Projecting coral reef futures under global warming and ocean acidification

The role of geomorphic zonation in long-term changes in coral-community structure on a Caribbean fringing reef

Ecological processes on coral reefs commonly have limited spatial and temporal scales and may not be recorded in their long-term geological history. The widespread degradation of Caribbean coral reefs over the last 40 years therefore provides an opportunity to assess the impact of more significant ecological changes on the geological and geomorphic structure of reefs. Here, we document the changing ecology of communities in a coral reef seascape within the context of its geomorphic zonation. By comparing basic ecological indices between historical and modern data we show that in 35 years the reef-front zone was transformed from a complex coral assemblage with a three-dimensional structure, to a size-homogenized and flattened one that is quasi indistinguishable from the adjacent non-accretional coral-ground zone. Today coral assemblages at Punta Maroma are characterized by the dominance of opportunistic species which are either tolerant to adverse environmental conditions, including sedimentation, or are known to be the first scleractinian species to recruit on disturbed reefs, implying they reflect a post-hurricane stage of adjustment. Despite an increase in similarity in ecological indices, the reef-front and coral-ground geomorphic zones still retain significant differences in coral assemblages and benthic habitat and are not homogeneous. The partial convergence of coral assemblages certainly has important consequences for the ecology and geological viability of the reef and its role in coastal protection, but environmental physical drivers continue to exert a fundamental role in the character and zonation of benthic communities of this reef seascape.

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.

Unfamiliar partnerships limit cnidarian holobiont acclimation to warming

Enhancing the resilience of corals to rising temperatures is now a matter of urgency, leading to growing efforts to explore the use of heat tolerant symbiont species to improve their thermal resilience. The notion that adaptive traits can be retained by transferring the symbionts alone, however, challenges the holobiont concept, a fundamental paradigm in coral research. Holobiont traits are products of a specific community (holobiont) and all its co-evolutionary and local adaptations, which might limit the retention or transference of holobiont traits by exchanging only one partner. Here we evaluate how interchanging partners affect the short- and long-term performance of holobionts under heat stress using clonal lineages of the cnidarian model system Aiptasia (host and Symbiodiniaceae strains) originating from distinct thermal environments. Our results show that holobionts from more thermally variable environments have higher plasticity to heat stress, but this resilience could not be transferred to other host genotypes through the exchange of symbionts. Importantly, our findings highlight the role of the host in determining holobiont productivity in response to thermal stress and indicate that local adaptations of holobionts will likely limit the efficacy of interchanging unfamiliar compartments to enhance thermal tolerance.

New approaches to species delimitation and population structure of anthozoans: Two case studies of octocorals using ultraconserved elements and exons

As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological variation and slowly evolving molecular markers confound species identification. New approaches to species delimitation in corals are needed to overcome these challenges. Here, we test whether target enrichment of ultraconserved elements (UCEs) and exons can be used for delimiting species boundaries and population structure within species of corals by focusing on two octocoral genera, Alcyonium and Sinularia, as exemplary case studies. We designed an updated bait set (29,181 baits) to target-capture 3,023 UCE and exon loci, recovering a mean of 1,910 ± 168 SD per sample with a mean length of 1,055 ± 208 bp. Similar numbers of loci were recovered from Sinularia (1,946 ± 227 SD) and Alcyonium (1,863 ± 177 SD). Species-level phylogenies were highly supported for both genera. Clustering methods based on filtered single nucleotide polymorphisms delimited species and populations that are congruent with previous allozyme, DNA barcoding, reproductive and ecological data for Alcyonium, and offered further evidence of hybridization among species. For Sinularia, results were congruent with those obtained from a previous study using restriction site associated DNA sequencing. Both case studies demonstrate the utility of target-enrichment of UCEs and exons to address a wide range of evolutionary and taxonomic questions across deep to shallow timescales in corals.

Micro-Fragmentation as an Effective and Applied Tool to Restore Remote Reefs in the Eastern Tropical Pacific

Coral reef ecosystems are continuously degraded by anthropogenic and climate change drivers, causing a widespread decline in reef biodiversity and associated goods and services. In response, active restoration methodologies and practices have been developed globally to compensate for losses due to reef degradation. Yet, most activities employ the gardening concept that uses coral nurseries, and are centered in easily-accessible reefs, with existing infrastructure, and impractical for coral reefs in remote locations. Here we evaluate the effectiveness of direct outplanting of coral micro-fragments (Pavona clavus and Pocillopora spp.) as a novel approach to restore remote reefs in the Islas Marías archipelago in the Eastern Tropical Pacific. Coral growth (height-width-tissue cover), survival percentage, extension rates (cm year⁻¹), skeletal density (g cm⁻³) and calcification rates (g cm⁻² year⁻¹) were assessed over 13 months of restoration. In spite of detrimental effects of Hurricane Willa, transplants showed a greater-than-twofold increase in all growth metrics, with ~58–61% survival rate and fast self-attachment (within ~3.9 months) for studied species, with Pocilloporids exhibiting higher extension, skeletal density, and calcification rates than Pavona. While comprehensive long-term studies are required, direct transplantation methodologies of coral micro-fragments are emerging as time-effective and affordable restoration tools to mitigate anthropogenic and climate change impacts in remote and marginal reefs.

Acclimatization Drives Differences in Reef-Building Coral Calcification Rates

Coral reefs are susceptible to climate change, anthropogenic influence, and environmental stressors. However, corals in Kāneʻohe Bay, Hawaiʻi have repeatedly shown resilience and acclimatization to anthropogenically-induced rising temperatures and increased frequencies of bleaching events. Variations in coral and algae cover at two sites—just 600 m apart—at Malaukaʻa fringing reef suggest genetic or environmental differences in coral resilience between sites. A reciprocal transplant experiment was conducted to determine if calcification (linear extension and dry skeletal weight) for dominant reef-building species, Montipora capitata and Porites compressa, varied between the two sites and whether or not parent colony or environmental factors were responsible for the differences. Despite the two sites representing distinct environmental conditions with significant differences between temperature, salinity, and aragonite saturation, M. capitata growth rates remained the same between sites and treatments. However, dry skeletal weight increases in P. compressa were significantly different between sites, but not across treatments, with linear mixed effects model results suggesting heterogeneity driven by environmental differences between sites and the parent colonies. These results provide evidence of resilience and acclimatization for M. capitata and P. compressa. Variability of resilience may be driven by local adaptations at a small, reef-level scale for P. compressa in Kāneʻohe Bay.

PhenoChip: A single-cell phenomic platform for high-throughput photophysiological analyses of microalgae

Photosynthetic microorganisms are key players in aquatic ecosystems with strong potential for bioenergy production, yet their systematic selection at the single-cell level for improved productivity or stress resilience ("phenotyping") has remained largely inaccessible. To facilitate the phenotyping of microalgae and cyanobacteria, we developed "PhenoChip," a platform for the multiparametric photophysiological characterization and selection of unicellular phenotypes under user-controlled physicochemical conditions. We used PhenoChip to expose single cells of the coral symbiont Symbiodinium to thermal and chemical treatments and monitor single-cell photophysiology via chlorophyll fluorometry. This revealed strain-specific thermal sensitivity thresholds and distinct pH optima for photosynthetic performance, and permitted the identification of single cells with elevated resilience toward rising temperature. Optical expulsion technology was used to collect single cells from PhenoChip, and their propagation revealed indications of transgenerational preservation of photosynthetic phenotypes. PhenoChip represents a versatile platform for the phenotyping of photosynthetic unicells relevant to biotechnology, ecotoxicology, and assisted evolution.

