Similar regional effects among local habitats on the structure of tropical reef fish and coral communities

Aim We examined data on corals and reef fishes to determine how particular local habitat types contribute to variation in community structure across regions covering gradients in species richness and how consistent this was over time. Location Great Barrier Reef (GBR), Australia. Methods We compared large‐scale (1300 km), long‐term (11 years) data on fishes and corals that were collected annually at fixed sites in three habitats (inshore, mid‐shelf and outer‐shelf reefs) and six regions (latitudinal sectors) along a gradient of regional species richness in both communities. We used canonical approaches to partition variation in community structure (sites × species abundance data matrices) into components associated with habitat, region and time and Procrustes analyses to assess the degree of concordance between coral and fish community structure. Results Remarkably similar patterns emerged for both fish and coral communities occupying the same sites. Reefs that had similar coral communities also had similar fish communities. The fraction of the community data that could be explained by regional effects, independent of pure habitat effects, was similar in both fish (33%) and coral (36.9%) communities. Pure habitat effects were slightly greater in the fish (31.3%) than in the coral (20.1%) community. Time explained relatively little variation (fish = 7.9%, corals = 9.6%) compared with these two spatial factors. Conclusions Our results indicate either that fish and coral communities were structured in similar ways by processes associated with region, habitat and time, or that the variation in fish community structure tracked variation associated with the coral communities at these sites and thereby reflects an indirect link between the environment and the structure of fish communities mediated by corals. Irrespective of the causes of such commonality, we demonstrate that community structure, not just species richness, can be related to both habitat differences and regional setting simultaneously.     

Coral reefs modify their seawater carbon chemistry – case study from a barrier reef (Moorea,French Polynesia)

Changes in the carbonate chemistry of coral reef waters are driven by carbon fluxes from two sources: concentrations of CO₂ in the atmospheric and source water, and the primary production/respiration and calcification/dissolution of the benthic community. Recent model analyses have shown that, depending on the composition of the reef community, the air‐sea flux of CO₂ driven by benthic community processes can exceed that due to increases in atmospheric CO₂ (ocean acidification). We field test this model and examine the role of three key members of benthic reef communities in modifying the chemistry of the ocean source water: corals, macroalgae, and sand. Building on data from previous carbon flux studies along a reef‐flat transect in Moorea (French Polynesia), we illustrate that the drawdown of total dissolved inorganic carbon (C_T) due to photosynthesis and calcification of reef communities can exceed the draw down of total alkalinity (A_T) due to calcification of corals and calcifying algae, leading to a net increase in aragonite saturation state (Ω_a). We use the model to test how changes in atmospheric CO₂ forcing and benthic community structure affect the overall calcification rates on the reef flat. Results show that between the preindustrial period and 1992, ocean acidification caused reef flat calcification rates to decline by an estimated 15%, but loss of coral cover caused calcification rates to decline by at least three times that amount. The results also show that the upstream–downstream patterns of carbonate chemistry were affected by the spatial patterns of benthic community structure. Changes in the ratio of photosynthesis to calcification can thus partially compensate for ocean acidification, at least on shallow reef flats. With no change in benthic community structure, however, ocean acidification depressed net calcification of the reef flat consistent with findings of previous studies.     

Fish community reassembly after a coral mass mortality: higher trophic groups are subject to increased rates of extinction

Since Gleason and Clements, our understanding of community dynamics has been influenced by theories emphasising either dispersal or niche assembly as central to community structuring. Determining the relative importance of these processes in structuring real‐world communities remains a challenge. We tracked reef fish community reassembly after a catastrophic coral mortality in a relatively unfished archipelago. We revisited the stochastic model underlying MacArthur and Wilson's Island Biogeography Theory, with a simple extension to account for trophic identity. Colonisation and extinction rates calculated from decadal presence‐absence data based on (1) species neutrality, (2) trophic identity and (3) site‐specificity were used to model post‐disturbance reassembly, and compared with empirical observations. Results indicate that species neutrality holds within trophic guilds, and trophic identity significantly increases overall model performance. Strikingly, extinction rates increased clearly with trophic position, indicating that fish communities may be inherently susceptible to trophic downgrading even without targeted fishing of top predators.     

