Benthic Composition Research Articles

Two tropical biodiversity hotspots, two different pathways for energy

Abstract Local factors, such as riparian vegetation and stream type, affect the structure and composition of benthic macroinvertebrate assemblages in streams. To better understand the effects of biomes on lotic ecosystems, we evaluated whether Atlantic Forest (AF) and Neotropical Savanna (NS) biomes showed distinct patterns in (i) benthic macroinvertebrate assemblage structure and (ii) the shredder functional feeding group. We predicted that (i) richness, density, biomass, instant secondary production, eco-exergy, and specific eco-exergy would be higher for benthic macroinvertebrate assemblages in AF stream sites than in NS sites. We also predicted that (ii) length, density, biomass, instant secondary production, eco-exergy, and specific eco-exergy would be higher for shredders in AF stream sites. We found that benthic macroinvertebrate assemblage composition and taxa richness were significantly different between stream sites in the two biomes, with the AF biome being the richest. But we found no differences in density, biomass, instant secondary production, eco-exergy, or specific eco-exergy between AF and NS stream sites. For AF shredders, the mean length, density, biomass, secondary production and eco-exergy were significantly higher than for NS stream sites. These differences were attributed to the quality of leaf litter, which was generally higher in AF than in NS stream sites. This indicates that the intrinsic characteristics of the AF and NS biomes act as structuring factors for benthic macroinvertebrate assemblages, influencing the structure and functioning of tropical lotic ecosystems.

Similarity in benthic habitat and fish assemblages in the upper mesophotic and shallow water reefs in the West Philippine Sea

AbstractThe South China Sea (SCS) is a biodiversity hotspot, however, most biodiversity surveys in the region are confined to shallow water reefs. Here, we studied the benthic habitat and fish assemblages in the upper mesophotic coral ecosystems (MCEs; 30–40 m) and SWRs (8–22 m) at three geographic locations (Luzon Strait; Palawan; and the Kalayaan Group of Islands) in the eastern SCS (also called the West Philippine Sea) using diver-based survey methods. Mean coral genera and fish species richness ranged from 17–25 (per 25 m2) and 11–17 (per 250 m2) in MCEs, respectively; although none of these were novel genera/species. Coral and fish assemblages were structured more strongly by location than by depth. Location differences were associated with the variability in benthic composition, wherein locations with higher hard coral cover had higher coral genera richness and abundance. Locations with higher algae and sand cover had higher diversity and density of fish herbivores and benthic invertivores. Fishing efforts may also have contributed to among-location differences as the highly exploited location had the lowest fish biomass. The low variation between depths may be attributed to the similar benthic composition at each location, the interconnectivity between depths due to hydrological conditions, fish motility, and the common fishing gears used in the Philippines that can likely extend beyond SWRs. Results imply that local-scale factors and anthropogenic disturbances probably dampen across-depth structuring in coral genera and fish species assemblages.

Global community breaks at 60 m on mesophotic coral reefs

AbstractAimMesophotic coral ecosystems (MCEs) are unique communities that support a high proportion of depth‐endemic species distinct from shallow‐water coral reefs. However, there is currently little consensus on the boundaries between shallow and mesophotic coral reefs and between upper versus lower MCEs because studies of these communities are often site specific. Here, we examine the ecological evidence for community breaks, defined here as species loss, in fish and benthic taxa between shallow reefs and MCEs globally.LocationGlobal MCEs.Time period1973–2017.Major taxa studiedMacrophytes, Porifera, Scleractinia, Hydrozoa, Octocorallia, Antipatharia and teleost fishes.MethodsWe used random‐effects models and breakpoint analyses on presence/absence data to identify regions of higher than expected species loss along a depth gradient of 1–69 m, based on a meta‐analysis of 26 studies spanning diverse photoautotrophic and heterotrophic taxa. We then investigated the extent to which points of high faunal turnover can be explained by environmental factors, including light, temperature and nutrient availability.ResultsWe found evidence for a community break, indicated by a significant loss of shallow‐water taxa, at ~ 60 m across several taxonomically and functionally diverse benthic groups and geographical regions. The breakpoint in benthic composition is best explained by decreasing light, which is correlated with the optical depths between 10 and 1% of surface irradiance. A concurrent shift in the availability of nutrients, both dissolved and particulate organic matter, and a shift from photoautotroph to heterotroph‐dominated assemblages also occurs at ~ 60 m depth.Main conclusionsWe found evidence for global community breaks across multiple benthic taxa at ~ 60 m depth, indicative of distinct community transitions between shallow and mesophotic coral ecosystems. Changes in the underwater light environment and the availability of trophic resources along the depth gradient are the most parsimonious explanations for the observed patterns.

