Relationships between coral reef substrata and fish

 The objective of this work is to identify which substrata characteristics (such as coral morphology, coral diversity, coral species richness, percentage coverage by live coral or by algae) influence the structure and abundance of fish communities. The study was carried out at Reunion Island, Indian Ocean, where six sites were sampled in two zones (reef flat and outer reef slope). Quantitative data were collected by visual census techniques, along a linear transect of 50 m for the substratum, and a belt of 50×2 m for the fish communities. Correspondence analysis (CA) and an optimising cluster analysis, called dynamic clustering method (DCM) were used to describe and compare fish assemblages with the benthic composition. The relationships between benthic and fish communities were examined using the classes revealed by the partitioning of the substratum with DCM. This partitioning allowed us to derive four classes of substratum: the non-disturbed reef flat, the non-disturbed outer reef slope, the perturbed reef habitat and the reef pass. The analysis of the partitioning based on the coral variables suggests that there are significant relationships between benthic and fish assemblages. Accepted: 26 July 1996     

The ecology,behaviour and physiology of fishes on coral reef flats,and the potential impacts of climate change

Reef flats, typically a low‐relief carbonate and sand habitat in shallow water leeward of the reef crest, are one of the most extensive zones on Pacific coral reefs. This shallow zone often supports an abundant and diverse fish assemblage that is exposed to more significant variations in physical factors, such as water depth and movement, temperature and ultraviolet (UV) radiation levels, than most other reef fishes. This review examines the characteristics of reef flat fish assemblages, and then investigates what is known about how they respond to their biophysical environment. Because of the challenges of living in shallow, wave‐exposed water, reef flats typically support a distinct fish assemblage compared to other reef habitats. This assemblage clearly changes across tidal cycles as some larger species migrate to deeper water at low tide and other species modify their behaviour, but quantitative data are generally lacking. At least some reef flat fish species are well‐adapted to high temperatures, low oxygen concentrations and high levels of UV radiation. These behavioural and physiological adaptations suggest that there may be differences in the demographic processes between reef flat assemblages and those in deeper water. Indeed, there is some evidence that reef flats may act as nurseries for some species, but more research is required. Further studies are also required to predict the effects of climate change, which is likely to have multifaceted impacts on reef flats by increasing temperature, water motion and sediment load. Sea‐level rise may also affect reef flat fish assemblages and food webs by increasing the amount of time that larger species are able to forage in this zone. The lack of data on reef flats is surprising given their size and relative ease of access, and a better understanding of their functional role within tropical marine seascapes is urgently required.     

Reef fish assemblages in north-western Sri Lanka: distribution patterns and influences of fishing practises

The distribution and abundance of reef fishes in relation to habitat structure were studied within Bar Reef Marine Sanctuary (BRMS) and on an adjacent reef, disturbed by destructive fishing techniques, in north-western Sri Lanka, by visually censusing 135 species groups using fifty metre belt-transects. Two types of continental shelf patch-reefs are found in the study area: coral reefs and sandstone reefs, which are divided into distinct habitats, four for the coral reef (shallow reef flat, shallow patch reef, deep reef flat and Porites domes) and two for the sandstone reef (structured sandstone-reef and flat sandstone-reef). Fish assemblages varied in structure between reef types and among habitats within reef types. Functional aspects of habitat structure and composition, such as available food and shelter, seemed to be important factors influencing distribution patterns. The strongest separation in the organisation of fish assemblages in BRMS was between reef types: 19% of all species were confined to the coral-reef patches while 22% were restricted to the sandstone reef patches and 59% were represented on both reef types. In terms of distribution among habitats, 21% of all species were restricted to one habitat while only 1.5% were present in all. The highest density of fish was in the coral reef habitats while highest species diversity was found in the most structurally complex habitat: the structured sandstone-reef. This habitat also had the highest proportion of species with restricted distribution. Planktivores were the most abundant trophic group in BRMS, and the species composition of the group varied among habitats. The comparison of the disturbed reef with BRMS suggested that habitat alteration caused by destructive fishing methods has strongly influenced the fish community. Within the fished area the structure of the fish assemblages was more heterogeneous, fish abundance was lower by an order of magnitude and species numbers were lower than in BRMS.     

