Projecting coral reef futures under global warming and ocean acidification

Heat stress in symbiotic dinoflagellates: Implications on oxidative stress and cellular changes

Global warming has been shown to harmfully affect symbiosis between Symbiodiniaceae and other marine invertebrates. When symbiotic dinoflagellates (the genus Breviolum) were in vitro exposed to acute heat stress of +7 °C for a period of 5 days, the results revealed the negative impact on all physiological and other cellular parameters measured. Elevated temperatures resulted in a severe reduction in algal density of up to 9.5-fold, as well as pigment concentrations, indicating the status of the physiological stress and early signs of photo-bleaching. Reactive oxygen species (ROS) were increased in all heated dinoflagellate cells, while the antioxidant-reduced glutathione levels initially dropped on day one but increased under prolonged temperature stress. The cell viability parameters were reduced by 97 % over the heating period, with an increased proportion of apoptotic and necrotic cells. Autofluorescence (AF) for Cy5-PE 660-20 was reduced from 1.7-fold at day 1 to up to 50-fold drop at the end of heating time, indicating that the AF changes were highly sensitive to heat stress and that it could be an extremely sensitive tool for assessing the functionality of algal photosynthetic machinery. The addition of the drug 5-AZA-2'-deoxycytidine (5-AZA), which inhibits DNA methylation processes, was assessed in parallel and contributed to some alterations in algal cellular stress response. The presence of drug 5-AZA combined with the temperature stress had an additional impact on Symbiodiniaceae density and cell complexity, including the AF levels. These variations in cellular stress response under heat stress and compromised DNA methylation conditions may indicate the importance of this epigenetic mechanism for symbiotic dinoflagellate thermal tolerance adaptability over a longer period, which needs further exploration. Consequently, the increased ROS levels and changes in AF signals reported during ongoing heat stress in dinoflagellate cells could be used as early stress biomarkers in these microalgae and potentially other photosynthetic species.

Local adaptation of trophic strategy determined the tolerance of coral Galaxea fascicularis to environmental fluctuations

The escalation of global change has resulted in heightened frequencies and intensities of environmental fluctuations within coral reef ecosystems. Corals originating from marginal reefs have potentially enhanced their adaptive capabilities in response to these environmental variations through processes of local adaptation. However, the intricate mechanisms driving this phenomenon remain a subject of limited investigation. This study aimed to investigate how corals in Luhuitou reef, a representative relatively high-latitude reef in China, adapt to seasonal fluctuations in seawater temperature and light availability. We conducted a 190-day plantation experiment with the widespread species, Galaxea fascicularis, in Luhuitou local, and from Meiji reef, a typical offshore tropical reef, to Luhuitou as comparison. Drawing upon insights from physiological adaptations, we focused on fatty acid (FA) profiles to unravel the trophic strategies of G. fascicularis to cope with environmental fluctuations from two origins. Our main findings are threefold: 1) Native corals exhibited a stronger physiological resilience compared to those transplanted from Meiji. 2) Corals from both origins consumed large quantities of energy reserves in winter, during which FA profiles of local corals altered, while the change of FA profiles of corals from Meiji was probably due to the excessive consumption of saturated fatty acid (SFA). 3) The better resilience of native corals is related to high levels of functional polyunsaturated fatty acid (PUFA), while insufficient nutrient reserves, possibly due to weak heterotrophic ability, result in the obstruction of the synthesis pathway of PUFA for corals from Meiji, leading to their intolerance to environmental changes. Consequently, we suggest that the tolerance of G. fascicularis to environmental fluctuations is determined by their local adapted trophic strategies. Furthermore, our findings underscore the notion that the rapid adaptation of relatively high-latitude corals to seasonal environmental fluctuations might not be readily attainable for their tropical counterparts within a brief timeframe.

Corals that survive repeated thermal stress show signs of selection and acclimatization

Climate change is transforming coral reefs by increasing the frequency and intensity of marine heatwaves, often leading to coral bleaching and mortality. Coral communities have demonstrated modest increases in thermal tolerance following repeated exposure to moderate heat stress, but it is unclear whether these shifts represent acclimatization of individual colonies or mortality of thermally susceptible individuals. For corals that survive repeated bleaching events, it is important to understand how past bleaching responses impact future growth potential. Here, we track the bleaching responses of 1,832 corals in leeward Maui through multiple marine heatwaves and document patterns of coral growth and survivorship over a seven-year period. While we find limited evidence of acclimatization at population scales, we document reduced bleaching over time in specific individuals that is indicative of acclimatization, primarily in the stress-tolerant taxa Porites lobata. For corals that survived both bleaching events, we find no relationship between bleaching response and coral growth in three of four taxa studied. This decoupling suggests that coral survivorship is a better indicator of future growth than is a coral's bleaching history. Based on these results, we recommend restoration practitioners in Hawai'i focus on colonies of Porites and Montipora with a proven track-record of growth and survivorship, rather than devote resources toward identifying and cultivating bleaching-resistant phenotypes in the lab. Survivorship followed a latitudinal thermal stress gradient, but because this gradient was small, it is likely that local environmental factors also drove differences in coral performance between sites. Efforts to reduce human impacts at low performing sites would likely improve coral survivorship in the future.

Mass mortality of diadematoid sea urchins in the Red Sea and Western Indian Ocean

Sea urchins are primary herbivores on coral reefs, regulating algal biomass and facilitating coral settlement and growth.1,2,3,4,5,6,7,8,9,10,11,12 Recurring mass mortality events (MMEs) of Diadema species Gray, 1825 have been recorded globally,13,14,15,16,17,18,19,20,21,22,23 the most notorious and ecologically significant of which occurred in the Caribbean in 1983,14,17,19,20 contributing to the shift from coral to algal-dominated ecosystems.17,24,25 Recently, first evidence of Diadema setosum mass mortality was reported from the eastern Mediterranean Sea.23 Here, we report extensive mass mortalities of several diadematoid species inhabiting the Red Sea and Western Indian Ocean (WIO)26,27,28 including first evidence of mortalities in the genus Echinothrix Peters, 1853. Mortalities initiated in the Gulf of Aqaba on December 2022 and span the Red Sea, the Gulf of Oman, and the Western Indian Ocean (Réunion Island), with population declines reaching 100% at some sites. Infected individuals are characterized by spine loss and tissue necrosis, resulting in exposed skeletons (i.e., tests) and mortality. Molecular diagnostics of the 18S rRNA gene confirm the presence of a waterborne scuticociliate protozoan most closely related to Philaster apodigitiformis in infected specimens-identical to the pathogen found in the 2022 Caribbean mass mortality of Diadema antillarum.13,15,18 Collapse of these key benthic grazers in the Red Sea and Western Indian Ocean may lead to algal dominance over corals, threatening the stability of coral reefs on a regional scale.29,30,31,32 We issue a warning regarding the further expansion of mortalities and call for immediate monitoring and conservation efforts for these key ecological species.

Triggers, cascades, and endpoints: connecting the dots of coral bleaching mechanisms

The intracellular coral-dinoflagellate symbiosis is the engine that underpins the success of coral reefs, one of the most diverse ecosystems on the planet. However, the breakdown of the symbiosis and the loss of the microalgal symbiont (i.e. coral bleaching) due to environmental changes are resulting in the rapid degradation of coral reefs globally. There is an urgent need to understand the cellular physiology of coral bleaching at the mechanistic level to help develop solutions to mitigate the coral reef crisis. Here, at an unprecedented scope, we present novel models that integrate putative mechanisms of coral bleaching within a common framework according to the triggers (initiators of bleaching, e.g. heat, cold, light stress, hypoxia, hyposalinity), cascades (cellular pathways, e.g. photoinhibition, unfolded protein response, nitric oxide), and endpoints (mechanisms of symbiont loss, e.g. apoptosis, necrosis, exocytosis/vomocytosis). The models are supported by direct evidence from cnidarian systems, and indirectly through comparative evolutionary analyses from non-cnidarian systems. With this approach, new putative mechanisms have been established within and between cascades initiated by different bleaching triggers. In particular, the models provide new insights into the poorly understood connections between bleaching cascades and endpoints and highlight the role of a new mechanism of symbiont loss, i.e. 'symbiolysosomal digestion', which is different from symbiophagy. This review also increases the approachability of bleaching physiology for specialists and non-specialists by mapping the vast landscape of bleaching mechanisms in an atlas of comprehensible and detailed mechanistic models. We then discuss major knowledge gaps and how future research may improve the understanding of the connections between the diverse cascade of cellular pathways and the mechanisms of symbiont loss (endpoints).

Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont

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

Synergistic response to climate stressors in coral is associated with genotypic variation in baseline expression

As environments are rapidly reshaped due to climate change, phenotypic plasticity plays an important role in the ability of organisms to persist and is considered an especially important acclimatization mechanism for long-lived sessile organisms such as reef-building corals. Often, this ability of a single genotype to display multiple phenotypes depending on the environment is modulated by changes in gene expression, which can vary in response to environmental changes via two mechanisms: baseline expression and expression plasticity. We used transcriptome-wide expression profiling of eleven genotypes of common-gardened Acropora cervicornis to explore genotypic variation in the expression response to thermal and acidification stress, both individually and in combination. We show that the combination of these two stressors elicits a synergistic gene expression response, and that both baseline expression and expression plasticity in response to stress show genotypic variation. Additionally, we demonstrate that frontloading of a large module of coexpressed genes is associated with greater retention of algal symbionts under combined stress. These results illustrate that variation in the gene expression response of individuals to climate change stressors can persist even when individuals have shared environmental histories, affecting their performance under future climate change scenarios.

Unique high-temperature tolerance mechanisms of zoochlorellae Symbiochlorum hainanensis derived from scleractinian coral Porites lutea

Global warming is a key issue that causes coral bleaching mainly because of the thermosensitivity of zooxanthellae. Compared with the well-studied zooxanthellae Symbiodiniaceae in coral holobionts, we rarely know about other coral symbiotic algae, let alone their thermal tolerance. In this study, a zoochlorellae, Symbiochlorum hainanensis, isolated from the coral Porites lutea, was proven to have a threshold temperature of 38°C. Meanwhile, unique high-temperature tolerance mechanisms were suggested by integrated transcriptomics and real-time quantitative PCR, physiological and biochemical analyses, and electron microscopy observation. Under heat stress, S. hainanensis shared some similar response strategies with zooxanthellae Effrenium sp., such as increased ascorbate peroxidase, glutathione peroxidase, superoxide dismutase activities and chlorophyll a, thiamine, and thiamine phosphate contents. In particular, more chloroplast internal layered structure, increased CAT activity, enhanced selenate reduction, and thylakoid assembly pathways were highlighted for S. hainanensis's high-temperature tolerance. Notably, it is the first time to reveal a whole selenate reduction pathway from SeO42- to Se2- and its contribution to the high-temperature tolerance of S. hainanensis. These unique mechanisms, including antioxidation and maintaining photosynthesis homeostasis, efficiently ensure the high-temperature tolerance of S. hainanensis than Effrenium sp. Compared with the thermosensitivity of coral symbiotic zooxanthellae Symbiodiniaceae, this study provides novel insights into the high-temperature tolerance mechanisms of coral symbiotic zoochlorellae S. hainanensis, which will contribute to corals' survival in the warming oceans caused by global climate change.

IMPORTANCE

The increasing ocean temperature above 31°C-32°C might trigger a breakdown of the coral-Symbiodiniaceae symbioses or coral bleaching because of the thermosensitivity of Symbiodiniaceae; therefore, the exploration of alternative coral symbiotic algae with high-temperature tolerance is important for the corals' protection under warming oceans. This study proves that zoochlorellae Symbiochlorum hainanensis can tolerate 38°C, which is the highest temperature tolerance known for coral symbiotic algae to date, with unique high-temperature tolerance mechanisms. Particularly, for the first time, an internal selenium antioxidant mechanism of coral symbiotic S. hainanensis to high temperature was suggested.

Systematic review of the uncertainty of coral reef futures under climate change

Climate change impact syntheses, such as those by the Intergovernmental Panel on Climate Change, consistently assert that limiting global warming to 1.5 °C is unlikely to safeguard most of the world's coral reefs. This prognosis is primarily based on a small subset of available models that apply similar 'excess heat' threshold methodologies. Our systematic review of 79 articles projecting coral reef responses to climate change revealed five main methods. 'Excess heat' models constituted one third (32%) of all studies but attracted a disproportionate share (68%) of citations in the field. Most methods relied on deterministic cause-and-effect rules rather than probabilistic relationships, impeding the field's ability to estimate uncertainty. To synthesize the available projections, we aimed to identify models with comparable outputs. However, divergent choices in model outputs and scenarios limited the analysis to a fraction of available studies. We found substantial discrepancies in the projected impacts, indicating that the subset of articles serving as a basis for climate change syntheses may project more severe consequences than other studies and methodologies. Drawing on insights from other fields, we propose methods to incorporate uncertainty into deterministic modeling approaches and propose a multi-model ensemble approach to generating probabilistic projections for coral reef futures.

Diversification of refugia types needed to secure the future of coral reefs subject to climate change

Identifying locations of refugia from the thermal stresses of climate change for coral reefs and better managing them is one of the key recommendations for climate change adaptation. We review and summarize approximately 30 years of applied research focused on identifying climate refugia to prioritize the conservation actions for coral reefs under rapid climate change. We found that currently proposed climate refugia and the locations predicted to avoid future coral losses are highly reliant on  excess heat metrics, such as degree heating weeks. However, many existing alternative environmental, ecological, and life-history variables could be used to identify other types of refugia that lead to the desired diversified portfolio for coral reef conservation. To improve conservation priorities for coral reefs, there is a need to evaluate and validate the predictions of climate refugia with long-term field data on coral abundance, diversity, and functioning. There is also the need to identify and safeguard locations displaying resistance toprolonged exposure to heat waves and the ability to recover quickly after thermal exposure. We recommend using more metrics to identify a portfolio of potential refugia sites for coral reefs that can avoid, resist, and recover from exposure to high ocean temperatures and the consequences of climate change, thereby shifting past efforts focused on avoidance to a diversified risk-spreading portfolio that can be used to improve strategic coral reef conservation in a rapidly warming climate.

A Meta-analysis Reveals Global Change Stressors Potentially Aggravate Mercury Toxicity in Marine Biota

Growing evidence demonstrates that global change can modulate mercury (Hg) toxicity in marine organisms; however, the consensus on such effect is lacking. Here, we conducted a meta-analysis to evaluate the effects of global change stressors on Hg biotoxicity according to the IPCC projections (RCP 8.5) for 2100, including ocean acidification (-0.4 units), warming (+4 °C), and their combination (acidification-warming). The results indicated an overall aggravating effect (ln RRΔ = -0.219) of global change on Hg toxicity in marine organisms, while the effect varied with different stressors; namely, acidification potentially alleviates Hg biotoxicity (ln RRΔ = 0.117) while warming and acidification-warming have an aggravating effect (ln RRΔ = -0.328 and -0.097, respectively). Moreover, warming increases Hg toxicity in different trophic levels, i.e., primary producers (ln RRΔ = -0.198) < herbivores (ln RRΔ = -0.320) < carnivores (ln RRΔ = -0.379), implying increasing trends of Hg biomagnification through the food web. Notably, ocean hypoxia appears to boost Hg biotoxicity, although it was not considered in our meta-analysis because of the small sample size. Given the persistent global change and combined effects of these stressors in marine environments, multigeneration and multistressor research is urgently needed to fully disclose the impacts of global change on Hg pollution and its risk.

Past disturbances and local conditions influence the recovery rates of coral reefs

Corals are being increasingly subjected to marine heatwaves. Theory suggests that increasing the intensity of disturbances reduces recovery rates, which inspired us to examine the recovery rates of coral cover following marine heatwaves, cyclones, and other disturbances at 1921 study sites, in 58 countries and three oceans, from 1977 to 2020. In the Atlantic Ocean, coral cover has decreased fourfold since the 1970s, and recovery rates following disturbances have been relatively slow, except in the Antilles. By contrast, reefs in the Pacific and Indian Oceans have maintained coral cover and recovery rates over time. There were positive relationships between rates of coral recovery and prior cyclone and heatwave frequency, and negative relationships between rates of coral recovery and macroalgae cover and distance to shore. A recent increase in the variance in recovery rates in some ecoregions of the Pacific and Indian Oceans suggests that some reefs in those ecoregions may be approaching a phase shift. While marine heatwaves are increasing in intensity and frequency, our results suggest that regional and local conditions influence coral recovery rates, and therefore, effective local management efforts can help reefs recover from disturbances.

