Thermal stress induces persistently altered coral reef fish assemblages

Geomorphological drivers of benthic community distribution on high energy temperate mesophotic and rariphotic reefs

Current knowledge of mesophotic benthic reef communities has predominantly focused on the distribution of sessile assemblages along the depth gradient. However, the influence of geomorphology on exposure to hydrodynamic processes may independently shape community assemblages, in addition to depth. We examined the distribution of sessile invertebrates at 50-150 m depths on exposed continental shelf reefs within a Marine Park in southwest Tasmania. Using marine still imagery and bathymetric mapping derivatives, we described the spatial response of biota to the prevailing hydrodynamic regime and geomorphology in this region, based on the growth forms of dominant morphospecies. The biota is exposed to large oceanic swells where high-wave energy mobilises sediments at depths of up to 140 m. As expected, the encrusting sponge morphospecies group was most prevalent but showed a niche habitat preference. Unlike wave-exposed reefs elsewhere, we observed a high cover of dominant morphospecies with three-dimensional growth forms alongside encrusting sponges over a wide range of depths. Notably, whip octocorals, cup-like, and tube sponge morphospecies groups had high cover on the most exposed slopes, while other groups such as encrusting and simple massive sponges were absent. However, this baseline assessment suggests there may be high species turnover due to the severe conditions during ocean storms, which may influence population dynamics. We recommend conducting future monitoring at ecologically relevant intervals to assess the natural variability in distribution due to local habitat effects.

Eat more, often: The capacity of piscivores to meet increased energy demands in warming oceans

Marine heatwaves (MHWs) profoundly disturb tropical coral reefs, imperilling species fitness and survival. Ectothermic piscivorous reef fishes are particularly vulnerable to MHWs since all aspects of their survival are dictated by ambient temperature. Severe +4 °C MHWs are projected to escalate daily energy demands by ~32-55 %, compelling piscivores to pursue larger or more frequent prey to survive. However, the feasibility of these responses have been questioned, as evolved predation and digestive strategies are constrained to specific prey types and sizes to safeguard residual aerobic scope (AS) during digestion for other vital processes. Instead, prevailing theory proposes appetite reductions at temperatures above optimal, preserving AS at the expense of growth and/or fitness. We investigated this dichotomy in the thermal foraging responses of Arc-eye hawkfish (Paracirrhites arcatus) and blacktail snapper (Lutjanus fulvus), evaluating energetic demand (standard metabolic rate, SMR), AS, appetite (meal mass intake), and capacity for digestion (specific dynamic action, SDA). Spanning a thermal gradient encompassing present-day winter (24.0 ± 0.1 °C), summer (27.5 ± 0.1 °C), and MHW (31.0 ± 0.1 °C), we show that SMR increased by ~65 % from winter to MHW for both species, while AS increased by ~31-67 %. Contrary to predictions of reduced appetite, both species consumed ~106 % larger meals, yielding a ~ 35-105 % greater SDA magnitude. Surprisingly, increased appetite did not encroach on residual AS as both species maintained the physiological flexibility to process larger meals while retaining ~45-60 % of AS at the post-prandial peak. Although larger meals take longer to digest, both species exhibited faster digestion with rising temperatures resulting in a maintained or shortened SDA duration during MHWs, simultaneously enabling increased feeding rates while preserving aerobic reserves to support heightened predation. Our findings underscore the physiological feasibility of increasing appetite for some piscivores, while highlighting the ecological challenge of increasing prey numbers and sizes amid declining prey densities and prey size-reductions caused by ocean warming.

Emergent patterns of reef fish diversity correlate with coral assemblage shifts along the Great Barrier Reef

Escalating climate and anthropogenic disturbances draw into question how stable large-scale patterns in biological diversity are in the Anthropocene. Here, we analyse how patterns of reef fish diversity have changed from 1995 to 2022 by examining local diversity and species dissimilarity along a large latitudinal gradient of the Great Barrier Reef and to what extent this correlates with changes in coral cover and coral composition. We find that reef fish species richness followed the expected latitudinal diversity pattern (i.e., greater species richness toward lower latitudes), yet has undergone significant change across space and time. We find declines in species richness at lower latitudes in recent periods but high variability at higher latitudes. Reef fish turnover continuously increased over time at all latitudes and did not show evidence of a return. Altered diversity patterns are characterised by heterogeneous changes in reef fish trophic groups across the latitudinal gradient. Shifts in coral composition correlate more strongly with reef fish diversity changes than fluctuations in coral cover. Our findings provide insight into the extent to which classic macroecological patterns are maintained in the Anthropocene, ultimately questioning whether these patterns are decoupling from their original underlying drivers.

