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Shallow coral reefs are being increasingly degraded as a result of natural and anthropogenic threats. Mesophotic coral ecosystems (MCEs) are an extension of shallow reefs at depths of ∼30–150 m that harbor depth generalists and specialists, acclimatized to changes in physical factors. A faunal break in MCEs occurs between upper (∼30–60 m) and lower (∼60–150 m) depths, representing transitional and endemic communities, respectively. The trophic ecology of MCEs shifts from autotrophic to heterotrophic processes with increasing depth, and trade-offs in the utilization of dissolved organic matter and particulate organic matter. While dispersal of MCE larvae could reseed degraded shallow reefs, genetic evidence is equivocal, suggesting site-specific connectivity patterns; anthropogenic disturbances at mesophotic depths indicate that MCEs may be as susceptible to stressors as shallow reefs are. The function and stability of mesophotic coral ecosystems (MCEs) have been extensively studied in recent years. These deep reefs are characterized by local physical processes, particularly the steep gradient in irradiance with increasing depth, and their impact on trophic resources. Mesophotic reefs exhibit distinct zonation patterns that segregate shallow reef biodiversity from ecologically unique deeper communities of endemic species. While mesophotic reefs are hypothesized as relatively stable refuges from anthropogenic stressors and a potential seed bank for degraded shallow reefs, these are site-specific features, if they occur at all. Mesophotic reefs are now known to be susceptible to many of the same stressors that are degrading shallow reefs, suggesting that they require their own specific conservation and management strategies. [ABSTRACT FROM AUTHOR]

Marine heat waves are having unprecedented impacts on reef-building corals worldwide. Corals within the same species have different sensitivity to heat stress, and part of this variation is due to genetic adaptation. Finding coral genotypes that underpin heat adaptation would allow the identification of adapted populations so that reef managers could protect and promote the spread of these adapted populations. Seascape genomics identifies candidate adaptive genotypes by associating variation in genotype frequencies across a reef system with historical thermal conditions. CRISPR/Cas9-based gene editing could assess and validate the functional roles of putative adaptive genotypes, and validated genotypes could then be used in conservation. Mass coral bleaching is one of the clearest threats of climate change to the persistence of marine biodiversity. Despite the negative impacts of bleaching on coral health and survival, some corals may be able to rapidly adapt to warming ocean temperatures. Thus, a significant focus in coral research is identifying the genes and pathways underlying coral heat adaptation. Here, we review state-of-the-art methods that may enable the discovery of heat-adaptive loci in corals and identify four main knowledge gaps. To fill these gaps, we describe an experimental approach combining seascape genomics with CRISPR/Cas9 gene editing to discover and validate heat-adaptive loci. Finally, we discuss how information on adaptive genotypes could be used in coral reef conservation and management strategies. [ABSTRACT FROM AUTHOR]

The Symbiodiniaceae have been coral symbionts for over 200 million years, yet they retain a facultative lifestyle because both the symbiotic and free-living stages offer unique selective advantages that ensure persistence of the algal lineage. There exists a dynamic competition and interaction between the coral host and algal symbionts that ensures survival of both under fluctuating environmental conditions. If algal symbiont-derived redox stress does not explain coral host bleaching, then it is possible that either or both partners generate a chemical cue that precipitates algal expulsion independent of malfunctions in their electron transport chains. We propose the 'stepping-stone model' as an explanation for the long-term and successful association between coral animals and their facultative algal symbionts, which in a stepwise manner creates novel Symbiodiniaceae lineages worldwide. The photosynthetic symbionts of corals sustain biodiverse reefs in nutrient-poor, tropical waters. Recent genomic data illuminate the evolution of coral symbionts under genome size constraints and suggest that retention of the facultative lifestyle, widespread among these algae, confers a selective advantage when compared with a strict symbiotic existence. We posit that the coral symbiosis is analogous to a 'bioreactor' that selects winner genotypes and allows them to rise to high numbers in a sheltered habitat prior to release by the coral host. Our observations lead to a novel hypothesis, the 'stepping-stone model', which predicts that local adaptation under both the symbiotic and free-living stages, in a stepwise fashion, accelerates coral alga diversity and the origin of endemic strains and species. [ABSTRACT FROM AUTHOR]

[Display omitted] • Corals support coral reef biodiversity by acting as hosts for symbionts. • Four major taxa of coral parasites were compared for their host specificity. • Totals of 203 coral-associated invertebrates and 335 host coral species were recorded. • Coral barnacles and gall crabs are more host-specific than serpulids and date mussels. • Coral symbionts in the Indo-Pacific are more host-specific than those in the Atlantic region. Coral-associated fauna predominantly consists of invertebrates and constitutes an important component of coral reef biodiversity. The symbionts depend on their hosts for food, shelter and substrate. They may act as parasites by feeding on their hosts, by overgowing their polyps, or by excavating their skeletons. Because some of these species partly reside inside their hosts, they may be cryptic and can easily be overlooked in biodiversity surveys. Since no quantitative overview is available about these inter-specific relationships, this present study adresses variation in host ranges and specificity across four large coral-associated taxa and between the Atlantic and Indo-Pacific oceans. These taxa are: coral barnacles (Pyrgomatidae, n = 95), coral gall crabs (Cryptochiridae, n = 54), tubeworms (Serpulidae, n = 31), and date mussels (Lithophaginae, n = 23). A total of 335 host coral species was recorded. An index of host specificity (S TD) was calculated per symbiont species, based on distinctness in taxonomic host range levels (species, genus, family, etc.). Mean indices were statistically compared among the four associated taxa and the two oceanic coral reef regions. Barnacles were the most host-specific, tubeworms the least. Indo-Pacific associates were approximately 10 times richer in species and two times more host-specific than their Atlantic counterparts. Coral families varied in the number of associates, with some hosting none. This variation could be linked to host traits (coral growth form, maximum host size) and is most probably also a result of the evolutionary history of the interspecific relationships. [ABSTRACT FROM AUTHOR]

Synthetic biology tools can be used to develop novel sustainability solutions for global ocean health challenges. Tailored microbial consortia can be designed to target plastic waste for biodegradation and upcycling. Engineering and altering coral holobiont dynamics may enhance coral reef resilience in the face of climate-induced extinction. CRISPR-based nucleic acid sensors can enable the rapid and inexpensive identification of toxic HAB events. Ocean health is faltering, its capability for regeneration and renewal being eroded by a steady pulse of anthropomorphic impacts. Plastic waste has infiltrated all ocean biomes, climate change threatens coral reefs with extinction, and eutrophication has unleashed vast algal blooms. In the face of these challenges, synthetic biology approaches may hold untapped solutions to mitigate adverse effects, repair ecosystems, and put us on a path towards sustainable stewardship of our planet. Leveraging synthetic biology tools would enable innovative engineering approaches to augment the natural adaptive capacity of ocean biological systems to cope with the swiftness of human-induced change. Here, we present a framework for developing synthetic biology solutions for the challenges of plastic pollution, coral bleaching, and harmful algal blooms. [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]

Suspended sediment is a significant threat to the Great Barrier Reef (GBR) ecosystem. This catchment pollutant stems primarily from terrestrial soil erosion. Bulk masses of sediments have potential to propagate from river plumes into the mid-shelf and outer-shelf regions. Existing sediment forecasting methods suffer from the problem of low-resolution predictions, making them unsuitable for wide area coverage. In this paper, a novel sediment distribution prediction model is proposed to augment existing water quality management programs for the GBR. This model is based on the state-of-the-art Transformer network in conjunction with the well-known finite element analysis. For model training, the emerging physics-informed neural network is employed to incorporate both simulated and measured sediment data. Our proposed Finite Element Transformer (FE-Transformer) model offers accurate predictions of sediment across the entire GBR. It provides unblurred outputs, which cannot be achieved with previous next-frame prediction models. This paves a way for accurate forecasting of sediment, which in turn may lead to improved water quality management for the GBR. • Vision Transformer is proposed for next-frame prediction. • Finite element analysis is integrated with the Vision Transformer. • Sediment distribution in the GBR is forecasted using the proposed FE-Transformer. • PINN is employed to merge sediment PDE solutions with in-situ measured data. • The proposed model produces highly accurate unblurred output frames. [ABSTRACT FROM AUTHOR]