Regulate or tolerate: Thermal strategy of a coral reef flat resident,the epaulette shark,Hemiscyllium ocellatum

Highly variable thermal environments, such as coral reef flats, are challenging for marine ectotherms and are thought to invoke the use of behavioural strategies to avoid extreme temperatures and seek out thermal environments close to their preferred temperatures. Common to coral reef flats, the epaulette shark (Hemiscyllium ocellatum) possesses physiological adaptations to hypoxic and hypercapnic conditions, such as those experienced on reef flats, but little is known regarding the thermal strategies used by these sharks. We investigated whether H. ocellatum uses behavioural thermoregulation (i.e., movement to occupy thermally favourable microhabitats) or tolerates the broad range of temperatures experienced on the reef flat. Using an automated shuttlebox system, we determined the preferred temperature of H. ocellatum under controlled laboratory conditions and then compared this preferred temperature to 6 months of in situ environmental and body temperatures of individual H. ocellatum across the Heron Island reef flat. The preferred temperature of H. ocellatum under controlled conditions was 20.7 ± 1.5°C, but the body temperatures of individual H. ocellatum on the Heron Island reef flat mirrored environmental temperatures regardless of season or month. Despite substantial temporal variation in temperature on the Heron Island reef flat (15–34°C during 2017), there was a lack of spatial variation in temperature across the reef flat between sites or microhabitats. This limited spatial variation in temperature creates a low-quality thermal habitat limiting the ability of H. ocellatum to behaviourally thermoregulate. Behavioural thermoregulation is assumed in many shark species, but it appears that H. ocellatum may utilize other physiological strategies to cope with extreme temperature fluctuations on coral reef flats. While H. ocellatum appears to be able to tolerate acute exposure to temperatures well outside of their preferred temperature, it is unclear how this, and other, species will cope as temperatures continue to rise and approach their critical thermal limits. Understanding how species will respond to continued warming and the strategies they may use will be key to predicting future populations and assemblages.     

Herbivorous fish assemblages and herbivory pressure on Laamu Atoll, Republic of Maldives

While herbivory is recognized as a fundamental process structuring coral reef communities, herbivore assemblages and processes are poorly described for reefs in the Indian Ocean region. We quantified herbivorous fish assemblage structure (abundance and diversity) in Laamu Atoll, Republic of Maldives, in four reef habitat types: faro reef flats, faro reef slopes, inner and outer atoll reef slopes (20 sites in total). Herbivorous fish assemblages, representing a total of 30 species, grouped strongly by habitat type, with the highest absolute abundance observed on faro reef flats and lowest abundance on inside atoll rim reef slopes. Removal of Thalassia seagrass blades by ambient herbivore assemblages was used in a bioassay to assess relative herbivory pressure among four habitat types (eight sites). Also, at one site a choice herbivory assay was performed to assess herbivore preference among four benthic plants across three depth zones. Relative herbivory, as indicated by Thalassia assays, was highest on inside atoll rim reef slopes and lowest on outside atoll rim reef slopes. Thalassia consumption did not correspond to overall herbivorous fish abundance, but corresponded more closely with parrotfish abundance. In the choice assays, herbivores showed strong preferences among plant types and consumption of most plant types was higher at mid-depth than in the shallow reef flat or deep reef knoll zones.     

Coral and fish distribution patterns in Mafia Island Marine Park, Tanzania: fish–habitat interactions

We examined coral reef communities at 11 sites within Mafia Island Marine Park using a point count method for substrate and visually censused belt transects for fish populations. Multivariate ordinations showed that the benthic habitat differed among reefs. The patterns were mainly attributed to variations in depth, hydrodynamics and benthic composition. In total, the substratum was dominated by dead coral (49%) and algae (25%), with a live coral cover of only 14%. Three hundred and ninety-four fish species belonging to 56 families were recorded. According to MDS-ordinations and RELATE procedures, fish assemblage composition varied among sites in concordance with the habitats provided. Sites with highest proportion of dead coral exhibited highest degree of dispersion in the multivariate ordinations of fish assemblages. Stepwise multiple regression was used to determine the proportion of variance among sites which could be explained by depth, exposure, rugosity, substrate diversity, branching substrate, live coral cover, dead coral cover and different types of algae. The results showed that habitat variables explained up to 92% of the variation in species numbers and in total, and taxon-specific, abundance. Live coral cover was the foremost predictor of both numerical and species abundance, as well as of corallivores, invertivores, planktivores and of the families Pomacentridae, Chaetodontidae and Pomacanthidae. Our results suggest that habitat characteristics play a dominant role in determining fish assemblage composition on coral reefs.     