Epilithic algal composition and the functioning of Anthropocene coral reefs

Epilithic algae dominate cover on coral reefs globally, forming a critical ecological interface between the benthos and reef organisms. Yet, the drivers of epilithic algal composition, and how composition relates to the distribution of key taxa, remain unclear. We develop a novel metric, the Epilithic Algal Ratio, based on turf cover relative to total epilithic algae cover, and use this metric to assess cross-scale patterns. We reveal water quality and hydrodynamics as the key environmental drivers of the Epilithic Algal Ratio across the Great Barrier Reef (GBR), and reefs globally. On the GBR, the abundance of herbivorous fishes and juvenile corals were also related to the Epilithic Algal Ratio, suggesting that reefs with long-dense turfs support fewer herbivores and corals. Ultimately, epilithic algae represent the interface through which the effects of declining water quality, which impacts a third of reefs globally, can reverberate up through coral reefs, compromising their functioning.

Increased resilience and a regime shift reversal through repeat mass coral bleaching

Ecosystems are substantially changing in response to ongoing climate change. For example, coral reefs have declined in coral dominance, with some reefs undergoing regime shifts to non-coral states. However, reef responses may vary through multiple heat stress events, with the rarity of long-term ecological datasets rendering such understanding uncertain. Assessing coral reefs across the inner Seychelles islands using a 28-year dataset, we document faster coral recovery from the 2016 than the 1998 marine heatwave event. Further, compositions of benthic and fish communities were more resistant to change following the more recent heat stress, having stabilized in a persistent altered state, with greater herbivory, following the 1998 climate disturbance. Counter to predictions, a macroalgal-dominated reef that had regime-shifted following the 1998 disturbance is transitioning to a coral-dominated state following the 2016 heat stress. Collectively, these patterns indicate that reef systems may be more resilient to repeat heatwave events than anticipated.

Global impacts of marine heatwaves on coastal foundation species

With increasingly intense marine heatwaves affecting nearshore regions, foundation species are coming under increasing stress. To better understand their impacts, we examine responses of critical, habitat-forming foundation species (macroalgae, seagrass, corals) to marine heatwaves in 1322 shallow coastal areas located across 85 marine ecoregions. We find compelling evidence that intense, summer marine heatwaves play a significant role in the decline of foundation species globally. Critically, detrimental effects increase towards species warm-range edges and over time. We also identify several ecoregions where foundation species don't respond to marine heatwaves, suggestive of some resilience to warming events. Cumulative marine heatwave intensity, absolute temperature, and location within a species' range are key factors mediating impacts. Our results suggest many coastal ecosystems are losing foundation species, potentially impacting associated biodiversity, ecological function, and ecosystem services provision. Understanding relationships between marine heatwaves and foundation species offers the potential to predict impacts that are critical for developing management and adaptation approaches.

Tropical fishery nutrient production depends on biomass-based management

The need to enhance nutrient production from tropical ecosystems to feed the poor could potentially create a new framework for fisheries science and management. Early recommendations have included targeting small fishes and increasing the species richness of fish catches, which could represent a departure from more traditional approaches such as biomass-based management. To test these recommendations, we compared the outcomes of biomass-based management with hypothesized factors influencing nutrient density in nearshore artisanal fish catches in the Western Indian Ocean. We found that enhancing nutrient production depends primarily on achieving biomass-based targets. Catches dominated by low- and mid-trophic level species with smaller body sizes and faster turnover were associated with modest increases in nutrient densities, but the variability in nutrient density was small relative to human nutritional requirements. Therefore, tropical fishery management should focus on restoring biomass to achieve maximum yields and sustainability, particularly for herbivorous fishes.

Competition Increases Risk of Species Extinction during Extreme Warming

AbstractTemperature and interspecific competition are fundamental drivers of community structure in natural systems and can interact to affect many measures of species performance. However, surprisingly little is known about the extent to which competition affects extinction temperatures during extreme warming. This information is important for evaluating future threats to species from extreme high-temperature events and heat waves, which are rising in frequency and severity around the world. Using experimental freshwater communities of rotifers and ciliates, this study shows that interspecific competition can lower the threshold temperature at which local extinction occurs, reducing time to extinction during periods of sustained warming by as much as 2 weeks. Competitors may lower extinction temperatures by altering biochemical characteristics of the natural environment that affect temperature tolerance (e.g., levels of dissolved oxygen, nutrients, and metabolic wastes) or by accelerating population decline through traditional effects of resource depletion on life history parameters that affect population growth rates. The results suggest that changes in community structure in space and time could drive variability in upper thermal limits.

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.

