A depth refugium from catastrophic coral bleaching prevents regional extinction

Measuring multi-year changes in the Symbiodiniaceae algae in Caribbean corals on coral-depleted reefs

Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from nine species were marked and sampled in 2017. Of these colonies, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes (2017) and the regional onset of stony coral tissue loss disease (2019). While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together, these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals.

Depth variation in benthic community response to repeated marine heatwaves on remote Central Indian Ocean reefs

Coral reefs are increasingly impacted by climate-induced warming events. However, there is limited empirical evidence on the variation in the response of shallow coral reef communities to thermal stress across depths. Here, we assess depth-dependent changes in coral reef benthic communities following successive marine heatwaves from 2015 to 2017 across a 5-25 m depth gradient in the remote Chagos Archipelago, Central Indian Ocean. Our analyses show an overall decline in hard and soft coral cover and an increase in crustose coralline algae, sponge and reef pavement following successive marine heatwaves on the remote reef system. Our findings indicate that the changes in benthic communities in response to elevated seawater temperatures varied across depths. We found greater changes in benthic group cover at shallow depths (5-15 m) compared with deeper zones (15-25 m). The loss of hard coral cover was better predicted by initial thermal stress, while the loss of soft coral was associated with repeated thermal stress following successive warming events. Our study shows that benthic communities extending to 25 m depth were impacted by successive marine heatwaves, supporting concerns about the resilience of shallow coral reef communities to increasingly severe climate-driven warming events.

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

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

Oceanic differences in coral-bleaching responses to marine heatwaves

Anomalously high ocean temperatures have increased in frequency, intensity, and duration over the last several decades because of greenhouse gas emissions that cause global warming and marine heatwaves. Reef-building corals are sensitive to such temperature anomalies that commonly lead to coral bleaching, mortality, and changes in community structure. Yet, despite these overarching effects, there are geographical differences in thermal regimes, evolutionary histories, and past disturbances that may lead to different bleaching responses of corals within and among oceans. Here we examined the overall bleaching responses of corals in the Atlantic, Indian, and Pacific Oceans, using both a spatially explicit Bayesian mixed-effects model and a deep-learning neural-network model. We used a 40-year global dataset encompassing 23,288 coral-reef surveys at 11,058 sites in 88 countries, from 1980 to 2020. Focusing on ocean-wide differences we assessed the relationships between the percentage of bleached corals and different temperature-related metrics alongside a suite of environmental variables. We found that while high sea-surface temperatures were consistently, and strongly, related to coral bleaching within all oceans, there were clear geographical differences in the relationships between coral bleaching and most environmental variables. For instance, there was an increase in coral bleaching with depth in the Atlantic Ocean whereas the opposite was observed in the Indian Ocean, and no clear trend could be seen in the Pacific Ocean. The standard deviation of thermal-stress anomalies was negatively related to coral bleaching in the Atlantic and Pacific Oceans, but not in the Indian Ocean. Globally, coral bleaching has progressively occurred at higher temperatures over the last four decades within the Atlantic, Indian, and Pacific Oceans, although, again, there were differences among the three oceans. Together, such patterns highlight that historical circumstances and geographical differences in oceanographic conditions play a central role in contemporary coral-bleaching responses.

Benthic Characterization of Mesophotic Communities Based on Optical Depths in the Southern Mexican Pacific Coast (Oaxaca)

The distinction between shallow coral reefs and mesophotic coral ecosystems (MCEs) has not been fully clarified yet. The original definition of MCEs, by depths of 30–150 m, fixes their bathymetrical limits and fails to accommodate environmental and biological variation. Recent studies have indicated that water transparency and light availability may explain why MCEs do not occur at fixed depths but vary among localities. This study aimed to evaluate the presence and distribution of MCEs, along the central coast of Oaxaca, through optical depths and the associated benthic community. Using MODIS-Aqua satellite data (Kd490), we estimated the mesophotic optical depths monthly (z10%, z1%, z0.1%), over the last four years. In addition, to characterize benthic community structure, we conducted underwater photo quadrat surveys at two locations on the southern Mexican Pacific coast from 10 to 55 m depth. Significant differences between depths and locations were found in benthic communities. Furthermore, the lower distribution of photosynthetic taxa was different between the two locations but indicative to the z10% and z1% in both cases. Those differences were associated with the upwelling season, which reduces, drastically and differentially, the light availability for benthic communities between the two locations and limits the development of MCEs on the central coast of Oaxaca.

The Hidden Diversity of Temperate Mesophotic Ecosystems from Central Chile (Southeastern Pacific Ocean) Assessed through Towed Underwater Videos

The largely unexplored diversity in temperate mesophotic ecosystems (TME, ~30–150 m depth) has attracted much attention over the past years. However, the number of studies and knowledge of TME diversity and ecology remains limited and geographically restricted. The absence of information on how assemblages vary across environmental gradients and with depth for most regions also limits our capacity to delimit conservation areas and devise management plans effectively. This study focuses on TME from central Chile and describes the depth distribution of reef fishes and benthic invertebrates and algae for the first time. Through the analysis of towed underwater video surveys between 4.7–95.5 m in multiple sites, we show that total reef fish density and richness decrease with depth but increase with local topographic complexity. The depth-related density varies among fish species and trophic groups, and it reverses in the case of Sebastes oculatus, which increases in density with depth. Sponges and gorgonians dominate benthic assemblages below 20 m depth, and brachiopods and anemones increase below 40 and 60 m, respectively. Some of these species form animal forests which, to some extent, replace the shallow-water kelp forests as structural habitat providers. Nevertheless, the reef fish and benthic community do not show a clear structure with depth or across studied sites. We highlight the urgency to intensify and expand the quantitative characterization of these communities, through this and other methodologies, to better define ecological patterns and advance towards conservation plans for TME, including the Souteastern Pacific region.