Relationships among map resolution, fish assemblages, and habitat variables in a coral reef ecosystem

Benthic maps are broad-scale characterizations that lack the detailed environmental attributes which have been the focus of most prior empirical studies linking reef fish and habitat. We used multivariate analyses to quantify correlations among fish assemblages, local habitat variables, and reef types depicted in benthic maps. Benthic maps of a study system in the U.S. Virgin Islands with high (100 m² minimum mapping unit) and low (4,048 m² minimum mapping unit) spatial resolution, respectively, were evaluated. Benthic maps depicted six reef types and two shelf positions (lagoon vs. shelf). Fish assemblages and local environmental variables were quantified at random sites throughout the landscape by diver surveys. Multivariate ordination based on either fish assemblages or environmental data did not result in well-separated groups of sites. Mapped reef types were not associated with distinct values of either local environmental variables or fish assemblages. Reef types exhibited substantial overlap in ordination plots based on benthic characteristics with groupings based on fish assemblages showing even greater overlap. Ordination patterns involving reef type were largely the same for both low- and high-resolution maps. In contrast, sites showed clear groups for lagoon and shelf in ordinations based on both environmental variables and fish assemblage composition, respectively. These results suggest that knowledge of the overall fish assemblage or fine-scale environmental characteristics could not be used to predict reef type depicted in benthic maps or vice versa. In contrast, reef zone could be used to predict fish assemblage or fine-scale environmental variables and vice versa.     

Variation in the structure of epifaunal invertebrate assemblages among coral hosts

The high biodiversity of coral reefs is attributable to the many invertebrate groups which live in symbiotic relationships with other reef organisms, particularly those which associate with the living coral habitat. However, few studies have examined the diversity and community structure of coral-dwelling invertebrates and how they vary among coral species. This study quantified the species richness and composition of animals associated with four common species of branching corals (Acropora nasuta, A. millepora, Pocillopora damicornis, and Seriatopora hystrix) at Lizard Island in the northern Great Barrier Reef. One hundred and seventy-eight nominal species from 12 different phyla were extracted across 50 replicate colonies of each coral host. A single coral colony, approximately 20 cm in diameter, harbored as many as 73 individuals and 24 species. There were substantial differences in invertebrate species composition among coral hosts of different families as well as genera. Twenty-seven species (15% of all taxa collected) were found on only one of the four different coral species, which may potentially indicate some level of specialization among coral hosts. The distinct assemblages on different coral species, and the presence of potential specialists, suggests invertebrate communities will be sensitive to the differential loss of branching coral species resulting from coral reef degradation.     

The role of the reef flat in coral reef trophodynamics: Past,present, and future

The reef flat is one of the largest and most distinctive habitats on coral reefs, yet its role in reef trophodynamics is poorly understood. Evolutionary evidence suggests that reef flat colonization by grazing fishes was a major innovation that permitted the exploitation of new space and trophic resources. However, the reef flat is hydrodynamically challenging, subject to high predation risks and covered with sediments that inhibit feeding by grazers. To explore these opposing influences, we examine the Great Barrier Reef (GBR) as a model system. We focus on grazing herbivores that directly access algal primary productivity in the epilithic algal matrix (EAM). By assessing abundance, biomass, and potential fish productivity, we explore the potential of the reef flat to support key ecosystem processes and its ability to maintain fisheries yields. On the GBR, the reef flat is, by far, the most important habitat for turf‐grazing fishes, supporting an estimated 79% of individuals and 58% of the total biomass of grazing surgeonfishes, parrotfishes, and rabbitfishes. Approximately 59% of all (reef‐wide) turf algal productivity is removed by reef flat grazers. The flat also supports approximately 75% of all grazer biomass growth. Our results highlight the evolutionary and ecological benefits of occupying shallow‐water habitats (permitting a ninefold population increase). The acquisition of key locomotor and feeding traits has enabled fishes to access the trophic benefits of the reef flat, outweighing the costs imposed by water movement, predation, and sediments. Benthic assemblages on reefs in the future may increasingly resemble those seen on reef flats today, with low coral cover, limited topographic complexity, and extensive EAM. Reef flat grazing fishes may therefore play an increasingly important role in key ecosystem processes and in sustaining future fisheries yields.     