Protection promotes energetically efficient structures in marine communities

The sustainability of marine communities is critical for supporting many biophysical processes that provide ecosystem services that promote human well-being. It is expected that anthropogenic disturbances such as climate change and human activities will tend to create less energetically-efficient ecosystems that support less biomass per unit energy flow. It is debated, however, whether this expected development should translate into bottom-heavy (with small basal species being the most abundant) or top-heavy communities (where more biomass is supported at higher trophic levels with species having larger body sizes). Here, we combine ecological theory and empirical data to demonstrate that full marine protection promotes shifts towards top-heavy energetically-efficient structures in marine communities. First, we use metabolic scaling theory to show that protected communities are expected to display stronger top-heavy structures than disturbed communities. Similarly, we show theoretically that communities with high energy transfer efficiency display stronger top-heavy structures than communities with low transfer efficiency. Next, we use empirical structures observed within fully protected marine areas compared to disturbed areas that vary in stress from thermal events and adjacent human activity. Using a nonparametric causal-inference analysis, we find a strong, positive, causal effect between full marine protection and stronger top-heavy structures. Our work corroborates ecological theory on community development and provides a quantitative framework to study the potential restorative effects of different candidate strategies on protected areas.

Marine heatwaves are not a dominant driver of change in demersal fishes

Marine heatwaves have been linked to negative ecological effects in recent decades1,2. If marine heatwaves regularly induce community reorganization and biomass collapses in fishes, the consequences could be catastrophic for ecosystems, fisheries and human communities3,4. However, the extent to which marine heatwaves have negative impacts on fish biomass or community composition, or even whether their effects can be distinguished from natural and sampling variability, remains unclear. We investigated the effects of 248 sea-bottom heatwaves from 1993 to 2019 on marine fishes by analysing 82,322 hauls (samples) from long-term scientific surveys of continental shelf ecosystems in North America and Europe spanning the subtropics to the Arctic. Here we show that the effects of marine heatwaves on fish biomass were often minimal and could not be distinguished from natural and sampling variability. Furthermore, marine heatwaves were not consistently associated with tropicalization (gain of warm-affiliated species) or deborealization (loss of cold-affiliated species) in these ecosystems. Although steep declines in biomass occasionally occurred after marine heatwaves, these were the exception, not the rule. Against the highly variable backdrop of ocean ecosystems, marine heatwaves have not driven biomass change or community turnover in fish communities that support many of the world's largest and most productive fisheries.

Mixed-species groups of herbivorous reef fishes show variable responses to ecosystem perturbations in the Lakshadweep Islands, India

Herbivorous reef fishes provide a vital function in reef ecosystems by removing algae and making space available to coral recruits. The high abundance of herbivores in the reefs of the Lakshadweep islands has potentially aided in reef recovery and helped avoid a phase shift to an algal-dominated system, despite most areas having suffered massive coral losses. Mixed-species grouping in herbivores could potentially benefit both the participant species and the reef ecosystem by improving foraging efficiency. We examined the grouping propensity and species richness for three types of herbivore groups after a mass-bleaching event in 2010 and a mass recruitment event in 2015. The species richness and number of parrotfish groups, as well as the grouping propensity of common species, declined starkly across years, indicating that these groups may have formed in response to the mass-bleaching event, slowly diminishing as the reefs recovered. Conversely, large surgeonfish, which varied in richness and propensity across islands and aspect, are probably influenced by local processes. Small surgeonfish only increased in species richness and number in 2015, which may have been in response to the recruitment event. Thus, herbivorous fishes may respond differently to local ecosystem perturbations and play different roles in reef recovery. This article is part of the theme issue 'Mixed-species groups and aggregations: shaping ecological and behavioural patterns and processes'.

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

Extreme heatwave drives topography-dependent patterns of mortality in a bed-forming intertidal barnacle, with implications for associated community structure

Heatwave frequency and intensity will increase as climate change progresses. Intertidal sessile invertebrates, which often form thermally benign microhabitats for associated species, are vulnerable to thermal stress because they have minimal ability to behaviourally thermoregulate. Understanding what factors influence the mortality of biogenic species and how heatwaves might impact their ability to provide habitat is critical. Here, we characterize the community associated with the thatched barnacle, Semibalanus cariosus (Pallass, 1788), in British Columbia (BC), Canada. Then, we investigate what site-level and plot-level environmental factors explained variations in barnacle mortality resulting from an unprecedented regional heatwave in BC, Canada. Furthermore, we used a manipulative shading experiment deployed prior to the heatwave to examine the effect of thermal stress on barnacle survival and recruitment and the barnacle-associated community. We identified 50 taxa inhabiting S. cariosus beds, with variations in community composition between sites. Site-scale variables and algal canopy cover did not predict S. cariosus mortality, but patch-scale variation in substratum orientation did, with more direct solar irradiance corresponding with higher barnacle mortality. The shading experiment demonstrated that S. cariosus survival, barnacle recruitment, and invertebrate community diversity were higher under shades where substratum temperatures were lower. Associated community composition also differed between shaded and non-shaded plots, suggesting S. cariosus was not able to fully buffer acute thermal stress for its associated community. While habitat provisioning by intertidal foundation species is an important source of biodiversity, these species alone may not be enough to prevent substantial community shifts following extreme heatwaves. As heatwaves become more frequent and severe, they may further reduce diversity via the loss of biogenic habitat, and spatial variation in these impacts may be substantial.