Upwelling, climate change, and the shifting geography of coral reef development

The eastern tropical Pacific is oceanographically unfavorable for coral-reef development. Nevertheless, reefs have persisted there for the last 7000 years. Rates of vertical accretion during the Holocene have been similar in the strong-upwelling Gulf of Panamá (GoP) and the adjacent, weak-upwelling Gulf of Chiriquí (GoC); however, seasonal upwelling in the GoP exacerbated a climate-driven hiatus in reef development in the late Holocene. The situation is now reversed and seasonal upwelling in the GoP currently buffers thermal stress, creating a refuge for coral growth. We developed carbonate budget models to project the capacity of reefs in both gulfs to keep up with future sea-level rise. On average, the GoP had significantly higher net carbonate production rates than the GoC. With an estimated contemporary reef-accretion potential (RAP) of 5.5 mm year^-1, reefs in the GoP are projected to be able to keep up with sea-level rise if CO₂ emissions are reduced, but not under current emissions trajectories. With an estimated RAP of just 0.3 mm year^-1, reefs in the GoC are likely already unable to keep up with contemporary sea-level rise in Panamá (1.4 mm year^-1). Whereas the GoP has the potential to support functional reefs in the near-term, our study indicates that their long-term persistence will depend on reduction of greenhouse gases.

Hidden heatwaves and severe coral bleaching linked to mesoscale eddies and thermocline dynamics

The severity of marine heatwaves (MHWs) that are increasingly impacting ocean ecosystems, including vulnerable coral reefs, has primarily been assessed using remotely sensed sea-surface temperatures (SSTs), without information relevant to heating across ecosystem depths. Here, using a rare combination of SST, high-resolution in-situ temperatures, and sea level anomalies observed over 15 years near Moorea, French Polynesia, we document subsurface MHWs that have been paradoxical in comparison to SST metrics and associated with unexpected coral bleaching across depths. Variations in the depth range and severity of MHWs was driven by mesoscale (10s to 100s of km) eddies that altered sea levels and thermocline depths and decreased (2007, 2017 and 2019) or increased (2012, 2015, 2016) internal-wave cooling. Pronounced eddy-induced reductions in internal waves during early 2019 contributed to a prolonged subsurface MHW and unexpectedly severe coral bleaching, with subsequent mortality offsetting almost a decade of coral recovery. Variability in mesoscale eddy fields, and thus thermocline depths, is expected to increase with climate change, which, along with strengthening and deepening stratification, could increase the occurrence of subsurface MHWs over ecosystems historically insulated from surface ocean heating by the cooling effects of internal waves.

Coral-bleaching responses to climate change across biological scales

The global impacts of climate change are evident in every marine ecosystem. On coral reefs, mass coral bleaching and mortality have emerged as ubiquitous responses to ocean warming, yet one of the greatest challenges of this epiphenomenon is linking information across scientific disciplines and spatial and temporal scales. Here we review some of the seminal and recent coral-bleaching discoveries from an ecological, physiological, and molecular perspective. We also evaluate which data and processes can improve predictive models and provide a conceptual framework that integrates measurements across biological scales. Taking an integrative approach across biological and spatial scales, using for example hierarchical models to estimate major coral-reef processes, will not only rapidly advance coral-reef science but will also provide necessary information to guide decision-making and conservation efforts. To conserve reefs, we encourage implementing mesoscale sanctuaries (thousands of km² ) that transcend national boundaries. Such networks of protected reefs will provide reef connectivity, through larval dispersal that transverse thermal environments, and genotypic repositories that may become essential units of selection for environmentally diverse locations. Together, multinational networks may be the best chance corals have to persist through climate change, while humanity struggles to reduce emissions of greenhouse gases to net zero.

Marine heatwaves impair the thermal refugia potential of marginal reefs in the northern South China Sea

Frequent marine heatwaves (MHWs), concurrent with climate warming, threaten global low-latitude, pristine coral reefs, leading to growing interest in identifying marginal coral reefs (relatively high-latitude and/or turbid reef environments) that can serve as thermal refugia from mass coral bleaching. However, the thermal refugia potential of marginal reefs remains controversial. We evaluated the thermal refugia potential of inshore reefs in the northern South China Sea (nSCS), a globally typical marginal reef system, by characterizing the long-term trend of MHW intensity and frequency and assessing thermal stress during a mass bleaching event in summer 2020. An unprecedented peak intensity of around 20 °C-weeks of cumulative heat stress, associated with a prolonged anomalous western Pacific subtropical high (WPSH) and weakened monsoon activity, induced record-breaking bleaching. The geographical variability of bleaching was strongly related to the extent of heat exposure and satellite-derived temperature anomalies. Under ongoing global warming, the frequency and intensity of MHWs over nSCS coral habitats show a markedly increasing trend, especially during the last decade. Intense MHWs and coral bleaching have already occurred throughout all El Niño-Southern Oscillation (ENSO) phases (e.g., 2010, 2015, and 2020). Climate change has pushed marginal coral reefs to or beyond the limits of their resilience, and frequent MHW events have amplified the increasing risk of thermal stress. There are no long-term thermal refugia for marginal reefs in the nSCS.

