IntroductionCoral reefs face unprecedented structural reorganisation following climate-induced mass mortality. While net coral loss is well-documented, the resulting spatial arrangement of surviving communities remains understudied. This study characterises the spatial organisation, functional composition, and environmental drivers of benthic communities on the western seaward reefs of Aldabra Atoll, Seychelles, using data from 2022.MethodsUsing 300, high-resolution 1 m2 video-still quadrats across two depth contours (8 m and 15 m), we integrated genus-level identification with life-history strategies (LHS) and substrate stability analysis.ResultsOur data revealed that the reefs were overwhelmingly dominated by stress-tolerant, massive corals, reflecting a resilient, post-disturbance state following historical thermal anomalies. However, multivariate dispersion (patchiness) significantly increased with depth highlighting the role of environmental filtering. We identified four spatial organisational “signatures” among organisms and abiotic features. Using the Variance-to-Mean Ratio (VMR), we identified a deterministic shift in spatial signatures: from shallow aggregated frameworks to deeper, fragmented nucleated patches. Statistical niche modelling confirmed that substrate stability acts as a physical bottleneck; Isopora spp. exhibited an extreme affinity for rock pavement, while Goniopora spp. dominated mobile rubble.DiscussionOur results demonstrate that post-bleaching recovery in Aldabra is partly driven by niche-driven environmental filtering rather than purely stochastic neutral drift.

ABSTRACT Marine sponges as natural samplers of environmental DNA (eDNA) are receiving growing attention as an untapped source of biodiversity data. However, little is known about the state of DNA (e.g., cellular or extracellular) that is captured by these samples and how this compares to conventional aquatic eDNA samples. Here, we present an artificial spiking experiment where DNA in cellular and extracellular states was added into tanks containing two sponge species. Aquatic eDNA samples and sponge natural sampler DNA (nsDNA) samples were collected over 7 days and DNA from the two states was quantified in each sample using quantitative real‐time PCR (qPCR). We found that there was a significant interaction between DNA state and sample type (eDNA and nsDNA), with lower detection and concentration of extracellular DNA, compared to cellular DNA, found in nsDNA samples. We also found that detection rate and concentration of DNA were significantly lower in nsDNA than in eDNA overall. During methodological testing, PCR inhibition was observed in both sponge species; this was prohibitive in one of the species. Further work to investigate the degree of PCR inhibition during nsDNA metabarcoding is important to understand its impact on the communities resolved using nsDNA methods. Synthesis and applications. We show that nsDNA may originate from a subset of the DNA present in environmental media, potentially providing a more stable picture of local communities. Natural samplers provide a promising option for hard‐to‐reach environments and for retrieving biodiversity data from archived samples; however, further work and optimization are required to understand what is and is not well represented by this sample type compared to widely applied aquatic eDNA approaches.

Abstract Environmental DNA (eDNA) metabarcoding has been widely employed to describe biological communities in the marine environment and to compare the richness and diversity of sites across large spatial scales. However, fine‐scale temporal eDNA dynamics are poorly understood and the time of eDNA sample collection is rarely reported in publications. Here, we collected surface eDNA samples every 6 h, for 3 days, at two coral reef sites to assess fine‐scale changes in the eukaryotic communities detected. Distinct eukaryotic communities were detected at two sites within the same lagoon. Sampling time was found to have a significant effect on ESV and class richness, both peaking during the 1 p.m. sampling time at both sites. Sampling time also had a significant effect on the detection of eukaryotic taxa, with relative read frequency showing clear diurnal patterns in line with the migratory behavior of planktonic groups. Other groups of organisms showed considerable variation in read frequency, highlighting the dynamic nature of marine eukaryotic communities and potential stochasticity of eDNA detections. For eukaryotic communities, eDNA samples can provide a “snapshot” of contemporary biodiversity and provide information on short‐term community dynamics on hyperdiverse coral reefs. However, our findings add to growing evidence that sampling time should be clearly considered and reported in marine eDNA studies and that multiple samples from the same site are needed to facilitate more robust comparisons across sites.

