Effects of territorial damselfish on an algal-dominated coastal coral reef

Territorial damselfish are important herbivores on coral reefs because they can occupy a large proportion of the substratum and modify the benthic community to promote the cover of food algae. However, on coastal coral reefs damselfish occupy habitats that are often dominated by unpalatable macroalgae. The aim of this study was to examine whether damselfish can maintain distinctive algal assemblages on a coastal reef that is seasonally dominated by Sargassum (Magnetic Island, Great Barrier Reef). Here, three abundant species (Pomacentrus tripunctatus, P. wardi and Stegastes apicalis) occupied up to 60% of the reef substrata. All three species promoted the abundance of food algae in their territories. The magnitudes of the effects varied among reef zones, but patterns were relatively stable over time. Damselfish appear to readily co-exist with large unpalatable macroalgae as they can use it as a substratum for promoting the growth of palatable epiphytes. Damselfish territories represent patches of increased epiphyte load on macroalgae, decreased sediment cover, and enhanced cover of palatable algal turf.     

Maintenance of fish diversity on disturbed coral reefs

Habitat perturbations play a major role in shaping community structure; however, the elements of disturbance-related habitat change that affect diversity are not always apparent. This study examined the effects of habitat disturbances on species richness of coral reef fish assemblages using annual surveys of habitat and 210 fish species from 10 reefs on the Great Barrier Reef (GBR). Over a period of 11 years, major disturbances, including localised outbreaks of crown-of-thorns sea star (Acanthaster planci), severe storms or coral bleaching, resulted in coral decline of 46–96% in all the 10 reefs. Despite declines in coral cover, structural complexity of the reef framework was retained on five and species richness of coral reef fishes maintained on nine of the disturbed reefs. Extensive loss of coral resulted in localised declines of highly specialised coral-dependent species, but this loss of diversity was more than compensated for by increases in the number of species that feed on the epilithic algal matrix (EAM). A unimodal relationship between areal coral cover and species richness indicated species richness was greatest at approximately 20% coral cover declining by 3–4 species (6–8% of average richness) at higher and lower coral cover. Results revealed that declines in coral cover on reefs may have limited short-term impact on the diversity of coral reef fishes, though there may be fundamental changes in the community structure of fishes.     

Community structure and biogeography of shore fishes in the Gulf of Aqaba,Red Sea

Shore fish community structure off the Jordanian Red Sea coast was determined on fringing coral reefs and in a seagrass-dominated bay at 6 m and 12 m depths. A total of 198 fish species belonging to 121 genera and 43 families was recorded. Labridae and Pomacentridae dominated the ichthyofauna in terms of species richness and Pomacentridae were most abundant. Neither diversity nor species richness was correlated to depth. The abundance of fishes was higher at the deep reef slope, due to schooling planktivorous fishes. At 12 m depth abundance of fishes at the seagrass-dominated site was higher than on the coral reefs. Multivariate analysis demonstrated a strong influence on the fish assemblages by depth and benthic habitat. Fish species richness was positively correlated with hard substrate cover and habitat diversity. Abundance of corallivores was positively linked with live hard coral cover. The assemblages of fishes were different on the shallow reef slope, deep reef slope and seagrass meadows. An analysis of the fish fauna showed that the Gulf of Aqaba harbours a higher species richness than previously reported. The comparison with fish communities on other reefs around the Arabian Peninsula and Indian Ocean supported the recognition of an Arabian subprovince within the Indian Ocean. The affinity of the Arabian Gulf ichthyofauna to the Red Sea is not clear. Received in revised form: 2 November 2001 Electronic Publication     

Fish assemblages on artificial and natural reefs in the Flower Garden Banks National Marine Sanctuary, USA