Past the Precipice? Projected Coral Habitability Under Global Heating

Coral reefs are rapidly declining due to local environmental degradation and global climate change. In particular, corals are vulnerable to ocean heating. Anomalously hot sea surface temperatures (SSTs) create conditions for severe bleaching or direct thermal death. We use SST observations and CMIP6 model SST to project thermal conditions at reef locations at a resolution of 1 km, a 16-fold improvement over prior studies, under four climate emissions scenarios. We use a novel statistical downscaling method which is significantly more skillful than the standard method, especially at near-coastal pixels where many reefs are found. For each location we present projections of thermal departure (TD, the date after which a location with steadily increasing heat exceeds a given thermal metric) for severe bleaching recurs every 5 years (TD5Y) and every 10 years (TD10Y), accounting for a range of post-bleaching reef recovery/degradation. As of 2021, we find that over 91% and 79% of 1 km² reefs have exceeded TD10Y and TD5Y, respectively, suggesting that widespread long-term coral degradation is no longer avoidable. We project 99% of 1 km² reefs to exceed TD5Y by 2034, 2036, and 2040 under SSP5-8.5, SSP3-7.0, and SSP2-4.5 respectively. We project that 2%-5% of reef locations remain below TD5Y at 1.5°C of mean global heating, but 0% remain at 2.0°C. These results demonstrate the importance of further improving ecological projection capacity for climate-vulnerable marine and terrestrial species and ecosystems, including identifying refugia and guiding conservation efforts. Ultimately, saving coral reefs will require rapidly reducing and eliminating greenhouse gas emissions.

A community and functional comparison of coral and reef fish assemblages between four decades of coastal urbanisation and thermal stress

Urbanized coral reefs experience anthropogenic disturbances caused by coastal development, pollution, and nutrient runoff, resulting in turbid, marginal conditions in which only certain species can persist. Mortality effects are exacerbated by increasingly regular thermal stress events, leading to shifts towards novel communities dominated by habitat generalists and species with low structural complexity.

There is limited data on the turnover processes that occur due to this convergence of anthropogenic stressors, and how novel urban ecosystems are structured both at the community and functional levels. As such, it is unclear how they will respond to future disturbance events.

Here, we examine the patterns of coral reef community change and determine whether ecosystem functions provided by specialist species are lost post‐disturbance. We present a comparison of community and functional trait‐based changes for scleractinian coral genera and reef fish species assemblages subject to coastal development, coastal modification, and mass bleaching between two time periods, 1975–1976 and 2018, in Nakagusuku Bay, Okinawa, Japan.

We observed an increase in fish habitat generalists, a dominance shift from branching to massive/sub‐massive corals and increasing site‐based coral genera richness between years. Fish and coral communities significantly reassembled, but functional trait‐based multivariate space remained constant, indicating a turnover of species with similar traits. A compression of coral habitat occurred, with shallow (<5 m) and deep (>8 m) coral genera shifting towards the mid‐depths (5–8 m).

We show that although reef species assemblages altered post disturbance, new communities retained similar ecosystem functions. This result could be linked to the stressors experienced by urban reefs, which reflect those that will occur at an increasing frequency globally in the near future. Yet, even after shifts to disturbed communities, these fully functioning reef systems may maintain high conservation value.

Community similarity and species overlap between habitats provide insight into the deep reef refuge hypothesis

The deep reef refuge hypothesis (DRRH) postulates that mesophotic coral ecosystems (MCEs) may provide a refuge for shallow coral reefs (SCRs). Understanding this process is an important conservation tool given increasing threats to coral reefs. To establish a better framework to analyze the DRRH, we analyzed stony coral communities in American Sāmoa across MCEs and SCRs to describe the community similarity and species overlap to test the foundational assumption of the DRRH. We suggest a different approach to determine species as depth specialists or generalists that changes the conceptual role of MCEs and emphasizes their importance in conservation planning regardless of their role as a refuge or not. This further encourages a reconsideration of a broader framework for the DRRH. We found 12 species of corals exclusively on MCEs and 183 exclusively on SCRs with another 63 species overlapping between depth zones. Of these, 19 appear to have the greatest potential to serve as reseeding species. Two additional species are listed under the U.S. Endangered Species Act, Acropora speciosa and Fimbriaphyllia paradivisa categorized as an occasional deep specialist and a deep exclusive species, respectively. Based on the community distinctiveness and minimal species overlap of SCR and MCE communities, we propose a broader framework by evaluating species overlap across coral reef habitats. This provides an opportunity to consider the opposite of the DRRH where SCRs support MCEs.

Strong horizontal and vertical connectivity in the coral Pocillopora verrucosa from Ludao, Taiwan, a small oceanic island

Mesophotic habitats could be sheltered from natural and anthropogenic disturbances and act as reproductive refuges, providing propagules to replenish shallower populations. Molecular markers can be used as proxies evaluating the connectivity and inferring population structure and larval dispersal. This study characterizes population structure as well as horizontal and vertical genetic connectivity of the broadcasting coral Pocillopora verrucosa from Ludao, a small oceanic island off the eastern coast of Taiwan. We genotyped 75 P. verrucosa specimens from three sites (Gongguan, Dabaisha, and Guiwan) at three depth ranges (Shallow: 7-15 m, Mid-depth: 23-30 m, and Deep: 38-45 m), spanning shallow to upper mesophotic coral reefs, with eight microsatellite markers. F-statistics showed a moderate differentiation (FST = 0.106, p<0.05) between two adjacent locations (Dabaisha 23-30 and Dabaisha 38-45 m), but no differentiation elsewhere, suggesting high levels of connectivity among sites and depths. STRUCTURE analysis showed no genetic clustering among sites or depths, indicating that all Pocillopora individuals could be drawn from a single panmictic population. Simulations of recent migration assigned 30 individuals (40%) to a different location from where they were collected. Among them, 1/3 were assigned to deeper locations, 1/3 to shallower populations and 1/3 were assigned to the right depth but a different site. These results suggest high levels of vertical and horizontal connectivity, which could enhance the recovery of P. verrucosa following disturbances around Ludao, a feature that agrees with demographic studies portraying this species as an opportunistic scleractinian.