Diversification dynamics of a common deep-sea octocoral family linked to the Paleocene-Eocene thermal maximum

The deep-sea has experienced dramatic changes in physical and chemical variables in the geological past. However, little is known about how deep-sea species richness responded to such changes over time and space. Here, we studied the diversification dynamics of one of the most diverse octocorallian families inhabiting deep sea benthonic environments worldwide and sustaining highly diverse ecosystems, Primnoidae. A newly dated species-level phylogeny was constructed to infer their ancestral geographic locations and dispersal rates initially. Then, we tested whether their global and regional (the Southern Ocean) diversification dynamics were mediated by dispersal rate and abiotic factors as changes in ocean geochemistry. Finally, we tested whether primnoids showed changes in speciation and extinction at discrete time points. Our results suggested primnoids likely originated in the southwestern Pacific Ocean during the Lower Cretaceous ∼112 Ma, with further dispersal after the physical separation of continental landmasses along the late Mesozoic and Cenozoic. Only the speciation rate of the Southern Ocean primnoids showed a significant correlation to ocean chemistry. Moreover, the Paleocene-Eocene thermal maximum marked a significant increase in the diversification of primnoids at global and regional scales. Our results provide new perspectives on the macroevolutionary and biogeographic patterns of an ecologically important benthic organism typically found in deep-sea environments.

Analysis of marine diversity and anthropogenic pressures on Seixas coral reef ecosystem (northeastern Brazil)

Coral reefs, vital and ecologically significant ecosystems, are among the most jeopardized marine environments in the Atlantic Ocean, particularly along the northeastern coast of Brazil. The persistent lack of effective management and conservation has led to fragmented information on reef use and pressures, hindering the understanding of these ecosystems' health. Major difficulties and challenges include inadequate data, diverse anthropogenic pressures, and the complex interaction between marine species. This study sought to bridge this knowledge gap by conducting a comprehensive analysis of marine diversity and anthropogenic pressures, specifically focusing on Seixas coral reef near João Pessoa city, an area notably impacted by tourism. Utilizing 25 monitoring transects, subdivided into 1 m2 quadrants, the marine diversity was meticulously evaluated through innovative procedures including (a) sedimentological and geochemical field surveys, (b) application of Shannon-Weaver diversity and Simpson dominance indices, (c) cluster analysis, (d) species identification of macroalgae, coral, and fish, and (e) an examination of anthropogenic interactions and pressures on the coral reef. The assessment encompassed three distinct zones: Back Reef, Reef Top, and Fore Reef, and identified a total of 25 species across 15 genera and 10 fish families. The findings revealed the prevalence of brown macroalgae, fish, and coral, with heightened abundance of red macroalgae in the Fore Reef, which also exhibited the greatest diversity (2.816) and dominance (0.894). Original achievements include the identification of specific spatial variations, recognition of the anthropogenic factors leading to ecological changes, and the formulation of evidence-based recommendations. The study concludes that escalating urbanization and burgeoning daily tourist visits to the reef have exacerbated negative impacts on Seixas coral reef's marine ecosystem. These insights underscore the urgent need for strategic planning and resource management to safeguard the reef's biodiversity and ecological integrity.

Morphological and genetic mechanisms underlying the plasticity of the coral Porites astreoides across depths in Bermuda

The widespread decline of shallow-water coral reefs has fueled interest in assessing whether mesophotic reefs can act as refugia replenishing deteriorated shallower reefs through larval exchange. Here we explore the morphological and molecular basis facilitating survival of planulae and adults of the coral Porites astreoides (Lamarck, 1816; Hexacorallia: Poritidae) along the vertical depth gradient in Bermuda. We found differences in micro-skeletal features such as bigger calyxes and coarser surface of the skeletal spines in shallow corals. Yet, tomographic reconstructions reveal an analogous mineral distribution between shallow and mesophotic adults, pointing to similar skeleton growth dynamics. Our study reveals patterns of host genetic connectivity and minimal symbiont depth-zonation across a broader depth range than previously known for this species in Bermuda. Transcriptional variations across life stages showed different regulation of metabolism and stress response functions, unraveling molecular responses to environmental conditions at different depths. Overall, these findings increase our understanding of coral acclimatory capability across broad vertical gradients, ultimately allowing better evaluation of the refugia potential of mesophotic reefs.

Coral Reef Population Genomics in an Age of Global Change

Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, gene flow, and hybridization have played and will continue to play an important role in the adaptation or extinction of coral reef taxa in the face of rapid environmental change, but research remains exceptionally limited compared to the urgent needs. Critical areas for future investigation include understanding evolutionary potential and the mechanisms of local adaptation, developing historical baselines, and building greater research capacity in the countries where most reef diversity is concentrated.

Seasonal coral-algae interactions drive White Mat Syndrome coral disease outbreaks

Ocean warming drives not only the increase of known coral disease prevalence but facilitates the emergence of new undescribed ones too. As climate change is restructuring coral ecosystems, novel biological interactions could lead to an increase in coral disease in both tropical and marginal coral communities. White Mat Syndrome (WMS) represents one such emerging coral disease, with outbreaks associated with high algal interactions and seasonal summer temperatures. However, the mechanisms behind its pathogenesis, modes of transmission and causative pathogens remain to be identified. Ex situ infection experiments pairing the coral Porites heronensis together with local potential contributory factors show that the macroalga Gelidium elegans hosts and proliferates the WMS microbial mat. This pathogenic consortium then infects adjacent corals, leading to their mortality. WMS was also observed to transmit following the fragmentation of the microbial mat, which was able to infect healthy corals. Sulfur-cycling bacteria (i.e., Beggiatoa, Desulfobacter sp., Arcobacteraceae species) and the free-living spirochete Oceanospirochaeta sediminicola were found consistently in both WMS and G. elegans consortia, suggesting they are putative pathogens of WMS. The predicted functional roles of these pathogenic consortia showed degradative processes, hinting that tissue lyses could drive mat formation and spread. Coral-algae interactions will rise due to ongoing ocean warming and coral ecosystem degradation, likely promoting the virulence and prevalence of algal-driven coral diseases.

Standardization of in situ coral bleaching measurements highlights the variability in responses across genera, morphologies, and regions

Marine heatwaves and regional coral bleaching events have become more frequent and severe across the world's oceans over the last several decades due to global climate change. Observational studies have documented spatiotemporal variation in the responses of reef-building corals to thermal stress within and among taxa across geographic scales. Although many tools exist for predicting, detecting, and quantifying coral bleaching, it remains difficult to compare bleaching severity (e.g., percent cover of bleached surface areas) among studies and across species or regions. For this review, we compiled over 2,100 in situ coral bleaching observations representing 87 reef-building coral genera and 250 species of common morphological groups from a total of 74 peer-reviewed scientific articles, encompassing three broad geographic regions (Atlantic, Indian, and Pacific Oceans). While bleaching severity was found to vary by region, genus, and morphology, we found that both genera and morphologies responded differently to thermal stress across regions. These patterns were complicated by (i) inconsistent methods and response metrics across studies; (ii) differing ecological scales of observations (i.e., individual colony-level vs. population or community-level); and (iii) temporal variability in surveys with respect to the onset of thermal stress and the chronology of bleaching episodes. To improve cross-study comparisons, we recommend that future surveys prioritize measuring bleaching in the same individual coral colonies over time and incorporate the severity and timing of warming into their analyses. By reevaluating and standardizing the ways in which coral bleaching is quantified, researchers will be able to track responses to marine heatwaves with increased rigor, precision, and accuracy.

Assessment of macrobenthos diversity and a zoning proposal for Seixas coral reefs (northeastern Brazil)

Coral reefs worldwide are under severe threat due to their inherent fragility and urgent need for conservation. The escalating tourism in coral reefs significantly impacts the marine ecosystem's biodiversity and conservation. This study analyzed the diversity and conservation status of macrobenthos in the Seixas coral reef, located in northeastern Brazil, and proposed a zoning plan. We employed monitoring protocols adapted from the Reef Check Program, the Rapid Assessment Protocol for Atlantic and Gulf Reefs, and the Protocol for Monitoring Coastal Benthic Habitats. Species identification was carried out by analyzing 25 transects, each divided into 1 m2 grids, with photos recorded for each grid, totaling 625 photos. Margalef, Shannon-Weaver, Simpson, and Pielou indices were used to analyze species distribution and diversity. The results indicated Dictyotaceae, Sargassaceae, and Corallinaceae as prevalent families. This research offers decision-makers a snapshot of species distribution in the Seixas coral reefs, providing a non-destructive, efficient methodology for assessing environmental impacts on coastal coral reefs.