Effects of future climate on coral-coral competition

As carbon dioxide (CO₂) levels increase, coral reefs and other marine systems will be affected by the joint stressors of ocean acidification (OA) and warming. The effects of these two stressors on coral physiology are relatively well studied, but their impact on biotic interactions between corals are poorly understood. While coral-coral interactions are less common on modern reefs, it is important to document the nature of these interactions to better inform restoration strategies in the face of climate change. Using a mesocosm study, we evaluated whether the combined effects of ocean acidification and warming alter the competitive interactions between the common coral Porites astreoides and two other mounding corals (Montastraea cavernosa or Orbicella faveolata) common in the Caribbean. After 7 days of direct contact, P. astreoides suppressed the photosynthetic potential of M. cavernosa by 100% in areas of contact under both present (~28.5°C and ~400 μatm pCO₂) and predicted future (~30.0°C and ~1000 μatm pCO₂) conditions. In contrast, under present conditions M. cavernosa reduced the photosynthetic potential of P. astreoides by only 38% in areas of contact, while under future conditions reduction was 100%. A similar pattern occurred between P. astreoides and O. faveolata at day 7 post contact, but by day 14, each coral had reduced the photosynthetic potential of the other by 100% at the point of contact, and O. faveolata was generating larger lesions on P. astreoides than the reverse. In the absence of competition, OA and warming did not affect the photosynthetic potential of any coral. These results suggest that OA and warming can alter the severity of initial coral-coral interactions, with potential cascading effects due to corals serving as foundation species on coral reefs.

Environmentally-induced parental or developmental conditioning influences coral offspring ecological performance

The persistence of reef building corals is threatened by human-induced environmental change. Maintaining coral reefs into the future requires not only the survival of adults, but also the influx of recruits to promote genetic diversity and retain cover following adult mortality. Few studies examine the linkages among multiple life stages of corals, despite a growing knowledge of carryover effects in other systems. We provide a novel test of coral parental conditioning to ocean acidification (OA) and tracking of offspring for 6 months post-release to better understand parental or developmental priming impacts on the processes of offspring recruitment and growth. Coral planulation was tracked for 3 months following adult exposure to high pCO2 and offspring from the second month were reciprocally exposed to ambient and high pCO2 for an additional 6 months. Offspring of parents exposed to high pCO2 had greater settlement and survivorship immediately following release, retained survivorship benefits during 1 and 6 months of continued exposure, and further displayed growth benefits to at least 1 month post release. Enhanced performance of offspring from parents exposed to high conditions was maintained despite the survivorship in both treatments declining in continued exposure to OA. Conditioning of the adults while they brood their larvae, or developmental acclimation of the larvae inside the adult polyps, may provide a form of hormetic conditioning, or environmental priming that elicits stimulatory effects. Defining mechanisms of positive acclimatization, with potential implications for carry over effects, cross-generational plasticity, and multi-generational plasticity, is critical to better understanding ecological and evolutionary dynamics of corals under regimes of increasing environmental disturbance. Considering environmentally-induced parental or developmental legacies in ecological and evolutionary projections may better account for coral reef response to the chronic stress regimes characteristic of climate change.

Successful application of a novel technique to quantify negative impacts of derelict fishing nets on Northwestern Hawaiian Island reefs

The remote and uninhabited Northwestern Hawaiian Islands (NWHI) contain 70% of the shallow water coral reefs in the United States and are regularly exposed to derelict fishing nets. These nets snag on the shallow reefs, damaging or killing benthic communities. However, no data exist to quantify this impact. Here we use a novel application of photogrammetry, Structure-from-Motion (SfM), to calculate benthic cover from mosaic images at net-impact and control sites. Net-impact sites had significantly higher cover of bare substrate, sand, and crustose coralline algae and significantly lower coral and macroalgae cover compared to control sites. These differences were unrelated to net size and fouling. Our study demonstrates the utility of using SfM to efficiently quantify impacts of derelict fishing nets. Revisiting these sites will be essential to document how the reef recovers to further our understanding of the lasting impacts of derelict fishing nets on coral reef habitats.

Science-based approach to using growth rate to assess coral performance and restoration outcomes

One response to the coral reef crisis has been human intervention to enhance selection on the fittest corals through cultivation. This requires genotypes to be identified for intervention, with a primary basis for this choice being growth: corals that quickly grow on contemporary reefs might be future winners. To test for temporal stability of growth as a predictor of future performance, genotypes of the coral Porites spp. were grown in common gardens in Mo'orea, French Polynesia. Growth was measured every two to four months throughout 2018, and each period was used as a predictor of growth over the subsequent period. Area-normalized growth explained less than 29% of the variance in subsequent growth, but for biomass-normalized growth this increased to 45-60%, and was highest when summer growth was used to predict autumn growth. The capacity of initial growth to predict future performance is dependent on the units of measurement and the time of year in which it is measured. The final choice of traits to quantify performance must be informed through consideration of the species and the normalization that best capture the information inherent in the biological processes mediating variation in traits values.

Impact of Climate Change on Nearshore Waves at a Beach Protected by a Barrier Reef

Barrier reefs dissipate most incoming wind-generated waves and, as a consequence, regulate the morphodynamics of its inbounded shorelines. The coastal protective capacity of reefs may nevertheless be compromised by climate change effects, such as reef degradation and sea-level rise. To assess the magnitude of these climate change effects, an analysis of the waves propagating across the barrier reef is carried out in Flic-en-Flac beach, Mauritius, based on scenarios of future sea levels and predicted coral reef condition. In the study, both the mean wave climate and extreme event conditions are considered. The results show that lower coral structure complexity jointly with higher water levels allow for higher waves to pass over the reef and, therefore, to reach the shoreline. In addition, modeling for cyclonic conditions showed that nearshore waves would also increase in height, which could lead to major coastal morphodynamic changes. Measures aimed at preserving the coral reef may allow the system to accommodate for the gradual climatic changes forecasted while keeping its coastal protective function.

The effects of ultraviolet radiation and climate on oil toxicity to coral reef organisms - A review

Oil pollution remains a significant local threat to shallow tropical coral reef environments, but the environmental conditions typical of coral reefs are rarely considered in oil toxicity testing and risk assessments. Here we review the effects of three environmental co-factors on petroleum oil toxicity towards coral reef organisms, and show that the impacts of oil pollution on coral reef taxa can be exacerbated by environmental conditions commonly encountered in tropical reef environments. Shallow reefs are routinely exposed to high levels of ultraviolet radiation (UVR), which can substantially increase the toxicity of some oil components through phototoxicity. Exposure to UVR represents the most likely and harmful environmental co-factor reviewed here, leading to an average toxicity increase of 7.2-fold across all tests reviewed. The clear relevance of UVR co-exposure and its strong influence on tropical reef oil toxicity highlights the need to account for UVR as a standard practice in future oil toxicity studies. Indeed, quantifying the influence of UVR on toxic thresholds of oil to coral reef species is essential to develop credible oil spill risk models required for oil extraction developments, shipping management and spill responses in the tropics. The few studies available indicate that co-exposure to elevated temperature and low pH, both within the range of current daily and seasonal fluctuations and/or projected under continued climate change, can increase oil toxicity on average by 3.0- and 1.3-fold, respectively. While all three of the reviewed environmental co-factors have the potential to substantially increase the impacts of oil pollution in shallow reef environments, their simultaneous effects have not been investigated. Assessments of the combined effects of oil pollution, UVR, temperature and low pH will become increasingly important to identify realistic hazard thresholds suitable for future risk assessments over the coming century.