Reef benthos of Seychelles - A field guide

Background

During the 2019 First Descent: Seychelles Expedition, shallow and deep reef ecosystems of the Seychelles Outer Islands were studied by deploying a variety of underwater technologies to survey their benthic flora and fauna. Submersibles, remotely operated vehicles (ROVs) and SCUBA diving teams used stereo-video camera systems to record benthic communities during transect surveys conducted at 10 m, 30 m, 60 m, 120 m, 250 m and 350 m depths. In total, ~ 45 h of video footage was collected during benthic transect surveys, which was subsequently processed using annotation software in order to assess reef biodiversity and community composition. Here, we present a photographic guide for the visual identification of the marine macrophytes, corals, sponges and other common invertebrates that inhabit Seychelles’ reefs. It is hoped that the resulting guide will aid marine biologists, conservationists, managers, divers and naturalists with the coarse identification of organisms as seen in underwater footage or live in the field.

New information

A total of 184 morphotypes (= morphologically similar individuals) were identified belonging to Octocorallia (47), Porifera (35), Scleractinia (32), Asteroidea (19), Echinoidea (10), Actiniaria (9), Chlorophyta (8), Antipatharia (6), Hydrozoa (6), Holothuroidea (5), Mollusca (2), Rhodophyta (2), Tracheophyta (2), Annelida (1), Crinoidea (1), Ctenophora (1), Ochrophyta (1) and Zoantharia (1). Out of these, we identified one to phylum level, eight to class, 14 to order, 27 to family, 110 to genus and 24 to species. This represents the first attempt to catalogue the benthic diversity from shallow reefs and up to 350 m depth in Seychelles.

Isolated reefs support stable fish communities with high abundances of regionally fished species

Anthropogenic impacts at isolated and inaccessible reefs are often minimal, offering rare opportunities to observe fish assemblages in a relatively undisturbed state. The remote Rowley Shoals are regarded as one of the healthiest reef systems in the Indian Ocean with demonstrated resilience to natural disturbance, no permanent human population nearby, low visitation rates, and large protected areas where fishing prohibitions are enforced. We used baited remote underwater video systems (BRUVS) to quantify fish assemblages and the relative abundance of regionally fished species within the lagoon, on the slope and in the mesophotic habitat at the Rowley Shoals at three times spanning 14 years and compared abundances of regionally fished species and the length distributions of predatory species to other isolated reefs in the northeast Indian Ocean. Fish assemblage composition and the relative abundance of regionally fished species were remarkably stable through time. We recorded high abundances of regionally fished species relative to other isolated reefs, including globally threatened humphead Maori wrasse (Cheilinus undulatus) and bumphead parrotfish (Bolbometopon muricatum). Length distributions of fish differed among habitats at the Rowley Shoals, suggesting differences in ontogenetic shifts among species. The Cocos (Keeling) Islands typically had larger-bodied predatory species than at the Rowley Shoals. Differences in geomorphology, lagoonal habitats, and fishing history likely contribute to the differences among remote reefs. Rowley Shoals is a rare example of a reef system demonstrating ecological stability in reef fish assemblages during a time of unprecedented degradation of coral reefs.

Reproductive Output, Synchrony across Depth and Influence of Source Depth in the Development of Early Life stages of Kelp

Ecklonia radiata is the main foundation species in Australian temperate reefs, yet little has been published on its reproduction and how this may change across its depth range (1-50+ m). In this study, we examined differences in sporophyte morphology and zoospore production during a reproductive season and across four depths (7, 15, 25, and 40 m). Additionally, we examined differences in germination rate, survival, and morphological traits of gametophytes obtained from these four depths, cultured under the same light and temperature conditions. Multivariate morphology of sporophytes differed significantly between deep (~40 m) and shallow sites (7 and 15 m), but individual morphological traits were not significantly different across depths. Total spore production was similar across depths but the peak of zoospore release was observed in February at 15 m of depth (6,154 zoospores · mm-2 of tissue) and the minimum observed in January at 7, 25, and 40 m (1,141, 987, and 214 zoospores · mm-2 of tissue, respectively). The source depth of zoospores did not have an influence in the germination rate or the survival of gametophytes, and only gametophytes sourced from 40 m sites presented significantly less surface area and number of branches. Overall, these results indicate that E. radiata's reproductive performance does not change across its depth range and that kelp beds reproducing in deeper areas may contribute to the replenishment of their shallow counterparts. We propose that deep kelps may constitute a mechanism of resilience against climate change and anthropogenic disturbances.

Severe coral bleaching of Siderastrea stellata at the only atoll in the South Atlantic driven by sequential Marine Heatwaves

Abstract: Threatened by global warming and extreme climatic events, such as El Niño Southern Oscillation (ENSO) and Marine Heatwaves (MHW), coral reefs worldwide faced the worst bleaching and mortality event between 2014 and 2017, induced by the 2015/2016 ENSO. We evaluated the impacts of ENSO and MHW episodes on bleaching and mortality frequencies of Siderastrea stellata at Rocas Atoll, Southwestern Atlantic, using visual censuses conducted in 2016, 2017 and 2019. Bleaching rate varied significantly along the sampling period (11.71% in 2016, 1.52% in 2017, and 88% in 2019), but mortality was always less than 4%. Bleaching events in Atlantic reefs have been constantly associated with ENSO, until these recent events of the last two years. We suggest that MHW were probably the primary driver of the observed bleaching, especially in 2019, when much higher bleaching rates were observed than in ENSO periods. Although Southwestern Atlantic massive corals are considered more resistant to thermal stress than reefs corals worldwide, the strong events registered since 2019 highlight the need for continuous monitoring to better understand coral bleaching dynamics and improve predictions on the effects of global change in the region.