Post-bleaching alterations in coral reef communities

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

Safeguarding nutrients from coral reefs under climate change

The sustainability of coral reef fisheries is jeopardized by complex and interacting socio-ecological stressors that undermine their contribution to food and nutrition security. Climate change has emerged as one of the key stressors threatening coral reefs and their fish-associated services. How fish nutrient concentrations respond to warming oceans remains unclear but these responses are probably affected by both direct (metabolism and trophodynamics) and indirect (habitat and species range shifts) effects. Climate-driven coral habitat loss can cause changes in fish abundance and biomass, revealing potential winners and losers among major fisheries targets that can be predicted using ecological indicators and biological traits. A critical next step is to extend research focused on the quantity of available food (fish biomass) to also consider its nutritional quality, which is relevant to progress in the fields of food security and malnutrition. Biological traits are robust predictors of fish nutrient content and thus potentially indicate how climate-driven changes are expected to impact nutrient availability within future food webs on coral reefs. Here, we outline future research priorities and an anticipatory framework towards sustainable reef fisheries contributing to nutrition-sensitive food systems in a warming ocean.

Tracking widespread climate-driven change on temperate and tropical reefs

Warming seas, marine heatwaves, and habitat degradation are increasingly widespread phenomena affecting marine biodiversity, yet our understanding of their broader impacts is largely derived from collective insights from independent localized studies. Insufficient systematic broadscale monitoring limits our understanding of the true extent of these impacts and our capacity to track these at scales relevant to national policies and international agreements. Using an extensive time series of co-located reef fish community structure and habitat data spanning 12 years and the entire Australian continent, we found that reef fish community responses to changing temperatures and habitats are dynamic and widespread but regionally patchy. Shifts in composition and abundance of the fish community often occurred within 2 years of environmental or habitat change, although the relative importance of these two mechanisms of climate impact tended to differ between tropical and temperate zones. The clearest of these changes on temperate and subtropical reefs were temperature related, with responses measured by the reef fish thermal index indicating reshuffling according to the thermal affinities of species present. On low latitude coral reefs, the community generalization index indicated shifting dominance of habitat generalist fishes through time, concurrent with changing coral cover. Our results emphasize the importance of maintaining local ecological detail when scaling up datasets to inform national policies and global biodiversity targets. Scaled-up ecological monitoring is needed to discriminate among increasingly diverse drivers of large-scale biodiversity change and better connect presently disjointed systems of biodiversity observation, indicator research, and governance.

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.

Climate-induced increases in micronutrient availability for coral reef fisheries

Climate change is transforming coral reefs, threatening supply of essential dietary micronutrients from small-scale fisheries to tropical coastal communities. Yet the nutritional value of reef fisheries and climate impacts on micronutrient availability remain unclear, hindering efforts to sustain food and nutrition security. Here, we measure nutrient content in coral reef fishes in Seychelles and show that reef fish are important sources of selenium and zinc and contain levels of calcium, iron, and omega-3 fatty acids comparable with other animal-source foods. Using experimental fishing, we demonstrate that iron and zinc are enriched in fishes caught on regime-shifted macroalgal habitats, whereas selenium and omega-3 varied among species. We find substantial increases in nutrients available to fisheries over two decades following coral bleaching, particularly for iron and zinc after macroalgal regime shifts. Our findings indicate that, if managed sustainably, coral reef fisheries could remain important micronutrient sources along tropical coastlines despite escalating climate impacts.

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Coral reef fishes are important sources of essential dietary nutrients

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Nutrients available to fisheries increased after mass coral bleaching

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Iron and zinc were higher in reef fishes caught on macroalgal habitats

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Coral reefs can remain key sources of nutritious food despite climate impacts

Tropical small-scale fisheries supply nutritious and affordable seafood to hundreds of millions of people, including catches from coral reefs that are vulnerable to marine heatwaves. Climate changes therefore threaten seafood supply in places where food insecurity is most prevalent, but what is the nutrient value of climate-impacted coral reefs? We analyzed nutrient content of 43 tropical reef fish species in Seychelles and found that coral reef fish contain similar levels of iron, selenium, and zinc as chicken, pork, and beef and higher levels of calcium and omega-3 fatty acids. By integrating nutrient data with fish surveys collected before and after mass coral bleaching, we show that high post-bleaching fish biomass led to greater nutrient supply for fisheries, particularly for iron and zinc. Sustainable management of reef fisheries can therefore continue to support tropical food and nutrition security, despite climate impacts to reef ecosystems.

