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     

Modelling sponge species diversity using a morphological predictor: a tropical test of a temperate model

The contribution of sponges to marine surveys is often underestimated due to problems of identification, synonymous species and limited numbers of specialists in the field. Bell & Barnes (2001) illustrated how sponge morphological diversity (diversity of body forms) might be used as a predictor of sponge species diversity and richness. This study investigated these relationships at six tropical West Indian Ocean localities in a number of habitat types. These habitats included tropical coral reefs, soft substratum (seagrass, mangrove and sand), caves and boulders. Sampling was undertaken at three depth zones in coral reef habitats only (intertidal, 10–15 m and 20–25 m), with the other habitats sampled in less than 10m of water. Species diversity and richness were significantly correlated (P < 0.05) with morphological diversity at all localities and depths in coral reef and soft substratum habitats. However, no significant correlation was found between these variables in cave or boulder habitats. The slope of the linear regression found between morphological diversity and species diversity did not significantly differ between coral reef, soft substratum and temperate reef (data taken from Bell & Barnes 2001) habitats. Similarly coral reefs showed the same relationship between morphological diversity and species richness as temperate reefs, however the relationship between morphological diversity and species richness was significantly different at both habitats compared with soft substratum environments. Sponge morphological diversity therefore may be more useful as a predictor of sponge species diversity, rather than species richness, as the former relationship is common between more habitats than the latter.     

Phase shift to algal dominated communities at mesophotic depths associated with lionfish (<Emphasis Type="Italic">Pterois volitans</Emphasis>) invasion on a Bahamian coral reef

Mesophotic coral reefs (30–150 m) have been assumed to be physically and biologically connected to their shallow-water counterparts, and thus may serve as refugia for important taxonomic groups such as corals, sponges, and fish. The recent invasion of the Indo–Pacific lionfish (Pterois volitans) onto shallow reefs of the Caribbean and Bahamas has had significant, negative, effects on shallow coral reef fish populations. In the Bahamas, lionfish have extended their habitat range into mesophotic depths down to 91 m where they have reduced the diversity of several important fish guilds, including herbivores. A phase shift to an algal dominated (>50% benthic cover) community occurred simultaneously with the loss of herbivores to a depth of 61 m and caused a significant decline in corals and sponges at mesophotic depths. The effects of this invasive lionfish on mesophotic coral reefs and the subsequent changes in benthic community structure could not be explained by coral bleaching, overfishing, hurricanes, or disease independently or in combination. The significant ecological effects of the lionfish invasion into mesophotic depths of coral reefs casts doubt on whether these communities have the resilience to recover themselves or contribute to the recovery of their shallow water counterparts as refugia for key coral reef taxa.     

Beta diversity of cold-water coral reef communities off western Scotland

Spatial heterogeneity in coral reef communities is well documented. This “species turnover” (beta diversity) on shallow warm-water reefs strongly conforms to spatial gradients in the environment as well as spatially autocorrelated biotic processes such as dispersal and competition. But the extent to which the environment and spatial autocorrelation create beta diversity on deep cold-water coral reefs such as those formed by Lophelia pertusa (Scleractinia) is unknown. The effects of remotely sensed and ground-truthed data were tested on the community composition of sessile suspension-feeding communities from the Mingulay Reef Complex, a landscape of inshore Lophelia reefs off the Scottish west coast. Canonical correspondence analysis determined that a statistically significant proportion (68%) of the variance in community composition could be explained by remotely sensed environmental variables (northerly and easterly aspect, seabed rugosity, depth), ground-truthed environmental variables (species richness and reef macrohabitat) and geospatial location. This variation was further partitioned into fractions explained by pure effects of the environment (51%), spatially structured environmental variables (12%) and spatial autocorrelation (5%). Beta diversity in these communities reflected the effects of both measured and unmeasured and spatially dependent environmental variables that vary across the reef complex, i.e., hydrography. Future work will quantify the significance and relative contributions of these variables in creating beta diversity in these rich communities.     

Predators reduce abundance and species richness of coral reef fish recruits via non-selective predation

Predators have important effects on coral reef fish populations, but their effects on community structure have only recently been investigated and are not yet well understood. Here, the effect of predation on the diversity and abundance of young coral reef fishes was experimentally examined in Moorea, French Polynesia. Effects of predators were quantified by monitoring recruitment of fishes onto standardized patch reefs in predator-exclosure cages or uncaged reefs. At the end of the 54-day experiment, recruits were 74% less abundant on reefs exposed to predators than on caged ones, and species richness was 42% lower on reefs exposed to predators. Effects of predators varied somewhat among families, however, rarefaction analysis indicated that predators foraged non-selectively among species. These results indicate that predation can alter diversity of reef fish communities by indiscriminately reducing the abundance of fishes soon after settlement, thereby reducing the number of species present on reefs.     