 Visual censusing was used to characterize fish assemblages on artificial and natural reefs located within the boundaries of the Flower Garden Banks National Marine Sanctuary (FGBNMS) in the northwestern Gulf of Mexico. Emphasis was placed on determining spatial and temporal patterns in habitat utilization by fishes on an offshore artificial reef (Mobil Platform HI-A389A). Overall, 43 species were observed during diurnal surveys in the upper 24 m of the artificial reef. Midwater pelagic fishes (i.e., carangids and scombrids) accounted for over 50% of all taxa enumerated on the artificial reef; however, these taxa were transient members of the assemblage and were observed infrequently. Labrids, pomacentrids, and serranids were the dominant reef-dependent taxa. Distinct trends in vertical, diel, and seasonal abundances were observed for juvenile and adult fishes. Of the three designated depth zones (upper 1.5–9.0, middle 9.0–16.5; lower 16.5–24.0 m), abundance and species diversity were lowest in the upper zone. Nocturnal counts were characterized by a marked reduction or complete absence of most species, due in part to twilight cover-seeking and movement activities. Seasonal variation in community composition and species abundance (May versus September) was primarily due to recruitment of juveniles (0-age fishes) to the artificial reef in late summer. Increases in total fish abundance (all taxa combined) coincided with both increasing habitat rugosity and degree of fouling. Species richness on natural coral reefs in the FGBNMS was higher than on the artificial reef. Unlike the artificial reef, fish assemblages on the natural reefs were dominated by a single family (Pomacentridae) which accounted for over 50% of all individuals observed. Accepted: 1 August 1996     

Impact of cyclones on hard coral and metapopulation structure,connectivity and genetic diversity of coral reef fish

Cyclones have one of the greatest effects on the biodiversity of coral reefs and the associated species. But it is unknown how stochastic alterations in habitat structure influence metapopulation structure, connectivity and genetic diversity. From 1993 to 2018, the reefs of the Capricorn Bunker Reef group in the southern part of the Great Barrier Reef were impacted by three tropical cyclones including cyclone Hamish (2009, category 5). This resulted in substantial loss of live habitat-forming coral and coral reef fish communities. Within 6–8 years after cyclones had devastated, live hard corals recovered by 50–60%. We show the relationship between hard coral cover and the abundance of the neon damselfish (Pomacentrus coelestis), the first fish colonizing destroyed reefs. We present the first long-term (2008–2015 years corresponding to 16–24 generations of P. coelestis) population genetic study to understand the impact of cyclones on the meta-population structure, connectivity and genetic diversity of the neon damselfish. After the cyclone, we observed the largest change in the genetic structure at reef populations compared to other years. Simultaneously, allelic richness of genetic microsatellite markers dropped indicating a great loss of genetic diversity, which increased again in subsequent years. Over years, metapopulation dynamics were characterized by high connectivity among fish populations associated with the Capricorn Bunker reefs (2200 km²); however, despite high exchange, genetic patchiness was observed with annual strong genetic divergence between populations among reefs. Some broad similarities in the genetic structure in 2015 could be explained by dispersal from a source reef and the related expansion of local populations. This study has shown that alternating cyclone-driven changes and subsequent recovery phases of coral habitat can greatly influence patterns of reef fish connectivity. The frequency of disturbances determines abundance of fish and genetic diversity within species.

     

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.     

The influence of coral reef benthic condition on associated fish assemblages

Accumulative disturbances can erode a coral reef's resilience, often leading to replacement of scleractinian corals by macroalgae or other non-coral organisms. These degraded reef systems have been mostly described based on changes in the composition of the reef benthos, and there is little understanding of how such changes are influenced by, and in turn influence, other components of the reef ecosystem. This study investigated the spatial variation in benthic communities on fringing reefs around the inner Seychelles islands. Specifically, relationships between benthic composition and the underlying substrata, as well as the associated fish assemblages were assessed. High variability in benthic composition was found among reefs, with a gradient from high coral cover (up to 58%) and high structural complexity to high macroalgae cover (up to 95%) and low structural complexity at the extremes. This gradient was associated with declining species richness of fishes, reduced diversity of fish functional groups, and lower abundance of corallivorous fishes. There were no reciprocal increases in herbivorous fish abundances, and relationships with other fish functional groups and total fish abundance were weak. Reefs grouping at the extremes of complex coral habitats or low-complexity macroalgal habitats displayed markedly different fish communities, with only two species of benthic invertebrate feeding fishes in greater abundance in the macroalgal habitat. These results have negative implications for the continuation of many coral reef ecosystem processes and services if more reefs shift to extreme degraded conditions dominated by macroalgae.     