Warming Rates Alter Sequence of Disassembly in Experimental Communities

AbstractThe frequency, intensity, and duration of periods of extreme environmental warming are expected to rise over the next hundred years and play an increasing role in species loss resulting from climate change, and yet we know little about their potential future effects on variability in the composition of communities. This study analyzed patterns of species loss in a community of four rotifers and six ciliates exposed to different rates of extreme warming. Temperature of loss was positively correlated with warming rates for all species, consistent with theoretical frameworks suggesting that lower rates of warming increase exposure time and cumulative thermal stress at each temperature. The sequence of species loss during extreme warming depended on the environmental warming rate (i.e., warming rates had the capacity to drive reversals in the relative thermal tolerances of species), and changes in the sequence of species loss driven by the warming rate resulted in substantial variability in community composition. The results suggest that differences in warming rates across space and time may increase variability in community composition in ecosystems increasingly disturbed by extreme temperature, potentially altering interspecific interactions, the abiotic environment, and ecosystem function. Several ecological mechanisms may be responsible, singly or together, for changes in the sequence of species loss at different rates of warming, including (a) differences among species in their sensitivity to the intensity and duration of heat exposure, (b) the effects of warming rates on temperature-dependent interspecific interactions, and (c) differences in opportunities for evolution among species and across warming rates.

Parrotfish corallivory on stress-tolerant corals in the Anthropocene

Cumulative anthropogenic stressors on tropical reefs are modifying the physical and community structure of coral assemblages, altering the rich biological communities that depend on this critical habitat. As a consequence, new reef configurations are often characterized by low coral cover and a shift in coral species towards massive and encrusting corals. Given that coral numbers are dwindling in these new reef systems, it is important to evaluate the potential influence of coral predation on these remaining corals. We examined the effect of a key group of coral predators (parrotfishes) on one of the emerging dominant coral taxa on Anthropocene reefs, massive Porites. Specifically, we evaluate whether the intensity of parrotfish predation on this key reef-building coral has changed in response to severe coral reef degradation. We found evidence that coral predation rates may have decreased, despite only minor changes in parrotfish abundance. However, higher scar densities on small Porites colonies, compared to large colonies, suggests that the observed decrease in scarring rates may be a reflection of colony-size specific rates of feeding scars. Reduced parrotfish corallivory may reflect the loss of small Porites colonies, or changing foraging opportunities for parrotfishes. The reduction in scar density on massive Porites suggests that the remaining stress-tolerant corals may have passed the vulnerable small colony stage. These results highlight the potential for shifts in ecological functions on ecosystems facing high levels of environmental stress.

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

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

Microbial Shift in the Enteric Bacteriome of Coral Reef Fish Following Climate-Driven Regime Shifts

Replacement of coral by macroalgae in post-disturbance reefs, also called a “coral-macroalgal regime shift”, is increasing in response to climate-driven ocean warming. Such ecosystem change is known to impact planktonic and benthic reef microbial communities but few studies have examined the effect on animal microbiota. In order to understand the consequence of coral-macroalgal shifts on the coral reef fish enteric bacteriome, we used a metabarcoding approach to examine the gut bacteriomes of 99 individual fish representing 36 species collected on reefs of the Inner Seychelles islands that, following bleaching, had either recovered to coral domination, or shifted to macroalgae. While the coral-macroalgal shift did not influence the diversity, richness or variability of fish gut bacteriomes, we observed a significant effect on the composition (R2 = 0.02; p = 0.001), especially in herbivorous fishes (R2 = 0.07; p = 0.001). This change is accompanied by a significant increase in the proportion of fermentative bacteria (Rikenella, Akkermensia, Desulfovibrio, Brachyspira) and associated metabolisms (carbohydrates metabolism, DNA replication, and nitrogen metabolism) in relation to the strong turnover of Scarinae and Siganidae fishes. Predominance of fermentative metabolisms in fish found on macroalgal dominated reefs indicates that regime shifts not only affect the taxonomic composition of fish bacteriomes, but also have the potential to affect ecosystem functioning through microbial functions.