• Understanding spatial and temporal trends of diversity is crucial for conservation. • This study analyses long-term data from 1986 to 2020 on Singapore reefs. • Taxonomic and phylogenetic diversity increased but functional diversity declined. • Reefs shifted towards dominance of stress-tolerant traits such as slow growth. • Trait-based approaches at finer taxonomic resolution will enhance reef monitoring. Coral reefs provide a multitude of ecosystem functions owing to the high levels of biodiversity they host. Coral species, as the foundation of shallow-water reefs, differ in their contributions toward the functioning of the ecosystem due in part to the disparate phylogenetic histories of scleractinian lineages. Understanding the spatial patterns and temporal trajectories of these biodiversity facets, as well as their interrelationships, is critical for more targeted conservation strategies in the face of widespread habitat degradation and climate change. Here, we analyse long-term benthic data spanning 1986 through 2020 on coral reefs in Singapore, which have been impacted by decades of urbanisation-related and thermal stressors, to test for differences between coral biodiversity facets—specifically, taxonomic, phylogenetic (evolutionary relatedness between species), and functional (occupancy of functional trait space) richness and diversity. Analyses show that taxonomic and phylogenetic richness and diversity measures increased over the 35-year period despite declines during major bleaching events. Yet, while taxonomic and phylogenetic diversity increased, functional richness and diversity declined over the same period. Community-weighted trait measures indicate a shift towards dominance of more stress-tolerant traits such as slower growth rates, smaller corallite sizes, and massive colony forms. Together, these trends highlight the effects of chronic urban stressors alongside major bleaching events impacting reef assemblages. Critically, such assemblage shifts and functional diversity declines were masked by increasing taxonomic diversity, which is most commonly assessed, and could erode ecosystem resilience. The temporal decoupling of the biodiversity facets examined here underscore the need for more comprehensive monitoring of reefs through a combination of trait-based approaches alongside traditional field surveys at finer taxonomic resolution. [ABSTRACT FROM AUTHOR]

Coastal marine environments are some of the most productive and overexploited ecosystems on earth. Coastal ecosystems, like oyster and coral reefs, need physical structures to establish and habitat destruction has led to the destabilization of reef structures resulting in massive biodiversity losses. For decades, researchers have utilized PolyVinyl Chloride (PVC) panels as artificial larval settlement panels to study recruitment and community dynamics in these incredibly important ecosystems. Unfortunately, PVC itself is relatively toxic, the panels are smooth which makes it difficult for larval settlement, and it can take months to see establishment because larvae need settlement cues on PVC from biofilm development. This study assessed the use of 3D printed panels constructed out of plant-based biodegradable materials as an alternative to PVC panels. Panels constructed of three different corn-based polylactic acid (PLA) materials (white impact modified, gray impact modified, wood pulp) were tested at a well monitored site along the Long Island Sound in Connecticut, US. Overall, the 3D printed panels had equal or higher recruitment compared to the PVC panels. Beyond the normal application of panels for ecological assessment of local settlement, this work highlights that using innovative, biodegradable panels has strong potential in reestablishing these overburdened yet critical ecosystems. Additionally, the 3D printed panels were economically beneficial to use, which increases equity in this conservation crisis field as material expense can be cost prohibitive. • Novel method to monitor invertebrate communities using 3D printed plant-based biodegradable panels. • Panels made from different corn-based polylactic acid (PLA) materials were tested for recruitment efficacy compared to PVC. • Overall, the 3D printed panels had equal or higher recruitment compared to the PVC panels. • Beyond application for ecological assessment of local settlement, biodegradable panels have strong potential for restoration use. [ABSTRACT FROM AUTHOR]

The Amazon Reef System (ARS) is one of the most important shallow and mesophotic reef ecosystems in the South Atlantic Ocean. The ARS consists mainly of extensive beds of calcareous algae interspersed by assemblages of octocorals and sponges. The enormous freshwater discharge from the Amazon River forms a plume along the extensive Amazon continental shelf, for which the hydroid community is still largely unknown. The aim of this study is to document the diversity and distribution of hydroids from the ARS, as well as to infer the influence of the plume on species composition in the different zones. Samples were collected at ninety-six stations between 15 and 240 m deep on the Amazon shelf. A total of 37 species were recorded in the studied area. Hydroid assemblages are richer in zones under lower river plume influence, and species composition differs significantly between zones with and without plume influence (PERMANOVA, p = 0.0025). The dissolved oxygen and nitrate ranges were the environmental variables significantly correlated with the hydroid distribution. This study is the first surveying the hydroid species composition and richness in the ARS, highlighting the presence of a typical reef biota and that further faunal studies in underexplored areas of the Atlantic should reveal the distribution of many poorly known hydroids species. • This study is the first survey of hydroid species richness in the Amazon shelf. • Hydroid assemblages are richer in zones under less river plume influence. • Species composition differs between zones with and without plume influence. • Dissolved oxygen and nitrate were significantly correlated with the distribution. • The results indicate that there is a typical reef biota in the Amazon shelf. [ABSTRACT FROM AUTHOR]

Sexual reproduction of reef–building corals is vital for coral reef ecosystem recovery. Corals allocate limited energy to growth and reproduction, when being under environmental disturbance, which ultimately shapes the community population dynamics. In the present study, energetic and physiological parameters of both parental colonies and larvae of the coral Pocillopora damicornis were measured during their reproduction stage under four temperatures; 28 °C (low–temperature acclimation, LA), 29 °C (control temperature, CT), 31 °C (high–temperature acclimation, HA), and 32 °C (heat stress, HS). The results showed temperature changes altered the larvae release timing and fecundity in P. damicornis. Parental colonies exposed to the LA treatment exhibited reduced investment in reproduction and released fewer larvae, while retaining more energy for their development. However, each larva acquired higher energy and symbiont densities enabling survival through longer planktonic periods before settlement. In contrast, parental colonies exposed to the HA treatment had increased investment for reproduction and larvae output, while per larva gained less energy to mitigate the threat of higher temperature. Furthermore, the energy allocation processes restructured fatty acids concentration and composition in both parental colonies and larvae as indicated by shifts in membrane fluidity under adaptable temperature changes. Notably, parental colonies from the HS treatment expended more energy in response to heat stress, resulting in adverse effects, especially after larval release. Our study expands the current knowledge on the energy allocation strategies of P. damicornis and how it is impacted by temperature. Parental colonies employed different energy allocation strategies under distinct temperature regimes to optimize their development and offspring success, but under heat stress, both were compromised. Lipid metabolism is essential for the success of coral reproduction and further understanding their response to heat stress can improve intervention strategies for coral reef conservation in warmer future oceans. • Temperature changes alter the energy allocation of P. damicornis. • Parental colonies release fewer but more robust larvae under low temperature. • Parental colonies increased investment for reproduction under high temperature. • FAs restructured in both parents and larvae to adapt to temperature changes. • Parental colonies have an adverse effect under 32 °C, especially after larval release. [ABSTRACT FROM AUTHOR]

Cold water corals (CWC) provide habitats for many organisms including demersal fish. Bottom trawl observations have indicated a co-occurrence of the fish Helicolenus dactylopterus with CWC reefs, but a detailed understanding of this relation is lacking. To better understand the nature of this relation we have analyzed 85 video-lines from ROV dives conducted at 25–1700 m depth off Morocco, Mauritania, and Senegal in 2020 and 2021. We annotated abundance, size, and behavior of the 552 specimens observed (32% juveniles and 68% adults), of these 82% occurred in CWC habitats at 400–600 m depth. Both juveniles and adults were observed standing on the seafloor. Our observations are discussed considering available knowledge on feeding ecology and life cycle of H. dactylopterus. Our findings show that CWC provides an essential habitat for this species at least during parts of its lifecycle, however, more behavioral studies are needed for an in-depth understanding of this association. • Our study shows that both juveniles and adults of H. dactylopterus are present within CWC habitats in the region. • TCWC habitats plays an important role by protecting H. dactylopterus females and juveniles against predation and currents. • This study increases our understanding of CWC reefs as habitat for H. dactylopterus and the need for reef protection. [ABSTRACT FROM AUTHOR]

Coral bleaching events are becoming increasingly common worldwide, causing widespread coral mortality. However, not all colonies within the same coral taxa show sensitivity to bleaching events, and the current understanding of the metabolic mechanisms underlying thermal bleaching in corals remains limited. We used untargeted metabolomics to analyze the biochemical processes involved in the survival of two bleaching phenotypes of the common corals Pavona decussata and Acropora pruinosa , during a severe bleaching event in the northern South China Sea in 2020. During thermal bleaching, P. decussata and A. pruinosa significantly accumulated energy products such as succinate and EPA, antioxidants and inflammatory markers, and reduced energy storage substances like glutamate and thymidine. KEGG analysis revealed enrichment of energy production pathways such as ABC transporters, nucleotide metabolism and lipid metabolism, suggesting the occurrence of oxidative stress and energy metabolism disorders in bleached corals. Notably, heat stress exerted distinct effects on metabolic pathways in the two coral species, e.g., P. decussata activating carbohydrate metabolism pathways like glycolysis and the TCA cycle, along with amino acid metabolism pathways, whereas A. pruinosa significantly altered the content of multiple small peptides affected amino acid metabolism. Furthermore, the osmoregulatory potential of corals correlates with their ability to survive in heat-stress environments in the wild. This study provides valuable insights into the metabolic mechanisms linked to thermal tolerance in reef-building corals, contributes to the understanding of corals' adaptive potential to heat stress induced by global warming and lays the foundation for developing targeted conservation strategies in the future. • Metabolic profiles differed between unbleached and bleached corals. • Bleached corals consumed energy reserves like nucleotides and lipids. • Coral bleaching led to oxidative damage and immune response activation. • Osmotic substances were crucial in coral response to heat stress. • New insights into metabolic response of reef-building corals to heat stress. [ABSTRACT FROM AUTHOR]