Effect of Phase Shift from Corals to Zoantharia on Reef Fish Assemblages

Consequences of reef phase shifts on fish communities remain poorly understood. Studies on the causes, effects and consequences of phase shifts on reef fish communities have only been considered for coral-to-macroalgae shifts. Therefore, there is a large information gap regarding the consequences of novel phase shifts and how these kinds of phase shifts impact on fish assemblages. This study aimed to compare the fish assemblages on reefs under normal conditions (relatively high cover of corals) to those which have shifted to a dominance of the zoantharian Palythoa cf. variabilis on coral reefs in Todos os Santos Bay (TSB), Brazilian eastern coast. We examined eight reefs, where we estimated cover of corals and P. cf. variabilis and coral reef fish richness, abundance and body size. Fish richness differed significantly between normal reefs (48 species) and phase-shift reefs (38 species), a 20% reduction in species. However there was no difference in fish abundance between normal and phase shift reefs. One fish species, Chaetodon striatus, was significantly less abundant on normal reefs. The differences in fish assemblages between different reef phases was due to differences in trophic groups of fish; on normal reefs carnivorous fishes were more abundant, while on phase shift reefs mobile invertivores dominated.     

Interactions between coral restoration and fish assemblages: implications for reef management

Corals create complex reef structures that provide both habitat and food for many fish species. Because of numerous natural and anthropogenic threats, many coral reefs are currently being degraded, endangering the fish assemblages they support. Coral reef restoration, an active ecological management tool, may help reverse some of the current trends in reef degradation through the transplantation of stony corals. Although restoration techniques have been extensively reviewed in relation to coral survival, our understanding of the effects of adding live coral cover and complexity on fishes is in its infancy with a lack of scientifically validated research. This study reviews the limited data on reef restoration and fish assemblages, and complements this with the more extensive understanding of complex interactions between natural reefs and fishes and how this might inform restoration efforts. It also discusses which key fish species or functional groups may promote, facilitate or inhibit restoration efforts and, in turn, how restoration efforts can be optimised to enhance coral fish assemblages. By highlighting critical knowledge gaps in relation to fishes and restoration interactions, the study aims to stimulate research into the role of reef fishes in restoration projects. A greater understanding of the functional roles of reef fishes would also help inform whether restoration projects can return fish assemblages to their natural compositions or whether alternative species compositions develop, and over what timeframe. Although alleviation of local and global reef stressors remains a priority, reef restoration is an important tool; an increased understanding of the interactions between replanted corals and the fishes they support is critical for ensuring its success for people and nature.     

The Eocene fishes of Monte Bolca: the earliest coral reef fish assemblage

The fish assemblage from the Eocene deposits of Monte Bolca, Northern Italy, are compared with those of Recent coral reefs. A family-level taxonomic definition of a Recent coral reef fish assemblage is formulated to permit direct comparisons. On this basis, the Monte Bolca fishes represent the earliest clearly defined coral reef fish assemblage. Quantitative analyses of the relative abundance of fish families revealed significant differences between the two assemblages. The Bolca assemblage has Mesozoic links (Pycnodontiformes) and non-perciform taxa are relatively abundant, particularly the Beryciformes (Holocentridae). However, Bolca represents the earliest record of a perciform-dominated benthic fish assemblage (68.4% of all non-clupeid taxa). Within the Perciformes, the abundance of the major reef fish lineages (higher squamipinnes and Labroidei) differs markedly between the two assemblages. The numerical dominance of labroid fishes on coral reefs appears to have been a relatively recent occurrence.     

Otolith growth of Springer's demoiselle, Chrysiptera springeri (Pomacentridae, Allen & Lubbock), on a protected and non-protected coral reef

The structural complexity of coral reefs is important for their function as shelter and feeding habitats for coral reef fishes, but physical disturbance by human activities often reduce complexity of the reefs by selectively destroying fragile and more complex coral species. The damselfish Springer's demoiselle Chrysiptera springeri primarily utilize complex coral heads for shelter and are hence vulnerable to human disturbance. In order to evaluate the potential effect of habitat degradation on juvenile fish growth, coral reef cover, fish age at settling and otolith growth, juvenile Springer's demoiselle was investigated on a protected and non‐protected coral reef in Darvel Bay, Borneo. The protected reef had higher coverage of complex branching corals and exhibited a more complex 3‐dimensional structure than the non‐protected reef. Springer's demoiselle settled at the same age on non‐protected and protected reefs. The growth rates of the otoliths from Springer's demoiselle were similar during the pre‐settlement period on the two reefs (manova , P > 0.05), but from age 20 to 48 days (post‐settlement period) the otolith growth rate of juveniles on the non‐protected reef was reduced compared to those from the protected reef (manova , P = 0.017). However, the differences in the otolith size, and by inference, fish size, after 48 days were small. The small effect of habitat degradation on growth is likely related to the fact that the Springer's demoiselles collected on the non‐protected reef were associated with the few remaining complex coral heads. Increased foraging‐predation tradeoffs on the non‐protected reef may decrease food intake and growth of juvenile Springer's demoiselle, but the main effect of habitat degradation on their abundance is likely to be related to lack of suitable shelter, and consequently reduced carrying capacity, on disturbed reefs.     