Collapsing ecosystem functions on an inshore coral reef

Ecosystem functions underpin productivity and key services to humans, such as food provision. However, as the severity of environmental stressors intensifies, it is becoming increasingly unclear if, and to what extent, critical functions and services can be sustained. This issue is epitomised on coral reefs, an ecosystem at the forefront of environmental transitions. We provide a functional profile of a coral reef ecosystem, linking time-series data to quantified processes. The data reveal a prolonged collapse of ecosystem functions in this previously resilient system. The results suggest that sediment accumulation in algal turfs has led to a decline in resource yields to herbivorous fishes and a decrease in fish-based ecosystem functions, including a collapse of both fish biomass and productivity. Unfortunately, at present, algal turf sediment accumulation is rarely monitored nor managed in coral reef systems. Our examination of functions through time highlights the value of directly assessing functions, their potential vulnerability, and the capacity of algal turf sediments to overwhelm productive high-diversity coral reef ecosystems.

Global tropical reef fish richness could decline by around half if corals are lost

Reef fishes are a treasured part of marine biodiversity, and also provide needed protein for many millions of people. Although most reef fishes might survive projected increases in ocean temperatures, corals are less tolerant. A few fish species strictly depend on corals for food and shelter, suggesting that coral extinctions could lead to some secondary fish extinctions. However, secondary extinctions could extend far beyond those few coral-dependent species. Furthermore, it is yet unknown how such fish declines might vary around the world. Current coral mass mortalities led us to ask how fish communities would respond to coral loss within and across oceans. We mapped 6964 coral-reef-fish species and 119 coral genera, and then regressed reef-fish species richness against coral generic richness at the 1° scale (after controlling for biogeographic factors that drive species diversification). Consistent with small-scale studies, statistical extrapolations suggested that local fish richness across the globe would be around half its current value in a hypothetical world without coral, leading to more areas with low or intermediate fish species richness and fewer fish diversity hotspots.

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.

Recovery disparity between coral cover and the physical functionality of reefs with impaired coral assemblages

The ecology and structure of many tropical coral reefs have been markedly altered over the past few decades. Although long-term recovery has been observed in terms of coral cover, it is not clear how novel species configurations shape reef functionality in impaired reefs. The identities and life-history strategies of the corals species that recover are essential for understanding reef functional dynamics. We used a species identity approach to quantify the physical functionality outcomes over a 13 year period across 56 sites in the Mexican Caribbean. This region was affected by multiple stressors that converged and drastically damaged reefs in the early 2000s. Since then, the reefs have shown evidence of a modest recovery of coral cover. We used Bayesian linear models and annual rates of change to estimate temporal changes in physical functionality and coral cover. Moreover, a functional diversity framework was used to explore changes in coral composition and the traits of those assemblages. Between 2005 and 2018, physical functionality increased at a markedly lower rate compared to that of coral cover. The disparity between recovery rates depended on the identity of the species that increased (mainly non-framework and foliose-digitate corals). No changes in species dominance or functional trait composition were observed, whereas non-framework building corals consistently dominated most reefs. Although the observed recovery of coral cover and functional potential may provide some ecological benefits, the long-term effects on reef frameworks remain unclear, as changes in the cover of key reef-building species were not observed. Our findings are likely to be representative of many reefs across the wider Caribbean basin, as declines in coral cover and rapid increases in the relative abundance of weedy corals have been reported regionally. A coral identity approach to assess species turnover is needed to understand and quantify changes in the functionality of coral reefs.

Long-term ecological changes in fishes and macro-invertebrates in the world's warmest coral reefs

The Arabian Gulf is a natural laboratory for examining the consequences of large-scale disturbances due to global warming on coral reef ecosystems because of its extreme temperature regime. Using a coral reef monitoring time series extending from 1985 to 2015, we examined the long-term ecological changes in fish and macro-invertebrate communities as these habitats suffered heat shocks. We used a GLMM modelling framework to obtain clean annual signals in community indicators from noisy data. We also visualized temporal change in the taxonomic composition of fishes and macro-invertebrates. A phase shift from predominantly reef-building corals to barren grounds occurred between 1996 and 2000. Macro-invertebrates responded rapidly, and most of associated indicators recovered to pre-shift levels in 15 years. Fishes generally had lagged responses to the phase shift and had shifted to a new state with lower abundance, as well as different species composition. Increased levels of herbivory first by macro-invertebrates, mostly sea urchins, and then fishes, could have suppressed macro-algae expansion and consequently led to the dominance of barren ground. When the phase shift occurred, most of the 14 fish families declined in abundance while macro-invertebrate groups increased. Fish families able to utilize non-coral habitats appeared more resilient to the disturbances and subsequent coral degradation. Unlike other regions, we observed high resilience of the coral-dependent butterflyfishes to coral loss, possibly due to local migration from other less-impacted coral reefs. We hypothesized a top-down control mechanism mediated by predation by fishes has contributed to shaping the temporal and spatial patterns of the macro-invertebrates. Our results also revealed differences in spatial preferences among fishes and macro-invertebrate groups, which could be used to set priorities and develop effective conservation and management strategies.