Direct Air Capture of CO2 Using Amine/Alumina Sorbents at Cold Temperature

Rising CO2 emissions are responsible for increasing global temperatures causing climate change. Significant efforts are underway to develop amine-based sorbents to directly capture CO2 from air (called direct air capture (DAC)) to combat the effects of climate change. However, the sorbents' performances have usually been evaluated at ambient temperatures (25 °C) or higher, most often under dry conditions. A significant portion of the natural environment where DAC plants can be deployed experiences temperatures below 25 °C, and ambient air always contains some humidity. In this study, we assess the CO2 adsorption behavior of amine (poly(ethyleneimine) (PEI) and tetraethylenepentamine (TEPA)) impregnated into porous alumina at ambient (25 °C) and cold temperatures (-20 °C) under dry and humid conditions. CO2 adsorption capacities at 25 °C and 400 ppm CO2 are highest for 40 wt% TEPA-incorporated γ-Al2O3 samples (1.8 mmol CO2/g sorbent), while 40 wt % PEI-impregnated γ-Al2O3 samples exhibit moderate uptakes (0.9 mmol g-1). CO2 capacities for both PEI- and TEPA-incorporated γ-Al2O3 samples decrease with decreasing amine content and temperatures. The 40 and 20 wt % TEPA sorbents show the best performance at -20 °C under dry conditions (1.6 and 1.1 mmol g-1, respectively). Both the TEPA samples also exhibit stable and high working capacities (0.9 and 1.2 mmol g-1) across 10 cycles of adsorption-desorption (adsorption at -20 °C and desorption conducted at 60 °C). Introducing moisture (70% RH at -20 and 25 °C) improves the CO2 capacity of the amine-impregnated sorbents at both temperatures. The 40 wt% PEI, 40 wt % TEPA, and 20 wt% TEPA samples show good CO2 uptakes at both temperatures. The results presented here indicate that γ-Al2O3 impregnated with PEI and TEPA are potential materials for DAC at ambient and cold conditions, with further opportunities to optimize these materials for the scalable deployment of DAC plants at different environmental conditions.

Simultaneous warming and acidification limit population fitness and reveal phenotype costs for a marine copepod

Phenotypic plasticity and evolutionary adaptation allow populations to cope with global change, but limits and costs to adaptation under multiple stressors are insufficiently understood. We reared a foundational copepod species, Acartia hudsonica, under ambient (AM), ocean warming (OW), ocean acidification (OA), and combined ocean warming and acidification (OWA) conditions for 11 generations (approx. 1 year) and measured population fitness (net reproductive rate) derived from six life-history traits (egg production, hatching success, survival, development time, body size and sex ratio). Copepods under OW and OWA exhibited an initial approximately 40% fitness decline relative to AM, but fully recovered within four generations, consistent with an adaptive response and demonstrating synergy between stressors. At generation 11, however, fitness was approximately 24% lower for OWA compared with the AM lineage, consistent with the cost of producing OWA-adapted phenotypes. Fitness of the OWA lineage was not affected by reversal to AM or low food environments, indicating sustained phenotypic plasticity. These results mimic those of a congener, Acartia tonsa, while additionally suggesting that synergistic effects of simultaneous stressors exert costs that limit fitness recovery but can sustain plasticity. Thus, even when closely related species experience similar stressors, species-specific costs shape their unique adaptive responses.

Three-dimensional species distribution modelling reveals the realized spatial niche for coral recruitment on contemporary Caribbean reefs

The three-dimensional structure of habitats is a critical component of species' niches driving coexistence in species-rich ecosystems. However, its influence on structuring and partitioning recruitment niches has not been widely addressed. We developed a new method to combine species distribution modelling and structure from motion, and characterized three-dimensional recruitment niches of two ecosystem engineers on Caribbean coral reefs, scleractinian corals and gorgonians. Fine-scale roughness was the most important predictor of suitable habitat for both taxa, and their niches largely overlapped, primarily due to scleractinians' broader niche breadth. Crevices and holes at mm scales on calcareous rock with low coral cover were more suitable for octocorals than for scleractinian recruits, suggesting that the decline in scleractinian corals is facilitating the recruitment of octocorals on contemporary Caribbean reefs. However, the relative abundances of the taxa were independent of the amount of suitable habitat on the reef, emphasizing that niche processes alone do not predict recruitment rates.

9000 years of change in coral community structure and accretion in Belize reefs, western Atlantic

Tropical coral reefs, as prominent marine diversity hotspots, are in decline, and long-term studies help to improve understanding of the effects of global warming, sea-level rise, ocean acidification, deterioration of water quality, and disease. Here, we evaluated relative coral abundance and reef accretion rates over the past 9000 years in Belize barrier and atoll reefs, the largest reef system in the Atlantic Ocean. Acropora palmata and Orbicella spp. have been the most common corals. The abundance of competitive, fast-growing acroporids was constant over multi-millennial timescales. A decline in A. cervicornis abundance, however, and three centennial-scale gaps in A. palmata occurrence, suggest that the modern decline in acroporids was not unprecedented. Stress-tolerant corals predominate at the beginning of Holocene successions. Following the improvement of environmental conditions after inundation of the reef pedestal, their abundance has decreased. The abundance of weedy corals has increased during the Holocene underlining the importance of fecundity for the coral community. Reef-accretion rate, as calculated based on 76 new U-series age dates, has decreased over the Holocene and the mean value of 3.36 m kyr-1 is at the lower end of global reef growth compilations and predicted future rates of rise in sea level.

Regional and global climate risks for reef corals: Incorporating species-specific vulnerability and exposure to climate hazards

Climate change is driving rapid and widespread erosion of the environmental conditions that formerly supported species persistence. Existing projections of climate change typically focus on forecasts of acute environmental anomalies and global extinction risks. The current projections also frequently consider all species within a broad taxonomic group together without differentiating species-specific patterns. Consequently, we still know little about the explicit dimensions of climate risk (i.e., species-specific vulnerability, exposure and hazard) that are vital for predicting future biodiversity responses (e.g., adaptation, migration) and developing management and conservation strategies. Here, we use reef corals as model organisms (n = 741 species) to project the extent of regional and global climate risks of marine organisms into the future. We characterise species-specific vulnerability based on the global geographic range and historical environmental conditions (1900-1994) of each coral species within their ranges, and quantify the projected exposure to climate hazard beyond the historical conditions as climate risk. We show that many coral species will experience a complete loss of pre-modern climate analogs at the regional scale and across their entire distributional ranges, and such exposure to hazardous conditions are predicted to pose substantial regional and global climate risks to reef corals. Although high-latitude regions may provide climate refugia for some tropical corals until the mid-21st century, they will not become a universal haven for all corals. Notably, high-latitude specialists and species with small geographic ranges remain particularly vulnerable as they tend to possess limited capacities to avoid climate risks (e.g., via adaptive and migratory responses). Predicted climate risks are amplified substantially under the SSP5-8.5 compared with the SSP1-2.6 scenario, highlighting the need for stringent emission controls. Our projections of both regional and global climate risks offer unique opportunities to facilitate climate action at spatial scales relevant to conservation and management.

Decadal stability in coral cover could mask hidden changes on reefs in the East Asian Seas

Coral reefs in the Central Indo-Pacific region comprise some of the most diverse and yet threatened marine habitats. While reef monitoring has grown throughout the region in recent years, studies of coral reef benthic cover remain limited in spatial and temporal scales. Here, we analysed 24,365 reef surveys performed over 37 years at 1972 sites throughout East Asia by the Global Coral Reef Monitoring Network using Bayesian approaches. Our results show that overall coral cover at surveyed reefs has not declined as suggested in previous studies and compared to reef regions like the Caribbean. Concurrently, macroalgal cover has not increased, with no indications of phase shifts from coral to macroalgal dominance on reefs. Yet, models incorporating socio-economic and environmental variables reveal negative associations of coral cover with coastal urbanisation and sea surface temperature. The diversity of reef assemblages may have mitigated cover declines thus far, but climate change could threaten reef resilience. We recommend prioritisation of regionally coordinated, locally collaborative long-term studies for better contextualisation of monitoring data and analyses, which are essential for achieving reef conservation goals.