Multi-scale spatial and partitioning analyses of the reef-fish community composition of the Yucatan fringing reef system

Coral reef and reef-fish communities are complex systems that have spatial structures that are influenced by multiple factors and processes that interact at several scales. We analysed composition data of reef-fish communities in the Yucatan Peninsula fringing reef system using a hierarchical multi-scale survey design to elucidate the origins of the species distribution patterns through multivariate canonical ordination and partitioning analysis. Twelve reef sites were surveyed along the fringing reef system, nested in three sectors, each with distinctive human interests (tourism, fishing, protection). Line transects were placed on reef lagoon, reef front, reef slope and reef terrace habitat for a total of 480 transects. The communities were composed of many rare and some dominant species (e.g., Thalasoma bifasciatum, Acanthurus bahianus, A. coeruleus, Sparisoma aurofrenatum). Redundancy analyses revealed that environmental variables explained between 11% and 22% of the variation in fish community data according to the habitat analysed. Spatial variables, represented by the geographic coordinates of transects, explained a low percentage (2–5%) of variation in the fish community data. Among the environmental variables that significantly explained (P < 0.05) the patterns of variation on the fish community were depth, topographical complexity, and the percentage of the substratum covered by algae, calcareous floor, rock and rubble. Although the total explained variation and proportion of the variation explained by each set of variables were consistently low, most of the effects on the fish community composition data were significant. Explanations are proposed concerning those results. Evincing the distribution patterns on the biological systems of multi-species as well as the causes that shape them is key for conservation planning and essential in highly threatened regions, such as the Caribbean coast of the Yucatan Peninsula.     

Fishing degrades size structure of coral reef fish communities

Fishing pressure on coral reef ecosystems has been frequently linked to reductions of large fishes and reef fish biomass. Associated impacts on overall community structure are, however, less clear. In size‐structured aquatic ecosystems, fishing impacts are commonly quantified using size spectra, which describe the distribution of individual body sizes within a community. We examined the size spectra and biomass of coral reef fish communities at 38 US‐affiliated Pacific islands that ranged in human presence from near pristine to human population centers. Size spectra ‘steepened’ steadily with increasing human population and proximity to market due to a reduction in the relative biomass of large fishes and an increase in the dominance of small fishes. Reef fish biomass was substantially lower on inhabited islands than uninhabited ones, even at inhabited islands with the lowest levels of human presence. We found that on populated islands size spectra exponents decreased (analogous to size spectra steepening) linearly with declining biomass, whereas on uninhabited islands there was no relationship. Size spectra were steeper in regions of low sea surface temperature but were insensitive to variation in other environmental and geomorphic covariates. In contrast, reef fish biomass was highly sensitive to oceanographic conditions, being influenced by both oceanic productivity and sea surface temperature. Our results suggest that community size structure may be a more robust indicator than fish biomass to increasing human presence and that size spectra are reliable indicators of exploitation impacts across regions of different fish community compositions, environmental drivers, and fisheries types. Size‐based approaches that link directly to functional properties of fish communities, and are relatively insensitive to abiotic variation across biogeographic regions, offer great potential for developing our understanding of fishing impacts in coral reef ecosystems.     

Patterns in the distribution of the crinoid community at Davies Reef on the central Great Barrier Reef

The crinoid community of Davies Reef, a midshelf reef in the central Great Barrier Reef, was systematically sampled in all major crinoid habitats. A total of 294 individuals of 27 species-level taxa was found in 25 sites across the reef. Of these 27 taxa, 20 were confidently assigned to known species. The 25 sitesx27 taxa matrix was subjected to an array of pattern extraction and diagnostic techniques — numerical classification, ordination and minimum spanning trees — to elucidate the structure of the community. These analyses revealed a consistent structure characterized by a species-rich ensemble around the periphery of the reef which was attenuated towards the inside of the reef. This structure contrasts strongly with the patterns seen in other major reef communities, such as hard and soft corals, fish or sponges. In these communities, different parts of the reef are characterized by distinctive sets of species, a depthbased zonation of the communities is evident, and the fore-reef slope typically supports a different ensemble from the back-reef slope. We conclude that the crinoid community offers a significant opportunity to observe the coral reef ecosystem from a different perspective.     

