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Fluorescence imaging of benthic communities is a widely used tool for determining the rate of hard coral recruitment in tropical reefs. Whilst fluorescent proteins are well-studied in scleractinian corals, less is understood about their distribution and function in other sessile reef invertebrates. This short study examines fluorescence images of benthic communities on Autonomous Reef Monitoring Structures (ARMS) from a remote and protected Indian Ocean reef system. We compare the abundance of adult and juvenile hard corals across three sites and between the topside and underside of ARMS recruitment plates. We also discuss observations of skeletal fluorescence in sponges, as well as uneven green fluorescent protein (GFP) concentrations across adult coral colonies. Our findings provide an insight into the recovery of shallow reefs previously hit by severe bleaching events and highlight the potential of ARMS fluorescence imaging for the analysis of cryptobenthic communities.

Coral reef sessile organisms inhabiting cryptic spaces and cavities of the reef matrix perform vital and varied functional roles but are often understudied in comparison to those on exposed surfaces. Here, we assess the composition of cryptobenthic taxa from three remote tropical reef sites (Central Indian Ocean) alongside a suite of in situ environmental parameters to determine if, or how, significant patterns of diversity are shaped by local abiotic factors. To achieve this, we carried out a point-count analysis of autonomous reef monitoring structure (ARMS) plate images and employed in situ instrumentation to recover long-term (12 months) profiles of flow velocity, wave heights, temperature, dissolved oxygen, and salinity, and short-term (3 weeks) profiles of light and pH. We recovered distinct environmental profiles between sampling sites and observed that ocean-facing reefs experienced frequent but short-lived cooling internal wave events and that these were key in shaping in situ temperature variability. By comparing temperature and wave height profiles recovered using in situ loggers with ex situ models, we discovered that global satellite products either failed to recover site-specific profiles or both over- and underestimated actual in situ conditions. We found that site choice and recruitment plate face (top or bottom) significantly impacted the percentage cover of bryozoans, gastropods, soft and calcified tube worms, as well as crustose coralline algae (CCA) and fleshy red, brown, and green encrusting macroalgae on ARMS. We observed significant correlations between the abundance of bryozoans, CCA, and colonial tunicates with lower mean temperature and higher mean dissolved oxygen profiles observed across sites. Red and brown encrusting macroalgae abundance correlated significantly with medium-to-high flow velocities and wave height profiles, as well as higher pH and dissolved oxygen. This study provides the first insight into cryptobenthic communities in the Chagos Archipelago marine-protected area and adds to our limited understanding of tropical reef sessile communities and their associations with environmental parameters in this region. With climate change accelerating the decline of reef ecosystems, integrating analyses of cryptobenthic organisms and in situ physicochemical factors are needed to understand how reef communities, if any, may withstand the impacts of climate change.

We present the first mitochondrial genomes from Chagos Archipelago, Indian Ocean, of three putative species of reef forming Acropora (Acropora aff. tenuis, Acropora aff. cytherea and Acropora aff. orbicularis). The circular genome consists respectively of 18,334 bp, 18,353 bp and 18,584 bp. All mitochondrial genomes recovered comprise 13 protein-coding genes, two transfer RNA genes and two ribosomal RNA genes, with an overall GC content ranging from 37.9% to 38.0%. These new genomic data contribute to our increased understanding of genus Acropora and its species boundaries, ultimately aiding species monitoring and conservation efforts.

Mesophotic coral ecosystems (MCEs; reefs 30–150 m depth) are poorly studied, with existing research heavily geographically biased away from the most species-rich reef regions. Yet, MCEs are of high interest because of their unique species and potential to act as refuges from the impacts of fishing. Using baited remote underwater video systems, we surveyed reef fish communities from 2 to 85 m depths throughout the Raja Ampat archipelago in West Papua, Indonesia—an area considered the heart of the Coral Triangle where coral reef biodiversity is greatest. We sought to provide the first assessment of fish communities across this depth gradient in the region and identify whether human population density and market access differently affected fish abundance based on depth. Here we show that—similar to shallow reefs—Raja Ampat MCEs are exceptionally diverse, with 152 fish species recorded at depths greater than 40 m. We found that fish community structures were highly depth driven, with declines in fish abundance at increased depth. In contrast to previous studies elsewhere in the world, we found that the proportion of planktivores declined across the shallow reef to MCE depth gradient. While greater human population density correlated with lower Epinephelidae and Lutjanidae abundance (two key fisheries families), we did not find evidence that MCEs provide a depth refuge from fishing. Surprisingly, we also found that fish abundance declined at greater distances from the major regional market—likely caused by historical fisheries pressure in more remote areas. These results both expand upon and contrast some previously established MCE-depth patterns and human impact patterns on fish communities, suggesting that regional context and historical pressures matters. Our findings highlight the need for future MCE studies within the Coral Triangle region.