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.     

Is increased calcarinid (foraminifera) abundance indicating a larger role for macro-algae in Indonesian Plio-Pleistocene coral reefs?

An important question in coral reef ecology is whether algal abundance in coral reef eco-systems is a natural phenomenon, or has increased as a result of coral reef degradation ultimately resulting in coral–algal regime shifts. Regime shifts, from coral to macro-algae dominated, alter the three-dimensional habitat structure in coral reef ecosystems. Surprisingly, few studies have looked at the effects for species that inhabit the reefs without being the architects of the three-dimensional structure. In this study the effects of a change in habitat characteristics on the community structure of large benthic foraminifera (LBF) is compared between an area with high (Kepulauan Seribu) and lower (Spermonde Archipelago) anthropogenic influence. The results indicate a general relationship between habitat and LBF assemblage structure. The largest difference was observed in shallow habitats. Habitats dominated by algae are inhabited by a specific group of LBF, the Calcarinidae, and domination of this group increases with higher algal prevalence. The fossil record of this group indicates that they evolved following a major change in settings of the central Indo-West-Pacific coral reefs from land detached platforms to fringing reefs, about 5 million years ago. Understanding the biotic response to this transition in reef morphology and the associated increase in terrestrially derived nutrients forms an excellent challenge to gain insights in present-day threats to coral reef ecosystems.     

Coral community structure and risk assessment of high-latitude reefs at Sodwana Bay,South Africa

The importance of studying coral communities at different spatial scales is acknowledged in a growing volume of scientific literature, and principles of landscape ecology were thus used to elucidate the patterns in coral community structure on the high-latitude reefs in South Africa. These reefs are at the southernmost distribution of this fauna in Africa, are surprisingly species rich, and represent a biodiversity peak in this fauna south of the equator, regardless of the marginal nature of the environment. Coral community patterns were identified on and between the reefs at Sodwana Bay, justifying the grouping of reef areas in distinct zones. A number of landscape components were identified, ranging from the entire reef complex (10 km scale), individual reefs (1 km scales) and reef zones, to components that were separated using multivariate statistical analysis of transect data. These components transcended spatial similarities, e.g. the fore-reef on Five-mile Reef was not similar to the fore-reef on Seven-mile Reef, but was rather grouped with the reef flat on Two-mile Reef. This information was “translated” into an index of management intervention, based on risk assessment, and was generated using parameters that measure susceptibility to crown-of-thorns feeding, bleaching, diver-related damage and swell-induced breakage. We also assessed was the time elapsed since the last major disturbance and the proximity to the only boat launch site, a proxy measure of continuous disturbance. The risk assessment suggested that conservation management is most needed in the stable and “climax” coral communities that are usually characterised by a near-equal mix of hard and soft corals at maximal coral species diversity.     

Coral bleaching, reef fish community phase shifts and the resilience of coral reefs

The 1998 global coral bleaching event was the largest recorded historical disturbance of coral reefs and resulted in extensive habitat loss. Annual censuses of reef fish community structure over a 12-year period spanning the bleaching event revealed a marked phase shift from a prebleach to postbleach assemblage. Surprisingly, we found that the bleaching event had no detectable effect on the abundance, diversity or species richness of a local cryptobenthic reef fish community. Furthermore, there is no evidence of regeneration even after 5–35 generations of these short-lived species. These results have significant implications for our understanding of the response of coral reef ecosystems to global warming and highlight the importance of selecting appropriate criteria for evaluating reef resilience.     

Mid-Holocene coral community data as baselines for understanding contemporary reef ecological states

Land-use changes and associated deteriorations in water quality are cited as major drivers of marine ecosystem change, and can modify community abundance and diversity on coral reefs. This study uses palaeoecological data derived from a mid-Holocene age coral reef in the Wet Tropics region of Australia's Great Barrier Reef to develop a record of coral community composition and diversity, from a period that significantly pre-dates European settlement in the region. Major changes in catchment sediment and nutrient yields since European settlement have been documented, and thus the data presented provides a baseline against which to compare contemporary ecological datasets. Natural variations in coral assemblage composition, as preserved in core records, clearly occurred in this mid-Holocene reef and were associated with the reef shallowing to sea level as it accreted vertically. Comparisons between modern and mid-Holocene coral community data from equivalent water depths did not reveal marked shifts in coral community composition and diversity, suggesting the long-term persistence of a resilient coral assemblage over these time periods.     