Adaptive responses and local stressor mitigation drive coral resilience in warmer, more acidic oceans

Coral reefs have great biological and socioeconomic value, but are threatened by ocean acidification, climate change and local human impacts. The capacity for corals to adapt or acclimatize to novel environmental conditions is unknown but fundamental to projected reef futures. The coral reefs of Kāne'ohe Bay, Hawai'i were devastated by anthropogenic insults from the 1930s to 1970s. These reefs experience naturally reduced pH and elevated temperature relative to many other Hawaiian reefs which are not expected to face similar conditions for decades. Despite catastrophic loss in coral cover owing to human disturbance, these reefs recovered under low pH and high temperature within 20 years after sewage input was diverted. We compare the pH and temperature tolerances of three dominant Hawaiian coral species from within Kāne'ohe Bay to conspecifics from a nearby control site and show that corals from Kāne'ohe are far more resistant to acidification and warming. These results show that corals can have different pH and temperature tolerances among habitats and understanding the mechanisms by which coral cover rebounded within two decades under projected future ocean conditions will be critical to management. Together these results indicate that reducing human stressors offers hope for reef resilience and effective conservation over coming decades.

Paradise lost: End-of-century warming and acidification under business-as-usual emissions have severe consequences for symbiotic corals

Despite recent efforts to curtail greenhouse gas emissions, current global emission trajectories are still following the business-as-usual representative concentration pathway (RCP) 8.5 emission pathway. The resulting ocean warming and acidification have transformative impacts on coral reef ecosystems, detrimentally affecting coral physiology and health, and these impacts are predicted to worsen in the near future. In this study, we kept fragments of the symbiotic corals Acropora intermedia (thermally sensitive) and Porites lobata (thermally tolerant) for 7 weeks under an orthogonal design of predicted end-of-century RCP8.5 conditions for temperature and pCO2 (3.5°C and 570 ppm above present-day, respectively) to unravel how temperature and acidification, individually or interactively, influence metabolic and physiological performance. Our results pinpoint thermal stress as the dominant driver of deteriorating health in both species because of its propensity to destabilize coral-dinoflagellate symbiosis (bleaching). Acidification had no influence on metabolism but had a significant negative effect on skeleton growth, particularly when photosynthesis was absent such as in bleached corals or under dark conditions. Total loss of photosynthesis after bleaching caused an exhaustion of protein and lipid stores and collapse of calcification that ultimately led to A. intermedia mortality. Despite complete loss of symbionts from its tissue, P. lobata maintained small amounts of photosynthesis and experienced a weaker decline in lipid and protein reserves that presumably contributed to higher survival of this species. Our results indicate that ocean warming and acidification under business-as-usual CO2 emission scenarios will likely extirpate thermally sensitive coral species before the end of the century, while slowing the recovery of more thermally tolerant species from increasingly severe mass coral bleaching and mortality. This could ultimately lead to the gradual disappearance of tropical coral reefs globally, and a shift on surviving reefs to only the most resilient coral species.

Combined stress of ocean acidification and warming influence survival and drives differential gene expression patterns in the Antarctic pteropod, Limacina helicina antarctica

The ecologically important thecosome pteropods in the Limacina spp. complex have recently been the focus of studies examining the impacts global change factors - e.g., ocean acidification (OA) and ocean warming (OW) - on their performance and physiology. This focus is driven by conservation concerns where the health of pteropod populations is threatened by the high susceptibility of their shells to dissolution in low aragonite saturation states associated with OA and how coupling of these stressors may push pteropods past the limits of physiological plasticity. In this manipulation experiment, we describe changes in the transcriptome of the Antarctic pteropod, Limacina helicina antarctica, to these combined stressors. The conditions used in the laboratory treatments met or exceeded those projected for the Southern Ocean by the year 2100. We made two general observations regarding the outcome of the data: (1) Temperature was more influential than pH in terms of changing patterns of gene expression, and (2) these Antarctic pteropods appeared to have a significant degree of transcriptomic plasticity to respond to acute abiotic stress in the laboratory. In general, differential gene expression was observed amongst the treatments; here, for example, transcripts associated with maintaining protein structure and cell proliferation were up-regulated. To disentangle the effects of OA and OW, we used a weighted gene co-expression network analysis to explore patterns of change in the transcriptome. This approach identified gene networks associated with OW that were enriched for transcripts proposed to be involved in increasing membrane fluidity at warmer temperatures. Together these data provide evidence that L.h.antarctica has a limited capacity to acclimate to the combined conditions of OA and OW used in this study. This reduced scope of acclimation argues for continued study of how adaptation to polar aquatic environments may limit the plasticity of present-day populations in responding to future environmental change.

Resilience in reef-building corals: The ecological and evolutionary importance of the host response to thermal stress

Coral reefs are under extreme threat due to a number of stressors, but temperature increases due to changing climate are the most severe. Rising ocean temperatures coupled with local extremes lead to extensive bleaching, where the coral-algal symbiosis breaks down and corals may die, compromising the structure and function of reefs. Although the symbiotic nature of the coral colony has historically been a focus of research on coral resilience, the host itself is a foundational component in the response to thermal stress. Fixed effects in the coral host set trait baselines through evolutionary processes, acting on many loci of small effect to create mosaics of thermal tolerance across latitudes and individual coral reefs. These genomic differences can be strongly heritable, producing wide variation among clones of different genotypes or families of a specific larval cross. Phenotypic plasticity is overlaid on these baselines and a growing body of knowledge demonstrates the potential for acclimatization of reef-building corals through a variety of mechanisms that promote resilience and stress tolerance. The long-term persistence of coral reefs will require many of these mechanisms to adjust to warmer temperatures within a generation, bridging the gap to reproductive events that allow recombination of standing diversity and adaptive change. Business-as-usual climate scenarios will probably lead to the loss of some coral populations or species in the future, so the interaction between intragenerational effects and evolutionary pressure is critical for the survival of reefs.

Elevated ammonium delays the impairment of the coral-dinoflagellate symbiosis during labile carbon pollution

Labile dissolved organic carbon (DOC) is a major pollutant in coastal marine environments affected by anthropogenic impacts, and may significantly contribute to coral bleaching and subsequent mortality on coastal reefs. DOC can cause bleaching indirectly through the rapid proliferation of copiotrophic and pathogenic bacteria. Here we demonstrate that labile DOC compounds can also impair the coral-dinoflagellate symbiosis by directly affecting coral physiology on both the host and algal symbiont level. In a controlled aquarium experiment, we monitored over several weeks key physiological parameters of the tropical coral Stylophora pistillata exposed to ambient and elevated labile DOC levels (0.1 and 1.0 mM) in combination with low and high nitrogen (i.e. ammonium) conditions (0.2 and 4.0 μM). At the symbiont level, DOC exposure under low ammonium availability decreased the photosynthetic efficiency accompanied by ∼75 % Chl a and ∼50 % symbiont cell reduction. The photosynthetic functioning of the symbionts recovered once the DOC enrichment ceased indicating a reversible shift between autotrophic and heterotrophic metabolism. At the host level, the assimilation of exogenous DOC sustained the tissue carbon reserves, but induced a depletion of the nitrogen reserves, indicated by ∼35 % decreased protein levels. This suggests an imbalanced exogenous carbon to nitrogen supply with nitrogen potentially limiting host metabolism on the long-term. We also demonstrate that increased ammonium availability delayed DOC-induced bleaching likely by keeping symbionts in a photosynthetically competent state, which is crucial for symbiosis maintenance and coral survival. Overall, the present study provides further insights into how coastal pollution can de-stabilize the coral-algal symbiosis and cause coral bleaching. Therefore, reducing coastal pollution and sustaining ecological integrity are critical to strengthen the resilience of coral reefs facing climate change.