Structure of reef fish communities in Catalinas Islands and Ocotal beach, North Pacific of Costa Rica

The reefs are heterogeneous systems that maintain a high diversity of organisms. Fish community structure varies within and among reefs, so it would be expected that reef structure and heterogeneity should affect fish communities inhabiting reefs. Four reef patches at Catalinas Islands (Sur, La Pared, Roca Sucia and Sombrero) and one in Ocotal beach (10 degrees 28'45" N; 85 degrees 52'35" W) were studied with visual censuses (July-December 2003). The structure and composition of fishes between Catalinas islands and Ocotal beach were different, and habitat structure and composition explain most of the variance founded. The presence of the fleshy algae Caulerpa sertularioides in Ocotal, and the corals Tubastrea coccinea and Pocillopora spp. at Catalinas Island explained the variability among sites and how it affected fish community structure and composition. The butterfly fish Johnrandallia nigrirostris, damselfish Microspathodon dorsalis, and surgeon fish Prionurus punctatus were directly correlated with the ahermatipic coral Tubastrea coccinea in Roca Sucia reef, while the angel fish Holacanthus passer was associated to reefs with a major percentage of rocky substrate. Other species such as the damselfish Abudefduf troschelli and Halichoeres dispilus were more abundant at Ocotal, where the algae C sertularioides dominated. The number and abundance of reef fishes was directly correlated with the rugosity index at the reefs of Roca Sucia and Ocotal, but not at reefs of La Pared and Sombrero.     

Interactions between herbivorous fish guilds and their influence on algal succession on a coastal coral reef

Herbivory is an important mechanism affecting algal succession, particularly on coral reefs where the relationship between algae and corals is largely controlled by herbivores. However, different functional groups of herbivores may have contrasting effects on succession, which may explain different trajectories of coral reef recovery after disturbance. Here, the effects of different herbivore groups (roving herbivores = foragers and territorial damselfish = farmers) were isolated by a multi-factorial experiment carried out on a coastal coral reef with high macroalgal cover, high farmer densities and relatively low forager abundance. The effects of foragers and farmers were distinguished by monitoring algal succession on settlement tiles placed inside and outside exclusion cages, with orthogonal treatments established inside and outside damselfish territories (with appropriate cage controls). Within 12 months, algal assemblages on ungrazed tiles inside exclusion cages proceeded rapidly from fine filamentous turfs, to corticated algae, to tough erect (e.g. Amphiroa spp.) and foliose (e.g. Peyssonnellidae) calcified algae. Farmers had a dramatic impact on succession, essentially arresting the development of the algal community at a point where it was dominated by palatable filamentous algae of the genus Polysiphonia. Fleshy macroalgae such as Sargassum spp. were excluded from farmer territories. In contrast, foragers did not suppress fleshy macroalgae, but rather, appeared to decelerate succession and promote a relatively diverse assemblage. In contrast to forager-dominated reefs, farmer territories did not appear to function solely as forager exclusion areas or promote algal diversity as a result of intermediate grazing pressure. The relatively strong effects of farmers observed here may represent a future scenario for coral reefs that are increasingly subject to overfishing of large grazing fishes.     