Molecular phylogenetics has fundamentally altered our understanding of the taxonomy, systematics and biogeography of corals. Recently developed phylogenomic techniques have started to resolve species-level relationships in the diverse and ecologically important genus Acropora, providing a path to resolve the taxonomy of this notoriously problematic group. We used a targeted capture dataset (2032 loci) to investigate systematic relationships within an Acropora clade containing the putatively widespread species Acropora tenuis and its relatives. Using maximum likelihood phylogenies and genetic clustering of single nucleotide polymorphisms from specimens, including topotypes, collected across the Indo-Pacific, we show & GE; 11 distinct lineages in the clade, only four of which correspond to currently accepted species. Based on molecular, morphological and geographical evidence, we describe two new species; Acropora rongoi n. sp. and Acropora tenuissima n. sp. and remove five additional nominal species from synonymy. Systematic relationships revealed by our molecular phylogeny are incongruent with traditional morphological taxonomy and demonstrate that characters traditionally used to delineate species boundaries and infer evolutionary history are homoplasies. Furthermore, we show that species within this clade have much smaller geographical ranges and, consequently, population sizes than currently thought, a finding with profound implications for conservation and management of reef corals.

Many countries with tropical reef systems face hard choices preserving coral reefs in the face of climate change on limited budgets. One approach to maximising regional reef resilience is targeting management efforts and resources at reefs that export large numbers of larvae to other reefs. However, this requires reef connectivity to be quantified. To map coral connectivity in the Seychelles reef system we carried out a population genomic study of the Porites lutea species complex using 241 sequenced colonies from multiple islands. To identify oceanographic drivers of this connectivity and quantify variability, we further used a 2 km resolution regional ocean simulation coupled with a larval dispersal model to predict the flow of coral larvae between reef sites. Patterns of admixture and gene flow are broadly supported by model predictions, but the realised connectivity is greater than that predicted from model simulations. Both methods detected a biogeographic dispersal barrier between the Inner and Outer Islands of Seychelles. However, this barrier is permeable and substantial larval transport is possible across Seychelles, particularly for one of two putative species found in our genomic study. The broad agreement between predicted connectivity and observed genetic patterns supports the use of such larval dispersal simulations in reef system management in Seychelles and the wider region.

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.

Coral reefs are significantly threatened by multiple environmental stressors associated with climate change. While there is growing recognition of the importance of interacting stressors on coral reefs, so far this has been primarily limited to in situ studies. Satellite remote sensing has potential for investigating coral reef exposure to multiple environmental stressors at a global scale over multiple years; however, current satellite monitoring is primarily focused on thermal stress. Here we collate nine environmental variables (cloud cover, current, depth, salinity, wind, and four sea surface temperature‐based metrics) from readily available satellite datasets using the Google Earth Engine geospatial processing platform. Using ecological and health‐based thresholds obtained from the literature, we developed, using fuzzy logic (discontinuous functions), a Reef Environmental Stress Exposure Toolbox (RESET) for monitoring environmental stress exposure at multiple scales. Stress exposure scores for 3157 reefs were generated and mapped globally across 12 coral reef ecosystem regions. RESET was also applied to three case‐study reefs, 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 environmental stress exposure in these three regions. Depth, degree heating weeks, and SST anomaly were identified as the potential drivers of inter‐ and intra‐region variation in environmental stress exposure. Individual variables were then integrated into a multi‐metric index of combined stress exposure which corroborated temporal and spatial differences due to known disturbance events. RESET provides a open access, easily interpretable set of tools and associated indices for monitoring environmental stress exposure on coral reefs, designed to inform conservation and management decisions. As such RESET has broad potential to assist in the monitoring of our increasingly imperilled coral ecosystems, in particular, those that are remote or inaccessible.

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 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.

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.