Pervasive tandem duplications and convergent evolution shape coral genomes

BACKGROUND

Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species.

RESULTS

In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience.

CONCLUSIONS

At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

Diversity and Antimicrobial Activity of Intestinal Fungi from Three Species of Coral Reef Fish

Although intestinal microbiota play crucial roles in fish digestion and health, little is known about intestinal fungi in fish. This study investigated the intestinal fungal diversity of three coral reef fish (Lates calcarifer, Trachinotus blochii, and Lutjanus argentimaculatus) from the South China Sea using a culturable method. A total of 387 isolates were recovered and identified by sequencing their internal transcribed spacer sequences, belonging to 29 known fungal species. The similarity of fungal communities in the intestines of the three fish verified that the fungal colonization might be influenced by their surrounding environments. Furthermore, the fungal communities in different intestines of some fish were significantly different, and the number of yeasts in the hindgut was less than that in fore- and mid-intestines, suggesting that the distribution of fungi in fishes' intestines may be related to the physiological functions of various intestinal segments. In addition, 51.4% of tested fungal isolates exhibited antimicrobial activity against at least one marine pathogenic microorganism. Notably, isolate Aureobasidium pullulans SCAU243 exhibited strong antifungal activity against Aspergillus versicolor, and isolate Schizophyllum commune SCAU255 displayed extensive antimicrobial activity against four marine pathogenic microorganisms. This study contributed to our understanding of intestinal fungi in coral reef fish and further increased the library of fungi available for natural bioactive product screening.

Separate and combined effects of elevated pCO2 and temperature on the branching reef corals Acropora digitifera and Montipora digitata

Ocean acidification (OA) and warming (OW) are major global threats to coral reef ecosystems; however, studies on their combined effects (OA + OW) are scarce. Therefore, we evaluated the effects of OA, OW, and OA + OW in the branching reef corals Acropora digitifera and Montipora digitata, which have been found to respond differently to environmental changes. Our results indicate that OW has a greater impact on A. digitifera and M. digitata than OA and that the former species is more vulnerable to OW than the latter. OW was the main stressor for increased mortality and decreased calcification in the OA + OW group, and the effect of OA + OW was additive in both species. Our findings suggest that the relative abundance and cover of M. digitata are expected to increase whereas those of A. digitifera may decrease in the near future in Okinawa.

Response of resistant larvae of the coral Acropora tenuis to future thermal stress

Seawater temperatures are rising rapidly and severely due to climate change, negatively affecting coral reef communities. The persistence of coral populations depends on their success during the early life stages. Thermal conditioning during the larval stage can increase coral larvae's ability to tolerate high temperatures in subsequent stages. We studied the response of resistant larvae of Acropora tenuis to thermal stress to increase their thermal tolerance during the juvenile stage. Larvae were exposed to ambient (∼26 °C) and thermal stress (∼31 °C) temperatures. Then, settlement success on preconditioned tiles was determined. After 28 days at ambient temperature, the juveniles were exposed to thermal stress for 14 days, and their survival was assessed. Our results showed that thermal stress in the larval stage did not alter the thermal tolerance of juveniles, and they could not acclimate to heat stress. As a result, the summer's heat waves could potentially threaten their resilience.

Acid times in physiology: A systematic review of the effects of ocean acidification on calcifying invertebrates

The reduction in seawater pH from rising levels of carbon dioxide (CO₂) in the oceans has been recognized as an important force shaping the future of marine ecosystems. Therefore, numerous studies have reported the effects of ocean acidification (OA) in different compartments of important animal groups, based on field and/or laboratory observations. Calcifying invertebrates have received considerable attention in recent years. In the present systematic review, we have summarized the physiological responses to OA in coral, echinoderm, mollusk, and crustacean species exposed to predicted ocean acidification conditions in the near future. The Scopus, Web of Science, and PubMed databases were used for the literature search, and 75 articles were obtained based on the inclusion criteria. Six main physiological responses have been reported after exposure to low pH. Growth (21.6%), metabolism (20.8%), and acid-base balance (17.6%) were the most frequent among the phyla, while calcification and growth were the physiological responses most affected by OA (>40%). Studies show that the reduction of pH in the aquatic environment, in general, supports the maintenance of metabolic parameters in invertebrates, with redistribution of energy to biological functions, generating limitations to calcification, which can have severe consequences for the health and survival of these organisms. It should be noted that the OA results are variable, with inter and/or intraspecific differences. In summary, this systematic review offers important scientific evidence for establishing paradigms in the physiology of climate change in addition to gathering valuable information on the subject and future research perspectives.

Monitoring the Health of Coastal Environments in the Pacific Region-A Review

Coastal areas provide important ecological services to populations accessing, for example, tourism services, fisheries, minerals and petroleum. Coastal zones worldwide are exposed to multiple stressors that threaten the sustainability of receiving environments. Assessing the health of these valuable ecosystems remains a top priority for environmental managers to ensure the key stressor sources are identified and their impacts minimized. The objective of this review was to provide an overview of current coastal environmental monitoring frameworks in the Asia-Pacific region. This large geographical area includes many countries with a range of climate types, population densities and land uses. Traditionally, environmental monitoring frameworks have been based on chemical criteria set against guideline threshold levels. However, regulatory organizations are increasingly promoting the incorporation of biological effects-based data in their decision-making processes. Using a range of examples drawn from across the region, we provide a synthesis of the major approaches currently being applied to examine coastal health in China, Japan, Australia and New Zealand. In addition, we discuss some of the challenges and investigate potential solutions for improving traditional lines of evidence, including the coordination of regional monitoring programs, the implementation of ecosystem-based management and the inclusion of indigenous knowledge and participatory processes in decision-making.

Reactions of juvenile coral to three years of consecutive thermal stress

As global temperatures continue to rise, corals are being exposed to increasing heat stress throughout their early life stages; however, the impact of this phenomenon is poorly understood. We exposed the reef-building coral Acropora tenuis juveniles to ∼26-28 °C (control) and ∼ 31 °C (heat stress) for one week per year over three consecutive years. In the first year of heat stress, >96 % of juveniles survived despite symbiotic algal densities in juvenile corals declining. In comparison, survival rates in the third year of heat stress declined to 50 %. Survival rates under natural conditions after stress also gradually decreased in the stressed groups. The rate in the reduction of survivorship was prominent in the consecutive thermally stressed groups (juveniles stressed twice in two years). Symbiotic algal density and photosynthetic activity (Fv/Fm) also declined in stressed juvenile groups. However, heat stress did not significantly affect the growth of juveniles. In the third year of heat stress, temperature negatively affected the physiology of juveniles in terms of survivorship, brightness (an indicator of bleaching), symbiotic algal density, and photosynthetic efficiency. Stress across consecutive years appeared to cause the survivorship of juvenile corals to decline, with three years of stress contributing to the severe decline of a reef. In conclusion, A. tenuis juveniles are not able to acclimatize to heat stress, with successive heat waves of <7 days in the summer potentially negatively affecting resilience.

The Evolution of Coral Reef under Changing Climate: A Scientometric Review

In this scientometric review, we employ the Web of Science Core Collection to assess current publications and research trends regarding coral reefs in relation to climate change. Thirty-seven keywords for climate change and seven keywords for coral reefs were used in the analysis of 7743 articles on coral reefs and climate change. The field entered an accelerated uptrend phase in 2016, and it is anticipated that this phase will last for the next 5 to 10 years of research publication and citation. The United States and Australia have produced the greatest number of publications in this field. A cluster (i.e., focused issue) analysis showed that coral bleaching dominated the literature from 2000 to 2010, ocean acidification from 2010 to 2020, and sea-level rise, as well as the central Red Sea (Africa/Asia), in 2021. Three different types of keywords appear in the analysis based on which are the (i) most recent (2021), (ii) most influential (highly cited), and (iii) mostly used (frequently used keywords in the article) in the field. The Great Barrier Reef, which is found in the waters of Australia, is thought to be the subject of current coral reef and climate change research. Interestingly, climate-induced temperature changes in "ocean warming" and "sea surface temperature" are the most recent significant and dominant keywords in the coral reef and climate change area.