High macroalgal cover and low coral recruitment undermines the potential resilience of the world's southernmost coral reef assemblages

Coral reefs are under increasing pressure from anthropogenic and climate-induced stressors. The ability of reefs to reassemble and regenerate after disturbances (i.e., resilience) is largely dependent on the capacity of herbivores to prevent macroalgal expansion, and the replenishment of coral populations through larval recruitment. Currently there is a paucity of this information for higher latitude, subtropical reefs. To assess the potential resilience of the benthic reef assemblages of Lord Howe Island (31°32'S, 159°04'E), the worlds' southernmost coral reef, we quantified the benthic composition, densities of juvenile corals (as a proxy for coral recruitment), and herbivorous fish communities. Despite some variation among habitats and sites, benthic communities were dominated by live scleractinian corals (mean cover 37.4%) and fleshy macroalgae (20.9%). Live coral cover was higher than in most other subtropical reefs and directly comparable to lower latitude tropical reefs. Juvenile coral densities (0.8 ind.m(-2)), however, were 5-200 times lower than those reported for tropical reefs. Overall, macroalgal cover was negatively related to the cover of live coral and the density of juvenile corals, but displayed no relationship with herbivorous fish biomass. The biomass of herbivorous fishes was relatively low (204 kg.ha(-1)), and in marked contrast to tropical reefs was dominated by macroalgal browsing species (84.1%) with relatively few grazing species. Despite their extremely low biomass, grazing fishes were positively related to both the density of juvenile corals and the cover of bare substrata, suggesting that they may enhance the recruitment of corals through the provision of suitable settlement sites. Although Lord Howe Islands' reefs are currently coral-dominated, the high macroalgal cover, coupled with limited coral recruitment and low coral growth rates suggest these reefs may be extremely susceptible to future disturbances.     

Ecological condition of coral reef assemblages in the Cuban Archipelago

The condition of coral reefs in the Cuban Archipelago is poorly known. We aimed to analyse coral assemblages across 199 reef sites belonging to 12 localities. Crest and fore reefs were assessed using six metrics: species richness, density, coral cover, mortality, coral size and reef complexity. The condition of reefs varied across the archipelago from healthy to depleted reefs. The localities with best scores were Cienfuegos, Bahía de Cochinos and Cazones. These reefs have values of living coral cover (>20%) and complexity (>50?cm) similar to the best preserved Caribbean reefs. However, the majority of crest biotopes suffered important deterioration with old mortality of Acropora palmata populations and moderate coral cover (15%); although crest reefs still maintained their structural complexity. Despite moderate levels of coral cover in fore reefs (18%), their condition was alarming because 25% of the sites had cover below the recovery threshold of 10%, accumulated mortality and structural flattening. Compared with the 1980s, the species richness was roughly the same (42) for crest and fore reefs, although dominance has changed to widespread tolerant species. Coral reef assemblages varied at local and regional scales in similar magnitude, suggesting the combined effects of natural and anthropogenic drivers.     

Habitat type and complexity drive fish assemblages in a tropical seascape

Inshore marine seascapes support a diversity of interconnected habitats and are an important focus for biodiversity conservation. This study examines the importance of habitat attributes to fish assemblages across a mosaic of inshore habitats: coral reefs, rocky reefs, macroalgae beds and sand/rubble beds. Fishes and benthic habitats were surveyed at 34 sites around continental islands of the central Great Barrier Reef using baited remote underwater video stations (BRUVS). Species richness was influenced foremost by habitat type and also by structural complexity within habitat types. The most speciose assemblages occurred in coral and rocky reef habitats with high structural complexity, provided by the presence of coral bommies/overhangs, boulders and rock crevices. Nonetheless, macroalgae and sand/rubble beds also supported unique species, and therefore contributed to the overall richness of fish assemblages in the seascape. Most trophic groups had positive associations with complexity, which was the most important predictor for abundance of piscivorous fishes and mobile planktivores. There was significant differentiation of fish assemblages among habitats, with the notable exception of coral and rocky reefs. Species assemblages overlapped substantially between coral and rocky reefs, which had 60% common species, despite coral cover being lower on rocky reefs. This suggests that, for many species, rocky and coral substrates can provide equivalent habitat structure, emphasizing the importance of complexity in providing habitat refuges, and highlighting the contribution of rocky reefs to habitat provision within tropical seascapes. The results of this study support an emerging recognition of the collective value of habitat mosaics in inshore marine ecosystems.     