Coral reefs are critical ecosystems globally for marine fauna, biodiversity and through the services they provide to humanity. However, they are significantly threatened by anthropogenic stressors, such as climate change. By combining 9 environmental variables and ecological and health-based thresholds obtained from the available literature, we develop, using fuzzy logic (discontinuous functions), a Coral Reef Stress Exposure Index (CRSEI) for remotely monitoring coral reef exposure to environmental stressors. Our approach capitalises on the abundance of readily available satellite Earth Observation (EO) data available in the Google Earth Engine (GEE) cloud-based geospatial processing platform. CRSEI values from 3157 distinct reefs were generated and mapped across 12 important coral reef ecosystem regions. Quantitative analyses indicated that the index detected significant temporal differences in stress and was, therefore, able to capture historic change at a global scale. We also applied the CRSEI to three case-study reef ecosystems, previously well-monitored for stress and disturbance using other methods. PCA analysis indicated that depth, current, sea surface temperature (SST) and SST anomaly accounted for the greatest contribution to the variance in stress in these three regions. The CRSEI corroborated temporal and spatial differences in stress exposure from known disturbances within these reference regions, in addition to identifying the potential drivers of inter- and intra-region differences in stress, namely depth, degree heating weeks and SST anomaly. We discuss how the index can be further improved in future with site-specific thresholds for each stress variable, and the incorporation of additional variables not currently available in GEE. This index provides an open access tool, built around a free and powerful processing platform, that has broad potential to assist in the regular monitoring of our increasingly imperilled coral reef ecosystems, and, in particular, those that are remote or inaccessible.

Given the recent trend towards establishing very large marine protected areas (MPAs) and the high potential of these to contribute to global conservation targets, we review outcomes of the last decade of marine conservation research in the British Indian Ocean Territory (BIOT), one of the largest MPAs in the world. The BIOT MPA consists of the atolls of the Chagos Archipelago, interspersed with and surrounded by deep oceanic waters. Islands around the atoll rims serve as nesting grounds for sea birds. Extensive and diverse shallow and mesophotic reef habitats provide essential habitat and feeding grounds for all marine life, and the absence of local human impacts may improve recovery after coral bleaching events. Census data have shown recent increases in the abundance of sea turtles, high numbers of nesting seabirds and high fish abundance, at least some of which is linked to the lack of recent harvesting. For example, across the archipelago the annual number of green turtle clutches (Chelonia mydas) is ~ 20,500 and increasing and the number of seabirds is ~ 1 million. Animal tracking studies have shown that some taxa breed and/or forage consistently within the MPA (e.g. some reef fishes, elasmobranchs and seabirds), suggesting the MPA has the potential to provide long-term protection. In contrast, post-nesting green turtles travel up to 4000 km to distant foraging sites, so the protected beaches in the Chagos Archipelago provide a nesting sanctuary for individuals that forage across an ocean basin and several geopolitical borders. Surveys using divers and underwater video systems show high habitat diversity and abundant marine life on all trophic levels. For example, coral cover can be as high as 40–50%. Ecological studies are shedding light on how remote ecosystems function, connect to each other and respond to climate-driven stressors compared to other locations that are more locally impacted. However, important threats to this MPA have been identified, particularly global heating events, and Illegal, Unreported and Unregulated (IUU) fishing activity, which considerably impact both reef and pelagic fishes.