Object-Based Mapping of Coral Reef Habitats Using Planet Dove Satellites

High spatial resolution benthic habitat information is essential for coral reef protection and coastal environmental management. Satellite-based shallow benthic composition mapping offers a more efficient approach than traditional field measurements, especially given the advancements in high spatial and temporal resolution satellite imagery. The Planet Dove satellite constellation now has more than 150 instruments in orbit that offer daily coverage at high spatial resolution (3.7 m). The Dove constellation provides regularly updated imagery that can minimize cloud in tropical oceans where dense cloud cover persists. Daily image acquisition also provides an opportunity to detect time-sensitive changes in shallow benthic habitats following coral bleaching events, storms, and other disturbances. We developed an object-based coral reef habitat mapping approach for Dove and similar multispectral satellites that provides bathymetry estimation, bottom reflectance retrieval, and object-based classification to identify different benthic compositions in shallow coastal environments. We tested our approach in three study sites in the Dominican Republic using 18 Dove images. Benthic composition classification results were validated by field measurements (overall accuracy = 82%). Bathymetry and bottom reflectance significantly contributed to identifying benthic habitat classes with similar surface reflectance. This new object-based approach can be effectively applied to map and manage coral reef habitats.

Filamentous calcareous alga provides substrate for coral-competitive macroalgae in the degraded lagoon of Dongsha Atoll, Taiwan.

BackgroundThe chemically-rich seaweed Galaxaura is not only highly competitive with corals, but also provides substrate for other macroalgae. Its ecology and associated epiphytes remain largely unexplored. To fill this knowledge gap, we undertook an ecological assessment to explore the spatial variation, temporal dynamics, and diversity of epiphytic macroalgae of Galaxaura divaricata on patch reefs in the lagoon of Dongsha Atoll, a shallow coral reef ecosystem in the northern South China Sea that has been repeatedly impacted by mass coral bleaching events.MethodsTwelve spatially independent patch reefs in the Dongsha lagoon were first surveyed to assess benthic composition in April 2016, and then revisited to determine G. divaricata cover in September 2017, with one additional Galaxaura-dominated reef (site 9). Four surveys over a period of 17 months were then carried out on a degraded patch reef site to assess the temporal variation in G. divaricata cover. Epiphytic macroalgae associated with G. divaricata were quantified and identified through the aid of DNA barcoding at this degraded site.ResultsPatch reefs in the Dongsha lagoon were degraded, exhibiting relatively low coral cover (5–43%), but high proportions of macroalgae (13–58%) and other substrate (rubble and dead corals; 23–69%). The distribution of G. divaricata was heterogeneous across the lagoon, with highest abundance (16–41%) in the southeast area. Temporal surveys showed consistently high covers (mean ± SD = 16.9 ± 1.21%) of G. divaricata for 17 months. Additional photographic evidence suggested that overgrowth of G. divaricata can persist for 3.5 years. Yet, G. divaricata provides substrate to other macroalgae (e.g., Lobophora sp.) that also limit the growth of corals.ConclusionsOur study demonstrates that an allelopathic seaweed, such as G. divaricata, can overgrow degraded coral reefs for extended periods of time. By providing habitat for other harmful macroalgae, a prolonged Galaxaura overgrowth could further enhance the spread of macroalgae, and strengthen negative feedback loops, decreasing the recovery potential of degraded reefs.