Investigating the potential and mechanisms of thermal adaptability in scleractinian corals is critical for aiding corals in dealing with global warming and improving the efficiency of coral reef restoration efforts. Although thermal acclimation facilitates the resistance of branching corals to thermal stress, little is known about the physiological processes of massive and platy corals in the South China Sea or their ability to adapt to heat stress. In this study, we conducted indoor short-term thermal acclimation simulation experiments on three types of corals: massive Porites lutea , platy Pavona decussata , and branching Pocillopora damicornis. Subsequently, we studied the responses and adaptive mechanisms of the three corals to heat stress and explored the effects of short-term thermal acclimation using physiological and biochemical markers. The results showed that the three corals exhibited comparable phenotypic and physiological responses to heat stress, including tentacle retraction and decreases in zooxanthellae density, maximum quantum efficiency of photosystem II, and glutathione content, along with increases in antioxidant activity (catalase and superoxide dismutase), ammonium assimilation (glutamine synthetase), and apoptosis (lipid peroxide and caspase-3). Additionally, heat tolerance differed among the different species of coral. Furthermore, the physiological markers performed better in all three coral types after acclimation, and the effects of short-term acclimation decreased from P. lutea to P. damicornis to P. decussata. We propose that short-term thermal acclimation enhances the heat tolerance of corals by affecting their metabolism and antioxidant capacity. Leveraging short-term thermal acclimation in coral reef restoration efforts could help corals adapt to the threats posed by global warming and enhance restoration efficiency. • Coral reefs are in rapid decline in the context of global pressures. • Different types of scleractinian corals display similar responses to heat stress. • Short-term thermal acclimation enhances the coral antioxidant capacity. • Porites lutea and Pocillopora damicornis have better thermal acclimatization. [ABSTRACT FROM AUTHOR]

Reef corals rely on their symbiotic relationship with dinoflagellates of the family Symbiodiniaceae for their metabolic energy demands, but this relationship is sensitive to thermal stress which can induce bleaching. We investigated the flux of 14C-labeled photosynthate in the sea anemone Exaiptasia diaphana ('Aiptasia') - a model for the cnidarian-dinoflagellate symbiosis - under low, control and high temperatures (15, 25, 33 °C) when colonized by either its native symbiont Breviolum minutum or the non-native but thermally tolerant Durusdinium trenchii or Breviolum psygmophilum. B. psygmophilum formed the most thermally stable symbiosis, maintaining a higher population density, and fixing and translocating similar or more carbon than the other two species at both high and low temperatures. In contrast, anemones containing D. trenchii markedly bleached at both high and low temperatures, confirming the sensitivity of this host-symbiont pairing to thermal extremes. Elevated temperature led to a significant increase in the percentage of fixed carbon (%) translocated from the symbiont to the host with both Breviolum species, however the total amount of carbon released to the host by the symbiont population (translocated C per mg of host protein) remained consistent between elevated and control temperatures due to the reduced rate of total photosynthetic carbon fixation. The highest rates of photosynthesis and carbon translocation by the symbiont population were seen at the low temperature, reflecting the maintenance or elevation of photosynthesis and/or symbiont density relative to the control. Overall, our findings underscore the significance of symbiont identity in conjunction with host-symbiont specificity in dictating the thermal resilience of the cnidarian-dinoflagellate symbiosis and emphasizing the potential of B. psygmophilum as an interesting candidate for future studies. • Partner identity and specificity impact thermal response in a symbiotic cnidarian. • Breviolum psygmophilum was 'thermally flexible', forming the most stable symbiosis. • Durusdinium trenchii fully bleached at both high and low temperatures. • Cell-specific rates of photosynthesis were highest at low symbiont density. • This maintained carbon flux to the host at high temperature for two Breviolum spp. [ABSTRACT FROM AUTHOR]

[Display omitted] • The AI-2 synthesis genes have higher abundance in bleached coral than the healthy one. • AI-2 caused dysbiosis of the symbiotic microbiota and induced coral bleaching. • Infection by pathogenic bacteria was more prevalent in the presence of AI-2 signal. • Manipulation of AI-2 signalling pathway is a potential way to protect vulnerable corals. Symbiotic microorganisms play critical ecophysiological roles that facilitate the maintenance of coral health. Currently, information on the gene and protein pathways contributing to bleaching responses is lacking, including the role of autoinducers. Although the autoinducer AI-1 is well understood, information on AI-2 is insufficient. Here, we observed a 3.7–4.0 times higher abundance of the AI-2 synthesis gene luxS in bleached individuals relative to their healthy counterparts among reef-building coral samples from the natural environment. Laboratory tests further revealed that AI-2 contributed significantly to an increase in coral bleaching, altered the ratio of potential probiotic and pathogenic bacteria, and suppressed the antiviral activity of specific pathogenic bacteria while enhancing their functional potential, such as energy metabolism, chemotaxis, biofilm formation and virulence release. Structural equation modeling indicated that AI-2 influences the microbial composition, network structure, and pathogenic features, which collectively contribute to the coral bleaching status. Collectively, our results offer novel potential strategies for coral conservation based on a signal manipulation approach. [ABSTRACT FROM AUTHOR]

The El Niño-Southern Oscillation (ENSO) is the most influential climatic phenomenon on an interannual timescale. Studying the relationship between sea surface temperature (SST) and ENSO events during typical geological periods is helpful for understanding the trends of ENSO activities in the future, especially under the background of global warming. Here we quantitatively reconstructed a 115-year history of SST and ENSO activity around 282 ka during Marine Isotope Stage 8 (MIS8) by using the growth rate of Porites corals from Xisha Islands in the South China Sea. The results show that the average coral growth rate (6.0 ± 1.0 mm/yr (1σ)) around 282 ka was only 56.1% of the modern average value (10.7 ± 0.9 mm/yr; 1937–2014 CE), and the average SST (26.0 ± 0.3 °C (1σ)) was 0.7 ± 0.4 °C and 1.1 ± 0.4 °C lower than that in the Little Ice Age (LIA; 1520–1676 CE; 26.7 ± 0.2 °C) and the present (1937–2014; 27.1 ± 0.2 °C), respectively. The reconstructed results show that there was significant ENSO activity with moderate intensity or above at 282 ka, while the frequency of ENSO activity at that time was lower than that of the LIA and the present. This seems to indicate that the frequency of moderate intensity ENSO activity increases with rising SST. Given the current rapid warming, the future trend of ENSO activities deserves close attention. • The growth rate of Porites coral is a reliable paleoenvironmental proxy. • The coral growth rate at 282 ka was only equivalent to 56.1% of the present. • Coral–SST at 282 ka was 0.7 °C and 1.1 °C lower than the LIA and present, respectively. • The ENSO frequency at 282 ka was lower than the present. [ABSTRACT FROM AUTHOR]

Global coral reefs are currently facing widespread declines in calcification rates, a trend that underscores the need to understand variations between calcification in contemporary and ancient corals. This study investigates the changes in coral calcification over the last millennium by analyzing 21 subfossil and 11 modern coral samples from a marginal reef in the northern South China Sea. Our results reveal that although coral skeletal density has remained relatively stable, significant differences are evident in linear extension rates between the Medieval Climate Anomaly (MCA, 900–1300 CE) and the Little Ice Age (LIA, 1550–1850 CE), as well as between the pre- and post-industrial periods. This finding suggests that inshore Porites corals have greater resilience in their skeletal density compared to linear extension rates when responding to environmental changes. Our analysis indicates that sea surface temperature (SST) is the primary environmental driver influencing coral calcification, with a positive correlation observed between SST and both modern coral linear extension and calcification rates. In contrast, factors such as seawater pH, salinity, and total solar irradiance appear to have minimal impact on coral skeletal growth. Therefore, the lower linear extension and calcification rates observed in the LIA corals, as compared to the MCA corals, are likely due to the cooler temperatures during the LIA. We also hypothesize that the extended period of cold SST from the LIA to the early 20th century may have led to the reduced linear extension and calcification rates in modern corals, with recent warming insufficient to facilitate a return to the optimal skeletal growth observed during the MCA. • Coral calcification records for the last millennium. • Coral skeletal density shows stable variation. • Coral linear extension rates differ between the MCA and the LIA. • Declined calcification of modern corals outweighs their ancient counterparts. • Temperature plays a major role driving coral calcification. [ABSTRACT FROM AUTHOR]

