The future of resilience-based management in coral reef ecosystems

Fostering marine resilience through the reduction of anthropogenic pressures in temperate rocky reefs

Resilience is vital for maintaining the health of temperate coastal systems, especially in the Anthropocene era, where anthropogenic pressures such as pollution, physical impacts, and overfishing pose significant threats. However, the scarcity of studies addressing marine resilience hampers its effective management. To address this issue, we evaluated the resilience of 300 temperate rocky reefs situated in Southern Europe, considering biological, environmental, and anthropogenic factors. We identified 43 top resilient areas recommended for conservation and 39 bottom resilient areas that could benefit from reducing anthropogenic pressures. Given that our findings suggest that anthropogenic pressures unequally influence the resilience of bottom resilient areas, we followed their decreasing order of influence to simulate five management scenarios based on the cumulative reduction of these pressures. While different percentages of reduction in anthropogenic pressures were necessary to significantly enhance resilience in each scenario, we found that, regardless of the approach taken, a comparable percentage of bottom resilient areas-ranging from 17 % to 23 %-could be reclassified as moderate resilient areas. By advancing resilience knowledge in temperate rocky reefs, this research underscores the important role that reducing anthropogenic pressures plays in enhancing resilience but also provides valuable insights for their strategic management.

Coastal seawater turbidity and thermal stress control growth of reef-building Porites spp. corals in Fiji

Nearshore reefs, at the interface of land-sea interactions, provide essential ecosystem services, but are susceptible to multiple global and local stressors. These stressors can detrimentally impact coral growth and the continuity of the reef framework. Here, we analyse coral growth records (1998 - 2016) of massive Porites spp. colonies from nearshore reefs in Fiji. Our aim is to assess the role of thermal stress and turbidity on coral growth across a range of environments. Our findings reveal a negative linear relationship between linear extension and seawater turbidity across locations (GLM, R2 = 0.42, p < 0.001), indicating that average coral growth is significantly influenced by local environmental conditions. On interannual timescales, all locations experienced a 14% to 30% decrease in linear extension in response to acute thermal stress during the 2013 - 2016 period. This finding highlights the existence of compounding effects between water quality and thermal stress. We suggest that inshore, long-lived massive hard corals in areas of high turbidity are more vulnerable to increasing SSTs due to an already reduced mean growth. Integrated management strategies in these regions that considers managing for multiple, interacting local stressors are warranted to enhance resilience.

Metabolic Shifts and Muscle Remodeling as Pro-Survival and Energy Compensation Strategies in Photosymbiotic Giant Clams after Bleaching

Tropical photosymbiotic giant clams are increasingly threatened by climate change, leading to widespread bleaching. Decline in density of symbionts caused mortality events in symbiotic organisms; however, giant clams appear to exhibit prior survival capacity against these detrimental effects. It remains unclear whether giant clams can mitigate the adverse impacts of bleaching. Herein, we found that bleaching events after chronic heat stress induce remarkable changes and remodeling in symbiotic tissue of the giant clam Tridacna crocea. The density and structure of unique muscle fibers with high collagen content, observed in siphonal mantle of these animals, were negatively altered after heat stress. These changes were associated with a metabolic shift from carbohydrates and fatty acids to amino acids as the breakdown of collagen-rich muscle fibers can partially compensate for energy loss during bleaching. Such a shift was proposed to be regulated by AMP-activated protein kinase (AMPK) signaling and FoxO-atrogin pathways. Overall, our study highlights a pro-survival mechanism in giant clams through plastic regulation, which likely contributes to their relatively high environmental resilience during bleaching.

Conceptualizing social risk in relation to climate change and assisted ecosystem adaptation

Realizing positive social and environmental outcomes from assisted ecosystem adaptation requires the management of complex, uncertain, and ambiguous risks. Using assisted coral reef adaptation as a case study, this article presents a conceptual framework that defines social impacts as the physical and cognitive consequences for people of planned intervention and social risks as potential impacts transformed into objects of management through assessment and governance. Reflecting on its multiple uses in the literature, we consider "social risk" in relation to risks to individuals and communities, risks to First Peoples, risks to businesses or project implementation, possibilities for amplified social vulnerability, and risk perceptions. Although much of this article is devoted to bringing clarity to the different ways in which social risk manifests and to the multiple characters of risk and uncertainty, it is apparent that risk governance itself must be an inherently integrative and social process.

Patterns and implications of spatial covariation in herbivore functions on resilience of coral reefs

Persistent shifts to undesired ecological states, such as shifts from coral to macroalgae, are becoming more common. This highlights the need to understand processes that can help restore affected ecosystems. Herbivory on coral reefs is widely recognized as a key interaction that can keep macroalgae from outcompeting coral. Most attention has been on the role 'grazing' herbivores play in preventing the establishment of macroalgae, while less research has focused on the role of 'browsers' in extirpating macroalgae. Here we explored patterns, environmental correlates and state shift consequences of spatial co-variation in grazing and browsing functions of herbivorous fishes. Grazing and browsing rates were not highly correlated across 20 lagoon sites in Moorea, French Polynesia, but did cluster into 3 (of 4) combinations of high and low consumption rates (no site had low grazing but high browsing). Consumption rates were not correlated with grazer or browser fish biomass, but both were predicted by specific environmental variables. Experiments revealed that reversibility of a macroalgal state shift was strongly related to spatial variation in browsing intensity. Our findings provide insights and simple diagnostic tools regarding heterogeneity in top-down forcing that influences the vulnerability to and reversibility of shifts to macroalgae on coral reefs.

The Young and the Resilient: Investigating Coral Thermal Resilience in Early Life Stages

Global ocean warming is affecting keystone species distributions and fitness, resulting in the degradation of marine ecosystems. Coral reefs are one of the most diverse and productive marine ecosystems. However, reef-building corals, the foundational taxa of coral reef ecosystems, are severely threatened by thermal stress. Models predict 40-80% of global coral cover will be lost by 2100, which highlights the urgent need for widespread interventions to preserve coral reef functionality. There has been extensive research on coral thermal stress and resilience, but 95% of studies have focused on adult corals. It is necessary to understand stress during early life stages (larvae, recruits, and juveniles), which will better inform selective breeding programs that aim to replenish reefs with resilient stock. In this review, we surveyed the literature on coral thermal resilience in early life stages, and we highlight that studies have been conducted on relatively few species (commonly Acropora spp.) and in limited regions (mainly Australia). Reef-building coral management will be improved by comprehensively understanding coral thermal resilience and fitness across life stages, as well as in diverse species and regions.

How changes projected by climate models can inform climate adaptation and marine sanctuary management: A collaborative prototype methodology

Coral reefs are highly important ecosystems providing habitat for biodiverse marine life and numerous benefits for humans. However they face immense risks from climate change. To date, Representative Concentration Pathway (RCP) climate models have aided global discussions on possible policy responses to adapt to change, but tailored climate projections at a useful scale for environmental managers are often prohibitively expensive to produce. Our research addresses this problem by presenting a novel type of collaborative, participatory research that integrates 1) site specific climate metrics from the Community Earth System Model version 2 large ensemble (CESM2-LE), 2) ecosystem response models to determine Degree Heating Months and coral bleaching impacts, and 3) collaborative social science data from environmental manager engagement to see how managers in one of the most visited marine sanctuaries in the world are enacting adaptive governance, stewarding reefs through climate impacts of the future. Our research is valuable to decision-makers seeking opportunities for innovative policy responses to climate impacts focused on experimentation and dialogue.