Habitat dynamics,marine reserve status,and the decline and recovery of coral reef fish communities

Severe climatic disturbance events often have major impacts on coral reef communities, generating cycles of decline and recovery, and in some extreme cases, community‐level phase shifts from coral‐ to algal‐dominated states. Benthic habitat changes directly affect reef fish communities, with low coral cover usually associated with low fish diversity and abundance. No‐take marine reserves (NTRs) are widely advocated for conserving biodiversity and enhancing the sustainability of exploited fish populations. Numerous studies have documented positive ecological and socio‐economic benefits of NTRs; however, the ability of NTRs to ameliorate the effects of acute disturbances on coral reefs has seldom been investigated. Here, we test these factors by tracking the dynamics of benthic and fish communities, including the important fishery species, coral trout (Plectropomus spp.), over 8 years in both NTRs and fished areas in the Keppel Island group, Great Barrier Reef, Australia. Two major disturbances impacted the reefs during the monitoring period, a coral bleaching event in 2006 and a freshwater flood plume in 2011. Both disturbances generated significant declines in coral cover and habitat complexity, with subsequent declines in fish abundance and diversity, and pronounced shifts in fish assemblage structure. Coral trout density also declined in response to the loss of live coral, however, the approximately 2:1 density ratio between NTRs and fished zones was maintained over time. The only post‐disturbance refuges for coral trout spawning stocks were within the NTRs that escaped the worst effects of the disturbances. Although NTRs had little discernible effect on the temporal dynamics of benthic or fish communities, it was evident that the post‐disturbance refuges for coral trout spawning stocks within some NTRs may be critically important to regional‐scale population persistence and recovery.     

Hierarchical and scale‐dependent effects of fishing pressure and environment on the structure and size distribution of parrotfish communities

Parrotfishes are considered to have a major influence on coral reef ecosystems through grazing the benthic biota and are also primary fishery targets in the Indo‐Pacific. Consequently, the impact of human exploitation on parrotfish communities is of prime interest. As anthropogenic and environmental factors interact across spatial scales, sampling programs designed to disentangle these are required by both ecologists and resource managers. We present a multi‐scale examination of patterns in parrotfish assemblage structure, size distribution and diversity across eight oceanic islands of Micronesia. Results indicate that correlates of assemblage structure are scale‐dependent; biogeographic distributions of species and island geomorphology hierarchically influenced community patterns across islands whereas biophysical features and anthropogenic pressure influenced community assemblage structure at the within‐island scale. Species richness and phylogenetic diversity increased with greater broad‐scale habitat diversity associated with different island geomorphologies. However, within‐island patterns of abundance and biomass varied in response to biophysical factors and levels of human influence unique to particular islands. While the effect of fishing activities on community composition and phylogenetic diversity was obscured across island types, fishing pressure was the primary correlate of mean parrotfish length at all spatial scales. Despite widespread fishery‐induced pressure on Pacific coral reefs, the structuring of parrotfish communities at broad spatial scales remains a story largely dependent on habitat. Thus, we propose better incorporation of scale‐dependent habitat effects in future assessments of overexploitation on reef fish assemblages. However, strong community‐level responses within islands necessitate an improved understanding of the phylogenetic and functional consequences of altering community structure.     

Island biogeography of Caribbean coral reef fish

Aim The goal of our study was to test fundamental predictions of biogeographical theories in tropical reef fish assemblages, in particular relationships between fish species richness and island area, isolation and oceanographic variables (temperature and productivity) in the insular Caribbean. These analyses complement an analogous and more voluminous body of work from the tropical Indo‐Pacific. The Caribbean is more limited in area with smaller inter‐island distances than the Indo‐Pacific, providing a unique context to consider fundamental processes likely to affect richness patterns of reef fish. Location Caribbean Sea. Methods We compiled a set of data describing reef‐associated fish assemblages from 24 island nations across the Caribbean Sea, representing a wide range of isolation and varying in land area from 53 to 110,860 km². Regression‐based analyses compared the univariate and combined effects of island‐specific physical predictors on fish species richness. Results We found that diversity of reef‐associated fishes increases strongly with increasing island area and with decreasing isolation. Richness also increases with increasing nearshore productivity. Analyses of various subsets of the entire data set reveal the robustness of the richness data and biogeographical patterns. Main conclusions Within the relatively small and densely packed Caribbean basin, fish species richness fits the classical species–area relationship. Richness also was related negatively to isolation, suggesting direct effects of dispersal limitation in community assembly. Because oceanic productivity was correlated with isolation, however, the related effects of system‐wide productivity on richness cannot be disentangled. These results highlight fundamental mechanisms that underlie spatial patterns of biodiversity among Caribbean coral reefs, and which are probably also are functioning in the more widespread and heterogeneous reefs of the Indo‐Pacific.     