• Habitat degradation can lead to functional homogenization in herbivore assemblages. • Assemblage composition varies among islands that differ in human impacts. • Generalists, like Acanthurus nigrofuscus , are dominant in impacted sites. Habitat loss from human impacts can lead to functional homogenization, whereby natural communities become less diverse. Herbivorous coral reef fishes display varying specialization and unique functional roles among closely related taxa, making homogenization relevant to ecosystem function. To explore whether the functional homogeneity of herbivore assemblages correlate with human impacts, we combined an index of diet specialization and a functional trait matrix with fish abundance data for > 3000 sites across the Pacific that encompass intact to degraded coral reefs. We determined the relative abundance of specialized species and the functional dissimilarity in an assemblage. Assemblage composition varied between islands, regions, and human population densities, with generalist species such as Acanthurus nigrofuscus dominating in highly populated locations. Spatial patterns and variability in the relationship between herbivorous reef fish assemblages and human impacts showed local and indirect effects. Despite broad variability, herbivore diversity decreased with human impacts among populated islands, consistent with the hypothesis that human impacts can lead to functional homogenization of coral reef fish communities. [ABSTRACT FROM AUTHOR]

Over the years, coral reefs in the South China Sea have degraded and faced severe threats from rapid development, coral bleaching, and Crown-of-Thorns Starfish (COTS) outbreak. There is limited knowledge relating to the effects of anthropogenic disturbances and natural events on the coral reefs of Pulau Layang-Layang. This study aims to assess reef cover changes by utilizing Landsat satellite images spanning from 1989 to 2022. Using the object-based image analysis method, this study classified the reef cover into three categories: coral, rock and rubble, and sand. The supervised classification had an overall accuracy of 86.41–87.38 % and Tau's coefficients of 0.80–0.81. The results showed island development and construction of artificial bird sanctuary have led to an increase in coral cover. Furthermore, it was illustrated that the impact of COTS outbreaks in 2010 and 2020 differed significantly, with the latter showing no signs of recovery. Our study underscores the importance of timely intervention to mitigate the spread of COTS. This study provides insights into the resilience and vulnerability of these ecosystems in the face of various stressors. • Lack of studies in Pulau Layang-Layang to address reef cover changes due to anthropogenic and natural events. • Lowest coral cover in 1998 during global coral bleaching event. • COTS outbreaks in 2010 and 2020 differed, with no signs of recovery. [ABSTRACT FROM AUTHOR]

Coral bleaching is a major concern for the health and survival of coral reefs worldwide, as it can significantly reduce coral growth and increase coral susceptibility to disease. The coral reefs at Sodwana Bay, located on the northeastern coast of South Africa, have shown resilience to coral bleaching which has been attributed to cold water temperature anomalies observed at Sodwana. This study investigates the regional hydrodynamic processes associated with 63 temperature anomalies identified at Sodwana between 1994 and 2015. The study found that 65% of the anomalies are associated with remote upwelling of cold water near the Delagoa Peninsula, followed by advection from the Delagoa Bight towards the Sodwana region. The cold upwelled water advects directly from the peninsula along the shelf towards Sodwana or recirculates within the Delagoa Bight before advecting along the coastline to Sodwana. The remaining 35% of the anomalies were associated with local upwelling within the KwaZulu-Natal Bight south of Sodwana. The study also found that the separation of the strong intermittent southward stream from the Delagoa Peninsula is strongly linked to the upwelling at the Delagoa Peninsula. The cold upwelled water is then advected to the Sodwana region by regional flow patterns, resulting in a temperature anomaly at Sodwana. The local upwelling is similarly linked to an increase in the Agulhas Current velocity magnitude around Sodwana and flow separation of the current from the coastline at the northern extent of the KwaZulu-Natal Bight. The cross-correlations between the conditionally averaged flow fields associated with remote and local upwelling near the Delagoa Peninsula and the instantaneous flow fields at the time of the upwelling showed a positive correlation for all the anomalies over the 21 years. The anomalies associated with remote upwelling have an average correlation coefficient of 0.67 with a maximum correlation of 0.96. The anomalies associated with local upwelling have an average correlation coefficient of 0.74 with a maximum correlation of 0.98. This study shows that the unique geometry of the southeast African coastline is a key factor associated with the cold water temperature anomalies at Sodwana. The interaction between the regional hydrodynamics and coastline features such as the Delagoa and Natal Bights, are crucial for the upwelling that eventually leads to the cold water temperature anomalies at Sodwana. Without these coastline features and the intermittent strengthening of the southward streams along the coastline due to the high eddy kinetic energy associated with the region, it is likely that these temperature anomalies would not occur at Sodwana. Without these temperature anomalies, the Sodwana coral reefs would become more vulnerable to climate change and coral bleaching. • The Southeast African coastline drives cold water temperature anomalies at Sodwana. • Two upwelling mechanisms modulate temperature at Sodwana reefs. • Our results have strong implications for the survival of coral reefs within the context of climate change. [ABSTRACT FROM AUTHOR]

To better understand the long-term survival of modern coral reefs under global warming, the history of past coral bleaching events prior to modern marine ecological surveys must be investigated. Here, 11 dead Porites and 2 Porites with growth hiatuses growing in the 20th century were collected from the Nansha Islands, southern South China Sea (SCS) for monthly Sr/Ca, δ18O and δ13C analyses to explore the climatic conditions and metabolic information corresponding to these growth structures. Among the 13 episodes, the results showed that 8 mortalities occurred in the summers, coral MJ8 died in spring, and the other 2 mortalities and 2 growth hiatuses occurred in the cooling season. In addition to the dead surface of the coral mortalities, stress bands with significantly reduced growth rates could also be observed in the corals. Negative shifts in δ13C occurred prior to 5 coral mortalities and most stress bands were caused in summer, suggesting a sharp reduction in photosynthesis by decreased symbiotic zooxanthellae or photosynthetic pigments. Overall, the mortalities can be concluded to have occurred in summer and stress bands with abrupt δ13C decreases in the last century were mainly caused by thermal coral bleaching in the southern SCS. This in turn suggests that the repeated coral bleaching and mortalities occurred much earlier before the 1980s, which is a longer-term response to modern global warming during the last century. [ABSTRACT FROM AUTHOR]

Studies of communities that produce knowledge about the natural world have largely focused on groups working with or for academic scientists and conforming to the epistemic values of academic knowledge production. This paper details a community that produces natural knowledge outside of those parameters. The reef hobbyist community, a group that works with aquariums as a form of non-professional leisure, has developed historical narratives, publishing standards, and recognized forms of expertise that are not shared by academic scientists. However, their goal is to produce knowledge about coral systems and their hobby has resulted in a wealth of knowledge about coral husbandry. In this paper, I identify the structure of this community, highlight several prominent groups that make up the network of reef hobbyists, and trace the ways that they produce knowledge about the marine environment through their actions. This paper contributes to discussions about diverse ways of knowing and differing forms of knowledge production in the history and philosophy of science. By examining the history and practices of a well-developed knowledge community outside of academic science, I hope to call attention to the ways that philosophers and historians have centered academic science and its structure and use of knowledge, even in conversations about non-professional knowledge producers. This paper pushes scholars to think more deeply about the way knowledge is developed in non-academic groups. [ABSTRACT FROM AUTHOR]

Coral reefs are rapidly declining because of widespread mass coral bleaching causing extensive coral mortality. Elevated seawater temperatures are the main drivers of coral bleaching, and climate change is increasing the frequency and severity of destructive marine heatwaves. Efforts to enhance coral thermal bleaching tolerance can be targeted at the coral host or at coral-associated microorganisms (e.g., dinoflagellate endosymbionts and bacteria). The literature on experimental evolution of bacteria suggests that it has value as a tool to increase coral climate resilience. We provide a workflow on how to experimentally evolve coral-associated bacteria to confer thermal tolerance to coral hosts and emphasize the value of implementing this approach in coral reef conservation and restoration efforts. Coral mortality has drastically increased in recent years because of climate change, and there is increasing evidence that coral-associated bacteria play a role in coral thermal tolerance. Approaches targeted at coral-associated microorganisms aim to provide corals with tools to adapt more quickly to increasing temperatures. This includes the inoculation of corals with probiotic bacteria. Experimental evolution is a powerful method whereby organisms are maintained under given selection pressures for many generations, hence forcing adaptation. Microorganisms can be evolved very quickly because of their short generation time. Coral-bleaching-related selection pressures, such as oxidative stress, have successfully enhanced antioxidant capacity in candidate bacteria. Application of such approaches could increase antioxidant capacity in coral-targeted probiotics and enhance coral climate resilience. [ABSTRACT FROM AUTHOR]