Depth moderates loss of marine foundation species after an extreme marine heatwave: could deep temperate reefs act as a refuge?

Marine heatwaves (MHWs) have been documented around the world, causing widespread mortality of numerous benthic species on shallow reefs (less than 15 m depth). Deeper habitats are hypothesized to be a potential refuge from environmental extremes, though we have little understanding of the response of deeper benthic communities to MHWs. Here, we show how increasing depth moderates the response of seaweed- and coral-dominated benthic communities to an extreme MHW across a subtropical–temperate biogeographical transition zone. Benthic community composition and key habitat-building species were characterized across three depths (15, 25 and 40 m) before and several times after the 2011 Western Australian MHW to assess resistance during and recovery after the heatwave. We found high natural variability in benthic community composition along the biogeographic transition zone and across depths with a clear shift in the composition after the MHW in shallow (15 m) sites but a lot less in deeper communities (40 m). Most importantly, key habitat-building seaweeds such as Ecklonia radiata and Syctothalia dorycarpa which had catastrophic losses on shallow reefs, remained and were less affected in deeper communities. Evidently, deep reefs have the potential to act as a refuge during MHWs for the foundation species of shallow reefs in this region.

Fish biodiversity patterns of a mesophotic-to-subphotic artificial reef complex and comparisons with natural substrates

Artificial reefs act as high-rugosity habitats and are often deployed to enhance fishing; however, the effects of man-made features on fish communities can be unpredictable and are poorly understood in deeper waters. In this study, we used a submersible to describe a deep-water artificial reef complex (93–245 m) off of Ewa Beach, Oahu, Hawaii, USA, and evaluated possible conservation and/or fisheries-related contributions. Sixty-eight species were recorded, with larger features supporting greater diversity of species. Species composition changed strongly with depth and a faunal break was detected from 113–137 m. While the features supported diverse fish communities, they were not similar to those on natural substrates, and were numerically dominated by only two species, Lutjanis kasmira and Chromis verater. Depth-generalist and endemic species were present at levels comparable to natural substrates, but were less abundant and species-rich than at biogenic Leptoseris reefs at similar depths. While the non-native L. kasmira was highly abundant, its presence and abundance were not associated with discernable changes in the fish community, and was not present deeper than 120 m. Finally, five species of commercially- and recreationally-important ‘Deep 7’ fisheries species were also observed, but the artificial reef complex was mostly too shallow to provide meaningful benefits.

The Rarity of Depth Refugia from Coral Bleaching Heat Stress in the Western and Central Pacific Islands

Some researchers have suggested that corals living in deeper reefs may escape heat stress experienced by shallow corals. We evaluated the potential of deep coral reef refugia from bleaching stress by leveraging a long record of satellite-derived sea surface temperature data with a temporal, spatial, and depth precision of in situ temperature records. We calculated an in situ stress metric using a depth bias-adjusted threshold for 457 coral reef sites among 49 islands in the western and central Pacific Ocean over the period 2001-2017. Analysis of 1,453 heating events found no meaningful depth refuge from heat stress down to 38 m, and no significant association between depth and subsurface heat stress. Further, the surface metric underestimated subsurface stress by an average of 39.3%, across all depths. Combining satellite and in situ temperature data can provide bleaching-relevant heat stress results to avoid misrepresentation of heat stress exposure at shallow reefs.

Upwelling buffers climate change impacts on coral reefs of the eastern tropical Pacific

Corals of the eastern tropical Pacific live in a marginal and oceanographically dynamic environment. Along the Pacific coast of Panamá, stronger seasonal upwelling in the Gulf of Panamá in the east transitions to weaker upwelling in the Gulf of Chiriquí in the west, resulting in complex regional oceanographic conditions that drive differential coral-reef growth. Over millennial timescales, reefs in the Gulf of Chiriquí recovered more quickly from climatic disturbances compared with reefs in the Gulf of Panamá. In recent decades, corals in the Gulf of Chiriquí have also had higher growth rates than in the Gulf of Panamá. As the ocean continues to warm, however, conditions could shift to favor the growth of corals in the Gulf of Panamá, where upwelling may confer protection from high-temperature anomalies. Here we describe the recent spatial and temporal variability in surface oceanography of nearshore environments in Pacific Panamá and compare those conditions with the dynamics of contemporary coral-reef communities during and after the 2016 coral-bleaching event. Although both gulfs have warmed significantly over the last 150 yr, the annual thermal maximum in the Gulf of Chiriquí is increasing faster, and ocean temperatures there are becoming more variable than in the recent past. In contrast to historical trends, we found that coral cover, coral survival, and coral growth rates were all significantly higher in the Gulf of Panamá. Corals bleached extensively in the Gulf of Chiriquí following the 2015-2016 El Niño event, whereas upwelling in the Gulf of Panamá moderated the high temperatures caused by El Niño, allowing the corals largely to escape thermal stress. As the climate continues to warm, upwelling zones may offer a temporary and localized refuge from the thermal impacts of climate change, while reef growth in the rest of the eastern tropical Pacific continues to decline.