The plasticity of gonad development of sexual reproduction in a scleractinian coral, Porites lichen

Metazoans have evolved a complexity of sexual system and gonad development, however, sexual reproduction of scleractinian corals is not well understood. This study aimed to address the sexual system and gametogenesis in Porites lichen, a common species in the Indo-West Pacific. This study represents the first description of sexual system, which were determined by histological analysis of the samples collected in northern Taiwan. In addition, female and hermaphroditic colonies were separately cultured in aquarium to further monitor the release of eggs/larvae and thereby confirm the breeding system. The results demonstrate that P. lichen is a polygamodioecious brooder and displays seasonal gametogenesis and embryogenesis that ends in late summer. In hermaphroditic colonies, male polyps are predominant and hermaphroditic polyps make up a very small percent (1%-19.3%). In addition, two new gametogenic features were observed from the histological analysis: 1) oocytes developed within the spermaries in hermaphroditic polyps during the early stage of gametogenesis and 2) melanin granular cells were clustered in spermaries in both male and hermaphroditic colonies. This study demonstrated the plasticity of gametogenesis and melanin related cells appeared in corals, which provides an important information to explore hormones and molecular mechanism involving in gonadal arrangement and production of melanin for further studies.

High heritability of coral calcification rates and evolutionary potential under ocean acidification

Estimates of heritability inform evolutionary potential and the likely outcome of many management actions, but such estimates remain scarce for marine organisms. Here, we report high heritability of calcification rate among the eight most dominant Hawaiian coral species under reduced pH simulating future ocean conditions. Coral colonies were sampled from up to six locations across a natural mosaic in seawater chemistry throughout Hawai'i and fragmented into clonal replicates maintained under both ambient and high pCO2 conditions. Broad sense heritability of calcification rates was high among all eight species, ranging from a low of 0.32 in Porites evermanni to a high of 0.61 in Porites compressa. The overall results were inconsistent with short-term acclimatization to the local environment or adaptation to the mean or ideal conditions. Similarly, in 'local vs. foreign' and 'home vs. away' tests there was no clear signature of local adaptation. Instead, the data are most consistent with a protected polymorphism as the mechanism which maintains differential pH tolerance within the populations. Substantial individual variation, coupled with high heritability and large population sizes, imply considerable scope for natural selection and adaptive capacity, which has major implications for evolutionary potential and management of corals in response to climate change.

A New Application of Internet of Things and Cloud Services in Analytical Chemistry: Determination of Bicarbonate in Water

In a constantly evolving world, new technologies such as Internet of Things (IoT) and cloud-based services offer great opportunities in many fields. In this paper we propose a new approach to the development of smart sensors using IoT and cloud computing, which open new interesting possibilities in analytical chemistry. According to IoT philosophy, these new sensors are able to integrate the generated data on the existing IoT platforms, so that information may be used whenever needed. Furthermore, the utilization of these technologies permits one to obtain sensors with significantly enhanced features using the information available in the cloud. To validate our new approach, a bicarbonate IoT-based smart sensor has been developed. A classical CO₂ ion selective electrode (ISE) utilizes the pH information retrieved from the cloud and then provides an indirect measurement of bicarbonate concentration, which is offered to the cloud. The experimental data obtained are compared to those yielded by three other classical ISEs, with satisfactory results being achieved in most instances. Additionally, this methodology leads to lower-consumption, low-cost bicarbonate sensors capable of being employed within an IoT application, for instance in the continuous monitoring of HCO₃^- in rivers. Most importantly, this innovative application field of IoT and cloud approaches can be clearly perceived as an indicator for future developments over the short-term.

Assessing the Resilience Potential of Inshore and Offshore Coral Communities in the Western Gulf of Thailand

Coral reefs in the Gulf of Thailand have experienced severe coral bleaching events and anthropogenic disturbances during the last two decades. This study assessed the resilience potential of coral communities at Ko Losin offshore reef sites and Mu Ko Chumphon nearshore coral reefs, in the south of Thailand, by conducting field surveys on the live coral cover, hard substratum composition and diversity and density of juvenile corals. Most study sites had higher percentages of live coral cover compared to dead coral cover. Some inshore and offshore reef sites showed low resilience to coral bleaching events. The total densities of juvenile corals at the study sites were in the range of 0.89–3.73 colonies/m2. The density of the juvenile corals at most reef sites was not dependent on the live coral cover of adult colonies in a reef, particularly for the Acropora communities. We suggest that Ko Losin should be established as a marine protected area, and Mu Ko Chumphon National Park should implement its management plans properly to enhance coral recovery and promote marine ecotourism. Other measures, such as shading, should be also applied at some coral reefs during bleaching periods.

Conservation evidence from climate-related stressors in the deep-time marine fossil record

Conservation of marine species requires the ability to predict the effects of climate-related stressors in an uncertain future. Experiments and observations in modern settings provide crucial information, but lack temporal scale and cannot anticipate emergent effects during ongoing global change. By contrast, the deep-time fossil record contains the long-term perspective at multiple global change events that can be used, at a broad scale, to test hypothesized effects of climate-related stressors. For example, geologically rapid carbon cycle disruption has often caused crises in reef ecosystems, and selective extinctions support the hypothesis that greater activity levels promote survival. Geographical patterns of extinction and extirpation were more variable than predicted from modern physiology, with tropical and temperate extinction peaks observed at different ancient events. Like any data source, the deep-time record has limitations but also provides opportunities that complement the limitations of modern and historical data. In particular, the deep-time record is the best source of information on actual outcomes of climate-related stressors in natural settings and over evolutionary timescales. Closer integration of modern and deep-time evidence can expand the types of hypotheses testable with the fossil record, yielding better predictions of extinction risk as climate-related stressors continue to intensify in future oceans. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'

Refugia under threat: Mass bleaching of coral assemblages in high-latitude eastern Australia

Environmental anomalies that trigger adverse physiological responses and mortality are occurring with increasing frequency due to climate change. At species' range peripheries, environmental anomalies are particularly concerning because species often exist at their environmental tolerance limits and may not be able to migrate to escape unfavourable conditions. Here, we investigated the bleaching response and mortality of 14 coral genera across high-latitude eastern Australia during a global heat stress event in 2016. We evaluated whether the severity of assemblage-scale and genus-level bleaching responses was associated with cumulative heat stress and/or local environmental history, including long-term mean temperatures during the hottest month of each year (SST_LTMAX ), and annual fluctuations in water temperature (SST_VAR ) and solar irradiance (PARZ_VAR ). The most severely-bleached genera included species that were either endemic to the region (Pocillopora aliciae) or rare in the tropics (e.g. Porites heronensis). Pocillopora spp., in particular, showed high rates of immediate mortality. Bleaching severity of Pocillopora was high where SST_LTMAX was low or PARZ_VAR was high, whereas bleaching severity of Porites was directly associated with cumulative heat stress. While many tropical Acropora species are extremely vulnerable to bleaching, the Acropora species common at high latitudes, such as A. glauca and A. solitaryensis, showed little incidence of bleaching and immediate mortality. Two other regionally-abundant genera, Goniastrea and Turbinaria, were also largely unaffected by the thermal anomaly. The severity of assemblage-scale bleaching responses was poorly explained by the environmental parameters we examined. Instead, the severity of assemblage-scale bleaching was associated with local differences in species abundance and taxon-specific bleaching responses. The marked taxonomic disparity in bleaching severity, coupled with high mortality of high-latitude endemics, point to climate-driven simplification of assemblage structures and progressive homogenisation of reef functions at these high-latitude locations.