Okeanomitos corallinicola gen. and sp. nov. (Nostocales, Cyanobacteria), a new toxic marine heterocyte-forming Cyanobacterium from a coral reef

Cyanobacterial mats supplanting coral and spreading coral diseases in tropical reefs, intensified by environmental shifts caused by human-induced pressures, nutrient enrichment, and global climate change, pose grave risks to the survival of coral ecosystems. In this study, we characterized Okeanomitos corallinicola gen. and sp. nov., a newly discovered toxic marine heterocyte-forming cyanobacterium isolated from a coral reef ecosystem of the South China Sea. Phylogenetic analysis, based on the 16S rRNA gene and the secondary structure of the 16S-23S rRNA intergenic region, placed this species in a clade distinct from closely related genera, that is, Sphaerospermopsis stricto sensu, Raphidiopsis, and Amphiheterocytum. The O. corallinicola is a marine benthic species lacking gas vesicles, distinguishing it from other members of the Aphanizomenonaceae family. The genome of O. corallinicola is large and exhibits diverse functional capabilities, potentially contributing to the resilience and adaptability of coral reef ecosystems. In vitro assays revealed that O. corallinicola demonstrates notable cytotoxic activity against various cancer cell lines, suggesting its potential as a source of novel anticancer compounds. Furthermore, the identification of residual saxitoxin biosynthesis function in the genome of O. corallinicola, a marine cyanobacteria, supports the theory that saxitoxin genes in cyanobacteria and dinoflagellates may have been horizontally transferred between them or may have originated from a shared ancestor. Overall, the identification and characterization of O. corallinicola provides valuable contributions to cyanobacterial taxonomy, offering novel perspectives on complex interactions within coral reef ecosystems.

Contributions of the IUCN Red List of Ecosystems to risk-based design and management of protected and conserved areas in Africa

Protected and conserved areas (PCAs) are key ecosystem management tools for conserving biodiversity and sustaining ecosystem services and social cobenefits. As countries adopt a 30% target for protection of land and sea under the Global Biodiversity Framework of the United Nations Convention on Biological Diversity, a critical question emerging is, which 30%? A risk-based answer to this question is that the 30% that returns the greatest reductions in risks of species extinction and ecosystem collapse should be protected. The International Union for Conservation of Nature (IUCN) Red List protocols provide practical methods for assessing these risks. All species, including humans, depend on the integrity of ecosystems for their well-being and survival. Africa is strategically important for ecosystem management due to convergence of high ecosystem diversity, intense pressures, and high levels of human dependency on nature. We reviewed the outcomes (e.g., applications of ecosystem red-list assessments to protected-area design, conservation planning, and management) of a symposium at the inaugural African Protected Areas Congress convened to discuss roles of the IUCN Red List of Ecosystems in the design and management of PCAs. Recent progress was made in ecosystem assessment, with 920 ecosystem types assessed against the IUCN Red List criteria across 21 countries. Although these ecosystems spanned a diversity of environments across the continent, the greatest thematic gaps were for freshwater, marine, and subterranean realms, and large geographic gaps existed in North Africa and parts of West and East Africa. Assessment projects were implemented by a diverse community of government agencies, nongovernmental organizations, and researchers. The assessments have influenced policy and management by informing extensions to and management of formal protected area networks supporting decision-making for sustainable development, and informing ecosystem conservation and threat abatement within boundaries of PCAs and in surrounding landscapes and seascapes. We recommend further integration of risk assessments in environmental policy and enhanced investment in ecosystem red-list assessment to fill current gaps.

Protecting Great Barrier Reef resilience through effective management of crown-of-thorns starfish outbreaks

Resilience-based management is essential to protect ecosystems in the Anthropocene. Unlike large-scale climate threats to Great Barrier Reef (GBR) corals, outbreaks of coral-eating crown-of-thorns starfish (COTS; Acanthaster cf. solaris) can be directly managed through targeted culling. Here, we evaluate the outcomes of a decade of strategic COTS management in suppressing outbreaks and protecting corals during the 4th COTS outbreak wave at reef and regional scales (sectors). We compare COTS density and coral cover dynamics during the 3rd and 4th outbreak waves. During the 4th outbreak wave, sectors that received limited to no culling had sustained COTS outbreaks causing significant coral losses. In contrast, in sectors that received timely and sufficient cull effort, coral cover increased substantially, and outbreaks were suppressed with COTS densities up to six-fold lower than in the 3rd outbreak wave. In the Townsville sector for example, despite exposure to comparable disturbance regimes during the 4th outbreak wave, effective outbreak suppression coincided with relative increases in sector-wide coral cover (44%), versus significant coral cover declines (37%) during the 3rd outbreak wave. Importantly, these estimated increases span entire sectors, not just reefs with active COTS control. Outbreaking reefs with higher levels of culling had net increases in coral cover, while the rate of coral loss was more than halved on reefs with lower levels of cull effort. Our results also indicate that outbreak wave progression to adjoining sectors has been delayed, probably via suppression of COTS larval supply. Our findings provide compelling evidence that proactive, targeted, and sustained COTS management can effectively suppress COTS outbreaks and deliver coral growth and recovery benefits at reef and sector-wide scales. The clear coral protection outcomes demonstrate the value of targeted manual culling as both a scalable intervention to mitigate COTS outbreaks, and a potent resilience-based management tool to "buy time" for coral reefs, protecting reef ecosystem functions and biodiversity as the climate changes.

Multi-Chemical Omics Analysis of the Symbiodiniaceae Durusdinium trenchii under Heat Stress

The urgency of responding to climate change for corals necessitates the exploration of innovative methods to swiftly enhance our understanding of crucial processes. In this study, we employ an integrated chemical omics approach, combining elementomics, metabolomics, and volatilomics methodologies to unravel the biochemical pathways associated with the thermal response of the coral symbiont, Symbiodiniaceae Durusdinium trenchii. We outline the complimentary sampling approaches and discuss the standardised data corrections used to allow data integration and comparability. Our findings highlight the efficacy of individual methods in discerning differences in the biochemical response of D. trenchii under both control and stress-inducing temperatures. However, a deeper insight emerges when these methods are integrated, offering a more comprehensive understanding, particularly regarding oxidative stress pathways. Employing correlation network analysis enhanced the interpretation of volatile data, shedding light on the potential metabolic origins of volatiles with undescribed functions and presenting promising candidates for further exploration. Elementomics proves to be less straightforward to integrate, likely due to no net change in elements but rather elements being repurposed across compounds. The independent and integrated data from this study informs future omic profiling studies and recommends candidates for targeted research beyond Symbiodiniaceae biology. This study highlights the pivotal role of omic integration in advancing our knowledge, addressing critical gaps, and guiding future research directions in the context of climate change and coral reef preservation.

Natural recovery of corals after severe disturbance

Ecosystem recovery from human-induced disturbances, whether through natural processes or restoration, is occurring worldwide. Yet, recovery dynamics, and their implications for broader ecosystem management, remain unclear. We explored recovery dynamics using coral reefs as a case study. We tracked the fate of 809 individual coral recruits that settled after a severe bleaching event at Lizard Island, Great Barrier Reef. Recruited Acropora corals, first detected in 2020, grew to coral cover levels that were equivalent to global average coral cover within just 2 years. Furthermore, we found that just 11.5 Acropora recruits per square meter were sufficient to reach this cover within 2 years. However, wave exposure, growth form and colony density had a marked effect on recovery rates. Our results underscore the importance of considering natural recovery in management and restoration and highlight how lessons learnt from reef recovery can inform our understanding of recovery dynamics in high-diversity climate-disturbed ecosystems.