Marine biodiversity from zero to a thousand meters at Clipperton Atoll (Île de La Passion), Tropical Eastern Pacific

Clipperton Atoll (Île de La Passion) is the only atoll in the Tropical Eastern Pacific (TEP) ecoregion and, owing to its isolation, possesses several endemic species and is likely an important stepping stone between Oceania, the remainder of the TEP, including other oceanic islands and the west coast of Central America. We describe the biodiversity at this remote atoll from shallow water to depths greater than one thousand meters using a mixture of technologies (SCUBA, stereo baited remote underwater video stations, manned submersible, and deep-sea drop cameras). Seventy-four unique taxa of invertebrates were identified during our expedition. The majority (70%) of these taxa were confined to the top 400 m and consisted mostly of sessile organisms. Decapod crustaceans and black corals (Antipatharia) had the broadest depth ranges, 100–1,497 m and 58–967 m, respectively. Decapods were correlated with the deepest depths, while hard corals were correlated with the shallow depths. There were 96 different fish taxa from 41 families and 15 orders, of which 70% were restricted to depths <200 m. While there was a decreasing trend in richness for both fish and invertebrate taxa with depth, these declines were not linear across the depth gradient. Instead, peaks in richness at ∼200 m and ∼750 m coincided with high turnover due to the appearance of new taxa and disappearance of other taxa within the community and is likely associated with the strong oxygen minimum zone that occurs within the region. The overall depth effect was stronger for fishes compared with invertebrates, which may reflect ecological preferences or differences in taxonomic resolution among groups. The creation of a no-take marine reserve 12 nautical miles around the atoll in 2016 will help conserve this unique and relatively intact ecosystem, which possesses high predator abundance.

Genetic diversity increases with depth in red gorgonian populations of the Mediterranean Sea and the Atlantic Ocean

Background

In the ocean, the variability of environmental conditions found along depth gradients exposes populations to contrasting levels of perturbation, which can be reflected in the overall patterns of species genetic diversity. At shallow sites, resource availability may structure large, persistent and well-connected populations with higher levels of diversity. In contrast, the more extreme conditions, such as thermal stress during heat waves, can lead to population bottlenecks and genetic erosion, inverting the natural expectation. Here we examine how genetic diversity varies along depth for a long-lived, important ecosystem-structuring species, the red gorgonian, Paramuricea clavata.

Methods

We used five polymorphic microsatellite markers to infer differences in genetic diversity and differentiation, and to detect bottleneck signs between shallow and deeper populations across the Atlantic Ocean and the Mediterranean Sea. We further explored the potential relationship between depth and environmental gradients (temperature, ocean currents, productivity and slope) on the observed patterns of diversity by means of generalized linear mixed models.

Results

An overall pattern of higher genetic diversity was found in the deeper sites of the Atlantic Ocean and the Mediterranean Sea. This pattern was largely explained by bottom temperatures, with a linear pattern of decreasing genetic diversity with increasing thermal stress. Genetic differentiation patterns showed higher gene flow within sites (i.e., shallow vs. deeper populations) than between sites. Recent genetic bottlenecks were found in two populations of shallow depths.

Discussion

Our results highlight the role of deep refugial populations safeguarding higher and unique genetic diversity for marine structuring species. Theoretical regression modelling demonstrated how thermal stress alone may reduce population sizes and diversity levels of shallow water populations. In fact, the examination of time series on a daily basis showed the upper water masses repeatedly reaching lethal temperatures for P. clavata. Differentiation patterns showed that the deep richer populations are isolated. Gene flow was also inferred across different depths; however, not in sufficient levels to offset the detrimental effects of surface environmental conditions on genetic diversity. The identification of deep isolated areas with high conservation value for the red gorgonian represents an important step in the face of ongoing and future climate changes.

Modeling impacts of climate change on the potential habitat of an endangered Brazilian endemic coral: Discussion about deep sea refugia

Climate and environmental conditions are determinant for coral distribution and their very existence. When changes in such conditions occur, their effects on distribution can be predicted through species distribution models, anticipating suitable habitats for the subsistence of species. Mussismilia harttii is one of the most endangered Brazilian endemic reef-building corals, and in increasing risk of extinction. Herein, species distribution models were used to determine the present and future potential habitats for M. harttii. Estimations were made through the maximum entropy approach, predicting suitable habitat losses and gains by the end of the 21st century. For this purpose, species records published in the last 20 years and current and future environmental variables were correlated. The best models were chosen according to the Akaike information criterion (AIC) and evaluated through the partial ROC (AUCratio), a new approach which uses independent occurrence data. Both approaches showed that the models performed satisfactorily in predicting potential habitat areas for the species. Future projections were made using the International Panel on Climate Change (IPCC) scenarios for 2100, with different levels of greenhouse gas emission. Representative Concentration Pathways (RCPs) were used to model the Future Potential Habitat (FPH) of M. harttii in two different scenarios: stabilization of emissions (RCP 4.5) and increase of emissions (RCP 8.5). According to the results, shallow waters to the south of the study area concentrate most of the current potential habitats for the species. However, in future scenarios, there was a loss of suitable areas in relation to the Current Potential Habitat (RCP 4.5 46% and RCP 8.5 59%), whereas there is a southward shift of the suitable areas. In all scenarios of FPH, the temperature was the variable with the greatest contribution to the models (> 35%), followed by the current velocity (> 33%) and bathymetry (>29%). In contrast, there is an increase of deep (50-75 m) suitable areas FPH scenarios, mainly in the southern portion of its distribution, at Abrolhos Bank (off Espirito Santo State). These deeper sites might serve as refugia for the species in global warming scenarios. Coral communities at such depths would be less susceptible to impacts of climate change on temperature and salinity. However, the deep sea is not free from human impacts and measures to protect deeper ecosystems should be prioritized in environmental policies for Brazilian marine conservation, especially the Abrolhos Bank, due to its importance for M. harttii.