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

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

Direct and indirect effects of climate change-amplified pulse heat stress events on coral reef fish communities

Climate change-amplified temperature anomalies pose an imminent threat to coral reef ecosystems. While much focus has been placed on the effects of heat stress on scleractinian corals-including bleaching, mortality, and loss of reef structural complexity-and many studies have documented changes to reef fish communities arising indirectly from shifts in benthic composition, the direct impacts of heat stress on reef fish are much less well understood. Here, we quantify the direct and indirect effects of heat stress on reef fishes, using underwater visual censuses of coral reef fish communities conducted before, during, and after the 2015-2016 El Niño-induced global coral bleaching event. Surveys took place at the epicenter of this event, at 16 sites on Kiritimati (Republic of Kiribati; central equatorial Pacific) spanning across a gradient of local human disturbance. We expected that heat stress would have both direct and indirect negative effects on the reef fish community, with direct effects resulting from physiological stress during the event and indirect effects manifesting afterward as a consequence of coral mortality, and that the ability of fish communities to recover following the heat stress would depend on levels of local human disturbance. We found that total reef fish biomass and abundance declined by >50% during heat stress, likely as a result of vertical migration of fish to cooler waters. One year after the cessation of heat stress, however, total biomass, abundance, and species richness had recovered to, or even exceeded, pre-heat stress levels. However, the biomass of corallivores declined by over 70% following severe coral loss, and reefs exposed to higher levels of local human disturbance showed impaired recovery following the heat stress. These findings enhance understanding of the projected impacts of climate change-associated marine heatwaves on reef fishes, and highlight the interacting effects of local and global stressors on this vital component of coral reef ecosystems.

Habitat zonation on coral reefs: Structural complexity, nutritional resources and herbivorous fish distributions

Distinct zonation of community assemblages among habitats is a ubiquitous feature of coral reefs. The distribution of roving herbivorous fishes (parrotfishes, surgeonfishes and rabbitfishes) is a particularly clear example, with the abundance of these fishes generally peaking in shallow-water, high-energy habitats, regardless of the biogeographic realm. Yet, our understanding of the factors which structure this habitat partitioning, especially with regards to different facets of structural complexity and nutritional resource availability, is limited. To address this issue, we used three-dimensional photogrammetry and structure-from-motion technologies to describe five components of structural complexity (rugosity, coral cover, verticality, refuge density and field-of-view) and nutritional resource availability (grazing surface area) among habitats and considered how these factors are related to herbivorous fish distributions. All complexity metrics (including coral cover) were highest on the slope and crest. Nutritional resource availability differed from this general pattern and peaked on the outer-flat. Unexpectedly, when compared to the distribution of herbivorous fishes, none of the complexity metrics had a marked influence in the models. However, grazing surface area was a strong predictor of both the abundance and biomass of herbivorous fishes. The strong relationship between grazing surface area and herbivorous fish distributions indicates that nutritional resource availability may be one of the primary factors driving the distribution of roving herbivorous fishes. The lack of a relationship between complexity and herbivorous fishes, and a strong affinity of herbivorous fishes for low-complexity, algal turf-dominated outer-flat habitats, offers some cautious optimism that herbivory may be sustained on future, low-complexity, algal turf-dominated reef configurations.

Biodiversity increases ecosystem functions despite multiple stressors on coral reefs

Positive relationships between biodiversity and ecosystem functioning (BEF) highlight the importance of conserving biodiversity to maintain key ecosystem functions and associated services. Although natural systems are rapidly losing biodiversity due to numerous human-caused stressors, our understanding of how multiple stressors influence BEF relationships comes largely from small, experimental studies. Here, using remote assemblages of coral reef fishes, we demonstrate strong, non-saturating relationships of biodiversity with two ecosystem functions: biomass and productivity. These positive relationships were robust both to an extreme heatwave that triggered coral bleaching and to invasive rats which disrupt nutrient subsidies from native seabirds. Despite having only minor effects on BEF relationships, both stressors still decreased ecosystem functioning via other pathways. The extreme heatwave reduced biodiversity, which, due to the strong BEF relationships, ultimately diminished both ecosystem functions. Conversely, the loss of cross-system nutrient subsidies directly decreased biomass. These results demonstrate multiple ways by which human-caused stressors can reduce ecosystem functioning, despite robust BEF relationships, in natural high-diversity assemblages.