Evidence for managing herbivores for reef resilience

Herbivore management is an important tool for resilience-based approaches to coral reef conservation, and evidence-based science is needed to enact successful management. We synthesized data from multiple monitoring programs in Hawai'i to measure herbivore biomass and benthic condition over a 10-year period preceding any major coral bleaching. We analysed data from 20 242 transects alongside data on 27 biophysical and human drivers and found herbivore biomass was highly variable throughout Hawai'i, with high values in remote locations and the lowest values near population centres. Both human and biophysical drivers explained variation in herbivore biomass, and among the human drivers both fishing and land-based pollution had negative effects on biomass. We also found evidence that herbivore functional group biomass is strongly linked to benthic condition, and that benthic condition is sensitive to changes in herbivore biomass associated with fishing. We show that when herbivore biomass is below 80% of potential biomass, benthic condition is predicted to decline. We also show that a range of management actions, including area-specific fisheries regulations and gear restrictions, can increase parrotfish biomass. Together, these results provide lines of evidence to support managing herbivores as an effective strategy for maintaining or bolstering reef resilience in a changing climate.

Genomic signatures of disease resistance in endangered staghorn corals

White band disease (WBD) has caused unprecedented declines in the Caribbean Acropora corals, which are now listed as critically endangered species. Highly disease-resistant Acropora cervicornis genotypes exist, but the genetic underpinnings of disease resistance are not understood. Using transmission experiments, a newly assembled genome, and whole-genome resequencing of 76 A. cervicornis genotypes from Florida and Panama, we identified 10 genomic regions and 73 single-nucleotide polymorphisms that are associated with disease resistance and that include functional protein-coding changes in four genes involved in coral immunity and pathogen detection. Polygenic scores calculated from 10 genomic loci indicate that genetic screens can detect disease resistance in wild and nursery stocks of A. cervicornis across the Caribbean.

Coral reefs benefit from reduced land-sea impacts under ocean warming

Coral reef ecosystems are being fundamentally restructured by local human impacts and climate-driven marine heatwaves that trigger mass coral bleaching and mortality1. Reducing local impacts can increase reef resistance to and recovery from bleaching2. However, resource managers lack clear advice on targeted actions that best support coral reefs under climate change3 and sector-based governance means most land- and sea-based management efforts remain siloed4. Here we combine surveys of reef change with a unique 20-year time series of land-sea human impacts that encompassed an unprecedented marine heatwave in Hawai'i. Reefs with increased herbivorous fish populations and reduced land-based impacts, such as wastewater pollution and urban runoff, had positive coral cover trajectories predisturbance. These reefs also experienced a modest reduction in coral mortality following severe heat stress compared to reefs with reduced fish populations and enhanced land-based impacts. Scenario modelling indicated that simultaneously reducing land-sea human impacts results in a three- to sixfold greater probability of a reef having high reef-builder cover four years postdisturbance than if either occurred in isolation. International efforts to protect 30% of Earth's land and ocean ecosystems by 2030 are underway5. Our results reveal that integrated land-sea management could help achieve coastal ocean conservation goals and provide coral reefs with the best opportunity to persist in our changing climate.

Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses

The dominant benthic primary producers in coral reef ecosystems are complex holobionts with diverse microbiomes and metabolomes. In this study, we characterize the tissue metabolomes and microbiomes of corals, macroalgae, and crustose coralline algae via an intensive, replicated synoptic survey of a single coral reef system (Waimea Bay, O'ahu, Hawaii) and use these results to define associations between microbial taxa and metabolites specific to different hosts. Our results quantify and constrain the degree of host specificity of tissue metabolomes and microbiomes at both phylum and genus level. Both microbiome and metabolomes were distinct between calcifiers (corals and CCA) and erect macroalgae. Moreover, our multi-omics investigations highlight common lipid-based immune response pathways across host organisms. In addition, we observed strong covariation among several specific microbial taxa and metabolite classes, suggesting new metabolic roles of symbiosis to further explore.

Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation

Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here we analyzed samples from the Tara Pacific Expedition (2016-2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals-Pocillopora meandrina, Porites lobata, and Millepora cf. platyphylla-across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data, we can show that despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.

A metric-based framework for climate-smart conservation planning

Climate change is already having profound effects on biodiversity, but climate change adaptation has yet to be fully incorporated into area-based management tools used to conserve biodiversity, such as protected areas. One main obstacle is the lack of consensus regarding how impacts of climate change can be included in spatial conservation plans. We propose a climate-smart framework that prioritizes the protection of climate refugia-areas of low climate exposure and high biodiversity retention-using climate metrics. We explore four aspects of climate-smart conservation planning: (1) climate model ensembles; (2) multiple emission scenarios; (3) climate metrics; and (4) approaches to identifying climate refugia. We illustrate this framework in the Western Pacific Ocean, but it is equally applicable to terrestrial systems. We found that all aspects of climate-smart conservation planning considered affected the configuration of spatial plans. The choice of climate metrics and approaches to identifying refugia have large effects in the resulting climate-smart spatial plans, whereas the choice of climate models and emission scenarios have smaller effects. As the configuration of spatial plans depended on climate metrics used, a spatial plan based on a single measure of climate change (e.g., warming) will not necessarily be robust against other measures of climate change (e.g., ocean acidification). We therefore recommend using climate metrics most relevant for the biodiversity and region considered based on a single or multiple climate drivers. To include the uncertainty associated with different climate futures, we recommend using multiple climate models (i.e., an ensemble) and emission scenarios. Finally, we show that the approaches we used to identify climate refugia feature trade-offs between: (1) the degree to which they are climate-smart, and (2) their efficiency in meeting conservation targets. Hence, the choice of approach will depend on the relative value that stakeholders place on climate adaptation. By using this framework, protected areas can be designed with improved longevity and thus safeguard biodiversity against current and future climate change. We hope that the proposed climate-smart framework helps transition conservation planning toward climate-smart approaches.

Impacts of marine debris on coral reef ecosystem: A review for conservation and ecological monitoring of the coral reef ecosystem

Coral reefs are the most spectacular underwater creation of nature. It enhances ecosystem functioning and marine biodiversity while also ensuring the livelihood of millions of coastal communities worldwide. Unfortunately, marine debris poses a serious threat to ecologically sensitive reef habitats and their associated organisms. Over the past decade, marine debris has been regarded as a major anthropogenic threat to marine ecosystems and gained scientific attention around the globe. However, the sources, types, abundance, distribution, and potential consequences of marine debris on reef ecosystems are hardly known. The goal of this review is to provide an overview of the current status of marine debris in various reef ecosystems across the world, with special emphasis on its sources, abundance, distribution, species impacted, major categories, potential impacts and management strategies. Furthermore, the adhesion mechanisms of microplastics to coral polyps, diseases caused by microplastics and are also highlighted.

Microbial Interactions with Dissolved Organic Matter Are Central to Coral Reef Ecosystem Function and Resilience

To thrive in nutrient-poor waters, coral reefs must retain and recycle materials efficiently. This review centers microbial processes in facilitating the persistence and stability of coral reefs, specifically the role of these processes in transforming and recycling the dissolved organic matter (DOM) that acts as an invisible currency in reef production, nutrient exchange, and organismal interactions. The defining characteristics of coral reefs, including high productivity, balanced metabolism, high biodiversity, nutrient retention, and structural complexity, are inextricably linked to microbial processing of DOM. The composition of microbes and DOM in reefs is summarized, and the spatial and temporal dynamics of biogeochemical processes carried out by microorganisms in diverse reef habitats are explored in a variety of key reef processes, including decomposition, accretion, trophictransfer, and macronutrient recycling. Finally, we examine how widespread habitat degradation of reefs is altering these important microbe-DOM interactions, creating feedbacks that reduce reef resilience to global change.