Temperate macroalgae impacts tropical fish recruitment at forefronts of range expansion

Warming waters and changing ocean currents are increasing the supply of tropical fish larvae to temperature regions where they are exposed to novel habitats, namely temperate macroalgae and barren reefs. Here, we use underwater surveys on the temperate reefs of south-eastern (SE) Australia and western Japan (~33.5°N and S, respectively) to investigate how temperate macroalgal and non-macroalgal habitats influence recruitment success of a range of tropical fishes. We show that temperate macroalgae strongly affected recruitment of many tropical fish species in both regions and across three recruitment seasons in SE Australia. Densities and richness of recruiting tropical fishes, primarily planktivores and herbivores, were over seven times greater in non-macroalgal than macroalgal reef habitat. Species and trophic diversity (K-dominance) were also greater in non-macroalgal habitat. Temperate macroalgal cover was a stronger predictor of tropical fish assemblages than temperate fish assemblages, reef rugosities or wave exposure. Tropical fish richness, diversity and density were greater on barren reef than on reef dominated by turfing algae. One common species, the neon damselfish (Pomacentrus coelestis), chose non-macroalgal habitat over temperate macroalgae for settlement in an aquarium experiment. This study highlights that temperate macroalgae may partly account for spatial variation in recruitment success of many tropical fishes into higher latitudes. Hence, habitat composition of temperate reefs may need to be considered to accurately predict the geographic responses of many tropical fishes to climate change.

     

Short-term changes of fish assemblages observed in the near-pristine reefs of the Phoenix Islands

Climate change-related disturbances are increasingly recognized as critical threats to biodiversity and species abundance. On coral reefs, climate disturbances have known consequences for reef fishes, but it is often difficult to isolate the effect of coral bleaching from preceding or simultaneous disturbances such as fishing, pollution, and habitat loss. In this study, pre-bleaching surveys of fish family assemblages in the remote Phoenix Islands in 2002 are compared to post-bleaching in 2005, following severe thermal stress. Post-bleaching, total coral cover decreased substantially, as did the combined abundance of all fish families. Yet, changes in abundance for specific fish families were not uniform, and varied greatly from site to site. Of the 13 fish families examined, 3 exhibited significant changes in abundance from 2002 to 2005, regardless of site (Carangidae, Chaetodontidae, and serranid subfamily Epinephelinae). For these families, we explored whether changes in abundance were related to island type (island vs atoll) and/or declining coral cover (percent change). Carangidae on islands experienced larger changes in abundance than those on atolls, though declines in abundance over time were not associated with changes in live coral cover. In contrast, for Chaetodontidae, declines in abundance over time were most dramatic on atolls, and were also associated with changes in live coral cover. The remoteness of the Phoenix Islands excludes many typical local anthropogenic stressors as drivers of short-term changes; observed changes are instead more likely attributed to natural variation in fish populations, or associated with coral loss following the 2002–2003 major thermal stress event.     

Abrolhos bank reef health evaluated by means of water quality, microbial diversity, benthic cover, and fish biomass data

The health of the coral reefs of the Abrolhos Bank (Southwestern Atlantic) was characterized with a holistic approach using measurements of four ecosystem components: (i) inorganic and organic nutrient concentrations, [1] fish biomass, [1] macroalgal and coral cover and (iv) microbial community composition and abundance. The possible benefits of protection from fishing were particularly evaluated by comparing sites with varying levels of protection. Two reefs within the well-enforced no-take area of the National Marine Park of Abrolhos (Parcel dos Abrolhos and California) were compared with two unprotected coastal reefs (Sebasti?o Gomes and Pedra de Leste) and one legally protected but poorly enforced coastal reef (the "paper park" of Timbebas Reef). The fish biomass was lower and the fleshy macroalgal cover was higher in the unprotected reefs compared with the protected areas. The unprotected and protected reefs had similar seawater chemistry. Lower vibrio CFU counts were observed in the fully protected area of California Reef. Metagenome analysis showed that the unprotected reefs had a higher abundance of archaeal and viral sequences and more bacterial pathogens, while the protected reefs had a higher abundance of genes related to photosynthesis. Similar to other reef systems in the world, there was evidence that reductions in the biomass of herbivorous fishes and the consequent increase in macroalgal cover in the Abrolhos Bank may be affecting microbial diversity and abundance. Through the integration of different types of ecological data, the present study showed that protection from fishing may lead to greater reef health. The data presented herein suggest that protected coral reefs have higher microbial diversity, with the most degraded reef (Sebasti?o Gomes) showing a marked reduction in microbial species richness. It is concluded that ecological conditions in unprotected reefs may promote the growth and rapid evolution of opportunistic microbial pathogens.