Responses of medaka (Oryzias latipes) ammonia production and excretion to overcome acidified environments

Anthropogenic acidification of water is an on-going environmental disaster for freshwater fishes. Fishes rely on ammonia excretion to eliminate the excess acid and mitigate the harmful effects; however, it remains largely unknown how ammoniagenesis occurs and is coordinated with ammonia excretion upon acidic stress. Medaka (Oryzias latipes) was used to examine the effects of acidic stress on ammonia production and excretion. We reveal an undiscovered ammonia-producing cell type that is rich in glutaminase (GLS) and located adjacent to the ammonia-excreting ionocytes, Na⁺/H⁺ exchanger (NHE) cells, in the gills. The gills, comparing with other ammoniagenetic organs, is the quickest to respond to the acidic stress by triggering GLS-dependent ammonia production. The unique division of labor between GLS and NHE cells in the gills allows medaka to simultaneously upregulate GLS activity and ammonia excretion shortly after exposure to acidic environments. Pharmacological experiment with a GLS inhibitor abolished the activated ammonia excretion, further suggesting the essential role of the unique feature in the responses to acidic stress. Our study shades light on a novel physiological mechanism to timely and efficiently mitigate adverse effects of acidification, providing a new way to assess the impact of on-going environmental acidification on fish.

Acclimation potential of Acropora to mesophotic environment

Mesophotic coral ecosystems may serve as a refuge for reef-building corals to survive the ongoing climate change. Distribution of coral species changes during larval dispersal. However, the acclimation potential in the early life stages of corals at different depths is unknown. This study investigated the acclimation potential of four shallow Acropora species at different depths via the transplantation of larvae and early polyps settled on tiles to 5, 10, 20, and 40 m depths. We then examined physiological parameters, such as size, survival, growth rate, and morphological characteristics. The survival and size of juveniles of A. tenuis and A. valida at 40 m depth were significantly higher than those at other depths. In contrast, A. digitifera and A. hyacinthus showed higher survival rates at shallow depths. The morphology (i.e., size of the corallites) also varied among the depths. Collectively, the shallow coral larvae and juveniles displayed substantial plasticity at depth.

Global diversity patterns of larger benthic foraminifera under future climate change

Global warming threatens the viability of tropical coral reefs and associated marine calcifiers, including symbiont-bearing larger benthic foraminifera (LBF). The impacts of current climate change on LBF are debated because they were particularly diverse and abundant during past warm periods. Studies on the responses of selected LBF species to changing environmental conditions reveal varying results. Based on a comprehensive review of the scientific literature on LBF species occurrences, we applied species distribution modeling using Maxent to estimate present-day and future species richness patterns on a global scale for the time periods 2040-2050 and 2090-2100. For our future projections, we focus on Representative Concentration Pathway 6.0 from the Intergovernmental Panel on Climate Change, which projects mean surface temperature changes of +2.2°C by the year 2100. Our results suggest that species richness in the Central Indo-Pacific is two to three times higher than in the Bahamian ecoregion, which we have identified as the present-day center of LBF diversity in the Atlantic. Our future predictions project a dramatic temperature-driven decline in low-latitude species richness and an increasing widening bimodal latitudinal pattern of species diversity. While the central Indo-Pacific, now the stronghold of LBF diversity, is expected to be most pushed outside of the currently realized niches of most species, refugia may be largely preserved in the Atlantic. LBF species will face large-scale non-analogous climatic conditions compared to currently realized climate space in the near future, as reflected in the extensive areas of extrapolation, particularly in the Indo-Pacific. Our study supports hypotheses that species richness and biogeographic patterns of LBF will fundamentally change under future climate conditions, possibly initiating a faunal turnover by the late 21st century.

Coral bleaching resistance variation is linked to differential mortality and skeletal growth during recovery

The prevalence of global coral bleaching has focused much attention on the possibility of interventions to increase heat resistance. However, if high heat resistance is linked to fitness tradeoffs that may disadvantage corals in other areas, then a more holistic view of heat resilience may be beneficial. In particular, overall resilience of a species to heat stress is likely to be the product of both resistance to heat and recovery from heat stress. Here, we investigate heat resistance and recovery among individual Acropora hyacinthus colonies in Palau. We divided corals into low, moderate, and high heat resistance categories based on the number of days (4-9) needed to reach significant pigmentation loss due to experimental heat stress. Afterward, we deployed corals back onto a reef in a common garden 6-month recovery experiment that monitored chlorophyll a, mortality, and skeletal growth. Heat resistance was negatively correlated with mortality during early recovery (0-1 month) but not late recovery (4-6 months), and chlorophyll a concentration recovered in heat-stressed corals by 1-month postbleaching. However, moderate-resistance corals had significantly greater skeletal growth than high-resistance corals by 4 months of recovery. High- and low-resistance corals on average did not exhibit skeletal growth within the observed recovery period. These data suggest complex tradeoffs may exist between coral heat resistance and recovery and highlight the importance of incorporating multiple aspects of resilience into future reef management programs.

Similarities in biomass and energy reserves among coral colonies from contrasting reef environments

Coral reefs are declining worldwide, yet some coral populations are better adapted to withstand reductions in pH and the rising frequency of marine heatwaves. The nearshore reef habitats of Palau, Micronesia are a proxy for a future of warmer, more acidic oceans. Coral populations in these habitats can resist, and recover from, episodes of thermal stress better than offshore conspecifics. To explore the physiological basis of this tolerance, we compared tissue biomass (ash-free dry weight cm^-2), energy reserves (i.e., protein, total lipid, carbohydrate content), and several important lipid classes in six coral species living in both offshore and nearshore environments. In contrast to expectations, a trend emerged of many nearshore colonies exhibiting lower biomass and energy reserves than colonies from offshore sites, which may be explained by the increased metabolic demand of living in a warmer, acidic, environment. Despite hosting different dinoflagellate symbiont species and having access to contrasting prey abundances, total lipid and lipid class compositions were similar in colonies from each habitat. Ultimately, while the regulation of colony biomass and energy reserves may be influenced by factors, including the identity of the resident symbiont, kind of food consumed, and host genetic attributes, these independent processes converged to a similar homeostatic set point under different environmental conditions.

Restoration and coral adaptation delay, but do not prevent, climate-driven reef framework erosion of an inshore site in the Florida Keys

For reef framework to persist, calcium carbonate production by corals and other calcifiers needs to outpace loss due to physical, chemical, and biological erosion. This balance is both delicate and dynamic and is currently threatened by the effects of ocean warming and acidification. Although the protection and recovery of ecosystem functions are at the center of most restoration and conservation programs, decision makers are limited by the lack of predictive tools to forecast habitat persistence under different emission scenarios. To address this, we developed a modelling approach, based on carbonate budgets, that ties species-specific responses to site-specific global change using the latest generation of climate models projections (CMIP6). We applied this model to Cheeca Rocks, an outlier in the Florida Keys in terms of high coral cover, and explored the outcomes of restoration targets scheduled in the coming 20 years at this site by the Mission: Iconic Reefs restoration initiative. Additionally, we examined the potential effects of coral thermal adaptation by increasing the bleaching threshold by 0.25, 0.5, 1 and 2˚C. Regardless of coral adaptative capacity or restoration, net carbonate production at Cheeca Rocks declines heavily once the threshold for the onset of annual severe bleaching is reached. The switch from net accretion to net erosion, however, is significantly delayed by mitigation and adaptation. The maintenance of framework accretion until 2100 and beyond is possible under a decreased emission scenario coupled with thermal adaptation above 0.5˚C. Although restoration initiatives increase reef accretion estimates, Cheeca Rocks will only be able to keep pace with future sea-level rise in a world where anthropogenic CO₂ emissions are reduced. Present results, however, attest to the potential of restoration interventions combined with increases in coral thermal tolerance to delay the onset of mass bleaching mortalities, possibly in time for a low-carbon economy to be implemented and complementary mitigation measures to become effective.