The term “Anthropocene” has been suggested as the current epoch (denoting the current geological age) and is viewed as the period where human-based activity is the dominant influence on climate and the environment (Lewis and Maslin, 2015). Arguably, one of the most prevalent and visible effects of this anthropogenic activity has manifested in the equatorial tropics—where coral reef ecosystems have suffered alarming declines (Pandolfi et al., 2003; Hughes et al., 2017). For example, recent increases in mass bleaching events brought about by prolonged periods of elevated sea surface temperatures highlight a worrying trend, with predictions that over half of reefs will experience annual severe bleaching before 2050 (van Hooidonk et al., 2016). For this reason, coral reefs have often been referred to as “canaries in the coal mine” for the marine biome. Yet reefs continue to be crucial sources of food, protection, livelihoods, and cultural identity for many people around the world (Teh et al., 2013; Hicks and Cinner, 2014; Lau et al., 2019). It is therefore critical that the link between healthy reefs, food security, and sustainable community livelihoods is maintained into the future. This Research Topic represents the proceedings for the European Coral Reef Symposium (ECRS), which took place 13th–15th December, 2017 in Oxford, UK. ECRS was organised by the Reef Conservation United Kingdom (RCUK) committee, in association with the Zoological Society of London (ZSL), University of Oxford, and the International Coral Reef Society (ICRS). Over 550 coral reef scientists and conservationists joined the meeting for a series of talks, posters, and workshops. In addition to the papers in this Research Topic, ECRS provided a platform for many other coral reef-related events and outputs. For example, the symposium hosted the European launch of the 2018 International Year of the Reef on the 13th December 2017, and several of the workshops produced published outputs (e.g., Turner et al., 2019). In this editorial, we provide a brief history of RCUK—charting the course from inception in 1997 through to ECRS in 2017—including our sustainable conferencing efforts and commitments to diversity and inclusion. We strongly believe that all conferences should carefully consider sustainability, diversity, and inclusion and we hope our efforts will inspire and encourage other conference organisers to do the same. We then introduce the globally relevant coral reef science and conservation that has been presented at RCUK meetings and provide an overview of the papers submitted to this Research Topic. We close by highlighting our vision for RCUK into the future—and lay out how this can be applied to the upcoming Frontiers Spotlight Conference on Coral Reefs.

Mesophotic coral ecosystems (MCEs; reefs 30-150 m depth) are poorly studied, with existing research heavily geographically biased away from the most species-rich reef regions. Yet, MCEs are of high interest because of their unique species and potential to act as refuges from the impacts of fishing. Using baited remote underwater video systems, we surveyed reef fish communities from 2 to 85 m depths throughout the Raja Ampat archipelago in West Papua, Indonesia – an area considered the heart of the Coral Triangle where coral reef biodiversity is greatest. We sought to provide the first assessment of fish communities across this depth gradient in the region and identify whether human population density and market access differently affected fish abundance based on depth. Here we show that—similar to shallow reefs—Raja Ampat MCEs are exceptionally diverse, with 152 fish species recorded at depths greater than 40 m. We found that fish community structures were highly depth driven, with declines in fish abundance at increased depth. In contrast to previous studies elsewhere in the world, we found that the proportion of planktivores declined across the shallow reef to MCE depth gradient. While greater human population density correlated with lower Epinephelidae and Lutjanidae abundance (two key fisheries families), we did not find evidence that MCEs provide a depth refuge from fishing. Surprisingly, we also found that fish abundance declined at greater distances from the major regional market – likely caused by historical fisheries pressure in more remote areas. These results both expand upon and contrast some previously established MCE-depth patterns and human impact patterns on fish communities, suggesting that regional context and historical pressures matters. Our findings highlight the need for future MCE studies within the Coral Triangle region.

The Chagos Archipelago, located in the central Indian Ocean and officially known as the British Indian Ocean Territory, contains some of the most remote reefs in the Indian Ocean. The Chagos Archipelago is comprised of a series of atolls, including the largest atoll in the world, the Great Chagos Bank. Records from surveys of mesophotic coral ecosystems (MCEs; reefs 30–150 m depth) in Chagos stretch back to 1905, with more extensive work conducted in the 1970s and post-2010. Coral and fish communities vary considerably with depth and among habitat types. Coral cover generally declines with increased depth across the shallow reef to MCE depth gradient, though in several locations close to 100% scleractinian coral cover has been observed on MCEs. Consistent with earlier studies, we identify five coral species as indicative of Chagos MCEs. Recently collected fish community data are analyzed to illustrate, for the first time, patterns in reef fish species richness, abundance, biomass, and trophic groups across a shallow to upper-MCE depth gradient (0–60 m). Fish species richness, abundance, and biomass declined with increased depth, while richness, abundance, and trophic group patterns were also influenced by habitat type (seaward versus lagoonal reef). To date, the vast majority of MCE research in Chagos has focused on upper mesophotic depths. We recommend future work consider the full MCE depth range within the Chagos Archipelago.