High species richness and lineage diversity of reef corals in the mesophotic zone

Coral reefs are increasingly threatened by thermal bleaching and tropical storm events associated with rising sea surface temperatures. Deeper habitats offer some protection from these impacts and may safeguard reef-coral biodiversity, but their faunas are largely undescribed for the Indo-Pacific. Here, we show high species richness of scleractinian corals in mesophotic habitats (30-125 m) for the northern Great Barrier Reef region that greatly exceeds previous records for mesophotic habitats globally. Overall, 45% of shallow-reef species (less than or equal to 30 m), 78% of genera, and all families extended below 30 m depth, with 13% of species, 41% of genera, and 78% of families extending below 45 m. Maximum depth of occurrence showed a weak relationship to phylogeny, but a strong correlation with maximum latitudinal extent. Species recorded in the mesophotic had a significantly greater than expected probability of also occurring in shaded microhabitats and at higher latitudes, consistent with light as a common limiting factor. The findings suggest an important role for deeper habitats, particularly depths 30-45 m, in preserving evolutionary lineages of Indo-Pacific corals. Deeper reef areas are clearly more diverse than previously acknowledged and therefore deserve full consideration in our efforts to protect the world's coral reef biodiversity.

State of corals and coral reefs of the Galápagos Islands (Ecuador): Past, present and future

Coral populations and structural coral reefs have undergone severe reductions and losses respectively over large parts of the Galápagos Islands during and following the 1982-83 El Niño event. Coral tissue loss amounted to 95% across the Archipelago. Also at that time, all coral reefs in the central and southern islands disappeared following severe degradation and eventual collapse due primarily to intense bioerosion and low recruitment. Six sites in the southern islands have demonstrated low to moderate coral community (scattered colonies, but no carbonate framework) recovery. The iconic pocilloporid reef at Devil's Crown (Floreana Island) experienced recovery to 2007, then severe mortality during a La Niña cooling event, and is again (as of 2017) undergoing rapid recovery. Notable recovery has occurred at the central (Marchena) and northern islands (Darwin and Wolf). Of the 17 structural reefs first observed in the mid-1970s, the single surviving reef (Wellington Reef) at Darwin Island remains in a positive growth mode. The remainder either degraded to a coral community or was lost. Retrospective analyses of the age structure of corals killed in 1983, and isotopic signatures of the skeletal growth record of massive corals suggest the occurrence of robust coral populations during at least a 500-year period before 1983. The greatest potential threats to the recovery and persistence of coral reefs include: ocean warming and acidification, bioerosion, coral diseases, human population growth (increasing numbers of residents and tourists), overfishing, invasive species, pollution, and habitat destruction. Such a diverse spectrum of disturbances, acting alone or in combination, are expected to continue to cause local and archipelago-wide mortality and degradation of the coral reef ecosystem.

Species identity and depth predict bleaching severity in reef-building corals: shall the deep inherit the reef?

Mass bleaching associated with unusually high sea temperatures represents one of the greatest threats to corals and coral reef ecosystems. Deeper reef areas are hypothesized as potential refugia, but the susceptibility of Scleractinian species over depth has not been quantified. During the most severe bleaching event on record, we found up to 83% of coral cover severely affected on Maldivian reefs at a depth of 3-5 m, but significantly reduced effects at 24-30 m. Analysis of 153 species' responses showed depth, shading and species identity had strong, significant effects on susceptibility. Overall, 73.3% of the shallow-reef assemblage had individuals at a depth of 24-30 m with reduced effects, potentially mitigating local extinction and providing a source of recruits for population recovery. Although susceptibility was phylogenetically constrained, species-level effects caused most lineages to contain some partially resistant species. Many genera showed wide variation between species, including Acropora, previously considered highly susceptible. Extinction risk estimates showed species and lineages of concern and those likely to dominate following repeated events. Our results show that deeper reef areas provide refuge for a large proportion of Scleractinian species during severe bleaching events and that the deepest occurring individuals of each population have the greatest potential to survive and drive reef recovery.

Experimental evidence for reduced mortality of Agaricia lamarcki on a mesophotic reef

Mesophotic Coral Ecosystems (MCEs) may act as a refuge for impacted shallow reefs as some of the stressors affecting tropical reefs attenuate with depth. A less impacted population at depth could provide recruits to recolonise shallow reefs. Recently, disturbance has been reported on several mesophotic reefs including storm damage, biological invasions, and coral bleaching; calling into question the extent of deep reef refuges. We report on a reciprocal transplant experiment between shallow and mesophotic reefs in the Caribbean, which occurred during a period of coral bleaching. 102 fragments of Agaricia lamarcki were collected down a continuous depth gradient at two sites to a maximum depth of 60m. Fragments were transplanted to either a shallow or mesophotic station at a third site, with controls. This allowed the disaggregation of the effect of the disturbance experienced during the observation period, and any potential acclimation resulting from the historical location of a fragment. Mortality and bleaching were quantitatively assessed. We found the relocation depth of a coral fragment had the strongest effect on both survival and the degree of bleaching recorded. The site a fragment was collected from, and the original collection depth, failed to explain mortality or bleaching with statistical significance. This experiment provides support for the assumption that mesophotic corals may be protected in comparison to shallow reefs, in spite of the potential effects of differing susceptibilities to stress.