Post-bleaching alterations in coral reef communities

We explored the extent of post-bleaching impacts, caused by the 2014-2016 El Niño Southern Oscillation (ENSO) event, on benthic community structure (BCS) and herbivores (fish and sea urchins) on seven fringing reefs, with differing protection levels, in Zanzibar, Tanzania. Results showed post-bleaching alterations in BCS, with up to 68 % coral mortality and up to 48 % increase in turf algae cover in all reef sites. Herbivorous fish biomass increased after bleaching and was correlated with turf algae increase in some reefs, while the opposite was found for sea urchin densities, with significant declines and complete absence. The severity of the impact varied across individual reefs, with larger impact on the protected reefs, compared to the unprotected reefs. Our study provides a highly relevant reference point to guide future research and contributes to our understanding of post-bleaching impacts, trends, and evaluation of coral reef health and resilience in the region.

Review: An integrated framework for understanding ecological drought and drought resistance

Droughts are a frequent natural phenomenon that has amplified globally in the 21st century and are projected to become more common and extreme in the future. Consequently, this affects the progress of drought indices and frameworks to categorize drought conditions. Several drought-related indices and variables are required to capture different features of complex drought conditions. Therefore, we explained the signs of progress of ecological drought that were ecologically expressive to promote the integration between the research on and identification of water scarcity situations and analyzed different frameworks to synthesize the drought effects on species and ecosystems. Notably, we present an inclusive review of an integrated framework for an ecological drought. The ecological drought framework affords the advantage of improved methodologies for assessing ecological drought. This is supported by research on water-limited ecosystems that incorporated several drought-related elements and indicators to produce an integrated drought framework. In this framework, we combined multiple studies on drought recovery, early warning signs, and the effects of land management interferences, along with a schematic representation of a new extension of the framework into ecological systems, to contribute to the success and long-term sustainability of ecological drought adaptation, as well as on-the-ground examples of climate-informed ecological drought management in action for an integrated framework for ecological drought. This study provides an integrated approach to the understanding of ecological drought in line with accelerated scientific advancement to promote persistence and plan for a future that irretrievably exceeds the ecosystem thresholds and new multivariate drought indices.

Cold water and harmful algal blooms linked to coral reef collapse in the Eastern Tropical Pacific

Background

With conventional coral reef conservation methods proving ineffective against intensifying climate change, efforts have focussed on augmenting coral tolerance to warmer water-the primary driver of coral declines. We document coral cover and composition in relation to sea surface temperature (SST) over 25-years, of six marginal reefs in an upwelling area of Costa Rica's Eastern Tropical Pacific.

Methods

Using reef survey data and sea surface temperature (SST) dating back over 25-years, we document coral cover and composition of six marginal reefs in an upwelling area of Costa Rica's Eastern Tropical Pacific in relation to thermal highs and lows.

Results

A ubiquitous and catastrophic coral die-off event occurred in 2009, driven by SST minima and likely by the presence of extreme harmful algal blooms. Coral cover was dramatically reduced and coral composition shifted from dominant branching Pocillopora to massive Pavona, Porites, and Gardineroseris. The lack of coral recovery in the decade since indicates a breach in ecosystem tipping-point and highlights a need for resilience-based management (RBM) and restoration. We propose a locally tailored and globally scalable approach to coral reef declines that is founded in RBM and informed by coral health dynamics.

A roadmap to integrating resilience into the practice of coral reef restoration

Recent warm temperatures driven by climate change have caused mass coral bleaching and mortality across the world, prompting managers, policymakers, and conservation practitioners to embrace restoration as a strategy to sustain coral reefs. Despite a proliferation of new coral reef restoration efforts globally and increasing scientific recognition and research on interventions aimed at supporting reef resilience to climate impacts, few restoration programs are currently incorporating climate change and resilience in project design. As climate change will continue to degrade coral reefs for decades to come, guidance is needed to support managers and restoration practitioners to conduct restoration that promotes resilience through enhanced coral reef recovery, resistance, and adaptation. Here, we address this critical implementation gap by providing recommendations that integrate resilience principles into restoration design and practice, including for project planning and design, coral selection, site selection, and broader ecosystem context. We also discuss future opportunities to improve restoration methods to support enhanced outcomes for coral reefs in response to climate change. As coral reefs are one of the most vulnerable ecosystems to climate change, interventions that enhance reef resilience will help to ensure restoration efforts have a greater chance of success in a warming world. They are also more likely to provide essential contributions to global targets to protect natural biodiversity and the human communities that rely on reefs.

Coral reefs: The good and not so good news with future bright and dark spots for coral reefs through climate change

COMMENTARY ON Present and future bright and dark spots for coral reefs through climate change. This is a commentary on Sully et al., 2022, https://doi.org/10.1111/gcb.16083

Trait groups as management entities in a complex, multispecies reef fishery

Localized stressors compound the ongoing climate-driven decline of coral reefs, requiring natural resource managers to work with rapidly shifting paradigms. Trait-based adaptive management (TBAM) is a new framework to help address changing conditions by choosing and implementing management actions specific to species groups that share key traits, vulnerabilities, and management responses. In TBAM maintenance of functioning ecosystems is balanced with provisioning for human subsistence and livelihoods. We first identified trait-based groups of food fish in a Pacific coral reef with hierarchical clustering. Positing that trait-based groups performing comparable functions respond similarly to both stressors and management actions, we ascertained biophysical and socioeconomic drivers of trait-group biomass and evaluated their vulnerabilities with generalized additive models. Clustering identified 7 trait groups from 131 species. Groups responded to different drivers and displayed divergent vulnerabilities; human activities emerged as important predictors of community structuring. Biomass of small, solitary reef-associated species increased with distance from key fishing ports, and large, solitary piscivores exhibited a decline in biomass with distance from a port. Group biomass also varied in response to different habitat types, the presence or absence of reported dynamite fishing activity, and exposure to wave energy. The differential vulnerabilities of trait groups revealed how the community structure of food fishes is driven by different aspects of resource use and habitat. This inherent variability in the responses of trait-based groups presents opportunities to apply selective TBAM strategies for complex, multispecies fisheries. This approach can be widely adjusted to suit local contexts and priorities.

Marine protected areas do not buffer corals from bleaching under global warming

BACKGROUND

The rising temperature of the oceans has been identified as the primary driver of mass coral reef declines via coral bleaching (expulsion of photosynthetic endosymbionts). Marine protected areas (MPAs) have been implemented throughout the oceans with the aim of mitigating the impact of local stressors, enhancing fish biomass, and sustaining biodiversity overall. In coral reef regions specifically, protection from local stressors and the enhanced ecosystem function contributed by MPAs are expected to increase coral resistance to global-scale stressors such as marine heatwaves. However, MPAs still suffer from limitations in design, or fail to be adequately enforced, potentially reducing their intended efficacy. Here, we address the hypothesis that the local-scale benefits resulting from MPAs moderate coral bleaching under global warming related stress.

RESULTS

Bayesian analyses reveal that bleaching is expected to occur in both larger and older MPAs when corals are under thermal stress from marine heatwaves (quantified as Degree Heating Weeks, DHW), but this is partially moderated in comparison to the effects of DHW alone. Further analyses failed to identify differences in bleaching prevalence in MPAs relative to non-MPAs for coral reefs experiencing different levels of thermal stress. Finally, no difference in temperatures where bleaching occurs between MPA and non-MPA sites was found.