Atmospheric Nitrogen Deposition Increases the Possibility of Macroalgal Dominance on Remote Coral Reefs

AbstractField surveys in the Xisha and Zhongsha archipelagos, in the midnorthern South China Sea, show macroalgal dominance on remote reefs that were previously dominated by corals. This study was conducted to investigate the underlying mechanisms of this phenomenon. Benthic composition analyses indicated that macroalgae that are rare on pristine reefs dominated 27% of 81 study sites, and live coral cover dropped to 16.3% in 2015. Nearly one third of corals came into direct contact with macroalgae. Further analyses on the algal distribution patterns, nutrient fluxes, and air mass backward trajectories suggest that atmospheric nitrogen deposition is the major external supply of nutrients. The greater cover of macroalgae on the coral reefs coincides with the considerable atmospheric nitrogen deposition from the southwest during the summer monsoon. Moreover, the remote coral reefs hosted sevenfold greater macroalgae cover than the coastal coral reefs because atmospheric nitrogen assimilates effectively in the N limited and high visibility water. Macroalgae promotion is projected to grow with the increasing atmospheric nitrogen supply in the coming decade, which constitutes a larger stress on remote coral reefs.

Can ensemble techniques improve coral reef habitat classification accuracy using multispectral data?

Remote sensing has potential in studies of the benthic habitat and extracting the reflectance from the data of multispectral sensors, but traditional image classification techniques cannot provide coral habitat maps with adequate accuracy. This study tested five traditional and three ensemble classification techniques on QuickBird for mapping the benthic composition of coral reefs on the Lang Tengah Island (Malaysia). The common techniques, minimum distance, maximum likelihood, K-nearest neighbour, Fisher and parallelepiped techniques were compared with ensemble classifiers, such as majority voting (MV), simple averaging, and mode combination. The per-class accuracy of the habitat detection improved in the ensemble classifiers; in particular, the MV classifier achieved 95%, 65%, 75% and 95% accuracies for coral, sparse coral, coral rubble and sand, respectively. Ensembles increased the accuracy of the habitat mapping classification by 28%, relative to conventional techniques. Thus, the ensemble techniques can be preferred over the traditional for benthic habitat mapping.

Spatial and temporal changes in reef fish assemblages on disturbed coral reefs, north Pacific coast of Costa Rica

AbstractBenthic structure of coral reefs determines the availability of refuges and food sources. Therefore, structural changes caused by natural and anthropogenic disturbances can have negative impacts on reef‐associated communities. During the 1990s, coral reefs from Bahía Culebra were considered among the most diverse ecosystems along the Pacific coast of Costa Rica; however, recently they have undergone severe deterioration as consequence of chronic stressors such as El Niño‐Southern Oscillation and harmful algal blooms. Reef fish populations in this area have also been intensely exploited. This study compared reef fish assemblages during two periods (1995–1996 and 2014–2016), to determine whether they have experienced changes as a result of natural and anthropogenic disturbances. For both periods, benthic composition and reef fish abundance were recorded using underwater visual censuses. Live coral cover (LCC) decreased from 43.09 ± 18.65% in 1995–1996 to 1.25 ± 2.42% in 2014–2016 (U = 36, p < 0.05). Macroalgal cover (%) in 2014–2016 was sixfold higher than mean values reported for the Eastern Tropical Pacific region. Mean (±SD) fish species richness in 1995–1996 (36.67 ± 14.20) was higher than in 2014–2016 (23.00 ± 9.14; U = 20, p < 0.05). Over 40% of reef fish orders observed in 1995–1996 were not detected in the 2014–2016 surveys, including large‐bodied predators. Reduction in abundance of fish predators such as sharks, grunts, and snappers is likely attributed to changes in habitat structure. Herbivorous such as parrotfishes and pufferfishes increased their abundance at sites with low LCC, probably in response to predators decline and increased algal cover. These findings revealed significant degradation and drastic loss of structural complexity in coral reefs from Bahía Culebra, which now are dominated by macroalgae. The large reduction in structural complexity of coral reefs has resulted in the loss of diversity and key ecological roles (e.g., predation and herbivory), thus potentially reducing the resilience of the entire ecosystem.