Effects of coral restoration on fish communities: snapshots of long‐term,multiregional responses and implications for practice

Coral restoration is widely used around the world to address dramatic declines in coral cover; however, very few studies have looked specifically at the temporal response of fish assemblages (i.e. abundance and diversity) to coral restoration. Several critical reef functions and processes are driven by fishes, thereby making their recovery and responses around restoration structures key indicators of success. This study evaluates fish abundance and community composition on restoration plots following 8–12 years of restoration activity, in four locations (two Caribbean and two Indo‐Pacific). Responses were very complex with region‐, site‐, and body size‐specific patterns. Overall, fish abundance only increased in Indo‐Pacific sites where damselfish responded positively to increased coral cover and topographic complexity. Restoration effects on other fish families and particularly on larger bodied reef fish were negative or neutral at all locations. If restoration initiatives are going to substantively improve the condition and recovery of degraded reef fish communities, restoration efforts need to be planned, designed, and monitored based on fish‐specific habitat requirements and locally specific community dynamics.     

Volcanic ash supports a diverse bacterial community in a marine mesocosm

Shallow‐water coral reef ecosystems, particularly those already impaired by anthropogenic pressures, may be highly sensitive to disturbances from natural catastrophic events, such as volcanic eruptions. Explosive volcanic eruptions expel large quantities of silicate ash particles into the atmosphere, which can disperse across millions of square kilometres and deposit into coral reef ecosystems. Following heavy ash deposition, mass mortality of reef biota is expected, but little is known about the recovery of post‐burial reef ecosystems. Reef regeneration depends partly upon the capacity of the ash deposit to be colonised by waterborne bacterial communities and may be influenced to an unknown extent by the physiochemical properties of the ash substrate itself. To determine the potential for volcanic ash to support pioneer bacterial colonisation, we exposed five well‐characterised volcanic and coral reef substrates to a marine aquarium under low light conditions for 3 months: volcanic ash, synthetic volcanic glass, carbonate reef sand, calcite sand and quartz sand. Multivariate statistical analysis of Automated Ribosomal Intergenic Spacer Analysis (ARISA) fingerprinting data demonstrates clear segregation of volcanic substrates from the quartz and coral reef substrates over 3 months of bacterial colonisation. Overall bacterial diversity showed shared and substrate‐specific bacterial communities; however, the volcanic ash substrate supported the most diverse bacterial community. These data suggest a significant influence of substrate properties (composition, granulometry and colour) on bacterial settlement. Our findings provide first insights into physicochemical controls on pioneer bacterial colonisation of volcanic ash and highlight the potential for volcanic ash deposits to support bacterial diversity in the aftermath of reef burial, on timescales that could permit cascading effects on larval settlement.     

Patterns in the structural typology of benthic communities on two coral reefs of the central Great Barrier Reef

The morphological life-forms, that is to say, physiognomic-structural attributes, of two coral reef communities were used in a numerical analysis to determine the power of these attributes in recovering the underlying community structure. We used 17 attributes from the benthic communities at 6 reef slope sites on each of a midshelf and off-shore reef of the central Great Barrier Reef. These reefs had been previously well studied by traditional species-level means for several major taxonomic groups such as corals, fish and soft corals. Our multivariate analyses were able to recover broad patterns of between-reef affinity and discrete within-reef zonation patterns similar to those found in earlier studies, and in broad accord with the prevailing model of reef community structure, but with far greater efficacy. But perhaps more importantly, by placing all the benthos within the same context for the first time, our analyses were able to recover new patterns of community structure independent of the ones described earlier. This suggests that single-model explantations for the complex phenomena of coral reefs are likely to be inadequate.     