Ocean acidification during prefertilization chemical communication affects sperm success

Ocean acidification (OA) poses a major threat to marine organisms, particularly during reproduction when externally shed gametes are vulnerable to changes in seawater pH. Accordingly, several studies on OA have focused on how changes in seawater pH influence sperm behavior and/or rates of in vitro fertilization. By contrast, few studies have examined how pH influences prefertilization gamete interactions, which are crucial during natural spawning events in most externally fertilizing taxa. One mechanism of gamete interaction that forms an important component of fertilization in most taxa is communication between sperm and egg-derived chemicals. These chemical signals, along with the physiological responses in sperm they elicit, are likely to be highly sensitive to changes in seawater chemistry. In this study, we experimentally tested this possibility using the blue mussel, Mytilus galloprovincialis, a species in which females have been shown to use egg-derived chemicals to promote the success of sperm from genetically compatible males. We conducted trials in which sperm were allowed to swim in gradients of egg-derived chemicals under different seawater CO2 (and therefore pH) treatments. We found that sperm had elevated fertilization rates after swimming in the presence of egg-derived chemicals in low pH (pH 7.6) compared with ambient (pH 8.0) seawater. This observed effect could have important implications for the reproductive fitness of external fertilizers, where gamete compatibility plays a critical role in modulating reproduction in many species. For example, elevated sperm fertilization rates might disrupt the eggs' capacity to avoid fertilizations by genetically incompatible sperm. Our findings highlight the need to understand how OA affects the multiple stages of sperm-egg interactions and to develop approaches that disentangle the implications of OA for female, male, and population fitness.

Coral Reef Resilience in Taiwan: Lessons from Long-Term Ecological Research on the Coral Reefs of Kenting National Park (Taiwan)

Coral reefs in the Anthropocene are being subjected to unprecedented levels of stressors, including local disturbances—such as overfishing, habitat destruction, and pollution—and large-scale destruction related to the global impacts of climate change—such as typhoons and coral bleaching. Thus, the future of corals and coral reefs in any given community and coral-Symbiodiniaceae associations over time will depend on their level of resilience, from individual corals to entire ecosystems. Herein we review the environmental settings and long-term ecological research on coral reefs, based on both coral resilience and space, in Kenting National Park (KNP), Hengchun Peninsula, southern Taiwan, wherein fringing reefs have developed along the coast of both capes and a semi-closed bay, known as Nanwan, within the peninsula. These reefs are influenced by a branch of Kuroshio Current, the monsoon-induced South China Sea Surface Current, and a tide-induced upwelling that not only shapes coral communities, but also reduces the seawater temperature and creates fluctuating thermal environments which over time have favoured thermal-resistant corals, particularly those corals close to the thermal effluent of a nuclear power plant in the west Nanwan. Although living coral cover (LCC) has fluctuated through time in concordance with major typhoons and coral bleaching between 1986 and 2019, spatial heterogeneity in LCC recovery has been detected, suggesting that coral reef resilience is variable among subregions in KNP. In addition, corals exposed to progressively warmer and fluctuating thermal environments show not only a dominance of associated, thermally-tolerant Durusdinium spp. but also the ability to shuffle their symbiont communities in response to seasonal variations in seawater temperature without bleaching. We demonstrate that coral reefs in a small geographical range with unique environmental settings and ecological characteristics, such as the KNP reef, may be resilient to bleaching and deserve novel conservation efforts. Thus, this review calls for conservation efforts that use resilience-based management programs to reduce local stresses and meet the challenge of climate change.

Potential impacts of anthropogenic nutrient enrichment on coral reefs in the South China Sea: evidence from nutrient and chlorophyll a levels in seawater

Anthropogenic nutrient enrichment is considered to be one of the causes resulting in coral reef decline. In order to better understand the trophic status and to further explore the potential impacts of nutrients on the coral reef decline in the South China Sea (SCS), we investigated the nutrient and chlorophyll a (chl a) distributions in the surface water of reef areas across latitudes from 9-22° of the SCS. The results showed that nutrient and chl a concentrations in coastal reefs were obviously higher than those in the central and southern basin. Meanwhile, the investigation of two long-distance transects revealed an inshore-offshore nutrient decreasing trend. However, some offshore coral reefs, such as Yongxing Island, Huaguang Reef and Huangyan Island, were exceptions with relatively higher concentrations than in the surrounding reefs because of the ever-increasing human activity. Compared to other coral reefs worldwide, the nutrient concentration in reef regions of the northern and central SCS was obviously higher than that in healthy coral reefs, approaching that in unhealthy reef areas, which suggested that the present nutrient concentration may reach a risky level. Field survey showed a high ratio of macroalgal cover and coral cover in these reefs, and the significant correlation between the nutrient level and macroalgal cover indicated that elevated nutrients resulted in the phase shift from coral-dominated to macroalgal-dominated reef areas. On the other hand, a significant positive correlation between chl a in lagoons and the volume of lagoons indicated that the structural properties of large lagoons could enhance retention of nutrients and promote the growth of macroalgae, and human disturbance may aggravate the macroalgal overgrowth. Overall, anthropogenic nutrient enrichment has caused negative impacts on coral reefs of the SCS, such as regional macroalgal blooms in coastal reefs and disturbed remote reefs.

Extreme, but not moderate climate scenarios, impart sublethal effects on polyps of the Irukandji jellyfish, Carukia barnesi

Ocean acidification and warming, fueled by excess atmospheric carbon dioxide, can impose stress on marine organisms. Most studies testing the effects of climate change on marine organisms, however, use extreme climate projection scenarios, despite moderate projections scenarios being most likely to occur. Here, we examined the interactive effects of warming and acidification on reproduction, respiration, mobility and metabolic composition of polyps of the Irukandji jellyfish, Carukia barnesi, to determine the responses of a cubozoan jellyfish to moderate and extreme climate scenarios in Queensland, Australia. The experiment consisted two orthogonal factors: temperature (current 25 °C and future 28 °C) and pH (current (8.0) moderate (7.9) and extreme (7.7)). All polyps survived in the experiment but fewer polyps were produced in the pH 7.7 treatment compared to pH 7.9 and pH 8.0. Respiration rates were elevated in the lowest pH treatment throughout most of the experiment and polyps were approximately half as mobile in this treatment compared to pH 7.9 and pH 8.0, regardless of temperature. We identified metabolites occurring at significantly lower relative abundance in the lowest pH (i.e. glutamate, acetate, betaine, methylguanidine, lysine, sarcosine, glycine) and elevated temperature (i.e. proline, trigonelline, creatinine, mannose, acetate, betaine, methylguanidine, lysine, sarcosine) treatments. Glycine was the only metabolite exhibiting an interactive effect between pH and temperature. Our results suggest that C. barnesi polyps are unaffected by the most optimistic climate scenario and may tolerate even extreme climate conditions to some extent.

Development and application of a low-cost rapid assessment system for coastal benthic habitats

Information on community structure and spatial distribution of benthic habitats are important in marine conservation and management. Coral areas, often monitored by trained scuba divers, are of importance for the ecosystem goods and services they provide. The data gathered may, however, be limited due to cost and time constraints. These restrictions and the continuing decline in coral reef health contribute to the need to develop rapid methods to efficiently document the distribution and status of coral reefs. A Rapid Assessment Instrument for Coastal Benthic Habitats (ARAICoBeH) System was developed to enable large-scale but low-cost coastal benthic habitat characterization and mapping without compromising accuracy. Inquiries on community structure and status in coral-dominated areas are also possible with the data collected using the method. The instrument, as well as the data processing and mapping algorithm are described in detail in this paper. A comparative study was conducted between ARAICoBeH and the frequently used underwater photo transect method. Variables compared were percent coral cover, functional group diversity, community structure as well as time and monetary requirements. There were no significant differences in estimates of percent coral cover and diversity of benthic functional groups for majority of sites while estimates of community structure were very similar. ARAICoBeH is cheaper and requires less time to gather the same amount of data as that of the photo transect method. The spatial distribution of coastal benthic habitats and community structure of coral-dominated areas in El Nido, Palawan, Philippines, are included to illustrate the application of the method.