Floating pontoons create novel habitats for subtidal epibiota

Urban structures in the form of pontoons and pilings represent major coastal habitats for marine organisms and understanding the factors causing abundances of organisms to differ between these and natural habitat has been neglected in the study of coastal ecology. It has been proposed that composition of substrata explain differences previously described between subtidal assemblages of epibiota on rocky reef (sandstone) and pontoons (concrete) in Sydney Harbour, Australia. This study tested the hypothesis that differences in the composition of substratum (sandstone vs. concrete) independent of type of habitat (rocky reef vs. pontoon) affects the development of epibiotic assemblages. This was tested by experimentally providing substratum of the two types in both habitats. Epibiotic assemblages were unaffected by the composition of substratum but strongly affected by the type of habitat; demonstrating that pontoons constitute novel habitats for epibiota. This result highlights a need for determining how current ecological understanding of subtidal epibiota, which is heavily based on studies of urban structures (pilings and pontoons), relates to natural reef. Future tests of hypotheses about the nature of these differences will not only contribute to better ecological understanding of epibiota and their use of urban structures as habitats, but also to better predictions of future changes to the ecology of coastal habitats.     

Relationships between structural complexity,coral traits,and reef fish assemblages

With the ongoing loss of coral cover and the associated flattening of reef architecture, understanding the links between coral habitat and reef fishes is of critical importance. Here, we investigate whether considering coral traits and functional diversity provides new insights into the relationship between structural complexity and reef fish communities, and whether coral traits and community composition can predict structural complexity. Across 157 sites in Seychelles, Maldives, the Chagos Archipelago, and Australia’s Great Barrier Reef, we find that structural complexity and reef zone are the strongest and most consistent predictors of reef fish abundance, biomass, species richness, and trophic structure. However, coral traits, diversity, and life histories provided additional predictive power for models of reef fish assemblages, and were key drivers of structural complexity. Our findings highlight that reef complexity relies on living corals—with different traits and life histories—continuing to build carbonate skeletons, and that these nuanced relationships between coral assemblages and habitat complexity can affect the structure of reef fish assemblages. Seascape-level estimates of structural complexity are rapid and cost effective with important implications for the structure and function of fish assemblages, and should be incorporated into monitoring programs.     

Acanthaster planci outbreak: decline in coral health, coral size structure modification and consequences for obligate decapod assemblages

Although benthic motile invertebrate communities encompass the vast majority of coral reef diversity, their response to habitat modification has been poorly studied. A variety of benthic species, particularly decapods, provide benefits to their coral host enabling them to cope with environmental stressors, and as a result benefit the overall diversity of coral-associated species. However, little is known about how invertebrate assemblages associated with corals will be affected by global perturbations, (either directly or indirectly via their coral host) or their consequences for ecosystem resilience. Analysis of a ten year dataset reveals that the greatest perturbation at Moorea over this time was an outbreak of the corallivorous sea star Acanthaster planci from 2006 to 2009 impacting habitat health, availability and size structure of Pocillopora spp. populations and highlights a positive relationship between coral head size and survival. We then present the results of a mensurative study in 2009 conducted at the end of the perturbation (A. planci outbreak) describing how coral-decapod communities change with percent coral mortality for a selected coral species, Pocillopora eydouxi. The loss of coral tissue as a consequence of A. planci consumption led to an increase in rarefied total species diversity, but caused drastic modifications in community composition driven by a shift from coral obligate to non-obligate decapod species. Our study highlights that larger corals left with live tissue in 2009, formed a restricted habitat where coral obligate decapods, including mutualists, could subsist. We conclude that the size structure of Pocillopora populations at the time of an A. planci outbreak may greatly condition the magnitude of coral mortality as well as the persistence of local populations of obligate decapods.     