Mass coral bleaching causes biotic homogenization of reef fish assemblages

Global climate change is altering community composition across many ecosystems due to nonrandom species turnover, typically characterized by the loss of specialist species and increasing similarity of biological communities across spatial scales. As anthropogenic disturbances continue to alter species composition globally, there is a growing need to identify how species responses influence the establishment of distinct assemblages, such that management actions may be appropriately assigned. Here, we use trait‐based analyses to compare temporal changes in five complementary indices of reef fish assemblage structure among six taxonomically distinct coral reef habitats exposed to a system‐wide thermal stress event. Our results revealed increased taxonomic and functional similarity of previously distinct reef fish assemblages following mass coral bleaching, with changes characterized by subtle, but significant, shifts toward predominance of small‐bodied, algal‐farming habitat generalists. Furthermore, while the taxonomic or functional richness of fish assemblages did not change across all habitats, an increase in functional originality indicated an overall loss of functional redundancy. We also found that prebleaching coral composition better predicted changes in fish assemblage structure than the magnitude of coral loss. These results emphasize how measures of alpha diversity can mask important changes in the structure and functioning of ecosystems as assemblages reorganize. Our findings also highlight the role of coral species composition in structuring communities and influencing the diversity of responses of reef fishes to disturbance. As new coral species configurations emerge, their desirability will hinge upon the composition of associated species and their capacity to maintain key ecological processes in spite of ongoing disturbances.     

Consistent nutrient storage and supply mediated by diverse fish communities in coral reef ecosystems

Corals thrive in low nutrient environments and the conservation of these globally imperiled ecosystems is largely dependent on mitigating the effects of anthropogenic nutrient enrichment. However, to better understand the implications of anthropogenic nutrients requires a heightened understanding of baseline nutrient dynamics within these ecosystems. Here, we provide a novel perspective on coral reef nutrient dynamics by examining the role of fish communities in the supply and storage of nitrogen (N) and phosphorus (P). We quantified fish‐mediated nutrient storage and supply for 144 species and modeled these data onto 172 fish communities (71 729 individual fish), in four types of coral reefs, as well as seagrass and mangrove ecosystems, throughout the Northern Antilles. Fish communities supplied and stored large quantities of nutrients, with rates varying among ecosystem types. The size structure and diversity of the fish communities best predicted N and P supply and storage and N : P supply, suggesting that alterations to fish communities (e.g., overfishing) will have important implications for nutrient dynamics in these systems. The stoichiometric ratio (N : P) for storage in fish mass (~8 : 1) and supply (~20 : 1) was notably consistent across the four coral reef types (but not seagrass or mangrove ecosystems). Published nutrient enrichment studies on corals show that deviations from this N : P supply ratio may be associated with poor coral fitness, providing qualitative support for the hypothesis that corals and their symbionts may be adapted to specific ratios of nutrient supply. Consumer nutrient stoichiometry provides a baseline from which to better understand nutrient dynamics in coral reef and other coastal ecosystems, information that is greatly needed if we are to implement more effective measures to ensure the future health of the world's oceans.     

Spatial patterns of Yucatan reef fish communities: Testing models using a multi-scale survey design

Using a hierarchical multi-scale survey design, we examined the spatial patterns of reef fish communities and tested ecological models concerning the relative importance of reef geomorphology and anthropogenic pressure possibly driving community structure. Canonical redundancy analysis was used as a form of multivariate analysis of variance (MANOVA) to asses differences in reef fish community composition at two spatial scales: broad (10⁵ m) and intermediate (10⁴ m). Surveys were conducted on the east coast of the Yucatan Peninsula (Mexican Caribbean fringing reef), including regions and reefs which differed in geomophologic structure and human use. Seven hundred and fourteen line transects were distributed among 13 reef localities belonging to different regions established a priori. Transects covered four types of reef habitat: lagoon, front, slope, and terrace. Tests of significance were based on permutation procedures. Significant differences among regions were found for the lagoon, slope, and terrace fish communities, consistent with the geomorphologic model, but it is only in the reef lagoon that they were consistent with the anthropogenic model, which may indicate an effect of coastal human activities. Significant differences among reefs within regions were observed, which could be associated with local environmental gradients. Canonical nested MANOVA was an appropriate method for testing ecological hypotheses about the functioning of complex biological systems. The use of a surveying strategy that explicitly incorporated the spatial structure represents an important contribution of this paper to coral reef fish ecology.     