Spatial patterns and drivers of fish and benthic reef communities at São Tomé Island, Tropical Eastern Atlantic

AbstractMarine communities vary across spatial scales due to changes in habitat structure, wave exposure, depth and anthropogenic activities. Here, we quantitatively characterized, for the first time, the reef fish assemblages and benthic communities in six sites around São Tomé Island, in the Tropical Eastern Atlantic region. We performed 139 underwater visual census and 112 photo‐quadrats across six sites around the island to explore the relative importance of exposure, depth and topographic complexity as drivers of fish and benthic reef communities. Planktivores were the most important trophic group, in terms of both fish abundance and biomass. Small fishes (0–7 cm) dominated the abundance, whereas biomass was mainly concentrated in 8–15 and 16–30 cm body size classes. About 30% of the total benthic cover was composed of turf algae and circa of 28% of calcareous coralline algae, whereas corals were comparably less abundant (only 8%). Among these, Montastraea cavernosawas the most abundant coral (46% of the coral cover and 4% of total benthic cover). Wave exposure was the most important driver of the reef fish assemblages and was also important for benthic communities. Also, fish species composition seemed to respond, although weakly, to benthic composition. Topographic complexity had little effect on the indicators of fish assemblages but seemed to drive some changes in benthic cover. Overall, our results evidence the dominance of small planktivorous reef fish assemblages and of turf algal communities in São Tomé. Taken together, they support the idea of benthic communities shaped by wave action, with minor importance of corals, and of important energetic contribution from planktonic material. We also suggest that the relatively low biomass of medium and large fish species reflects the long‐term fishing pressure in São Tomé Island.

The influence of tourism-based provisioning on fish behavior and benthic composition

Distribution of non-natural food (provisioning) to attract fish, though popular in coral reef tourism, has often been discouraged due to its assumed adverse effects on fish health and behavior. However, the effects of provisioning on community structure, anti-predator, and foraging behavior of teleost fishes, as well as their potential to indirectly affect benthic organisms, are not yet clear. Here, we compared fish composition, wariness, foraging behavior of herbivorous fishes, and the benthic cover between provisioned and control sites. We found significant differences in fish abundance, species number, and composition at some locations, but not all. Although most provisioned herbivorous fish did not reduce their biting rates of benthic algae, provisioned sites still had higher coverage of green macroalgae. Our results dispute widely held presumptions on the effects of tourism-based provisioning on the ecology and behavior of teleost fishes, as well as the benthic cover. These findings suggest that while regulation of provisioning is necessary to manage and mitigate any deleterious outcomes, when moderated and monitored, it could still provide an educationally beneficial tool for coral reef ecotourism.

Environmental conditions and herbivore biomass determine coral reef benthic community composition: implications for quantitative baselines

Our ability to understand natural constraints on coral reef benthic communities requires quantitative assessment of the relative strengths of abiotic and biotic processes across large spatial scales. Here, we combine underwater images, visual censuses and remote sensing data for 1566 sites across 34 islands spanning the central-western Pacific Ocean, to empirically assess the relative roles of abiotic and grazing processes in determining the prevalence of calcifying organisms and fleshy algae on coral reefs. We used regression trees to identify the major predictors of benthic composition and to test whether anthropogenic stress at inhabited islands decouples natural relationships. We show that sea surface temperature, wave energy, oceanic productivity and aragonite saturation strongly influence benthic community composition; overlooking these factors may bias expectations of calcified reef states. Maintenance of grazing biomass above a relatively low threshold (~ 10–20 kg ha−1) may also prevent transitions to algal-dominated states, providing a tangible management target for rebuilding overexploited herbivore populations. Biophysical relationships did not decouple at inhabited islands, indicating that abiotic influences remain important macroscale processes, even at chronically disturbed reefs. However, spatial autocorrelation among inhabited reefs was substantial and exceeded abiotic and grazing influences, suggesting that natural constraints on reef benthos were superseded by unmeasured anthropogenic impacts. Evidence of strong abiotic influences on reef benthic communities underscores their importance in specifying quantitative targets for coral reef management and restoration that are realistic within the context of local conditions.