Can mesophotic reefs replenish shallow reefs? Reduced coral reproductive performance casts a doubt

Mesophotic coral ecosystems (i.e., deep coral reefs at 30-120 m depth) appear to be thriving while many shallow reefs in the world are declining. Amid efforts to understand and manage their decline, it was suggested that mesophotic reefs might serve as natural refuges and a possible source of propagules for the shallow reefs. However, our knowledge of how reproductive performance of corals alters with depth is sparse. Here, we present a comprehensive study of the reproductive phenology, fecundity, and abundance of seven reef-building conspecific corals in shallow and mesophotic habitats. Significant differences were found in the synchrony and timing of gametogenesis and spawning between shallow and mesophotic coral populations. Thus, mesophotic populations exhibited delayed or protracted spawning events, which led to spawning of the mesophotic colonies in large proportions at times where the shallow ones had long been depleted of reproductive material. All species investigated demonstrated a substantial reduction in fecundity and/or oocyte sizes at mesophotic depths (40-60 m). Two species (Seriatopora hystrix and Galaxea fascicularis) displayed a reduction in both fecundity and oocyte size at mesophotic depths. Turbinaria reniformis had only reduced fecundity and Acropora squarrosa and Acropora valida only reduced oocyte size. In Montipora verrucosa, reduced fecundity was found during one annual reproductive season while, in the following year, only reduced oocyte size was found. In contrast, reduced oocyte size in mesophotic populations of Acropora squarrosa was consistent along three studied years. One species, Acropora pharaonis, was found to be infertile at mesophotic depths along two studied years. This indicates that reproductive performance decreases with depth; and that although some species are capable of reproducing at mesophotic depths, their contribution to the replenishment of shallow reefs may be inconsequential. Reduced reproductive performance with depth, combined with the possible narrower tolerance to environmental factors, further suggests that mesophotic corals may in fact be more vulnerable than previously conceived. Furthermore, we posit that the observed temporal segregation in reproduction could lead to assortative mating, and this, in turn, may facilitate adaptive divergence across depth.

Mortality, recovery, and community shifts of scleractinian corals in Puerto Rico one decade after the 2005 regional bleaching event

This work analyzes the mortality, recovery, and shifts in the composition of scleractinian corals from Puerto Rico one decade after the 2005 regional coral bleaching event. Temporal and spatial patterns of coral community structure were examined using a stratified, non-random sampling approach based on five permanent transects per reef at 16 reef stations. A negative correlation between percent coral cover loss and light attenuation coefficient (Kd₄₉₀) was observed, suggesting that light attenuation, as influenced by water turbidity and depth, played a major role in coral protection during the bleaching event (“sunblock effect”). Responses of coral assemblages varied after the bleaching event, including shifts of cover from massive corals (Orbicella spp.) to opportunistic (Porites astreoides) and branching corals (Madracis auretenra, P. porites) and/or turf algae; partial recovery of reef substrate cover by O. annularis complex; and no measurable changes in coral assemblages before and after the event.

Polyp bailout in Pocillopora damicornis following thermal stress

Polyp bailout is an established but understudied coral stress response that involves the detachment of individual polyps from the colonial form as a means of escaping unfavourable conditions. This may influence both the mortality and asexual recruitment of coral genotypes across a range of species. It has been observed in response to numerous stressors including high salinity and low pH. Polyp expulsion in association with thermal stress has once been described in a geographically restricted, temperate species. We therefore cannot reliably apply this observation to tropical coral reefs around the world, which are increasingly under threat from thermal stress events. We present the first qualitative observation of polyp bailout following acute temperature shock  in a near-natural mesocosm experiment. Detached polyps show similar characteristics to those described in previous studies, including the retention of endosymbiotic zooxanthellae and the ability to disperse across short distances. This finding strongly suggests that polyp bailout occurs in tropical coral reef environments and warrants further detailed research into the implication of this response in terms of individual survival, rapid migration into cooler micro-habitats and local recruitment within the reef environment and its coral community.

27 years of benthic and coral community dynamics on turbid, highly urbanised reefs off Singapore

Coral cover on reefs is declining globally due to coastal development, overfishing and climate change. Reefs isolated from direct human influence can recover from natural acute disturbances, but little is known about long term recovery of reefs experiencing chronic human disturbances. Here we investigate responses to acute bleaching disturbances on turbid reefs off Singapore, at two depths over a period of 27 years. Coral cover declined and there were marked changes in coral and benthic community structure during the first decade of monitoring at both depths. At shallower reef crest sites (3–4 m), benthic community structure recovered towards pre-disturbance states within a decade. In contrast, there was a net decline in coral cover and continuing shifts in community structure at deeper reef slope sites (6–7 m). There was no evidence of phase shifts to macroalgal dominance but coral habitats at deeper sites were replaced by unstable substrata such as fine sediments and rubble. The persistence of coral dominance at chronically disturbed shallow sites is likely due to an abundance of coral taxa which are tolerant to environmental stress. In addition, high turbidity may interact antagonistically with other disturbances to reduce the impact of thermal stress and limit macroalgal growth rates.

Caribbean mesophotic coral ecosystems are unlikely climate change refugia

Deeper coral reefs experience reduced temperatures and light and are often shielded from localized anthropogenic stressors such as pollution and fishing. The deep reef refugia hypothesis posits that light-dependent stony coral species at deeper depths are buffered from thermal stress and will avoid bleaching-related mass mortalities caused by increasing sea surface temperatures under climate change. This hypothesis has not been tested because data collection on deeper coral reefs is difficult. Here we show that deeper (mesophotic) reefs, 30-75 m depth, in the Caribbean are not refugia because they have lower bleaching threshold temperatures than shallow reefs. Over two thermal stress events, mesophotic reef bleaching was driven by a bleaching threshold that declines 0.26 °C every +10 m depth. Thus, the main premise of the deep reef refugia hypothesis that cooler environments are protective is incorrect; any increase in temperatures above the local mean warmest conditions can lead to thermal stress and bleaching. Thus, relatively cooler temperatures can no longer be considered a de facto refugium for corals and it is likely that many deeper coral reefs are as vulnerable to climate change as shallow water reefs.