CONCLUSIONS

Our findings suggest that bleaching is likely to occur under global warming regardless of protected status. Thus, while protected areas have key roles for maintaining ecosystem function and local livelihoods, combatting the source of global warming remains the best way to prevent the decline of coral reefs via coral bleaching.

A tale of two reef systems: Local conditions, disturbances, coral life histories, and the climate catastrophe

Coral reefs have evolved over millennia to survive disturbances. Yet, in just a few decades chronic local pressures and the climate catastrophe have accelerated so quickly that most coral reefs are now threatened. Rising ocean temperatures and recurrent bleaching pose the biggest threat, affecting even remote and well-managed reefs on global scales. We illustrate how coral bleaching is altering reefs by contrasting the dynamics of adjacent reef systems over more than two decades. Both reef systems sit near the edge of northwest Australia's continental shelf, have escaped chronic local pressures and are regularly affected by tropical storms and cyclones. The Scott reef system has experienced multiple bleaching events, including mass bleaching in 1998 and 2016, from which it is unlikely to fully recover. The Rowley Shoals has maintained a high cover and diversity of corals and has not yet been impacted by mass bleaching. We show how the dynamics of both reef systems were driven by a combination of local environment, exposure to disturbances and coral life history traits, and consider future shifts in community structure with ongoing climate change. We then demonstrate how applying knowledge of community dynamics at local scales can aid management strategies to slow the degradation of coral reefs until carbon emissions and other human impacts are properly managed.

Contingency planning for coral reefs in the Anthropocene; The potential of reef safe havens

Reducing the global reliance on fossil fuels is essential to ensure the long-term survival of coral reefs, but until this happens, alternative tools are required to safeguard their future. One emerging tool is to locate areas where corals are surviving well despite the changing climate. Such locations include refuges, refugia, hotspots of resilience, bright spots, contemporary near-pristine reefs, and hope spots that are collectively named reef 'safe havens' in this mini-review. Safe havens have intrinsic value for reefs through services such as environmental buffering, maintaining near-pristine reef conditions, or housing corals naturally adapted to future environmental conditions. Spatial and temporal variance in physicochemical conditions and exposure to stress however preclude certainty over the ubiquitous long-term capacity of reef safe havens to maintain protective service provision. To effectively integrate reef safe havens into proactive reef management and contingency planning for climate change scenarios, thus requires an understanding of their differences, potential values, and predispositions to stress. To this purpose, I provide a high-level review on the defining characteristics of different coral reef safe havens, how they are being utilised in proactive reef management and what risk and susceptibilities they inherently have. The mini-review concludes with an outline of the potential for reef safe haven habitats to support contingency planning of coral reefs under an uncertain future from intensifying climate change.

A portfolio of climate-tailored approaches to advance the design of marine protected areas in the Red Sea

Intensified coastal development is compromising the health and functioning of marine ecosystems. A key example of this is the Red Sea, a biodiversity hotspot subjected to increasing local human pressures. While some marine-protected areas (MPAs) were placed to alleviate these stressors, it is unclear whether these MPAs are managed or enforced, thus providing limited protection. Yet, most importantly, MPAs in the Red Sea were not designed using climate considerations, likely diminishing their effectiveness against global stressors. Here, we propose to tailor the design of MPAs in the Red Sea by integrating approaches to enhance climate change mitigation and adaptation. First, including coral bleaching susceptibility could produce a more resilient network of MPAs by safeguarding reefs from different thermal regions that vary in spatiotemporal bleaching responses, reducing the risk that all protected reefs will bleach simultaneously. Second, preserving the basin-wide genetic connectivity patterns that are assisted by mesoscale eddies could further ensure recovery of sensitive populations and maintain species potential to adapt to environmental changes. Finally, protecting mangrove forests in the northern and southern Red Sea that act as major carbon sinks could help offset greenhouse gas emissions. If implemented with multinational cooperation and concerted effort among stakeholders, our portfolio of climate-tailored approaches may help build a network of MPAs in the Red Sea that protects more effectively its coastal resources against escalating coastal development and climate instability. Beyond the Red Sea, we anticipate this study to serve as an example of how to improve the utility of tropical MPAs as climate-informed conservation tools.

A Participatory Approach for Balancing Accuracy and Complexity in Modeling Resilience and Robustness

Robustness and resilience are widely used in the biological sciences and related disciplines to describe how systems respond to change. Robustness is the ability to tolerate change without adapting or moving to another state. Resilience refers to the ability for a system to sustain a perturbation and maintain critical functions. Robustness and resilience transcend levels of biological organization, though they do not scale directly across levels. We live in an era of novel stressors and unprecedented change, including climate change, emerging environmental contaminants, and changes to earth's biogeochemical and hydrological cycles. We envision a common framework for developing models to predict the robustness and resilience of biological functions associated with complex systems that can transcend disciplinary boundaries. Conceptual and quantitative models of robustness and resilience must consider cross-scale interactions of potentially infinite complexity, but it is impossible to capture everything within a single model. Here, we discuss the need to balance accuracy and complexity when designing models, data collection, and downstream analyses to study robustness and resilience. We also consider the difficulties in defining the spatiotemporal domain when studying robustness and resilience as an emergent property of a complex system. We suggest a framework for implementing transdisciplinary research on robustness and resilience of biological systems that draws on participatory stakeholder engagement methods from the fields of conservation and natural resources management. Further, we suggest that a common, simplified model development framework for describing complex biological systems will provide new, broadly relevant educational tools. Efficient interdisciplinary collaboration to accurately develop a model of robustness and resilience would enable rapid, context-specific assessment of complex biological systems with benefits for a broad range of societally relevant problems.

Optimizing coral reef recovery with context-specific management actions at prioritized reefs

Assisting the natural recovery of coral reefs through local management actions is needed in response to increasing ecosystem disturbances in the Anthropocene. There is growing evidence that commonly used resilience-based passive management approaches may not be sufficient to maintain coral reef key functions. We synthesize and discuss advances in coral reef recovery research, and its application to coral reef conservation and restoration practices. We then present a framework to guide the decision-making of reef managers, scientists and other stakeholders, to best support reef recovery after a disturbance. The overall aim of this management framework is to catalyse reef recovery, to minimize recovery times, and to limit the need for ongoing management interventions into the future. Our framework includes two main stages: first, a prioritization method for assessment following a large-scale disturbance, which is based on a reef's social-ecological values, and on a classification of the likelihood of recovery or succession resulting in degraded, novel, hybrid or historical states. Second, a flow chart to assist with determining management actions for highly valued reefs. Potential actions are chosen based on the ecological attributes of the disturbed reef, defined during ecological assessments. Depending on the context, management actions may include (1) substrata rehabilitation actions to facilitate natural coral recruitment, (2) repopulating actions using active restoration techniques, (3) resilience-based management actions and (4) monitoring coral recruitment and growth to assess the effectiveness of management interventions. We illustrate the proposed decision framework with a case study of typhoon-damaged eastern outer reefs in Palau, Micronesia. The decisions made following this framework lead to the conclusion that some reefs may not return to their historical state for many decades. However, if motivation and funds are available, new management approaches can be explored to assist coral reefs at valued locations to return to a functional state providing key ecosystem services.