Comparison of cryptobenthic reef fish communities among microhabitats in the Red Sea

Knowledge of community structure within an ecosystem is essential when trying to understand the function and importance of the system and when making related management decisions. Within the larger ecosystem, microhabitats play an important role by providing inhabitants with a subset of available resources. On coral reefs, cryptobenthic fishes encompass many groups and make up an important proportion of the biodiversity. However, these fishes are relatively small, exhibit extreme visual or behavioral camouflage, and, therefore, are often overlooked. We examined the differences in fish community structure between three common reef microhabitats (live hard coral, dead coral rubble, and sand) using ichthyocide stations in the central Red Sea. Using a combination of morphological and genetic (cytochrome oxidase I (COI) barcoding) techniques, we identified 326 individuals representing 73 species spread across 17 families, from fifteen 1 m2 quadrats. Fish assemblages in the three microhabitats were significantly different from each other. Rubble microhabitats yielded the highest levels of fish abundance, richness, and diversity, followed by hard coral, and then sand. The results show that benthic composition, even at a small scale, influences cryptobenthic communities. This study also provides new COI sequence data to public databases, in order to further the research of cryptobenthic fishes in the Red Sea region.

The dynamics of coral reef benthic and reef fish communities in Batam and Natuna Islands, Indonesia

ABSTRACTThe dynamics of coral reef benthic and fish communities and their relationship within the Batam and Natuna Islands were investigated in 2004, 2007, 2010 and 2013. Hard coral covers declined at both locations (Batam by 18.69% and Natuna by 16.50%) in 2013, after which a mass bleaching event occurred in 2010. This dramatically affected fish abundance, given that there was a decline of 39.18 individuals per transect in Batam but strangely there was an increase by 47.36 individuals per transect for Natuna. This increase might be related to the isolated location of Natuna, which prevented fishes from migration, especially juveniles. In the same year, the benthic compositions in both locations changed from Acroporidae dominated reefs to become less complex reefs. Following this, the fish composition became less diverse for Batam but in reverse for Natuna. The changes in benthic communities correlate significantly with fish functional group diversity for Batam and the abundance for Natuna. These differences might be related to geographical conditions and human impacts which are different between the locations, such as being surrounded by group of islands or open sea, and fishing activities. The communities are dynamic spatially and temporally as a result of natural conditions of the environment and human activities.

Estimating the footprint of pollution on coral reefs with models of species turnover.

Ecological communities typically change along gradients of human impact, although it is difficult to estimate the footprint of impacts for diffuse threats such as pollution. We developed a joint model (i.e., one that includes multiple species and their interactions with each other and environmental covariates) of benthic habitats on lagoonal coral reefs and used it to infer change in benthic composition along a gradient of distance from logging operations. The model estimated both changes in abundances of benthic groups and their compositional turnover, a type of beta diversity. We used the model to predict the footprint of turbidity impacts from past and recent logging. Benthic communities far from logging were dominated by branching corals, whereas communities close to logging had higher cover of dead coral, massive corals, and soft sediment. Recent impacts were predicted to be small relative to the extensive impacts of past logging because recent logging has occurred far from lagoonal reefs. Our model can be used more generally to estimate the footprint of human impacts on ecosystems and evaluate the benefits of conservation actions for ecosystems.

The lionfish Pterois sp. invasion: Has the worst-case scenario come to pass?

This review revisits the traits thought to have contributed to the success of Indo-Pacific lionfish Pterois sp. as an invader in the western Atlantic Ocean and the worst-case scenario about their potential ecological effects in light of the more than 150 studies conducted in the past 5 years. Fast somatic growth, resistance to parasites, effective anti-predator defences and an ability to circumvent predator recognition mechanisms by prey have probably contributed to rapid population increases of lionfish in the invaded range. However, evidence that lionfish are strong competitors is still ambiguous, in part because demonstrating competition is challenging. Geographic spread has likely been facilitated by the remarkable capacity of lionfish for prolonged fasting in combination with other broad physiological tolerances. Lionfish have had a large detrimental effect on native reef-fish populations in the northern part of the invaded range, but similar effects have yet to be seen in the southern Caribbean. Most other envisaged direct and indirect consequences of lionfish predation and competition, even those that might have been expected to occur rapidly, such as shifts in benthic composition, have yet to be realized. Lionfish populations in some of the first areas invaded have started to decline, perhaps as a result of resource depletion or ongoing fishing and culling, so there is hope that these areas have already experienced the worst of the invasion. In closing, we place lionfish in a broader context and argue that it can serve as a new model to test some fundamental questions in invasion ecology.