The Chagos Archipelago is geographically remote and isolated from most direct anthropogenic pressures. Here, we quantify the abundance and diversity of decapod crustaceans inhabiting dead coral colonies, representing a standardised microhabitat, across the Archipelago. Using morphological and molecular techniques we recorded 1868 decapods from 164 nominal species within 54 dead coral colonies, but total species estimates (Chao1 estimator) calculate at least 217 species. Galatheids were the most dominant taxa, though alpheids and hippolytids were also very abundant. 32% of species were rare, and 46% of species were found at only one atoll. This prevalence of rarer species has been reported in other cryptofauna studies, suggesting these assemblages maybe comprised of low-abundance species. This study provides the first estimate of diversity for reef cryptofauna in Chagos, which will serve as a useful baseline for global comparisons of coral reef biodiversity.

Outbreaks of the crown-of-thorns starfish (COTS), Acanthaster planci, have occurred at many locations throughout the Indo-Pacific and are a major contributor to widespread coral loss and reef degradation. The causes of outbreaks remain controversial, but are commonly attributed to anthropogenically elevated nutrients and/or over-fishing. If so, it seems unlikely that outbreaks would occur in reef systems that are largely isolated from anthropogenic disturbances. However, high densities of COTS were recently observed on reefs in the Chagos Archipelago, a remote group of atolls and banks within the central Indian Ocean, which experience very limited anthropogenic influence. Aggregations of COTS were first noticed at Eagle Island in 2012, which, although unquantified, appeared to be at outbreak levels, and very high densities (1624 km−2) were subsequently recorded at Danger Island in 2013. While these islands are uninhabited by humans, it is possible that nutrient inputs result from upwelling zones around the Archipelago, or high densities of breeding seabirds. Among islands within the Great Chagos Bank, densities of the red-footed booby Sula sula ranged from 8 to 7888 individuals km−2, with associated guano input ranging from 96 to 25,381 kg island−1 year−1. However, Danger and Eagle Islands where high COTS densities were recorded, had both high and low levels of guano production, respectively, which suggests that outbreaks may not be directly linked to guano nutrient enrichment. Other factors which might be responsible for intermittent COTS outbreaks should be considered in isolated reef systems such as the Chagos Archipelago.

Coral reefs are the most biodiverse marine ecosystem and one of the most threatened by global climate change impacts. The vast majority of diversity on reefs is comprised of small invertebrates that live within the reef structure, termed the cryptofauna. This component of biodiversity is hugely understudied, and many species remain undescribed. This study represents a rare analysis of assembly processes structuring a distinct group of cryptofauna, the Palaemonidae, in the Chagos Archipelago, a reef ecosystem under minimal direct human impacts in the central Indian Ocean. The Palaemonidae are a diverse group of Caridae (infraorder of shrimps) that inhabit many different niches on coral reefs and are of particular interest because of their varied habitat associations. Phylogenetic and trait diversity and phylogenetic signal were used to infer likely drivers of community structure. The mechanisms driving palaemonid community assembly and maintenance in the Chagos Archipelago showed distinct spatial patterns. At local scales, among coral colonies and among reefs fringing individual atolls, significant trait, and phylogenetic clustering patterns suggest environmental filtering may be a dominant ecological process driving Palaemonidae community structure, although local competition through equalizing mechanisms may also play a role in shaping the local community structure. Importantly, we also tested the robustness of phylogenetic diversity to changes in evolutionary information as multi‐gene phylogenies are resource intensive and for large families, such as the Palaemonidae, are often incomplete. These tests demonstrated a very modest impact on phylogenetic community structure, with only one of the four genes (PEPCK gene) in the phylogeny affecting phylogenetic diversity patterns, which provides useful information for future studies on large families with incomplete phylogenies. These findings contribute to our limited knowledge of this component of biodiversity in a marine locality as close to undisturbed by humans as can be found. It also provides a rare evaluation of phylogenetic diversity methods.

Mesophotic coral ecosystems (MCEs, reefs 30–150 m) are understudied, yet the limited research conducted has been biased towards large sessile taxa, such as scleractinian corals and sponges, or mobile taxa such as fishes. Here we investigate zooplankton communities on shallow reefs and MCEs around Utila on the southern Mesoamerican Barrier Reef using planktonic light traps. Zooplankton samples were sorted into broad taxonomic groups. Our results indicate similar taxonomic zooplankton richness and overall biomass between shallow reefs and MCEs. However, the abundance of larger bodied (>2 mm) zooplanktonic groups, including decapod crab zoea, mysid shrimps and peracarid crustaceans, was higher on MCEs than shallow reefs. Our findings highlight the importance of considering zooplankton when identifying broader reef community shifts across the shallow reef to MCE depth gradient.