Back to the future: Reintegrating biology to understand how past eco-evolutionary change can predict future outcomes

During the last few decades, biologists have made remarkable progress in understanding the fundamental processes that shape life. But despite the unprecedented level of knowledge now available, large gaps still remain in our understanding of the complex interplay of eco-evolutionary mechanisms across scales of life. Rapidly changing environments on Earth provide a pressing need to understand the potential implications of eco-evolutionary dynamics, which can be achieved by improving existing eco-evolutionary models and fostering convergence among the sub-fields of biology. We propose a new, data-driven approach that harnesses our knowledge of the functioning of biological systems to expand current conceptual frameworks and develop corresponding models that can more accurately represent and predict future eco-evolutionary outcomes. We suggest a roadmap toward achieving this goal. This long-term vision will move biology in a direction that can wield these predictive models for scientific applications that benefit humanity and increase the resilience of natural biological systems. We identify short, medium, and long-term key objectives to connect our current state of knowledge to this long-term vision, iteratively progressing across three stages: 1) utilizing knowledge of biological systems to better inform eco-evolutionary models, 2) generating models with more accurate predictions, and 3) applying predictive models to benefit the biosphere. Within each stage, we outline avenues of investigation and scientific applications related to the timescales over which evolution occurs, the parameter space of eco-evolutionary processes, and the dynamic interactions between these mechanisms. The ability to accurately model, monitor, and anticipate eco-evolutionary changes would be transformational to humanity's interaction with the global environment, providing novel tools to benefit human health, protect the natural world, and manage our planet's biosphere.

A survey of current trends and suggested future directions in coral transplantation for reef restoration

Coral transplantation has been used in reef restoration for several decades, but information on the type of projects, their scope, scale, and success is mostly limited to published scientific studies and technical reports. Many practitioners do not have the capacity to share their progress in peer-reviewed literature, yet likely have a wealth of information to share on how to improve the efficiency of transplantation efforts. In order to incorporate non-published data on coral transplantation projects and gain an overview of the general features of these projects, we conducted an initial systematic online survey of projects run by various practitioners. Surveyed projects (n = 50) covered most of the tropical belt and ranged in size from a few hundred transplanted corals to >5000 transplants. The most frequent source of coral fragments were corals already broken from some previous impact (“corals of opportunity”; 58% of projects), followed by fragments stored in different types of aquaculture systems (42% of projects). The use of sexual reproduction was very limited. Fast-growing, branching corals were used in 96% of projects, being by far the most common transplanted growth form. About half of the projects mentioned undertaking maintenance of the transplantation plots. The majority of projects undertook subsequent monitoring (80%), yet the available data indicates that duration of monitoring efforts was not adequate to evaluate long-term success. The findings underline that while some general principles for successful coral restoration projects are reasonably well established, others need to be mainstreamed better in order to improve the effectiveness of coral transplantation for reef restoration. This relates in particular to sustainable funding, adequate site assessment, and long-term monitoring using established protocols. Additional information is needed to better understand and address potential challenges with regards to the sourcing of transplants and use of slow-growing species. A better integration of practitioners is necessary to improve the understanding of coral transplantation effectiveness. The results underline a need to develop and use monitoring protocols that allow gauging and comparing the effectiveness of coral transplantation among various projects, as well as for accessible platform(s) to allow the exchange of experiences made in different projects. Regular surveys of restoration projects are recommended to collate and share information among practitioners. We provide a number of recommendations for items to include in future surveys.

The tropical Pacific Oceanscape: Current issues, solutions and future possibilities

Marine ecosystems across the world's largest ocean - the Pacific Ocean - are being increasingly affected by stressors such as pollution, overfishing, ocean acidification, coastal development and warming events coupled with rising sea levels and increasing frequency of extreme weather. These anthropogenic-driven stressors, which operate cumulatively at varying spatial and temporal scales, are leading to ongoing and pervasive degradation of many marine ecosystems in the Pacific Island region. The effects of global warming and ocean acidification threaten much of the region and impact on the socio-cultural, environmental, economic and human health components of many Pacific Island nations. Simultaneously, resilience to climate change is being reduced as systems are overburdened by other stressors, such as marine and land-based pollution and unsustainable fishing. Consequently, it is important to understand the vulnerability of this region to future environmental scenarios and determine to what extent management actions can help protect, and rebuild ecosystem resilience and maintain ecosystem service provision. This Special Issue of papers explores many of these pressures through case studies across the Pacific Island region, and the impacts of individual and cumulative pressures on the condition, resilience and survival of ecosystems and the communities that depend on them. The papers represent original work from across the tropical Pacific oceanscape, an area that includes 22 Pacific Island countries and territories plus Hawaii and the Philippines. The 39 papers within provide insights on anthropogenic pressures and habitat responses at local, national, and regional scales. The themes range from coastal water quality and human health, assessment of status and trends for marine habitats (e.g. seagrass and coral reefs), and the interaction of local pressures (pollution, overfishing) with increasing temperatures and climate variability. Studies within the Special Issue highlight how local actions, monitoring, tourism values, management, policy and incentives can encourage adaptation to anthropogenic impacts. Conclusions identify possible solutions to support sustainable and harmonious environment and social systems in the unique Pacific Island oceanscape.

The coral conservation crisis: interacting local and global stressors reduce reef resiliency and create challenges for conservation solutions

Coral reefs are one of the most productive and biodiverse ecosystems in the world. Humans rely on these coral reef ecosystems to provide significant ecological and economic resources; however, coral reefs are threatened by numerous local and global anthropogenic factors that cause significant environmental change. The interactions of these local and global human impacts may increase the rate of coral reef degradation. For example, there are many local influences (i.e., sedimentation and submarine groundwater discharge) that may exacerbate coral bleaching and mortality. Therefore, researchers and resource managers cannot limit their narratives and actions to mitigating a sole stressor. With the continued increase in greenhouse gas emissions, management strategies and restoration techniques need to account for the scale at which environmental change occurs. This review aims to outline the various local and global anthropogenic stressors threatening reef resiliency and address the recent disagreements surrounding present-day conservation practices. Unfortunately, there is no one solution to preserve and restore all coral reefs. Each coral reef region is challenged by numerous interactive stressors that affect its ecosystem response, recovery, and services in various ways. This review discusses, while global reef degradation occurs, local solutions should be implemented to efficiently protect the coral reef ecosystem services that are valuable to marine and terrestrial environments.

Genetic structure of a remnant Acropora cervicornis population

Amongst the global decline of coral reefs, hope spots such as Cordelia Bank in Honduras, have been identified. This site contains dense, remnant thickets of the endangered species Acropora cervicornis, which local managers and conservation organizations view as a potential source population for coral restoration projects. The aim of this study was to determine the genetic diversity of colonies across three banks within the protected area. We identified low genetic diversity (F_ST = 0.02) across the three banks, and genetic similarity of colonies ranged from 91.3 to 95.8% between the banks. Clonality rates were approximately 30% across the three banks, however, each genotype identified was unique to each bank. Despite the low genetic diversity, subtle genetic differences within and among banks were demonstrated, and these dense thickets were shown not to be comprised of a single or a few genotypes. The presence of multiple genotypes suggests A. cervicornis colonies from these banks could be used to maintain and enhance genetic diversity in restoration projects. Management of hope spots, such as Cordelia Bank, and the incorporation of genetic information into restoration projects to ensure genetic diversity within out-planted populations, will be critical in the ongoing challenge of conserving and preserving coral reefs.