To assess the stability of coral sand foundation in complex environments, the undrained monotonic and cyclic shear tests were conducted in the laboratory. The test results indicate that the coral sand exhibits pronounced inherent anisotropy in the vertical direction. Under complex consolidation conditions, significant stress–induced anisotropy can also be observed. With increasing generalized shear strain (γ g), both the generalized monotonic and cyclic shear modulus (G gm , G gd) exhibit a decreasing trend irrespective of consolidation ratio (k c) and inclinations of major principal stress (α c). Additionally, a strong linear relationship is evident between G gm and G gd , suggesting a consistent reduction pattern of G g for various loading modes. The investigation on the inclination of the failure line (φ FL) for monotonic and cyclic shear is also conducted. The test results show that consolidation conditions have minimal influence on φ FL during monotonic shear, but exert a significant impact on φ FL during cyclic shear. A novel index called the consolidation parameter (η) is proposed to quantitatively assess the relationship between k c , α c and φ FL. The average values of φ FL for cyclic shear increase with increasing η , indicating the non-failure zone of coral sand during undrained cyclic shear will shrink with higher values of k c and α c. • Coral sand has inherent and stress-induced anisotropy due to special particle shapes and complex consolidation conditions. • The shear modulus for coral sand reduces with increase of strain. The reduction mode varies under different stress states. • The consolidation states have no effect on the failure angle for monotonic shear, but has a significant impact on the failure angle for cyclic shear. • The consolidation parameter is proposed to quantify the relation between failure angle and consolidation state parameters. [ABSTRACT FROM AUTHOR]

Living coral cover is rapidly decreasing due to global climate change and local human impacts. Response to the ongoing transformation of coral reefs requires a deep understanding of the mechanisms that regulate community assembly and sustain biodiversity in these systems. The goal of this study is to test the persistence of Devonian reef communities across 70 sea-level fluctuation cycles. Abundance data were collected for in situ coral and calcareous sponge taxa found along 164 transects across two field localities within the Canning Basin, Western Australia. The Bray-Curtis dissimilarity index was used to quantify the dissimilarity in taxonomic composition among transects. Despite the notable persistence of reef communities over numerous cycles (ranging from 22 to 29 cycles) spanning hundreds of thousands of years, significant taxonomic shifts unfolded over millions of years, primarily driven by the diversity and composition of coral assemblages. This indicates that while reef communities exhibit persistence over intermediate time scales, they undergo changes in taxonomic composition over extended periods. The observed shifts in taxonomic composition likely reflect the profound changes in Earth-surface systems that occurred during the Devonian (i.e., fluctuations in global sea-surface temperatures and sea-level). Therefore, sustained abiotic processes can act to disrupt community structure over extended time scales as the threshold for community persistence is exceeded. This study helps establish baseline community composition dynamics in systems devoid of human influence and thus deepens our understanding of naturally occurring phase shifts. Understanding the factors that contribute to the persistence of community assembly across multiple scales is crucial for conserving coral reef ecosystems in the face of ongoing environmental changes. • Understanding community dynamics is shaped by the scale at which it is studied. • Reefs were studied across 70 sea-level fluctuation cycles. • Communities were persistent for up to 29 cycles before experiencing a phase shift. • Phase shifts could reflect global environmental changes during the Devonian. [ABSTRACT FROM AUTHOR]

The eastern oyster, Crassostrea virginica , is an ecologically and economically important species that is threatened by ongoing coastal ocean acidification. Oyster larvae are known to be more susceptible to acidification than either juvenile or adult life stages, but less is known about what levels of acidification induce a stress response and how this stress response changes with increasing acidification. Furthermore, little is known about population-level variability in acidification tolerance in C. virginica , making predictions of how this species will respond to future environmental scenarios difficult. To address these knowledge gaps, both whole animal and cellular metrics were used to quantify the acidification response of larvae produced by adults collected from Page Rock reef and Parrot's Rock reef, two spatially distinct reefs in adjacent tributaries of Chesapeake Bay. A comparison of Page Rock reef larvae among four acidification scenarios (pH 7.8, 7.5, 7.2, 7.0) revealed differences in shell length, total protein content, and triglyceride content, with growth increasingly impacted as acidification intensity increased. However, the sensitivity of these traits to acidification varied, where shell length was similarly impacted between pH 7.5 and 7.2, while protein and triglyceride content continued to decrease between these acidification scenarios. Triglyceride accumulation was most severely impacted under the lowest pH tested (pH 7.0), signaling that acidification could ultimately reduce the number of individuals successfully recruiting into the adult population if adequate energy stores cannot be accumulated for metamorphosis. A comparison of larvae between the two reefs at pH 7.8 and 7.2 revealed differences in survival, growth, and energy accumulation that suggest clear underlying physiological variations in larvae between reefs and unique sensitivities to acidification stress. These findings demonstrate that acidification tolerance within C. virginica can vary by population, which will have important implications for industry and conservation efforts as more resilient populations would make better candidates for future selective breeding efforts as well as restoration initiatives. • Larval oysters are threatened by ongoing ocean acidification. • Shell growth was the most sensitive metric to conditions of mild acidification. • Protein and triglyceride content were more insightful responses at lower pH. • Oyster populations differed in responses to conditions of acidification. • Physiology varied between oyster populations, even under control conditions. [ABSTRACT FROM AUTHOR]

There is an increasing need for conservation action to help degraded ecosystems recover from anthropogenic disturbances like climate change. Historically there has been a lack of recognition of First Nations peoples in marine genetic conservation, contributing to existing inequalities. To better understand First Nations' perspectives, specifically within Traditional Owner (TO) groups within Australia, a mixed-method approach (surveys and interviews) was used. Two groups along the Great Barrier Reef (GBR) were interviewed, including Lama Lama from the northern and Woppaburra from the southern GBR. Overall, perceptions varied within and between groups. There were differences in perception over equity of resource sharing in genetic conservation practices, including the sharing of coral offspring and their removal from one location to another group's Sea Country. There was, however, a strong sense of the "greater good" (benefits extending outside locations of individual groups). Their willingness to be included in most aspects of the conservation process was unanimous. These results highlight the importance of involvement of First Nations people in the decision-making process to ensure social equity in climate change conservation strategies in a way that respects local communities and cultures. [ABSTRACT FROM AUTHOR]

Bottom trawling significantly impacts benthic communities, reducing habitat complexity and biodiversity. The distribution and abundance of key species in the northeastern Gulf of Cádiz, Spanish waters of Atlantic Ocean, such as soft-bottom octocorals and burrowing megafauna, were examined using video observations and Spatial Distribution Models developed with Random Forest. The study was conducted in the Site of Community Importance " Volcanes de fango del golfo de Cádiz " focusing on depths between 300 and 950 metres depth. The effects of environmental variables and bottom trawling on octocoral distribution and abundance were assessed, and management strategies for habitat protection were proposed. Bottom trawling was found to decrease habitat suitability for large octocoral species while the abundance of Norway lobster was positively correlated with certain values of bottom trawling effort. The study suggests that bottom trawling causes significant reduction in octocoral distributions, substrate homogenization, and habitat differentiation. A 200 km2 area is recommended for a specific bottom trawling regulation to protect soft-bottom octocorals and support the recovery of commercial burrowing megafauna. • Soft-bottom octocorals and Nephrops norvegicus distributions were examined using video and Spatial Distribution Models. • Bottom trawling was found to decrease habitat suitability for large octocoral species. • N. norvegicus exhibit high densities in mud and trawling effort apparently does not significantly impact their density. • N. norvegicus abundance predictions was positively correlated with certain values of fishing effort. • A 200 km2 area is recommended for a specific bottom trawling regulation to protect soft-bottom octocorals. [ABSTRACT FROM AUTHOR]

Cnidarians may dominate benthic communities, as in the case of coral reefs that foster biodiversity and provide important ecosystem services. Polyps may feed by predating mesozooplantkon and large motile prey, but many species further obtain autotrophic nutrients from photosymbiosis. Anthropogenic disturbance, such as the rise of seawater temperature and turbidity, can lead to the loss of symbionts, causing bleaching. Prolonged periods of bleaching can induce mortality events over vast areas. Heterotrophy may allow bleached cnidarians to survive for long periods of time. We tested the reinforcement of heterotrophic feeding of bleached polyps of Exaiptasia diaphana fed with both small zooplantkon and large prey, in order to evaluate if heterotrophy allows this species to compensate the reduction of autotrophy. Conversely to expected, heterotrophy was higher in unbleached polyps (+54% mesozooplankton prey and +11% large prey). The increase of heterotrophic intake may not be always used as a strategy to compensate autotrophic depletion in bleached polyps. Such a resilience strategy might be more species-specific than expected. [Display omitted] • 45-days dark period induced bleaching in the sea anemone Exaiptasia diaphana. • Mesoplankton capture and collective large-prey predation ensured heterotrophic nutrient uptake. • Bleached anemones did not reinforce heterotrophy to overcome reduced autotrophy. • The increase of heterotrophy might be a resilience strategy more species-specific than expected. [ABSTRACT FROM AUTHOR]