Short-term improvement of heat tolerance in naturally growing Acropora corals in Okinawa

Mass bleaching and subsequent mortality of reef corals by heat stress has increased globally since the late 20th century, due to global warming. Some experimental studies have reported that corals may increase heat tolerance for short periods, but only a few such studies have monitored naturally-growing colonies. Therefore, we monitored the survival, growth, and bleaching status of Acropora corals in fixed plots by distinguishing individual colonies on a heat-sensitive reef flat in Okinawa, Japan. The level of heat stress, assessed by the modified version of degree heating week duration in July and August, when the seawater temperature was the highest, was minimally but significantly higher in 2017 than in 2016; however, the same colonies exhibited less bleaching and mortality in 2017 than in 2016. Another study conducted at the same site showed that the dominant unicellular endosymbiotic algal species did not change before and after the 2016 bleaching, indicating that shifting and switching of the Symbiodiniaceae community did not contribute to improved heat tolerance. Colonies that suffered from partial mortality in 2016 were completely bleached at higher rates in 2017 than those without partial mortality in 2016. The present results suggest that either genetic or epigenetic changes in coral hosts and/or algal symbionts, or the shifting or switching of microbes other than endosymbionts, may have improved coral holobiont heat tolerance.

Integrative Application of Transcriptomics and Metabolomics Provides Insights into Unsynchronized Growth in Sea Cucumber (Stichopus monotuberculatus)

Ever-increasing consumer demand for sea cucumbers mainly leads to huge damage to wild sea cucumber resources, including Stichopus monotuberculatus, which in turn exerts negative impacts on marine environments due to the lack of ecological functions performed by sea cucumbers. Aquaculture of sea cucumbers is an effective way to meet consumer demand and restore their resources. Unsynchronous growth is a prominent problem in the aquaculture of sea cucumbers which has concealed unelucidated molecular mechanisms until now. In this study, we carried out an integrative analysis of transcriptomics and metabolomics on fast-growing (SMF) and slow-growing (SMS) groups of S. monotuberculatus cultured in the same environmental conditions. The results revealed that a total of 2054 significantly differentially expressed genes (DEGs) were identified, which are mainly involved in fat digestion and absorption, histidine metabolism, arachidonic acid metabolism, and glutathione metabolism. 368 differential metabolites (DMs) were screened out between the SMF group and the SMS group; these metabolites are mainly involved in glycerophospholipid metabolism, purine metabolism, biosynthesis of unsaturated fatty acids, pyrimidine metabolism, arachidonic acid metabolism, and other metabolic pathways. The integrative analysis of transcriptomics and metabolomics of S. monotuberculatus suggested that the SMF group had a higher capacity for lipid metabolism and protein synthesis, and had a more frequent occurrence of apoptosis events, which are likely to be related to coping with environmental stresses. The results of this study provide potential values for the aquaculture of sea cucumbers which may promote their resource enhancement.

Bioaccumulation and trophic transfer of PAHs in tropical marine food webs from coral reef ecosystems, the South China Sea: Compositional pattern, driving factors, ecological aspects, and risk assessment

Multiple environmental pressures caused by global warming and human activities have aroused widespread concern about PAHs pollution in tropical marine coral reef regions (CRRs). However, the trophodynamics of PAHs in the food webs of the CRRs and the related influence factors have not been reported. This study investigated the occurrence, trophic amplification, and transmission of PAHs in various organisms selecting between at least representative species for each level in CRRs of the South China Sea (SCS); revealed their driving mechanisms; and explored the trophodynamics of PAHs in the food web of the coral reef ecosystem. Results showed that more PAHs can be accumulated in the mantle tissue of Tridacnidae, and the proportion of mantle tissue of Tridacnidae increases with the increase of latitude (y = 0.01x + 0.17, R² = 0.49, p < 0.05). Latitude drives the differential occurrence level and bioaccumulation of PAHs in tropical marine organisms, and also affects the trophodynamics of PAHs in aquatic ecosystem food webs. PAHs undergo trophic amplification in the food webs of tropical marine ecosystems represented by coral reefs, thus further aggravating the negative environmental impact on coral reef ecosystems. The cancer risk caused by accidental ingestion of PAHs by humans through consumption of seafood in CRRs is very low, but we should be alert to the biomagnification effect of PAHs.

Assessing the potential for demographic restoration and assisted evolution to build climate resilience in coral reefs

Interest is growing in developing conservation strategies to restore and maintain coral reef ecosystems in the face of mounting anthropogenic stressors, particularly climate warming and associated mass bleaching events. One such approach is to propagate coral colonies ex situ and transplant them to degraded reef areas to augment habitat for reef-dependent fauna, prevent colonization from spatial competitors, and enhance coral reproductive output. In addition to such "demographic restoration" efforts, manipulating the thermal tolerance of outplanted colonies through assisted relocation, selective breeding, or genetic engineering is being considered for enhancing rates of evolutionary adaptation to warming. Although research into such "assisted evolution" strategies has been growing, their expected performance remains unclear. We evaluated the potential outcomes of demographic restoration and assisted evolution in climate change scenarios using an eco-evolutionary simulation model. We found that supplementing reefs with pre-existing genotypes (demographic restoration) offers little climate resilience benefits unless input levels are large and maintained for centuries. Supplementation with thermally resistant colonies was successful at improving coral cover at lower input levels, but only if maintained for at least a century. Overall, we found that, although demographic restoration and assisted evolution have the potential to improve long-term coral cover, both approaches had a limited impact in preventing severe declines under climate change scenarios. Conversely, with sufficient natural genetic variance and time, corals could readily adapt to warming temperatures, suggesting that restoration approaches focused on building genetic variance may outperform those based solely on introducing heat-tolerant genotypes.

Indications of symbiotic state influencing melanin-synthesis immune response in the facultative coral Astrangia poculata

Increased ocean warming is causing detrimental impacts to tropical corals worldwide. Compounding the effects of heat stress, incidences of tropical coral disease have risen concurrently. While tropical coral responses to these impacts are well studied, temperate coral responses remain largely unknown. The present study focused on the immune response of the temperate coral Astrangia poculata to increased temperature and disease. Symbiotic and aposymbiotic A. poculata were collected from Narragansett Bay, Rhode Island (USA) in summer and winter seasons and exposed to control (18°C) versus elevated temperatures (26°C) in the presence of an immune stimulant (i.e. lipopolysaccharide) for a 12 h period. Prophenoloxidase (PPO) and melanin concentrations from the melanin-synthesis pathway were assessed via spectrophotometry to examine immune responses. While PPO measurements were higher on average in symbiotic corals compared with aposymbiotic corals, temperature and season did not significantly affect this metric. Melanin was significantly higher in symbiotic compared to aposymbiotic corals, implying that symbiotic state may be important for melanin-synthesis response. Conversely, melanin as an immune response may be of less importance in aposymbiotic A. poculata due to the potential capacity of other immune responses in this species. In addition, differences in resource allocation to immune investment as a result of symbiosis is plausible given melanin production observed within the present study. However, thermal stressors may reduce the overall influence of symbiosis on melanin production. Future studies should build upon these results to further understand the entirety of innate immunity responses in temperate coral species.

Antifouling coatings can reduce algal growth while preserving coral settlement

In the early stages after larval settlement, coral spat can be rapidly overgrown and outcompeted by algae, reducing overall survival for coral reef replenishment and supply for restoration programs. Here we investigated three antifouling (AF) coatings for their ability to inhibit algal fouling on coral settlement plugs, a commonly-used restoration substrate. Plugs were either fully or partially coated with the AF coatings and incubated in mesocosm systems with partial recirculation for 37 days to track fouling succession. In addition, settlement of Acropora tenuis larvae was measured to determine whether AF coatings were a settlement deterrent. Uncoated control plugs became heavily fouled, yielding only 4–8% bare substrate on upper surfaces after 37 days. During this period, an encapsulated dichlorooctylisothiazolinone (DCOIT)-coating was most effective in reducing fouling, yielding 61–63% bare substrate. Antiadhesive and cerium dioxide (CeO_2−x) nanoparticle (NP) coatings were less effective, yielding 11–17% and 2% bare substrate, respectively. Average settlement of A. tenuis larvae on the three types of AF-coated plugs did not statistically differ from settlement on uncoated controls. However, settlement on the NP-coating was generally the highest and was significantly higher than settlement found on the antiadhesive- and DCOIT-coating. Furthermore, on plugs only partially-covered with AF coatings, larval settlement on coated NP- areas was significantly higher than settlement on coated antiadhesive- and DCOIT-areas. These results demonstrate that AF coatings can reduce fouling intensity on biologically-relevant timescales while preserving robust levels of coral settlement. This represents an important step towards reducing fine-scale competition with benthic fouling organisms in coral breeding and propagation.