Disturbance type determines how connectivity shapes ecosystem resilience

Connectivity is fundamentally important for shaping the resilience of complex human and natural networks when systems are disturbed. Ecosystem resilience is, in part, shaped by the spatial arrangement of habitats, the permeability and fluxes between them, the stabilising functions performed by organisms, their dispersal traits, and the interactions between functions and stressor types. Controlled investigations of the relationships between these phenomena under multiple stressors are sparse, possibly due to logistic and ethical difficulties associated with applying and controlling stressors at landscape scales. Here we show that grazing performance, a key ecosystem function, is linked to connectivity by manipulating the spatial configuration of habitats in microcosms impacted by multiple stressors. Greater connectivity enhanced ecosystem function and reduced variability in grazing performance in unperturbed systems. Improved functional performance was observed in better connected systems stressed by harvesting pressure and temperature rise, but this effect was notably reversed by the spread of disease. Connectivity has complex effects on ecological functions and resilience, and the nuances should be recognised more fully in ecosystem conservation.

Using resilience assessments to inform the management and conservation of coral reef ecosystems

Climate change is causing the decline of coral reef ecosystems globally. Recent research highlights the importance of reducing CO₂ emissions in combination with implementing local management actions to support reef health and recovery, particularly actions that protect sites which are more resilient to extreme events. Resilience assessments quantify the ecological, social, and environmental context of reefs through the lens of resilience, i.e., the capacity of a system to absorb or withstand stressors such that the system maintains its structure and functions and has the capacity to adapt to future disturbances and changes. Resilience assessments are an important tool to help marine managers and decision makers anticipate changes, identify areas with high survival prospects, and prioritize management actions to support resilience. While being widely implemented, however, there has not yet been an evaluation of whether resilience assessments have informed coral reef management. Here, we assess the primary and gray literature and input from coral reef managers to map where resilience assessments have been conducted. We explore if and how they have been used to inform management actions and provide recommendations for improving the likelihood that resilience assessments will result in management actions and positive conservation outcomes. These recommendations are applicable to other ecosystems in which resilience assessments are applied and will become increasingly important as climate impacts intensify and reduce the window of opportunity for protecting natural ecosystems.

Seagrasses and seagrass habitats in Pacific small island developing states: Potential loss of benefits via human disturbance and climate change

Seagrasses provide a wide range of services including food provision, water purification and coastal protection. Pacific small island developing states (PSIDS) have limited natural resources, challenging economies and a need for marine science research. Seagrasses occur in eleven PSIDS and nations are likely to benefit in different ways depending on habitat health, habitat cover and location, and species presence. Globally seagrass habitats are declining as a result of anthropogenic impacts including climate change and in PSIDS pressure on already stressed coastal ecosystems, will likely threaten seagrass survival particularly close to expanding urban settlements. Improved coastal and urban planning at local, national and regional scales is needed to reduce human impacts on vulnerable coastal areas. Research is required to generate knowledge-based solutions to support effective coastal management and protection of the existing seagrass habitats, including strenghened documentation the socio-economic and environmental services they provide. For PSIDS, protection of seagrass service benefits requires six priority actions: seagrass habitat mapping, regulation of coastal and upstream development, identification of specific threats at vulnerable locations, a critique of cost-effective restoration options, research devoted to seagrass studies and more explicit policy development.

Population genetics of the brooding coral Seriatopora hystrix reveals patterns of strong genetic differentiation in the Western Indian Ocean

Coral reefs provide essential goods and services but are degrading at an alarming rate due to local and global anthropogenic stressors. The main limitation that prevents the implementation of adequate conservation measures is that connectivity and genetic structure of populations are poorly known. Here, the genetic diversity and connectivity of the brooding scleractinian coral Seriatopora hystrix were assessed at two scales by genotyping ten microsatellite markers for 356 individual colonies. S. hystrix showed high differentiation, both at large scale between the Red Sea and the Western Indian Ocean (WIO), and at smaller scale along the coast of East Africa. As such high levels of differentiation might indicate the presence of more than one species, a haploweb analysis was conducted with the nuclear marker ITS2, confirming that the Red Sea populations are genetically distinct from the WIO ones. Based on microsatellite analyses three groups could be distinguished within the WIO: (1) northern Madagascar, (2) south-west Madagascar together with one site in northern Mozambique (Nacala) and (3) all other sites in northern Mozambique, Tanzania and Kenya. These patterns of restricted connectivity could be explained by the short pelagic larval duration of S. hystrix, and/or by oceanographic factors, such as eddies in the Mozambique Channel (causing larval retention in northern Madagascar but facilitating dispersal from northern Mozambique towards south-west Madagascar). This study provides an additional line of evidence supporting the conservation priority status of the Northern Mozambique Channel and should inform coral reef management decisions in the region.

Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont

Coral microbiomes are critical to holobiont health and functioning, but the stability of host–microbial interactions is fragile, easily shifting from eubiosis to dysbiosis. The heat-induced breakdown of the symbiosis between the host and its dinoflagellate algae (that is, “bleaching”), is one of the most devastating outcomes for reef ecosystems. Yet, bleaching tolerance has been observed in some coral species. This review provides an overview of the holobiont’s diversity, explores coral thermal tolerance in relation to their associated microorganisms, discusses the hypothesis of adaptive dysbiosis as a mechanism of environmental adaptation, mentions potential solutions to mitigate bleaching, and suggests new research avenues. More specifically, we define coral bleaching as the succession of three holobiont stages, where the microbiota can (i) maintain essential functions for holobiont homeostasis during stress and/or (ii) act as a buffer to mitigate bleaching by favoring the recruitment of thermally tolerant Symbiodiniaceae species (adaptive dysbiosis), and where (iii) environmental stressors exceed the buffering capacity of both microbial and dinoflagellate partners leading to coral death.

Coral community life histories and population dynamics driven by seascape bathymetry and temperature variability

Temperature variability, habitat, coral communities, and fishing intensity are important factors influencing coral responses to climate change. Consequently, chronic and acute sea-surface temperatures (SSTs) and their interactions with habitat and fishing were studied along the East African coast (~400km) by evaluating changes over a ~25-year period in two major reef habitats-island and fringing reefs. These habitats had similar mean and standard deviation temperature measurements but differed in that islands had lower ocean heights and flatter and less right-skewed temperature distributions than fringing reefs. These patterns arise because islands are exposed to deep offshore water passing through deep channels while being protected from the open ocean storms and the strong inter-annual current temperature variability. Within these two seascapes, coral communities are shaped by population responses to the variable temperature distributions as determined by the taxa's associations with the competitive-stress-ruderal (CSR) life history groups. For example, competitive taxa were more abundant where temperature distributions were flat and lacked frequent warm water anomalies. In contrast, ruderal, weedy, and generalist taxa were more common where temperature distributions were centralized, standard deviations high, and warm water anomalies more frequent. Finally, stress-resistant taxa were more common in reefs with high temperature skew but flatter temperature distributions. The rare 1998 thermal anomaly impacted and disturbed the ruderal and stressed reef more than the competitive communities. Ruderal became more similar to stressed communities while the stressed community moved further from the mean before recovering towards the competitive community. Competitive taxa were more common on islands and the deeper fringing reef sites while ruderal were dominant in shallow fringing reef lagoons. Over time, islands were less disturbed than fringing reefs and maintained the highest coral cover, numbers of taxa, and most competitive or space-occupying taxa. However, some island reefs with a history of dynamite fishing aligned with the stress-resistant communities over the full study period. Compared to the in situ SST gauges at the study site, temperature proxies with global coverage were often good at estimating mean and standard deviations of the SSTs but much poorer at estimating the shape of the temperature distributions that reflect chronic and acute stress, as reflected by kurtosis and skewness metrics. Given that these stress variables were critical for understanding the impacts of rare climate disturbances, global climate models that use mean conditions are likely to be poor predictors of future impacts on corals, particularly their species and life history composition. Better predictions should be possible if appropriate chronic and acute stress metrics and their proxies are identified and used.