Coral reef habitat mapping: A combination of object-based image analysis and ecological modelling

Despite being one of the most important and well-studied coral reefs in the world, the full extent of coral habitat of the Great Barrier Reef (GBR) is not well mapped and there is no current and comprehensive map of the GBR's geomorphic zonation or benthic composition. This paper demonstrates an approach that integrates ecological coral habitat mapping with empirical modelling to map the geomorphic zonation and benthic composition of the “shallow offshore reefs” of the GBR, using the Capricorn Bunker Group (CBG) as a case study. The approach combined environmental data sets and geo-ecological rule sets to identify geomorphic zones. The benthic composition of individual geomorphic zones was mapped for: shallow reef flat zones, using object-based image analysis with context driven rules based on coral reef ecology; and reef slope zones, using levels of wave exposure to predict the distribution of coral types. The environmental data sets used were field-based benthic composition data, Landsat 8 OLI satellite image-derived bottom reflectance, water depth and slope (15 m × 15 m pixel size) data, reef impact data, and modelled wave exposure. The study showed that the combination of geomorphic-ecological rules and models with remote sensing imagery provided robust mapping results over a large (~2500 km2) reef system, of which 245 km2 was mapped as shallow coral reefs and 88 km2 of that was mapped as areas containing coral. Most importantly, the method produced defined the geomorphic zones and benthic composition of a study area that is significantly larger than the majority of coral reef remote sensing mapping projects previously published. With some modifications, the methods presented have the potential to be applied to the full extent of the shallow offshore reefs of the GBR, or any large reef globally. Monitoring and management of coral reefs for conservation and other purposes, at regional to global scales will benefit from the ability to produce and use this type of essential information on a regular basis.

Spatio-Temporal Patterns in the Coral Reef Communities of the Spermonde Archipelago, 2012–2014, II: Fish Assemblages Display Structured Variation Related to Benthic Condition

The Spermonde Archipelago is a complex of ~70 mostly populated islands off Southwest Sulawesi, Indonesia, in the center of the Coral Triangle. The reefs in this area are exposed to a high level of anthropogenic disturbances. Previous studies have shown that variation in the benthos is strongly linked to water quality and distance from the mainland. However, little is known about the fish assemblages of the region and if their community structure also follows a relationship with benthic structure and distance from shore. In this study, we used eight islands of the archipelago, varying in distance from 1-55 km relative to the mainland, and three years of surveys, to describe benthic and fish assemblages and to examine the spatial and temporal influence of benthic composition on the structure of the fish assemblages. Cluster analysis indicated that distinct groups of fish were associated with distance, while few species were present across the entire range of sites. Relating fish communities to benthic composition using a multivariate generalized linear model confirmed that fish groups relate to structural complexity (rugosity) or differing benthic groups; either algae, reef builders (coral and crustose coralline algae) or invertebrates and rubble. From these relationships we can identify sets of fish species that may be lost given continued degradation of the Spermonde reefs. Lastly, the incorporation of water quality, benthic and fish indices indicates that local coral reefs responded positively after an acute disturbance in 2013 with increases in reef builders and fish diversity over relatively short (one year) time frames. This study contributes an important, missing component (fish community structure) to the growing literature on the Spermonde Archipelago, a system that features environmental pressures common in the greater Southeast Asian region.