Cascading effects of climate change on recreational marine flats fishes and fisheries

Tropical and subtropical coastal flats are shallow regions of the marine environment at the intersection of land and sea. These regions provide myriad ecological goods and services, including recreational fisheries focused on flats-inhabiting fishes such as bonefish, tarpon, and permit. The cascading effects of climate change have the potential to negatively impact coastal flats around the globe and to reduce their ecological and economic value. In this paper, we consider how the combined effects of climate change, including extremes in temperature and precipitation regimes, sea level rise, and changes in nutrient dynamics, are causing rapid and potentially permanent changes to the structure and function of tropical and subtropical flats ecosystems. We then apply the available science on recreationally targeted fishes to reveal how these changes can cascade through layers of biological organization-from individuals, to populations, to communities-and ultimately impact the coastal systems that depend on them. We identify critical gaps in knowledge related to the extent and severity of these effects, and how such gaps influence the effectiveness of conservation, management, policy, and grassroots stewardship efforts.

Unraveling Moreton Bay reef history: An urban high-latitude setting for coral development

High-latitude habitats have become increasingly recognized as a potential climate refuge for coral communities, supporting both tropical and sub-tropical corals. Despite the increasing interest in the ecology of high-latitude corals, our current knowledge of their temporal dynamics is limited, especially within urbanized settings. Here, we examined the entire history of a high-latitude coral reef ecosystem in an urbanized setting. We surveyed Holocene fossil and modern coral communities along a water quality gradient in Moreton Bay, southeast Queensland, Australia, representing near-river (Wellington Point), intermediate (Peel Island) and near-oceanic (Myora Reef) environmental conditions. Reef accretion occurred during three discrete episodes from 7,400 to 5,800, 4,900 to 3,000, and 2,100 to 300 years BP, each separated by roughly 1,000-year hiatuses, where conditions were probably not favorable enough for reef accretion to occur. Episodic reef initiation and termination suggests strong environmental controls over reef development. Eastern Australian Holocene reef growth and cessation has been linked previously to sea level fluctuations and climatic regimes (e.g., ENSO). Within each reef building episode, there were few changes in coral assemblages over time. The fast growing and branching Acropora had a relative abundance greater than 90% in ten of the 13 sediment cores and all the submerged terrace excavations. However, substantial modification of adjacent coastal catchments from European colonization in the mid 1800’s resulted in increased sediment and nutrient discharge into the bay. This perturbation coincided with a greater abundance of stress-tolerant coral species (e.g., Dipsastraea, Goniastrea, and Goniopora) and the near extirpation of Acropora in the modern coral communities of near-river and intermediate sites due to poor water quality. In contrast, the modern coral assemblage at the near-oceanic site (Myora Reef) continues to be dominated by Acropora, likely due to the consistent oceanic input, resulting in lower sediment loading and higher water quality. In order for conditions for reef growth to improve, especially within the near-river portions of the bay, further sediment and nutrient runoff from anthropogenic land-use changes need to be mitigated. Given the historical abundance of Acropora, we recommend this genus be used as an indicator of natural resource management success in the bay.

Viable protoplast formation of the coral endosymbiont alga Symbiodinium spp. in a microfluidics platform

Symbiodiniaceae is an important dinoflagellate family which lives in endosymbiosis with reef invertebrates, including coral polyps, making them central to the holobiont. With coral reefs currently under extreme threat from climate change, there is a pressing need to improve our understanding on the stress tolerance and stress avoidance mechanisms of Symbiodinium spp. Reactive oxygen species (ROS) such as singlet oxygen are central players in mediating various stress responses; however, the detection of ROS using specific dyes is still far from definitive in intact Symbiodinium cells due to the hindrance of uptake of certain fluorescent dyes because of the presence of the cell wall. Protoplast technology provides a promising platform for studying oxidative stress with the main advantage of removed cell wall, however the preparation of viable protoplasts remains a significant challenge. Previous studies have successfully applied cellulose-based protoplast preparation in Symbiodiniaceae; however, the protoplast formation and regeneration process was found to be suboptimal. Here, we present a microfluidics-based platform which allowed protoplast isolation from individually trapped Symbiodinium cells, by using a precisely adjusted flow of cell wall digestion enzymes (cellulase and macerozyme). Trapped single cells exhibited characteristic changes in their morphology, cessation of cell division and a slight decrease in photosynthetic activity during protoplast formation. Following digestion and transfer to regeneration medium, protoplasts remained photosynthetically active, regrew cell walls, regained motility, and entered exponential growth. Elevated flow rates in the microfluidic chambers resulted in somewhat faster protoplast formation; however, cell wall digestion at higher flow rates partially compromised photosynthetic activity. Physiologically competent protoplasts prepared from trapped cells in microfluidic chambers allowed for the first time the visualization of the intracellular localization of singlet oxygen (using Singlet Oxygen Sensor Green dye) in Symbiodiniaceae, potentially opening new avenues for studying oxidative stress.

Photophysiological response of Symbiodiniaceae single cells to temperature stress

Photosynthetic dinoflagellates in the family Symbiodiniaceae engage in symbiosis with scleractinian corals. As coral ‘bleaching’ is partly governed by the thermal sensitivity of different Symbiodiniaceae lineages, numerous studies have investigated their temperature sensitivity. However, the systematic identification of single-cells with increased temperature resistance among these dinoflagellates has remained inaccessible, mostly due to a lack of technologies operating at the microscale. Here, we employed a unique combination of microfluidics, miniaturized temperature control, and chlorophyll fluorometry to characterize the single-cell heterogeneity among five representative species within the Symbiodiniaceae family under temperature stress. We monitored single-cell maximum quantum yields (F_v/F_m) of photosystem (PS) II under increasing temperature stress (22‒39 °C, + 1 °C every 15 min), and detected a significant F_v/F_m reduction at lineage-specific temperatures ranging from 28 °C to 34 °C alongside a 40- to 180- fold increase in intraspecific heterogeneity under elevated temperatures (>31 °C). We discovered that the initial F_v/F_m of a cell could predict the same cell’s ability to perform PSII photochemistry under moderate temperature stress (<32 °C), suggesting its use as a proxy for measuring the thermal sensitivity among Symbiodiniaceae. In combination, our study highlights the heterogeneous thermal sensitivity among photosynthetic Symbiodiniaceae and adds critical resolution to our understanding of temperature-induced coral bleaching.

Assessing the vulnerability of marine life to climate change in the Pacific Islands region

Our changing climate poses growing challenges for effective management of marine life, ocean ecosystems, and human communities. Which species are most vulnerable to climate change, and where should management focus efforts to reduce these risks? To address these questions, the National Oceanic and Atmospheric Administration (NOAA) Fisheries Climate Science Strategy called for vulnerability assessments in each of NOAA’s ocean regions. The Pacific Islands Vulnerability Assessment (PIVA) project assessed the susceptibility of 83 marine species to the impacts of climate change projected to 2055. In a standard Rapid Vulnerability Assessment framework, this project applied expert knowledge, literature review, and climate projection models to synthesize the best available science towards answering these questions. Here we: (1) provide a relative climate vulnerability ranking across species; (2) identify key attributes and factors that drive vulnerability; and (3) identify critical data gaps in understanding climate change impacts to marine life. The invertebrate group was ranked most vulnerable and pelagic and coastal groups not associated with coral reefs were ranked least vulnerable. Sea surface temperature, ocean acidification, and oxygen concentration were the main exposure drivers of vulnerability. Early Life History Survival and Settlement Requirements was the most data deficient of the sensitivity attributes considered in the assessment. The sensitivity of many coral reef fishes ranged between Low and Moderate, which is likely underestimated given that reef species depend on a biogenic habitat that is extremely threatened by climate change. The standard assessment methodology originally developed in the Northeast US, did not capture the additional complexity of the Pacific region, such as the diversity, varied horizontal and vertical distributions, extent of coral reef habitats, the degree of dependence on vulnerable habitat, and wide range of taxa, including data-poor species. Within these limitations, this project identified research needs to sustain marine life in a changing climate.