Simulating and Quantifying Multiple Natural Subsea CO2 Seeps at Panarea Island (Aeolian Islands, Italy) as a Proxy for Potential Leakage from Subseabed Carbon Storage Sites

Carbon dioxide (CO₂) capture and storage (CCS) has been discussed as a potentially significant mitigation option for the ongoing climate warming. Natural CO₂ release sites serve as natural laboratories to study subsea CO₂ leakage in order to identify suitable analytical methods and numerical models to develop best-practice procedures for the monitoring of subseabed storage sites. We present a new model of bubble (plume) dynamics, advection-dispersion of dissolved CO₂, and carbonate chemistry. The focus is on a medium-sized CO₂ release from 294 identified small point sources around Panarea Island (South-East Tyrrhenian Sea, Aeolian Islands, Italy) in water depths of about 40-50 m. This study evaluates how multiple CO₂ seep sites generate a temporally variable plume of dissolved CO₂. The model also allows the overall flow rate of CO₂ to be estimated based on field measurements of pH. Simulations indicate a release of ∼6900 t y^-1 of CO₂ for the investigated area and highlight an important role of seeps located at >20 m water depth in the carbon budget of the Panarea offshore gas release system. This new transport-reaction model provides a framework for understanding potential future leaks from CO₂ storage sites.

Application of the Ostrom framework in the analysis of a social-ecological system with multiple resources in a marine protected area

The framework proposed by Ostrom (2009) has become one of the most utilized tools to address the complexity of social-ecological systems. Most cases use this framework to analyze the systems from the perspective of a single resource unit. However, the livelihoods in several coastal communities are diverse, so that the users interact with multiple common-pool resources, which makes their analysis difficult. In this sense, it is important to identify the key elements of management to achieve the sustainable use of the resources. In this study, we were able to do this in a coastal community where commercial fishing, ecotourism, and recreational fishing coexist. The system of interest, located in the state of Quintana Roo, Mexico, was subdivided by resource type using a multi-method approach to data collection including surveys, interviews, and records review. A conceptual map was developed that shows how the second-tier variables are integrated through the governance and actors with the biophysical system. The actors involved in lobster fishing achieved a more complex governance system, followed by the ecotourism and recreational fishing; the complexity of the governance was related with the equity level of the actors. The analysis revealed the research gaps to develop management strategies and improve the sustainability of the system.

Immediate Effects of Hurricanes on a Diverse Coral/Mangrove Ecosystem in the U.S. Virgin Islands and the Potential for Recovery

Hurricanes Irma and Maria, two powerful storms that hit the U.S. Virgin Islands less than 2 weeks apart in September 2017, caused extensive damage to the natural resources on St. John. Damage was particularly severe in a unique mangrove/coral ecosystem in three bays within Virgin Islands Coral Reef National Monument, a National Park Service marine protected area. Many Red Mangrove (Rhizophora mangle) trees were uprooted and tossed into the sea, and the prop roots of others were stripped of corals, sponges and other marine life. No other mangrove area in the Caribbean is known to have so many scleractinian corals (about 30 species before the storms). Although many corals were overturned or buried in rubble, colonies of most of the species, including four that are listed as threatened under the U.S. Endangered Species Act, survived. Recovery of this ecosystem will depend on Red Mangrove propagules becoming established and producing prop roots to support rich marine life along with a canopy to provide the shade that was critical to the biodiversity that was present before the storms. Unlike in many situations where major disturbances reduce coral cover, the substrate that must be restored for full recovery to occur is a living substrate—the prop roots of the mangroves. Larvae of corals and sponges will need to recruit on to the roots. Future storms could hinder this process.

The role of chromatin dynamics under global warming response in the symbiotic coral model Aiptasia

Extreme weather events frequency and scale are altered due to climate change. Symbiosis between corals and their endosymbiotic-dinoflagellates (Symbiodinium) is susceptible to these events and can lead to what is known as bleaching. However, there is evidence for coral adaptive plasticity in the role of epigenetic that have acclimated to high-temperature environments. We have implemented ATAC-seq and RNA-seq to study the cnidarian-dinoflagellate model Exaptasia pallida (Aiptasia) and expose the role of chromatin-dynamics in response to thermal-stress. We have identified 1309 genomic sites that change their accessibility in response to thermal changes. Moreover, apo-symbiotic Aiptasia accessible sites were enriched with NFAT, ATF4, GATA3, SOX14, and PAX3 motifs and expressed genes related to immunological pathways. Symbiotic Aiptasia accessible sites were enriched with NKx3-1, HNF4A, IRF4 motifs and expressed genes related to oxidative-stress pathways. Our work opens a new path towards understanding thermal-stress gene regulation in association with gene activity and chromatin-dynamics.

Carbonic anhydrase activity as a potential biomarker for acute exposure to copper in corals

Coral reefs are subjected to climate change and are severely impacted by human activities, with copper (Cu) being a relevant physiological stressor for corals at local scale. The ecological relevance of parameters measured at biochemical or cellular level is now considered an extremely important feature in environmental studies, and can be used as early warning signs of environmental degradation. In this context, the effects of acute exposure (96 h) to Cu were assessed on the maximum photochemical efficiency of zooxanthellae (Fv/Fm) and on the activity of key enzymes [carbonic anhydrase (CA) and Ca-ATPase] involved in coral physiology using the scleractinian coral Mussismilia harttii as a biological model. Corals were exposed to different concentrations of dissolved Cu (4.6-19.4 μg/L) using two different experimental approaches: a laboratory closed system and a marine mesocosm system. Fv/Fm values and Ca - ATPase activity were not affect by exposure to Cu in any of the exposure systems. However, a significant reduction in CA activity was observed in corals exposed to 11.9 and 19.4 μg Cu/L in the laboratory and at all concentrations of Cu tested in the mesocosm system (4.6, 6.0 and 8.5 μg/L). Based on the sensitivity of this enzyme to the short period of exposure to sublethal concentrations of Cu in both experimental approaches, the present study suggests the use of CA activity as a potential biomarker to be used in biomarker-based environmental monitoring programs in coral reefs.

Coral Reef Change Detection in Remote Pacific Islands Using Support Vector Machine Classifiers

Despite the abundance of research on coral reef change detection, few studies have been conducted to assess the spatial generalization principles of a live coral cover classifier trained using remote sensing data from multiple locations. The aim of this study is to develop a machine learning classifier for coral dominated benthic cover-type class (CDBCTC) based on ground truth observations and Landsat images, evaluate the performance of this classifier when tested against new data, then deploy the classifier to perform CDBCTC change analysis of multiple locations. The proposed framework includes image calibration, support vector machine (SVM) training and tuning, statistical assessment of model accuracy, and temporal pixel-based image differencing. Validation of the methodology was performed by cross-validation and train/test split using ground truth observations of benthic cover from four different reefs. These four locations (Palmyra Atoll, Kingman Reef, Baker Island Atoll, and Howland Island) as well as two additional locations (Kiritimati Island and Tabuaeran Island) were then evaluated for CDBCTC change detection. The in-situ training accuracy against ground truth observations for Palmyra Atoll, Kingman Reef, Baker Island Atoll, and Howland Island were 87.9%, 85.7%, 69.2%, and 82.1% respectively. The classifier attained generalized accuracy scores of 78.8%, 81.0%, 65.4%, and 67.9% for the respective locations when trained using ground truth observations from neighboring reefs and tested against the local ground truth observations of each reef. The classifier was trained using the consolidated ground truth data of all four sites and attained a cross-validated accuracy of 75.3%. The CDBCTC change detection analysis showed a decrease in CDBCTC of 32% at Palmyra Atoll, 25% at Kingman Reef, 40% at Baker Island Atoll, 25% at Howland Island, 35% at Tabuaeran Island, and 43% at Kiritimati Island. This research establishes a methodology for developing a robust classifier and the associated Controlled Parameter Cross-Validation (CPCV) process for evaluating how well the model will generalize to new data. It is an important step for improving the scientific understanding of temporal change within coral reefs around the globe.