The Western Indian Continental Shelf (WICS) experiences upwelling during the Southwest Monsoon (SWM), leading to deoxygenation and acidification of subsurface waters. The region has patchy growth of corals, e.g. in the Grande Island and Angria Bank. Measurements made during the late SWM of 2022 reveal that the shelf waters around the Grande Island were subject to varying environmental conditions, viz. lower temperature (21.3–26.1°C), oxygen (0–4.9 mL L−1) and pH T (7.506–7.927). Complete anoxia was associated with sulphide build-up to a maximum of 5.9 μmol L−1 at 17 m depth. An additional episodic condition (high temperature, low oxygen and pH) also occurred associated presumably with a plankton bloom in April 2017. Hence, unlike the offshore coral site Angria Bank, waters around the Grande Island experiences extreme changes in physico-chemical conditions (e.g. Ω arg ∼1.2–1.8 during October 2022) seasonally as reported here. The biogeochemical conditions are however not as intense (Ω arg = 0.6) as observed along the eastern boundary upwelling system of the Pacific Ocean. • Waters around the Grande Island (harboring patchy coral growth) along the central west coast of India experience low- O 2 , pH, and temperature during seasonal upwelling, while episodes of low- O 2 and pH are observed during plankton blooms in the summer season. • Changes in benthic communities and a steady decline in coral cover associated with a sharp increase in the macro-algae and rubble were observed at the Grande Island. • Angria Bank, the offshore coral site, does not show extreme seasonal change in the environmental conditions, rather it shows open ocean biogeochemical characyteristics. [ABSTRACT FROM AUTHOR]

Previous studies have reported the correlations between bacterial communities and coral bleaching, but the knowledge of fungal roles in coral bleaching is still limited. In this study, the taxonomic and functional diversities of fungi in unbleached, partly bleached and bleached stony coral Acropora intermedia were investigated through the ITS-rRNA gene next-generation sequencing. An unexpected diversity of successfully classified fungi (a total of 167 fungal genera) was revealed in this study, and the partly bleached coral samples gained the highest fungal diversity, followed by bleached and unbleached coral samples. Among these fungi, 122 genera (nearly 73.2%) were rarely found in corals in previous studies, such as Calostoma and Morchella , which gave us a more comprehensive understanding of coral-associated fungi. Positively correlated fungal genera (Calostoma , Corticium , Derxomyces , Fusicolla , Penicillium and Vishniacozyma) and negative correlated fungal genera (Blastobotrys , Exophiala and Dacryopinax) with the coral bleaching were both detected. It was found that a series of fungal genera, dominant by Apiotrichum , a source of opportunistic infections, was significantly enriched; while another fungal group majoring in Fusicolla , a probiotic fungus, was distinctly depressed in the bleached coral. It was also noteworthy that the abundance of pathogenic fungi, including Fusarium , Didymella and Trichosporon showed a rising trend; while the saprotrophic fungi, including Tricladium , Botryotrichum and Scleropezicula demostrated a declining trend as the bleaching deteriorating. The rising of pathogenic fungi and the declining of saprotrophic fungi revealed the basic rules of fungal community transitions in the coral bleaching, but the mechanism of coral-associated fungal interactions still lacks further investigation. Overall, this is an investigation focused on the differences of fungal communities at taxonomic and functional levels in stony coral A. intermedia under different bleaching statuses, which provides a better comprehension of the correlations between fungal communities and the coral bleaching. • An unexpected diversity of successfully classified fungi in corals was revealed. • Positive and negative correlations of fungi with the coral bleaching were revealed. • Firstly investigated the fungal community differences in A. intermedia under different bleaching statuses. [ABSTRACT FROM AUTHOR]

Coral reef benthic communities have been mapped in broad categories, such as total coral cover, using remote sensing, yet we lack important details on how changes in benthic community composition translate to spectral changes observed in airborne and spaceborne data. Here, we carry out a spectral sensitivity analysis to enhance our quantitative understanding of benthic community reflectance spectra – or spectral communities – using a controlled simulation that incorporates field-based spectral libraries and endmember constituent modeling. Following the modeling phase, we apply the knowledge to the interpretation of airborne imaging spectroscopy data taken at 2 m resolution over two coral reefs in Hawaiʻi. We found that differences in organismic-scale spectra and their morphology contribute to patterns in the airborne data, enabling fine-scale differentiation between benthic community types. In doing so, we successfully determined the extent of two hyperdominant coral species (Porites lobata and Porites compressa) in the airborne data. Our findings suggest that imaging spectroscopy remains only partially explored for its potential in more detailed benthic mapping. Additional research that combines field- and remote sensing-based spectroscopy may advance ecosystem research and management on coral reefs. • A simulation that combines field-based spectra and endmember constituent modeling. • Sensitivity analyses of spectral variability in Hawaiian benthic communities. • Comparing modeled spectra with airborne imaging spectroscopy data. • Spectral signatures were found to discriminate between two dominant coral species. • High-order principal components revealed clustering based on benthic morphology. [ABSTRACT FROM AUTHOR]

Based on National Oceanic and Atmospheric Administration (NOAA) Coral Reef Conservation Program, climate change causes coral bleaching. In response to the high roughness of coral colonies and reduced current velocity, coral reefs in near-shore regions are susceptible to accumulation of pollutants or sediments. This threatens coral reef ecosystems and causes several challenges. Controlling the wave velocity, Turbulent Kinetic Energy (TKE), and vortical structures help enhance advection/diffusion of particles from coral reef zones. In the current study, a device inspired by a marine sponge (synthetic sponge), was designed. A suction/pumping function was devised through two concentric perforated cylinders to simulate this mechanism in the synthetic sponge. Several physical and numerical experiments (using OpenFOAM software considering RANS modeling) were carried out to investigate the effects of geometrical characteristics (i.e., cylinder and perforation diameters) of synthetic sponge on wave hydrodynamics. Accordingly, wave attenuation, mean horizontal and orbital velocities, turbulent kinetic energy, and vortex structures were evaluated. In summary, the results indicated that the pumping flow can act as an energy recovery downstream of the sponge, and the horizontal velocity and TKE growing in the water column due to generation of special vortices. Therefore, the current synthetic sponge can improve momentum transfer. • Perforation diameter has 60% contribution to the mean velocity in the mid-depth. • The small annular space traps water through the two concentric cylinders. • The secondary flow generation annihilates the spiral and turbulence of flow. • The pumping flow acts as a wave energy recovery in the downstream. [ABSTRACT FROM AUTHOR]

Seabed cover of organisms is an established metric for assessing the status of many vulnerable marine ecosystems. When deriving cover estimates from seafloor imagery, a source of uncertainty in capturing the true distribution of organisms is introduced by the inherent variability and bias of the annotation method used to extract ecological data. We investigated variability and bias in two common annotation methods for estimating organism cover, and the role of size selectivity in this variability. Eleven annotators estimated sparse cold-water coral cover in the same 96 images with both grid-based and manual segmentation annotation methods. The standard deviation between annotators was three times greater in the grid-based method compared to segmentation, and grid-based estimates from annotators tended to overestimate coral cover. Size selectivity biased the manual segmentation; the minimum size of colonies segmented varied between annotators fivefold. Two modelling techniques (based on Richard's selection curves and Gaussian processes) were used to impute areas where annotators identified colonies too small for segmentation. By imputing small coral sizes in segmentation estimates, the coefficient of variation between annotators was reduced by approximately 10%, and method bias (compared to a reference dataset) was reduced by up to 23%. Therefore, for sparse, low cover organisms, manual segmentation of images is recommended to minimise annotator variability and bias. Uncertainty in cover estimates may be further reduced by addressing size selectivity bias when annotating small organisms in images using a data-driven modelling technique. [Display omitted] • We assess annotator error in cover estimation from images with sparse coral cover. • Annotator variability in grid-based estimates was three times that of drawn areas. • Grid-based results overestimated coral cover by 45% above the reference dataset. • For drawn areas, missing sizes of smallest colonies led to 38% cover underestimation. • Model estimation of missing coral sizes reduced annotator variability by 10%. [ABSTRACT FROM AUTHOR]