A contemporary baseline record of the world's coral reefs

Addressing the global decline of coral reefs requires effective actions from managers, policymakers and society as a whole. Coral reef scientists are therefore challenged with the task of providing prompt and relevant inputs for science-based decision-making. Here, we provide a baseline dataset, covering 1300 km of tropical coral reef habitats globally, and comprised of over one million geo-referenced, high-resolution photo-quadrats analysed using artificial intelligence to automatically estimate the proportional cover of benthic components. The dataset contains information on five major reef regions, and spans 2012–2018, including surveys before and after the 2016 global bleaching event. The taxonomic resolution attained by image analysis, as well as the spatially explicit nature of the images, allow for multi-scale spatial analyses, temporal assessments (decline and recovery), and serve for supporting image recognition developments. This standardised dataset across broad geographies offers a significant contribution towards a sound baseline for advancing our understanding of coral reef ecology and thereby taking collective and informed actions to mitigate catastrophic losses in coral reefs worldwide.

Measurement(s)	ecosystem • coral reef • composition
Technology Type(s)	automated image annotation • machine learning
Factor Type(s)	year of data collection • geographic location
Sample Characteristic - Organism	Anthozoa • Algae • Porifera
Sample Characteristic - Environment	marine coral reef biome • marine coral reef fore reef
Sample Characteristic - Location	Atlantic Ocean • Eastern Australia • Indian Ocean • Southeast Asia • Pacific Ocean • Great Barrier Reef

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13007516

Coral Gardens Reef, Belize: A refugium in the face of Caribbean-wide Acropora spp. coral decline

Caribbean Acropora spp. corals have undergone a decline in cover since the second half of the twentieth century. Loss of these architecturally complex and fast-growing corals has resulted in significant, cascading changes to the character, diversity, and available eco-spaces of Caribbean reefs. Few thriving Acropora spp. populations exist today in the Caribbean and western North Atlantic seas, and our limited ability to access data from reefs assessed via long-term monitoring efforts means that reef scientists are challenged to determine resilience and longevity of existing Acropora spp. reefs. Here we used multiple dating methods to measure reef longevity and determine whether Coral Gardens Reef, Belize, is a refuge for Acropora cervicornis against the backdrop of wider Caribbean decline. We used a new genetic-aging technique to identify sample sites, and radiocarbon and high-precision uranium-thorium (U-Th) dating techniques to test whether one of the largest populations of extant A. cervicornis in the western Caribbean is newly established after the 1980s, or represents a longer-lived, stable population. We did so with respect for ethical sampling of a threatened species. Our data show corals ranging in age from 1910 (14C) or 1915 (230Th) to at least November 2019. While we cannot exclude the possibility of short gaps in the residence of A. cervicornis earlier in the record, the data show consistent and sustained living coral throughout the 1980s and up to at least 2019. We suggest that Coral Gardens has served as a refuge for A. cervicornis and that identifying other, similar sites may be critical to efforts to grow, preserve, conserve, and seed besieged Caribbean reefs.

Algal turf sediments limit the spatial extent of function delivery on coral reefs

The presence of key organisms is frequently associated with the delivery of specific ecosystem functions. Areas with such organisms are therefore often considered to have greater levels of these functions. While this assumption has been the backbone of coral reef ecosystem-based management approaches for decades, we currently have only a limited understanding of how fish presence equates to function on coral reefs and whether this relationship is susceptible to stressors. To assess the capacity of a stressor to shape function delivery we used a multi-scale approach ranging from tens of kilometres across the continental shelf of Australia's Great Barrier Reef, down to centimetres within a reef habitat. At each scale, we quantified the spatial extent of a model function (detritivory) by a coral reef surgeonfish (Ctenochaetus striatus) and its potential to be shaped by sediments. At broad spatial scales, C. striatus presence was correlated strongly with algal turf sediment loads, while at smaller spatial scales, function delivery appears to be constrained by algal turf sediment distributions. In all cases, sediment loads above ~250-500 g m^-2 were associated with a marked decrease in fish abundance or feeding activity, suggesting that a common ecological threshold lies within this range. Our results reveal a complex functional dynamic between proximate agents of function delivery (fish) and the ultimate drivers of function delivery (sediments), which emphasizes: a) weaknesses in the assumed links between fish presence and function, and b) the multi-scale capacity of algal turf sediments to shape reef processes. Unless direct extractive activities (e.g. fishing) are the main driver of function loss on coral reefs, managing to conserve fish abundance is unlikely to yield the desired outcomes. It only addresses one potential driver. Instead, management of both the agents that deliver functions (e.g. fishes), and the drivers that modify functions (e.g. sediments), is needed.

Coral reef restoration efforts in Latin American countries and territories

Coral reefs worldwide are degrading due to climate change, overfishing, pollution, coastal development, coral bleaching, and diseases. In areas where the natural recovery of an ecosystem is negligible or protection through management interventions insufficient, active restoration becomes critical. The Reef Futures symposium in 2018 brought together over 400 reef restoration experts, businesses, and civil organizations, and galvanized them to save coral reefs through restoration or identify alternative solutions. The symposium highlighted that solutions and discoveries from long-term and ongoing coral reef restoration projects in Spanish-speaking countries in the Caribbean and Eastern Tropical Pacific were not well known internationally. Therefore, a meeting of scientists and practitioners working in these locations was held to compile the data on the extent of coral reef restoration efforts, advances and challenges. Here, we present unpublished data from 12 coral reef restoration case studies from five Latin American countries, describe their motivations and techniques used, and provide estimates on total annual project cost per unit area of reef intervened, spatial extent as well as project duration. We found that most projects used direct transplantation, the coral gardening method, micro-fragmentation or larval propagation, and aimed to optimize or scale-up restoration approaches (51%) or provide alternative, sustainable livelihood opportunities (15%) followed by promoting coral reef conservation stewardship and re-establishing a self-sustaining, functioning reef ecosystems (both 13%). Reasons for restoring coral reefs were mainly biotic and experimental (both 42%), followed by idealistic and pragmatic motivations (both 8%). The median annual total cost from all projects was $93,000 USD (range: $10,000 USD-$331,802 USD) (2018 dollars) and intervened a median spatial area of 1 ha (range: 0.06 ha-8.39 ha). The median project duration was 3 years; however, projects have lasted up to 17 years. Project feasibility was high with a median of 0.7 (range: 0.5-0.8). This study closes the knowledge gap between academia and practitioners and overcomes the language barrier by providing the first comprehensive compilation of data from ongoing coral reef restoration efforts in Latin America.

Combining agent-based, trait-based and demographic approaches to model coral-community dynamics

The complexity of coral-reef ecosystems makes it challenging to predict their dynamics and resilience under future disturbance regimes. Models for coral-reef dynamics do not adequately account for the high functional diversity exhibited by corals. Models that are ecologically and mechanistically detailed are therefore required to simulate the ecological processes driving coral reef dynamics. Here, we describe a novel model that includes processes at different spatial scales, and the contribution of species' functional diversity to benthic-community dynamics. We calibrated and validated the model to reproduce observed dynamics using empirical data from Caribbean reefs. The model exhibits realistic community dynamics, and individual population dynamics are ecologically plausible. A global sensitivity analysis revealed that the number of larvae produced locally, and interaction-induced reductions in growth rate are the parameters with the largest influence on community dynamics. The model provides a platform for virtual experiments to explore diversity-functioning relationships in coral reefs.