contents (see Table 1 for keywords included in each topic). received little attention prior to 2005 (Figure 2A). The increased prominence of coral disease is likely associated with the increased profile of diseases emerging as a major scleractinian coral threat (Harvell et al., 1999; Sweet et al., 2012). Plastic pollution, despite a recent high profile (Villarrubia-Gómez et al., 2018; Stafford and Jones, 2019), has featured the least of all reef threats. The most common climate change-related impact mentioned in 21% of RCUK presentations has been coral bleaching (Figure 2B). Unsurprisingly, as the first RCUK conference occurred in November 1998—toward the end of the first reported global mass coral bleaching event (Wilkinson, 2000)— presentations discussed preliminary results of the impact of bleaching on coral reefs. These first conference presentation titles included phrases such as “catastrophic coral bleaching” and “can coral adapt to climate change” (RCUK, 1998). More presentations refer to bleaching than climate change throughout the time series (Figure 2B), likely reflecting the fact that bleaching is a sign of coral stress directly observable by researchers and can also be caused by non-climate change related processes, e.g., disease. Presentations related to bleaching were a mainstay of meetings from 1998 to 2016, while climate change became much more prominent after 2006 (Figure 2B). Whilst storm impacts and ocean acidification were mentioned in 7 and 3% of abstracts, respectively, presentations relating to ocean acidification were completely absent prior to 2008 (Figure 2B). From 1998 to 2016, over half (59%) of abstracts included reference to conservation ormanagement. Given that the original aim of RCUK included “promoting conservation...about coral reefs” and “ensuring that all reef related activities are conducted in a responsible manner”, it is encouraging to see a high number of abstracts either directly studying these issues or relating research to potential applied impact. Management issues (comprised of keywords “management”, “management capacity”, and “effectiveness”) were the most commonly mentioned terms— present in 35% of abstracts (Figure 2C), followed by conservation and people (both 30% of accepted abstracts). Sustainability and Marine Protected Areas (MPAs) were each mentioned in 14% of abstracts, with MPAs being the single biggest named conservation intervention discussed at RCUK. However, the use of community-based conservation approaches and enforcement have been noticeably lacking in past RCUK conferences (Figure 2C). Overall, there has been little change through time in the discussion of conservation and management approaches. RESEARCH TOPIC OVERVIEW This Research Topic “Coral Reefs in the Anthropocene” marks the 20th anniversary of RCUK, and was assembled jointly as a conference proceedings volume for ECRS and an open call via the Frontiers in Marine Science journal website for additional submissions. This Research Topic contains 20 papers involving 104 authors and covers many issues at the cutting-edge of reef science and conservation. Papers span basic and applied science, such as the diversity of coral holobionts, coral disease, nutrient impacts, recovery potential for coral reefs, and support for MPA expansions. Here, we briefly summarise each contribution and highlight their importance to the study of coral reefs. Coral reefs are built by stony corals that comprise metaorganisms, or so-called holobionts (Rohwer et al., 2002). For decades, the association between coral animals and their intracellular microalgal partners in the family Symbiodiniaceae has been the subject of intense research given that this symbiosis comprises the foundation of reef ecosystems (LaJeunesse et al., 2018). However, more recently, the role of bacteria in helping Frontiers in Marine Science | www.frontiersin.org June 2020 | Volume 7 | Article 364 9 Andradi-Brown et al. Editorial: Coral Reefs in the Anthropocene TABLE 1 |

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.

Studying scleractinian coral bleaching and recovery dynamics in remote, isolated reef systems offers an opportunity to examine impacts of global reef stressors in the absence of local human threats. Reefs in the Chagos Archipelago, central Indian Ocean, suffered severe bleaching and mortality in 2015 following a 7.5 maximum degree heating weeks (DHWs) thermal anomaly, causing a 60% coral cover decrease from 30% cover in 2012 to 12% in April 2016. Mortality was taxon specific, with Porites becoming the dominant coral genus post-bleaching because of an 86% decline in Acropora from 14 to 2% cover. Spatial heterogeneity in Acropora mortality across the Archipelago was significantly negatively correlated with variation in DHWs and with chlorophyll-a concentrations. In 2016, a 17.6 maximum DHWs thermal anomaly caused further damage, with 68% of remaining corals bleaching in May 2016, and coral cover further declining by 29% at Peros Banhos Atoll (northern Chagos Archipelago) from 14% in March 2016 to 10% in April 2017. We therefore document back-to-back coral bleaching and mortality events for two successive years in the remote central Indian Ocean. Our results indicate lower coral mortality in 2016 than 2015 despite a more severe thermal anomaly event in 2016. This could be caused by increased thermal resistance and resilience within corals surviving the 2015 thermal anomaly; however, high bleaching prevalence in 2016 suggests there remained a high sensitivity to bleaching. Similar coral mortality and community change were seen in the Chagos Archipelago following the 1998 global bleaching event, from which recovery took 10 yr. This relatively rapid recovery suggests high reef resiliency and indicates that the Archipelago’s lack of local disturbances will increase the probability that the reefs will again recover over time. However, as the return time between thermal anomaly events becomes shorter, this ability to recover will become increasingly compromised.

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.

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 potential to act as refuges from fisheries impacts. We surveyed MCEs in Raja Ampat, West Papua using baited remote underwater video, representing the largest MCE fish community survey ever conducted in the Coral Triangle region. Here we show that Raja Ampat MCEs are exceptionally fish species rich, with 152 fish species recorded – representing the greatest fish richness of any MCE previously surveyed. We find fish communities are highly depth driven, with declines in fish abundance and biomass at increased depth. In contrast to previous studies elsewhere in the world, we found that planktivores declined as a proportion of MCE community at increased depths. While greater human population density resulted in lower reef fish biomass, we found no evidence that MCEs provide a depth refuge from fisheries impacts. Our results suggest that previously established MCE-depth patterns may not hold true for Raja Ampat and highlight the need for future MCE studies within the Coral Triangle region.

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.