Use of a semi-automated object based analysis to map benthic composition, Heron Reef, Southern Great Barrier Reef

ABSTRACTCoral reef scientists and managers require detailed information of reef environments to develop, implement and evaluate management strategies. Maps showing the distribution of corals, seagrass, algae, sand, rubble and rock are an essential component of this information. Using a semi-automated, object-based image analysis (OBIA) approach this study created a benthic community map for Heron Reef (area: approximately 27 km2), Southern Great Barrier Reef, Australia. Benthic cover information was acquired for calibration and validation via georeferenced photograph transects, which coincided with high spatial resolution Quickbird-2 satellite image capture in 2007. Through combination of these data sets and modification of a semi-automated OBIA classification scheme previously developed for seagrass environments to account for the heterogeneous nature of reef benthic communities, a benthic community map was created for Heron Reef with an overall accuracy of 61.6%. The robustness and repeatability of our method provide future opportunity to apply the semi-automated approach to a time series of field and high spatial resolution image data sets to create a time series of benthic community maps for Heron Reef. The results presented in this study therefore open up the opportunity to assess and understand the spatial and temporal dynamics of the reef environment.

Patterns in reef fish assemblages: Insights from the Chagos Archipelago.

Understanding the drivers of variability in the composition of fish assemblages across the Indo-Pacific region is crucial to support coral reef ecosystem resilience. Whilst numerous relationships and feedback mechanisms between the functional roles of coral reef fishes and reef benthic composition have been investigated, certain key groups, such as the herbivores, are widely suggested to maintain reefs in a coral-dominated state. Examining links between fishes and reef benthos is complicated by the interactions between natural processes, disturbance events and anthropogenic impacts, particularly fishing pressure. This study examined fish assemblages and associated benthic variables across five atolls within the Chagos Archipelago, where fishing pressure is largely absent, to better understand these relationships. We found high variability in fish assemblages among atolls and sites across the archipelago, especially for key groups such as a suite of grazer-detritivore surgeonfish, and the parrotfishes which varied in density over 40-fold between sites. Differences in fish assemblages were significantly associated with variable levels of both live and recently dead coral cover and rugosity. We suggest these results reflect differing coral recovery trajectories following coral bleaching events and a strong influence of ‘bottom-up’ control mechanisms on fish assemblages. Species level analyses revealed that Scarus niger, Acanthurus nigrofuscus and Chlorurus strongylocephalos were key species driving differences in fish assemblage structure. Clarifying the trophic roles of herbivorous and detritivorous reef fishes will require species-level studies, which also examine feeding behaviour, to fully understand their contribution in maintaining reef resilience to climate change and fishing impacts.

Ecosystem regime shifts disrupt trophic structure.

Regime shifts between alternative stable ecosystem states are becoming commonplace due to the combined effects of local stressors and global climate change. Alternative states are characterized as substantially different in form and function from pre-disturbance states, disrupting the delivery of ecosystem services and functions. On coral reefs, regime shifts are typically characterized by a change in the benthic composition from coral to macroalgal dominance. Such fundamental shifts in the benthos are anticipated to impact associated fish communities that are reliant on the reef for food and shelter, yet there is limited understanding of how regime shifts propagate through the fish community over time, relative to initial or recovery conditions. This study addresses this knowledge gap using long-term data of coral reef regime shifts and recovery on Seychelles reefs following the 1998 mass bleaching event. It shows how trophic structure of the reef fish community becomes increasingly dissimilar between alternative reef ecosystem states (regime-shifted vs. recovering) with time since disturbance. Regime-shifted reefs developed a concave trophic structure, with increased biomass in base trophic levels as herbivorous species benefitted from increased algal resources. Mid trophic level species, including specialists such as corallivores, declined with loss of coral habitat, while biomass was retained in upper trophic levels by large-bodied, generalist invertivores. Recovering reefs also experienced an initial decline in mid trophic level biomass, but moved toward a bottom-heavy pyramid shape, with a wide range of feeding groups (e.g., planktivores, corallivores, omnivores) represented at mid trophic levels. Given the importance of coral reef fishes in maintaining the ecological function of coral reef ecosystems and their associated fisheries, understanding the effects of regime shifts on these communities is essential to inform decisions that enhance ecological resilience and economic sustainability.