The Draft Genome of an Octocoral, Dendronephthya gigantea

Coral reefs composed of stony corals are threatened by global marine environmental changes. However, soft coral communities of octocorallian species, appear more resilient. The genomes of several cnidarians species have been published, including from stony corals, sea anemones, and hydra. To fill the phylogenetic gap for octocoral species of cnidarians, we sequenced the octocoral, Dendronephthya gigantea, a nonsymbiotic soft coral, commonly known as the carnation coral. The D. gigantea genome size is ∼276 Mb. A high-quality genome assembly was constructed from PacBio long reads (29.85 Gb with 108× coverage) and Illumina short paired-end reads (35.54 Gb with 128× coverage) resulting in the highest N50 value (1.4 Mb) reported thus far among cnidarian genomes. About 12% of the genome is repetitive elements and contained 28,879 predicted protein-coding genes. This gene set is composed of 94% complete BUSCO ortholog benchmark genes, which is the second highest value among the cnidarians, indicating high quality. Based on molecular phylogenetic analysis, octocoral and hexacoral divergence times were estimated at 544 MYA. There is a clear difference in Hox gene composition between these species: unlike hexacorals, the Antp superclass Evx gene was absent in D. gigantea. Here, we present the first genome assembly of a nonsymbiotic octocoral, D. gigantea to aid in the comparative genomic analysis of cnidarians, including stony and soft corals, both symbiotic and nonsymbiotic. The D. gigantea genome may also provide clues to mechanisms of differential coping between the soft and stony corals in response to scenarios of global warming.

Place-based management can reduce human impacts on coral reefs in a changing climate

Declining natural resources have contributed to a cultural renaissance across the Pacific that seeks to revive customary ridge-to-reef management approaches to protect freshwater and restore abundant coral reef fisheries. We applied a linked land-sea modeling framework based on remote sensing and empirical data, which couples groundwater nutrient export and coral reef models at fine spatial resolution. This spatially explicit (60 × 60 m) framework simultaneously tracks changes in multiple benthic and fish indicators as a function of community-led marine closures, land-use and climate change scenarios. We applied this framework in Hā'ena and Ka'ūpūlehu, located at opposite ends of the Hawaiian Archipelago to investigate the effects of coastal development and marine closures on coral reefs in the face of climate change. Our results indicated that projected coastal development and bleaching can result in a significant decrease in benthic habitat quality and community-led marine closures can result in a significant increase in fish biomass. In general, Ka'ūpūlehu is more vulnerable to land-based nutrients and coral bleaching than Hā'ena due to high coral cover and limited dilution and mixing from low rainfall and wave power, except for the shallow and wave-sheltered back-reef areas of Hā'ena, which support high coral cover and act as nursery habitat for fishes. By coupling spatially explicit land-sea models with scenario planning, we identified priority areas on land where upgrading cesspools can reduce human impacts on coral reefs in the face of projected climate change impacts.

Proteomic Basis of Symbiosis: A Heterologous Partner Fails to Duplicate Homologous Colonization in a Novel Cnidarian- Symbiodiniaceae Mutualism

Reef corals and sea anemones form symbioses with unicellular symbiotic dinoflagellates. The molecular circumventions that underlie the successful intracellular colonization of hosts by symbionts are still largely unknown. We conducted proteomic analyses to determine molecular differences of Exaiptasia pallida anemones colonized by physiologically different symbiont species, in comparison with symbiont-free (aposymbiotic) anemones. We compared one homologous species, Symbiodinium linucheae, that is natively associated with the clonal Exaiptasia strain (CC7) to another heterologous species, Durusdinium trenchii, a thermally tolerant species that colonizes numerous coral species. This approach allowed the discovery of a core set of host genes that are differentially regulated as a function of symbiosis regardless of symbiont species. The findings revealed that symbiont colonization at higher densities requires circumvention of the host cellular immunological response, enhancement of ammonium regulation, and suppression of phagocytosis after a host cell in colonized. Furthermore, the heterologous symbionts failed to duplicate the same level of homologous colonization within the host, evidenced by substantially lower symbiont densities. This reduced colonization of D. trenchii correlated with its inability to circumvent key host systems including autophagy-suppressing modulators, cytoskeletal alteration, and isomerase activity. The larger capability of host molecular circumvention by homologous symbionts could be the result of a longer evolutionary history of host/symbiont interactions, which translates into a more finely tuned symbiosis. These findings are of great importance within the context of the response of reef corals to climate change since it has been suggested that coral may acclimatize to ocean warming by changing their dominant symbiont species.

Annual Thermal Stress Increases a Soft Coral's Susceptibility to Bleaching

Like scleractinian corals, soft corals contain photosymbionts (Family Symbiodiniaceae) that provide energy for the host. Recent thermal events have resulted in soft coral bleaching in four of five years on Guam, where they dominated back-reef communities. Soft coral bleaching was examined in Sinularia maxima, S. polydactyla, and their hybrid S. maxima x polydactyla. Results from annual field surveys indicated that S. maxima and the hybrid were more susceptible to bleaching than S. polydactyla, and this was related to differences in their Symbiodiniaceae communities in 2016 and 2017. The photosymbionts of S. polydactyla were apparently more stress tolerant and maintained higher photosynthetic potential through three years of bleaching, in contrast to the other species that exhibited a decline in photosynthetic potential after the first year of bleaching. Nonetheless, by the 2017 bleaching event all soft coral populations exhibited significant bleaching-mediated declines and loss of photosynthetic efficiency suggesting a declining resiliency to annual thermal stress events. While S. polydactyla initially looked to succeed the other species as the dominant space occupying soft coral on Guam back-reefs, cumulative bleaching events ultimately turned this "winner" into a "loser", suggesting the trajectory for coral reefs is towards continued loss of structure and function.

Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA

Marine environments face acute pressures from human impacts, often resulting in substantial changes in community structure. On the inshore Great Barrier Reef (GBR), palaeoecological studies show the collapse of the previously dominant coral Acropora from the impacts of degraded water quality associated with European colonization. Even more dramatic impacts can result in the replacement of corals by fleshy macroalgae on modern reefs, but their past distribution is unknown because they leave no fossil record. Here, we apply DNA metabarcoding and high-throughput sequencing of the 18S rDNA gene on palaeoenvironmental DNA (aeDNA) derived from sediment cores at two sites on Pandora Reef (GBR), to enhance palaeoecological studies by incorporating key soft-bodied taxa, including macroalgae. We compared temporal trends in this aeDNA record with those of coral genera derived from macrofossils. Multivariate analysis of 12 eukaryotic groups from the aeDNA community showed wide variability over the past 750 years. The occurrence of brown macroalgae was negatively correlated only with the dominant coral at both sites. The occurrence of coralline and green macroalgae was positively correlated with only the dominant coral at one of the sites, where we also observed a significant association between the whole coral community and the occurrence of each of the three macroalgae groups. Our results demonstrate that reef sediments can provide a valuable archive for understanding the past distribution and occurrence of important soft-bodied reef dwellers. Combining information from fossils and aeDNA provides an enhanced understanding of temporal changes of reefs ecosystems at decadal to millennial timescales.