Changing role of coral reef marine reserves in a warming climate

Coral reef ecosystems are among the first to fundamentally change in structure due to climate change, which leads to questioning of whether decades of knowledge regarding reef management is still applicable. Here we assess ecological responses to no-take marine reserves over two decades, spanning a major climate-driven coral bleaching event. Pre-bleaching reserve responses were consistent with a large literature, with higher coral cover, more species of fish, and greater fish biomass, particularly of upper trophic levels. However, in the 16 years following coral mortality, reserve effects were absent for the reef benthos, and greatly diminished for fish species richness. Positive fish biomass effects persisted, but the groups of fish benefiting from marine reserves profoundly changed, with low trophic level herbivores dominating the responses. These findings highlight that while marine reserves still have important roles on coral reefs in the face of climate change, the species and functional groups they benefit will be substantially altered.

It is unclear whether rapid climate change will alter the effectiveness of marine reserves. Here Graham et al. use a 20-year time-series from the Seychelles to show that marine reserves may not prevent climate-driven shifts in community composition, and that ecological responses to reserves are substantially altered.

Bleaching-driven reef community shifts drive pulses of increased reef sediment generation

The ecological impacts of coral bleaching on reef communities are well documented, but resultant impacts upon reef-derived sediment supply are poorly quantified. This is an important knowledge gap because these biogenic sediments underpin shoreline and reef island maintenance. Here, we explore the impacts of the 2016 bleaching event on sediment generation by two dominant sediment producers (parrotfish and Halimeda spp.) on southern Maldivian reefs. Our data identifies two pulses of increased sediment generation in the 3 years since bleaching. The first occurred within approximately six months after bleaching as parrotfish biomass and resultant erosion rates increased, probably in response to enhanced food availability. The second pulse occurred 1 to 3 years post-bleaching, after further increases in parrotfish biomass and a major (approx. fourfold) increase in Halimeda spp. abundance. Total estimated sediment generation from these two producers increased from approximately 0.5 kg CaCO3 m-2 yr-1 (pre-bleaching; 2016) to approximately 3.7 kg CaCO3 m-2 yr-1 (post-bleaching; 2019), highlighting the strong links between reef ecology and sediment generation. However, the relevance of this sediment for shoreline maintenance probably diverges with each producer group, with parrotfish-derived sediment a more appropriate size fraction to potentially contribute to local island shorelines.

Climatic and local stressor interactions threaten tropical forests and coral reefs

Tropical forests and coral reefs host a disproportionately large share of global biodiversity and provide ecosystem functions and services used by millions of people. Yet, ongoing climate change is leading to an increase in frequency and magnitude of extreme climatic events in the tropics, which, in combination with other local human disturbances, is leading to unprecedented negative ecological consequences for tropical forests and coral reefs. Here, we provide an overview of how and where climate extremes are affecting the most biodiverse ecosystems on Earth and summarize how interactions between global, regional and local stressors are affecting tropical forest and coral reef systems through impacts on biodiversity and ecosystem resilience. We also discuss some key challenges and opportunities to promote mitigation and adaptation to a changing climate at local and global scales. This article is part of the theme issue 'Climate change and ecosystems: threats, opportunities and solutions'.

Habitat complexity influences selection of thermal environment in a common coral reef fish

Coral reef species, like most tropical species, are sensitive to increasing environmental temperatures, with many species already living close to their thermal maxima. Ocean warming and the increasing frequency and intensity of marine heatwaves are challenging the persistence of reef-associated species through both direct physiological effects of elevated water temperatures and the degradation and loss of habitat structure following disturbance. Understanding the relative importance of habitat degradation and ocean warming in shaping species distributions is critical in predicting the likely biological effects of global warming. Using an automated shuttle box system, we investigated how habitat complexity influences the selection of thermal environments for a common coral reef damselfish, Chromis atripectoralis. In the absence of any habitat (i.e. control), C. atripectoralis avoided temperatures below 22.9 ± 0.8°C and above 31.9 ± 0.6°C, with a preferred temperature (T _pref) of 28.1 ± 0.9°C. When complex habitat was available, individual C. atripectoralis occupied temperatures down to 4.3°C lower (mean ± SE; threshold: 18.6 ± 0.7°C; T _pref: 18.9 ± 1.0°C) than control fish. Conversely, C. atripectoralis in complex habitats occupied similar upper temperatures as control fish (threshold: 31.7 ± 0.4°C; preference: 28.3 ± 0.7°C). Our results show that the availability of complex habitat can influence the selection of thermal environment by a coral reef fish, but only at temperatures below their thermal preference. The limited scope of C. atripectoralis to occupy warmer environments, even when associated with complex habitat, suggests that habitat restoration efforts in areas that continue to warm may not be effective in retaining populations of C. atripectoralis and similar species. This species may have to move to cooler (e.g. deeper or higher latitude) habitats under predicted future warming. The integration of habitat quality and thermal environment into conservation efforts will be essential to conserve of coral reef fish populations under future ocean warming scenarios.