Global warming is triggering significant shifts in temperate macroalgal communities worldwide, favoring small, warm-affinity species over large canopy-forming, cold-affinity species. The Cantabrian Sea, a region acutely impacted by climate change, is also witnessing this shift. This study delved into the impacts of increasing sea surface temperature on the subtidal macroalgal communities in the southeastern Bay of Biscay over the last four decades, by using data from the years 1982, 2007, 2014, and 2020. We found that temperature has shaped the community structure, with warm-affinity species steadily displacing their cold-affinity counterparts. Notably, new communities exhibited a profusion of smaller algal species, explaining the observed increased biodiversity within the area. In the last period investigated (2014–2020), we observed a partial recovery of the communities, coinciding with cooler sea surface temperatures. Shallow algal communities were more reactive to temperature variations than deeper communities, possibly associated with higher exposure to increased temperatures. Our study offered insights into the intricate relationship between the changes in ocean temperature and algal species in the southeastern Bay of Biscay, shedding light on the ongoing ecological shifts in this region. • SST increase drove shifts in community structure. • Turf-like species thrived with temperature changes; canopy-forming species declined. • SST had a more pronounced impact on shallow communities. • Macroalgal communities responded rapidly to temperature fluctuations. • Increased biodiversity was associated with the emergence of small-sized species. [ABSTRACT FROM AUTHOR]

Coral reef growth and recovery from bleaching depend on the onset and physiological maintenance of cnidarian-dinoflagellate symbiosis. Many cnidarian hosts can acquire new symbionts (family Symbiodiniaceae) from the environment. Symbiodiniaceae can be found at significant densities within other hosts and lesser densities as free-living populations on macroalgae, in sediments, and in the water column. The mechanisms underlining host selectivity towards symbionts are still under investigation, and even less is known about the timing and community composition when hosts uptake symbionts in their natural environments. This project studied symbiont diversity in environmental reservoirs and the progression of symbiont acquisition in bleached hosts. We first characterized various Symbiodiniaceae reservoirs in an estuarine habitat of Florida Bay at Key Largo, Florida. We then deployed bleached Exaiptasia sp. anemones in the habitat and recorded their recovery for three weeks, assessing symbiont density through cell counting and diversity via next-generation sequencing (NGS). We found that environmental reservoirs exhibit higher symbiont diversity but much lower densities than in hospite living reservoirs, highlighting the potential for healthy hosts as symbiont donors. We showed that the anemones can recover from bleaching using their residual leftover symbiont cells but recover 40% faster when also uptaking new symbionts from their environment, including non-homologous strains. We also report that symbiont shuffling can be observed in disturbed anemones in as little as three days, with decreasing symbiont density but higher symbiont diversity. Our data can guide future studies towards understanding small-scale dynamics and symbiont acquisition for cnidarians recovering from bleaching. • Environmental and in hospite symbiont communities are drastically different within Florida Bay. • Bleached anemones can recover from residual symbionts within the host. • Bleached anemones can recover using environmental reservoirs in the natural habitat. [ABSTRACT FROM AUTHOR]

Mass coral bleaching driven by climate change impacts coral reefs globally. As net zero emissions and a return to pre-industrial global temperatures are unlikely to occur in the near future, there is an urgent need to engineer intervention methods that can mitigate the risk of coral bleaching at different scales. Coral dietary enrichment and shade-based irradiance reduction have each been shown to reduce coral bleaching. Here, we tested the hypothesis that combining these two intervention methods could further reduce the risk and impact of bleaching using an outdoor experiment with fragments of the coral Hydnophora exesa. The experiment was set up over three orthogonal factors: shade (2 levels – 4 h of 30% shade and no shade), temperature (2 levels – 32.6 °C and 26.4 °C) and food type (2 levels – fatty-acid enriched and non-enriched Artemia). The provision of 30% shade for 4 h did not significantly affect any of the measured bleaching response variables, likely due to the low natural irradiance for all treatments throughout the experiment. Significant bleaching of H. exesa fragments occurred in the high-temperature treatments after 18 days of thermal stress. Feeding the corals Artemia enriched with omega-3 and omega-6 fatty acids had a minor impact on the proportion of fatty acids in the corals and resulted in a decline in chlorophyll a content and symbiont density. Overall, these results suggest that coral PUFA enrichment may have limited potential as a mitigation tool to minimise the risk of mass coral bleaching as numerous factors such as species and lipidome composition must be considered. In addition, we recommend that irradiance values higher than the natural light levels recorded during our experiment are required to effectively test the ability of shading technologies designed to reduce mass bleaching of coral reefs. • Hydnophora exesa did not respond positively to increased abundance of PUFAs. • PUFA enrichment may not be appropriate for some coral species. • Light was likely not a significant stress factor due to low irradiance levels. • Higher irradiance levels are needed to evaluate coral shading techniques. [ABSTRACT FROM AUTHOR]

The ability to map coral reef biodiversity from orbit would greatly advance marine spatial planning. Presently, reef biodiversity is measured in situ by divers, but this method is inefficient and expensive. Remote sensing techniques have been developed in the terrestrial realm to lever the "habitat heterogeneity hypothesis," which contends that the biodiversity of organisms is directly linked to the diversity of habitats which they occupy. Here, we evaluated this hypothesis using satellite-derived reef habitat maps across 880 shallow-water field stations distributed on a global transect through the Atlantic, Pacific, and Indian Oceans where we measured the taxonomic and functional diversity of reef fish and corals. Benthic habitat maps produced from WorldView-2 and PlanetScope were compared as proxies for coral reef species diversity. We found satellite-mapped habitat heterogeneity to be positively correlated with both fish (R ≤ 0.64) and coral diversity (R ≤ 0.56), at an optimum spatial scale between 110 and 320 ha, even when the data were partitioned across global biodiversity gradients. Best results were realized when using the WorldView-derived habitat maps, indicating that the enhanced spectral and radiometric resolution of this sensor is better poised for retrieving species biodiversity than PlanetScope. Our study offers an efficient method for monitoring coral reef ecosystems by leveraging satellite maps as a surrogate for species biodiversity. • Fish and coral diversity can be proxied from remotely sensed benthic habitat maps. • The optimum window size to measure habitat heterogeneity changes with map type. • Spectral definition of habitats was better constrained by WorldView-2 than Planet. • Habitat and species diversity relationships maintained over biodiversity gradients. • Best correlations between habitats and species found when habitats were connected. [ABSTRACT FROM AUTHOR]

Massive reef-building Porites corals are commonly studied to obtain long-term reconstructions of past sea surface temperature (SST) using temperature-sensitive elemental proxies, such as Sr/Ca or Li/Mg ratios. Most recently, a multi-proxy approach combining these two ratios (e.g. D'Olivo et al., 2018) and the Sr U method (DeCarlo et al., 2016) have proved to be more robust to reconstruct paleo-temperatures. To date, no study has been carried out on the application of these new approaches on the Diploastrea heliopora coral, another massive reef-building genus that can potentially provide longer temperature records. Moreover, only a few studies have assessed coral SST calibrations at the scale of the Indo-Pacific basin and compared SST reconstructions obtained from two massive coral genera from the same site. In this study, we investigated the elemental composition of the topmost portion of 34 modern tropical Porites and 6 Diploastrea colonies collected during the Tara Pacific expedition (2016–2018) from various hydrological contexts in the Pacific Ocean. We derived and discussed annual Sr/Ca, Li/Mg, combined Sr/Ca-Li/Mg and Sr/Ca-Li/Ca-Mg/Ca and Sr U vs. SST calibrations as well as potential intra-colonial and genus specific effects and evaluated the use of these basin-wide calibration equations. Overall, multi-ratio and multi-genera SST calibrations perform better than single-ratio calibrations and seem to improve temperature reconstructions. These new SST calibrations were applied to two colonies of Porites and Diploastrea collected from the same site in the North-West of the Palau archipelago located in the western Pacific Ocean to evaluate the applicability of universal calibrations based on different proxies and their combination. Coral-based SST records spanning the last 141 years show decadal changes and recent warming episodes that are related to major El Niño Southern Oscillation events. However, differences in reconstruction remain between both genera in the long-term trends, amplitudes, and absolute temperatures, depending on which genus or temperature proxy is considered. [ABSTRACT FROM AUTHOR]