Response of Pleistocene Coral Reefs to Environmental Change Over Long Temporal Scales

SYNOPSIS. TWO studies from the Pleistocene coral reef fossilrecord demonstrate the sensitivity of reef communities to bothlocal environmental parameters and habitat reduction. In thefirst study, Pleistocene reef coral assemblages from Papua NewGuinea show pronounced constancy in taxonomic composition andspecies diversity between 125 and 30 ka (thousand years). Spatialdifferences in reef coral community composition during successivehigh stands of sea level were greater among sites of the sameage than among reefs of different ages, even though global changesin sea level, atmospheric CO₂ concentration, tropical benthichabitat area, and temperature varied at each high sea levelstand. Thus, local environmental variation associated with runofffrom the land had greater influence on reef coral communitycomposition than variation in global climate and sea level.Proportional sampling from a regional species pool does notexplain the temporal persistence and local factors likely playeda major role. Examination of coral reef response to global changeshould not only involve regional diversity patterns but alsolocal ecological factors, and the interactive effects of localand global environmental change. In the second study, Pleistocene extinction of two widespread,strictly insular species of Caribbean reef corals, Pocilloporacf. palmata (Geister, 1975) and an organ-pipe growth form ofthe Montastraea "annularis" species complex, was natural anddid not involve gradual decrease in range and abundance, butwas sudden (thousands of years) throughout the entire range.One explanation is that sea level drop at the Last Glacial Maximum(LGM—18 ka) resulted in a threshold of habitat reduction,and caused disruption of coral metapopulation structure. Thresholdeffects predicted by metapopulation dynamics may also explainthe apparent paradox of the large amount of degraded modernreef habitat without any known modern-day reef coral extinctions.The rapid extinction of widespread Pleistocene species emphasizesthe vulnerability of reef corals in the face of present rapidenvironmental and climatic change.     

Relative Importance of Coral Cover,Habitat Complexity and Diversity in Determining the Structure of Reef Fish Communities

The structure of coral reef habitat has a pronounced influence on the diversity, composition and abundance of reef-associated fishes. However, the particular features of the habitat that are most critical are not always known. Coral habitats can vary in many characteristics, notably live coral cover, topographic complexity and coral diversity, but the relative effects of these habitat characteristics are often not distinguished. Here, we investigate the strength of the relationships between these habitat features and local fish diversity, abundance and community structure in the lagoon of Lizard Island, Great Barrier Reef. In a spatial comparison using sixty-six 2m² quadrats, fish species richness, total abundance and community structure were examined in relation to a wide range of habitat variables, including topographic complexity, habitat diversity, coral diversity, coral species richness, hard coral cover, branching coral cover and the cover of corymbose corals. Fish species richness and total abundance were strongly associated with coral species richness and cover, but only weakly associated with topographic complexity. Regression tree analysis showed that coral species richness accounted for most of the variation in fish species richness (63.6%), while hard coral cover explained more variation in total fish abundance (17.4%), than any other variable. In contrast, topographic complexity accounted for little spatial variation in reef fish assemblages. In degrading coral reef environments, the potential effects of loss of coral cover and topographic complexity are often emphasized, but these findings suggest that reduced coral biodiversity may ultimately have an equal, or greater, impact on reef-associated fish communities.     

Effectiveness of benthic foraminiferal and coral assemblages as water quality indicators on inshore reefs of the Great Barrier Reef, Australia

