spherulites, or randomly distributed. At the nano- and micro-scale, coral skeletons fill space as much as single crystals of aragonite. Based on these observations, we tentatively propose a spherulite formation mechanism in which growth front nucleation (GFN) of randomly oriented sprinkles, competition for space, and coarsening produce spherulites, rather than the previously assumed slightly misoriented nucleations termed "non-crystallographic branching". Phase-field simulations support this mechanism, and, using a minimal set of thermodynamic parameters, are able to reproduce all of the microstructural variation observed experimentally in all of the investigated coral skeletons. Beyond coral skeletons, other spherulitic systems, from aspirin to semicrystalline polymers and chocolate, may also form according to the mechanism for spherulite formation proposed here. STATEMENT OF SIGNIFICANCE: Understanding the fundamental mechanisms of spherulite nucleation and growth has broad ranging applications in the fields of metallurgy, polymers, food science, and pharmaceutical production. Using the skeletons of reef-building corals as a model system for investigating these processes, we propose a new spherulite growth mechanism that can not only explain the micro-structural diversity observed in distantly related coral species, but may point to a universal growth mechanism in a wide range of biologically and technologically relevant spherulitic materials systems.

With climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The Tara Pacific expedition (2016–2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while Porites corals increase the aragonite saturation state of the calcifying fluid (Ωcf) at higher temperatures to enhance their calcification capacity, Diploastrea show a steady homeostatic Ωcf across the Pacific temperature gradient. Thus, the extent to which Diploastrea responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus. [ABSTRACT FROM AUTHOR]

The impact of changing nutrient conditions on scleractinian coral-based geochemical proxies is poorly understood, despite the nutrient balance in many coral reefs being disturbed by anthropogenic activity. Here, the geochemical responses of tropical corals Acropora polystoma and Porites lichen to nutrient enrichment and depletion are examined following growth under cultured conditions, to assess the impact of nutrients on traditional geochemical proxies for both temperature and the coral internal carbonate system. The corals were exposed to four different nutrient treatments over a period of 140 days: (1) a replete treatment with optimal levels of nitrate (∼4.5 μM) and phosphate (∼0.6 μM), (2) a nutrient depleted treatment with negligible nitrate and phosphate, (3) a treatment with high nitrate (∼73 μM) and negligible phosphate, and (4) a treatment with high phosphate (∼5.7 μM) and negligible nitrate. Results suggest nutrients play a hitherto under-appreciated role in coral skeleton elemental (Li/Ca, B/Ca, Mg/Ca, Sr/Ca, Li/Mg) and isotopic (δ11B) composition, with the internal carbonate chemistry also impacted. For example, Mg/Ca and Sr/Ca are lower, and Li/Mg higher, in the nutrient imbalanced and deplete treatments compared to the replete treatment for both species. Disruption to the carbonate system in corals cultured under imbalanced nutrient conditions is best explained by a decrease in dissolved inorganic carbon flux to the extracellular calcifying medium. Variations in nutrient concentration — or nutrient imbalance — can have dramatic consequences on both reconstructed sea surface temperatures and ocean or calcification pH, with reconstructed temperatures varying from −7°C to +52 °C, and δ11B-derived pH by up to 0.13 pH units. The impact from anthropogenically-induced nutrient disturbances should therefore be considered when generating temporal records of environments using coral skeletal archives. [ABSTRACT FROM AUTHOR]