• Anabaena crude extract and laxaphycin B decrease larval survivorship and settlement. • Laxaphycins A and B interact to reduce coral larval survival and settlement. • In situ laxaphycin concentrations close to Anabaena are sufficient to inhibit coral recruitment. • Benthic cyanobacterial mats could be a cause of coral recruitment failure through allelopathy. Benthic cyanobacterial mats (BCMs) are becoming increasingly abundant on coral reefs worldwide. High growth rates and prolific toxin production give them the potential to cause widespread coral recruitment failure through allelopathic effects, but few studies have made the link between their toxicity for coral larvae and in situ toxin concentrations. Here we investigated the allelopathic effects of the benthic cyanobacterium Anabaena sp.1 on larvae of the coral Pocillopora acuta. This cyanobacterium produces several non-ribosomal cyclic lipopeptides of the laxaphycin family with cytotoxic properties. Therefore, we measured the concentration of laxaphycins A and B in Anabaena mats and in the water column and tested their effects on coral larvae. We found that Anabaena crude extract reduces both larval survivorship and settlement and that laxaphycin B reduces settlement. When larvae were exposed to both laxaphycins, there was a reduction in both larval survival and settlement. In the natural reef environment, laxaphycin A and B concentrations increased with increasing proximity to Anabaena mats, with concentrations being consistently above LC 50 and EC 50 thresholds within a 1 cm distance of the mats. This study demonstrates that laxaphycins reduce the survival and inhibit the settlement of coral larvae at concentrations found near Anabaena mats in situ. It further shows a combined effect between two cyanobacterial metabolites. As BCMs become more common, more of their secondary metabolites might be released in the water column. Their occurrence will lead to a reduction in coral recruitment rates, contributing to the continuing decline of coral reefs and shift in community structure. [ABSTRACT FROM AUTHOR]

The apparent ability of corals to acquire and maintain enhanced stress tolerance through a dose-dependent environmental memory, which may persist for multiple years, has critical implications for coral reef conservation research. Such responses are variable across coral species and environmental stressors, with primed corals exhibiting a modified response to secondary stress exposures. While the mechanisms underlying coral memory responses are poorly understood, they likely involve both the coral host and microbiome. With advances in molecular technologies, it is now possible to investigate potential memory mechanisms in non-model organisms, including transcriptional regulation through epigenetic modifications. We integrate evidence of coral environmental memory and suggest future research directions to evaluate the potential for this process to enhance coral resilience under climate change. Memory of a prior exposure to environmental stress can increase the tolerance of subsequent exposures, which is vital for sessile organisms. This phenomenon has been well described in terrestrial plants and there is evidence demonstrating environmental memory in marine organisms, particularly corals. Global climate change and local anthropogenic stressors have resulted in dramatic declines in many coral populations. Environmental memory may be an important mechanism for corals to cope with the rapidly changing climate, especially given their vulnerability to environmental stress. Increased coral stress tolerance has been observed across recurrent marine heatwaves and following experimentally applied stress exposures. Such 'stress hardening' methods have recently been highlighted as priority conservation interventions to enhance coral resilience. [ABSTRACT FROM AUTHOR]

The open-source geospatial analysis ecosystem in the R language has been growing exponentially, making R a key aspect of statistical analysis in Geographic Information Systems (GIS). In this paper, we present arcgisbinding , an open-source R package for R-ArcGIS integration, and its functionality, architecture, and use cases for environmental modeling applications. Integrating R and ArcGIS provides rich end-to-end geospatial analysis workflows and enables a variety of curated spatial and spatiotemporal data in Esri formats for use in the R community. arcgisbinding supports geospatial data input and output (I/O), on-the-fly data manipulation, conversion to frequently used spatial R data formats, and interactive data mapping capabilities via esri.leaflet. The package allows the creation of R-driven geoprocessing tools, R script tools, that can be executed in ArcGIS. Different integration patterns between R and ArcGIS are elaborated with a case study on modeling coral bleaching severity using near-live data feeds from NOAA's Coral Reef Watch. • The R package, arcgisbinding , enables easy geospatial data I/O between R and ArcGIS. • Package supports data pipelines for local and cloud-based OGC-compliant data. • Arcgisbinding enables integrating Esri technology such as arcpy and interactive mapping in spatial analysis workflows. • Case study elaborates on using live data feeds for near-live coral bleaching prediction. • Ordinal regression model shows the importance of magnitude and duration of sea surface temperature extremes. [ABSTRACT FROM AUTHOR]

Coral probiotics can improve the tolerance of corals to heat stress, thus mitigating the process of coral thermal bleaching. Sensitive and specific detection of coral probiotics at low abundances is highly desirable but remains challenging, especially for rapid and on-site detection of coral probiotics. Since the electrochemical biosensor has been recently used in the field of environmental DNA (eDNA) detection, herein, an efficient electrochemical biosensor was developed based on CoS 2 /CoSe 2 -NC HNCs electrode material with a specific DNA probe for the C. marina detection. After optimization, the lower limit of detection (LOD) values of such biosensors for the target DNA and genomic DNA were 1.58 fM and 6.5 pM, respectively. On this basis, a portable device was constructed for the practical detection of C. marina eDNA, and its reliability and accuracy were verified by comparison with the ddPCR method (P > 0.05). For each analysis, the average cost was only ∼ $1.08 and could be completed within 100 min with reliable sensitivity and specificity. Overall, the biosensor could reflect the protective effect of probiotics on coral heat stress, and the proposed technique will put new insights into the rapid and on-site detection of coral probiotics to assist corals against global warming. [ABSTRACT FROM AUTHOR]

[Display omitted] • The highly suitable region of coral was mainly distributed in north of 10°N. • Water velocity, sunlight, temperature, and dissolved oxygen affected coral survival. • Water velocity and nitrate content leaded to heterogeneity in coral distribution. • The exposure risk of corals in the southern Nansha was highest under all scenarios. Coral reefs represent distinctive yet vulnerable marine ecosystems. Recently, these ecosystems have faced threats and degradation from multiple factors. A comprehensive understanding of coral distribution and niche information forms the theoretical foundation for addressing the ongoing coral crisis. This study employed the MaxEnt model to predict coral distribution in the central and southern regions of the South China Sea (SCS), while also obtaining ecological niche information. Utilizing CMIP6 data, the future exposure risk of corals was evaluated under two forcing scenarios (SSP245 and SSP585). The findings revealed that the highly suitable areas for corals in the SCS were approximately 31,360 km2, mainly distributed in the middle and east of Xisha, Zhongsha Atoll, Huangyan Island, and the north of the Nansha Islands. The probability of coral presence in the north and west of Xisha and the south of Nansha was low. The key environmental factors exerting significant influences on coral occurrence included seawater temperature, photosynthetically active radiation, current velocity, and dissolved oxygen. Among them, seawater velocity and nitrate emerged as the primary factors discerning differences in coral fitness across the study regions, which also verified the results of principal component analysis. Under extreme scenarios predicted by the end of this century (SSP585-2090s), over 43 % of coral distribution areas would face the highest exposure risk, mainly concentrated in southern Nansha. The primary drivers of this increased risk were the substantial changes occurring in temperature, dissolved oxygen, and nitrate. This research serves as a reference for coral conservation under climate change in the future. [ABSTRACT FROM AUTHOR]

• Trophic flexibility of corals with different symbionts (PdC or PdD) was assessed. • PdC had a higher autotrophic capacity than PdD, despite lower symbiont density. • Trophic strategy of PdC was more flexible than that of PdD across seasons. • Corals relied more on autotrophy in summer, but heterotrophy in winter. • Symbiont genus can determine the nutritional strategy and adaptability of corals. Coral reefs are typically found in nutrient-limited waters, which may restrict the growth and expansion of corals. Nevertheless, corals are mixotrophs that may adjust to the variation in the availability of energy sources by switching their major nutritional mode between autotrophy (i.e., synthesizing their own food by symbionts) and heterotrophy (i.e., consuming external food sources). Such trophic plasticity may, however, be subject to symbiont genus and environmental conditions. Using a widespread coral species (Pocillopora damicornis), we examine how symbiont genus (Cladocopium vs. Durusdinium) affects the physiological traits (biomass, symbiont density, C:N ratio and chlorophyll content) of corals and their trophic strategy across seasons (summer and winter) based on stable isotope markers (δ13C and δ15N). We found that corals dominated by Cladocopium (PdC) had a lower symbiont density, but higher autotrophic capacity (higher cellular chlorophyll content and higher δ13C) than those by Durusdinium (PdD). Across seasons, the trophic strategy of PdC was flexible that the autotrophic capacity was reduced by 37.1 % from summer to winter, whereas the trophic strategy of PdD remained relatively unchanged. PdC had a greater heterotrophic capacity in winter, while PdD in summer. Our findings suggest that symbiont genus can determine the trophic flexibility of corals and drive trophic niche differentiation between conspecific corals. By adaptively changing trophic strategy, intraspecific competition of corals for energy sources can be reduced, possibly allowing them to persist in oligotrophic waters and adapt to the future oceanic climate. [ABSTRACT FROM AUTHOR]