Although the debate about coral reef decline focuses on global disturbances (e.g., increasing temperatures and acidification), local stressors (nutrient runoff and overfishing) continue to affect reef health and resilience. The effectiveness of foraminiferal and hard-coral assemblages as indicators of changes in water quality was assessed on 27 inshore reefs along the Great Barrier Reef. Environmental variables (i.e., several water quality and sediment parameters) and the composition of both benthic foraminiferal and hard-coral assemblages differed significantly between four regions (Whitsunday, Burdekin, Fitzroy, and the Wet Tropics). Grain size and organic carbon and nitrogen content of sediments, and a composite water column parameter (based on turbidity and concentrations of particulate matter) explained a significant amount of variation in the data (tested by redundancy analyses) in both assemblages. Heterotrophic species of foraminifera were dominant in sediments with high organic content and in localities with low light availability, whereas symbiont-bearing mixotrophic species were dominant elsewhere. A similar suite of parameters explained 89% of the variation in the FORAM index (a Caribbean coral reef health indicator) and 61% in foraminiferal species richness. Coral richness was not related to environmental setting. Coral assemblages varied in response to environmental variables, but were strongly shaped by acute disturbances (e.g., cyclones, Acanthaster planci outbreaks, and bleaching), thus different coral assemblages may be found at sites with the same environmental conditions. Disturbances also affect foraminiferal assemblages, but they appeared to recover more rapidly than corals. Foraminiferal assemblages are effective bioindicators of turbidity/light regimes and organic enrichment of sediments on coral reefs.     

Spatial predictability of juvenile fish species richness and abundance in a coral reef environment

Juvenile reef fish communities represent an essential component of coral reef ecosystems in the current focus of fish population dynamics and coral reef resilience. Juvenile fish survival depends on habitat characteristics and is, following settlement, the first determinant of the number of individuals within adult populations. The goal of this study was to provide methods for mapping juvenile fish species richness and abundance into spatial domains suitable for micro and meso-scale analysis and management decisions. Generalized Linear Models predicting juvenile fish species richness and abundance were developed according to spatial and temporal environmental variables measured from 10 m up to 10 km in the southwest lagoon of New Caledonia. The statistical model was further spatially generalized using a 1.5-m resolution, independently created, remotely sensed, habitat map. This procedure revealed that : (1) spatial factors at 10 to 100-m scale explained up to 71% of variability in juvenile species richness, (2) a small improvement (75%) was gained when a combination of environmental variables at different spatial and temporal scales was used and (3) the coupling of remotely sensed data, geographical information system tools and point-based ecological data showed that the highest species richness and abundance were predicted along a narrow margin overlapping the coral reef flat and adjacent seagrass beds. Spatially explicit models of species distribution may be relevant for the management of reef communities when strong relationships exist between faunistic and environmental variables and when models are built at appropriate scales.     

Species-specific habitat distribution of coral reef fish assemblages in relation to habitat characteristics in an Okinawan coral reef

We determined the species-specific habitat associations of coral reef fishes and environmental characteristics in an Okinawan coral reef in Japan. We focused on three families (Pomacentridae, Gobiidae and Labridae) and attempted to determine differences in habitat utilization. We selected six sites along the coast of Amitori Bay, from the entrance to the innermost part, in order to cover a wide range of habitat characteristics (exposed habitat, semi-exposed habitat and sheltered habitat). The species diversity of coral assemblages was greater at the exposed and semi-exposed habitats, whereas branching coral mostly covered the sheltered habitat. The environmental factors that determine the species-specific spatial association in fishes differed among families. Both biological characteristics (coral morphology and coral species diversity) and physical characteristics (water depth and wave exposure) affected the spatial association of pomacentrids and gobiids. In contrast, physical characteristics such as substrate complexity and water depth affected the species-specific spatial association of labrid species. Further study is needed to determine the ecological factors that regulate the species-specific habitat preference in Okinawan coral reefs.     

Ecology and Biodiversity of Coral Reef Polychaetes of Guam and Saipan,Mariana Islands.

Polychaetes collected from coral reefs and other coastal habitats on Guam and Saipan, and information from published studies bring the known number of species from these two islands to 101 and 15, respectively. Sediment and rock dwelling species collected, and those previously recorded, belong to 25 families. Polychaete assemblages are compared on the basis of species richness, genera in common, and trophic categories, with other West Pacific, Hawaiian and East Indian Ocean locations. Polychaetes from Guam are similar to those on reef flats of Hawaii, Enewetak, and Indonesia in faunal composition and density. Despite the limitations in comparable collecting effort and quantitative analyses for some of the areas, these coral reefs have similar complements of families and genera present, and proportions of four trophic categories.