Quantifying the Human Impacts on Papua New Guinea Reef Fish Communities across Space and Time

Describing the drivers of species loss and of community change are important goals in both conservation and ecology. However, it is difficult to determine whether exploited species decline due to direct effects of harvesting or due to other environmental perturbations brought about by proximity to human populations. Here we quantify differences in species richness of coral reef fish communities along a human population gradient in Papua New Guinea to understand the relative impacts of fishing and environmental perturbation. Using data from published species lists we categorize the reef fishes as either fished or non-fished based on their body size and reports from the published literature. Species diversity for both fished and non-fished groups decreases as the size of the local human population increases, and this relationship is stronger in species that are fished. Additionally, comparison of modern and museum collections show that modern reef communities have proportionally fewer fished species relative to 19^th century ones. Together these findings show that the reef fish communities of Papua New Guinea experience multiple anthropogenic stressors and that even at low human population levels targeted species experience population declines across both time and space.     

A geospatial assessment of the relationship between reef flat community calcium carbonate production and wave energy

The ability of benthic communities inhabiting coral reefs to produce calcium carbonate underpins the development of reef platforms and associated sedimentary landforms, as well as the fixation of inorganic carbon and buffering of diurnal pH fluctuations in ocean surface waters. Quantification of the relationship between reef flat community calcium carbonate production and wave energy provides an empirical basis for understanding and managing this functionally important process. This study employs geospatial techniques across the reef platform at Lizard Island, Great Barrier Reef, to (1) map the distribution and estimate the total magnitude of reef community carbonate production and (2) empirically ascertain the influence of wave energy on community carbonate production. A World-View-2 satellite image and a field data set of 364 ground referencing points are employed, along with data on physical reef characteristics (e.g. bathymetry, rugosity) to map and validate the spatial distribution of the four major community carbonate producers (live coral, carbonate sand, green calcareous macroalgae and encrusting calcified algae) across the reef platform. Carbonate production is estimated for the complete reef platform from the composition of these community components. A synoptic model of wave energy is developed using the Simulating WAves Nearshore (SWAN) two-dimensional model for the entire reef platform. The relationship between locally derived measures of carbonate production and wave energy is evaluated at both the global scale and local scale along spatial gradients of wave energy traversing the reef platform. A wave energy threshold is identified, below which carbonate production levels appear to increase with wave energy and above which mechanical forcing reduces community production. This implies an optimal set of hydrodynamic conditions characterized by wave energy levels of approximately 300 J m^?2, providing an empirical basis for management of potential changes in community carbonate production associated with climate change-driven increases in wave energy.     

Assessing coral reefs on a pacific-wide scale using the microbialization score

The majority of the world's coral reefs are in various stages of decline. While a suite of disturbances (overfishing, eutrophication, and global climate change) have been identified, the mechanism(s) of reef system decline remain elusive. Increased microbial and viral loading with higher percentages of opportunistic and specific microbial pathogens have been identified as potentially unifying features of coral reefs in decline. Due to their relative size and high per cell activity, a small change in microbial biomass may signal a large reallocation of available energy in an ecosystem; that is the microbialization of the coral reef. Our hypothesis was that human activities alter the energy budget of the reef system, specifically by altering the allocation of metabolic energy between microbes and macrobes. To determine if this is occurring on a regional scale, we calculated the basal metabolic rates for the fish and microbial communities at 99 sites on twenty-nine coral islands throughout the Pacific Ocean using previously established scaling relationships. From these metabolic rate predictions, we derived a new metric for assessing and comparing reef health called the microbialization score. The microbialization score represents the percentage of the combined fish and microbial predicted metabolic rate that is microbial. Our results demonstrate a strong positive correlation between reef microbialization scores and human impact. In contrast, microbialization scores did not significantly correlate with ocean net primary production, local chla concentrations, or the combined metabolic rate of the fish and microbial communities. These findings support the hypothesis that human activities are shifting energy to the microbes, at the expense of the macrobes. Regardless of oceanographic context, the microbialization score is a powerful metric for assessing the level of human impact a reef system is experiencing.