Light limitation selects for depth generalists in urbanised reef coral communities

Depth range is an important species trait for coral reef organisms, yet it remains to be quantified and analysed adequately among tropical coral species. Filling this knowledge gap is crucial as the depth limits of corals are related to important environmental factors such as light and temperature. Furthermore, the health and survivorship of corals may be threatened due to warming-induced sea-level rise, particularly for colonies living at the deeper limits of species depth ranges. Here we collected benthic and environmental data along the reef profile to characterise the depth ranges of coral species, and analysed species diversity and community structure in relation to possible depth-related biophysical parameters on the sediment-stressed reefs of Singapore. The results reveal clear environmental covariations with depth, expectedly with light availability showing the most marked decline as depth increases. Live coral cover, species richness and diversity are associated positively and significantly with light, which also structures coral communities along the reef profile more strongly than temperature or sediment levels. Relatedly, we detect species-specific depth distributions with two main strategies observed among coral species: shallow specialists and depth generalists. We suggest that corals in Singapore are unlikely to be impacted by light limitation specifically as sea level rises due to the wider depth range of the deeper species. Our data will inform conservation efforts especially in the selection of sites and depths for coral transplantation.

Nutrient pollution disrupts key ecosystem functions on coral reefs

There is a long history of examining the impacts of nutrient pollution and pH on coral reefs. However, little is known about how these two stressors interact and influence coral reef ecosystem functioning. Using a six-week nutrient addition experiment, we measured the impact of elevated nitrate (NO^-₃) and phosphate (PO^3-₄) on net community calcification (NCC) and net community production (NCP) rates of individual taxa and combined reef communities. Our study had four major outcomes: (i) NCC rates declined in response to nutrient addition in all substrate types, (ii) the mixed community switched from net calcification to net dissolution under medium and high nutrient conditions, (iii) nutrients augmented pH variability through modified photosynthesis and respiration rates, and (iv) nutrients disrupted the relationship between NCC and aragonite saturation state documented in ambient conditions. These results indicate that the negative effect of NO^-₃ and PO^3-₄ addition on reef calcification is likely both a direct physiological response to nutrients and also an indirect response to a shifting pH environment from altered NCP rates. Here, we show that nutrient pollution could make reefs more vulnerable to global changes associated with ocean acidification and accelerate the predicted shift from net accretion to net erosion.

Gene Expression Profiles of Two Coral Species with Varied Resistance to Ocean Acidification

Recent studies have indicated that various corals might have different degrees of resistance to elevated CO₂ levels. However, the underlying molecular mechanism accounting for these differences is still poorly understood. In this study, RNA-seq data were analyzed to identify differentially expressed genes in two coral species (Acropora austera and Acropora cerealis) in response to high CO₂ levels. The calcification rates were higher in high CO₂ treatment than the control in A. austera, but was not significantly different in A. cerealis. A KEGG database search revealed that in both coral species, most Ca²⁺ transporters were present in the calcium signaling pathway, which could be important in the CO₂ regulation of coral calcification. The gene expression levels of many CO₂ and HCO₃^- transporters were not affected by elevated CO₂. Nevertheless, high CO₂ levels did have an effect on the expression of certain Ca²⁺ transporters. The upregulation of Ca²⁺ transporters likely explained the higher resistance of A. austera to high CO₂ than A. cerealis.

A global analysis of coral bleaching over the past two decades

Thermal-stress events associated with climate change cause coral bleaching and mortality that threatens coral reefs globally. Yet coral bleaching patterns vary spatially and temporally. Here we synthesize field observations of coral bleaching at 3351 sites in 81 countries from 1998 to 2017 and use a suite of environmental covariates and temperature metrics to analyze bleaching patterns. Coral bleaching was most common in localities experiencing high intensity and high frequency thermal-stress anomalies. However, coral bleaching was significantly less common in localities with a high variance in sea-surface temperature (SST) anomalies. Geographically, the highest probability of coral bleaching occurred at tropical mid-latitude sites (15-20 degrees north and south of the Equator), despite similar thermal stress levels at equatorial sites. In the last decade, the onset of coral bleaching has occurred at significantly higher SSTs (∼0.5 °C) than in the previous decade, suggesting that thermally susceptible genotypes may have declined and/or adapted such that the remaining coral populations now have a higher thermal threshold for bleaching.

Resilience of Central Pacific reefs subject to frequent heat stress and human disturbance

Frequent occurrences of coral bleaching and associated coral mortality over recent decades have raised concerns about the survival of coral reefs in a warming planet. The El Niño-influenced coral reefs in the central Gilbert Islands of the Republic of Kiribati, which experience years with prolonged heat stress more frequently than 99% of the world's reefs, may serve as a natural model for coral community response to frequent heat stress. Here we use nine years of survey data (2004-2012) and a suite of remote sensing variables from sites along gradients of climate variability and human disturbance in the region to evaluate the drivers of coral community response to, and recovery from, multiple heat stress events. The results indicate that the extent of bleaching was limited during the 2009-2010 El Niño event, in contrast to a similar 2004-2005 event, and was correlated with incoming light and historical temperature variability, rather than heat stress. Spatial and temporal patterns in benthic cover suggest growing resistance to bleaching-level heat stress among coral communities subject to high inter-annual temperature variability and local disturbance, due to the spread of "weedy" and temperature-tolerant species (e.g., Porites rus) and the cloudy conditions in the region during El Niño events.

Thermal and Herbicide Tolerances of Chromerid Algae and Their Ability to Form a Symbiosis With Corals

Reef-building corals form an obligate symbiosis with photosynthetic microalgae in the family Symbiodiniaceae that meet most of their energy requirements. This symbiosis is under threat from the unprecedented rate of ocean warming as well as the simultaneous pressure of local stressors such as poor water quality. Only 1°C above mean summer sea surface temperatures (SSTs) on the Great Barrier Reef (GBR) can trigger the loss of Symbiodiniaceae from the host, and very low concentrations of the most common herbicide, diuron, can disrupt the photosynthetic activity of microalgae. In an era of rapid environmental change, investigation into the assisted evolution of the coral holobiont is underway in an effort to enhance the resilience of corals. Apicomplexan-like microalgae were discovered in 2008 and the Phylum Chromerida (chromerids) was created. Chromerids have been isolated from corals and contain a functional photosynthetic plastid. Their discovery therefore opens a new avenue of research into the use of alternative/additional photosymbionts of corals. However, only two studies to-date have investigated the symbiotic nature of Chromera velia with corals and thus little is known about the coral-chromerid relationship. Furthermore, the response of chromerids to environmental stressors has not been examined. Here we tested the performance of four chromerid strains and the common dinoflagellate symbiont Cladocopium goreaui (formerly Symbiodinium goreaui, ITS2 type C1) in response to elevated temperature, diuron and their combined exposure. Three of the four chromerid strains exhibited high thermal tolerances and two strains showed exceptional herbicide tolerances, greater than observed for any photosynthetic microalgae, including C. goreaui. We also investigated the onset of symbiosis between the chromerids and larvae of two common GBR coral species under ambient and stress conditions. Levels of colonization of coral larvae with the chromerid strains were low compared to colonization with C. goreaui. We did not observe any overall negative or positive larval fitness effects of the inoculation with chromerid algae vs. C. goreaui. However, we cannot exclude the possibility that chromerid algae may have more important roles in later coral life stages and recommend this be the focus of future studies.