Spatial structure of coral reef fish communities at Kudaka Island (Ryukyu Archipelago), Japan

The present study aimed to investigate the spatial structure of fish communities at juvenile and adult stages on coral reefs at Kudaka Island (Ryukyu Archipelago, Japan) and to relate spatial patterns in the structure of the fish communities to gradients in environmental variables. Diurnal visual censuses allowed us to record 2,602 juveniles belonging to 60 species and 1,543 adults belonging to 53 species from October to December 2005. The distribution of species highlighted that the juvenile community was organised into three distinct assemblages, rather than exhibiting gradual change in community structure along the cross-reef gradient. Correlations between spatial patterns of juvenile community and environmental variables revealed that the most significant factors explaining variation in community structure were coral rubble and coral slab. In contrast, the adult community was organised into one assemblage, and the most significant variation factors in community structure were depth, live coral in massive form, live coral in branched form, dead coral and sand. Overall, the present study showed that most juvenile and adult coral reef fish at Kudaka Island exhibited striking patterns in their distribution and depth and some biological factors (e.g., abundance of live coral, dead coral and coral rubble) might exert considerable influence on the distribution of fishes.     

Scale-dependent spatial variability of coral assemblages along the Florida Reef Tract

 Coral reef communities of the western Atlantic have changed over the past two to three decades, but the magnitude and causes of this change remain controversial. Part of the problem is that small-scale patterns observed on individual reefs have been erroneously extrapolated to landscape and geographic scales. Understanding how reef coral assemblages vary through space is an essential prerequisite to devising sampling strategies to track the dynamics of coral reefs through time. In this paper we quantify variation in the cover of hard corals in spur-and-groove habitats (13–19 m depth) at spatial scales spanning five orders of magnitude along the Florida Reef Tract. A videographic sampling program was conducted to estimate variances in coral cover at the following hierarchical levels and corresponding spatial scales: (1) among transects within sites (0.01- to 0.1-km scale), (2) among sites within reefs (0.5- to 2-km scale), (3) among reefs within sectors of the reef tract (10- to 20-km scale), and (4) among sectors of the reef tract (50- to 100-km scale). Coral cover displayed low variability among transects within sites and among sites within reefs. This means that transects from a site adequately represented the variability of the spur-and-groove habitat of the reef as a whole. Variability among reefs within sectors was highly significant, compared with marginally significant variability among sectors. Estimates from an individual reef, therefore, did not adequately characterize nearby reefs, nor did those estimates sufficiently represent variability at the scale of the sector. The structure and composition of coral reef communities is probably determined by the interaction of multiple forcing functions operating on a variety of scales. Hierarchical analyses of coral assemblages from other geographic locations have detected high variability at scales different from those in the present study. A multiscale analysis should, therefore, precede any management decisions regarding large reef systems such as the Florida Reef Tract. Accepted: 19 July 1999     

Coral Reefs at the Northernmost Tip of Borneo: An Assessment of Scleractinian Species Richness Patterns and Benthic Reef Assemblages

The coral reefs at the northernmost tip of Sabah, Borneo will be established under a marine protected area: the Tun Mustapha Park (TMP) by the end of 2015. This area is a passage where the Sulu Sea meets the South China Sea and it is situated at the border of the area of maximum marine biodiversity, the Coral Triangle. The TMP includes fringing and patch reefs established on a relatively shallow sea floor. Surveys were carried out to examine features of the coral reefs in terms of scleractinian species richness, and benthic reef assemblages following the Reef Check substrate categories, with emphasis on hard coral cover. Variation in scleractinian diversity was based on the species composition of coral families Fungiidae (n = 39), Agariciidae (n = 30) and Euphylliidae (n = 15). The number of coral species was highest at reefs with a larger depth gradient i.e. at the periphery of the study area and in the deep South Banggi Channel. Average live hard coral cover across the sites was 49%. Only 7% of the examined reefs had > 75% hard coral cover, while the majority of the reef sites were rated fair (51%) and good (38%). Sites with low coral cover and high rubble fragments are evidence of blast fishing, although the observed damage appeared old. Depth was a dominant factor in influencing the coral species composition and benthic reef communities in the TMP. Besides filling in the information gaps regarding species richness and benthic cover for reef areas that were previously without any data, the results of this study together with information that is already available on the coral reefs of TMP will be used to make informed decisions on zoning plans for conservation priorities in the proposed park.     

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.     

Bathymetry,water optical properties,and benthic classification of coral reefs using hyperspectral remote sensing imagery

The complexity and heterogeneity of shallow coastal waters over small spatial scales provides a challenging environment for mapping and monitoring benthic habitats using remote sensing imagery. Additionally, changes in coral reef community structure are occurring on unprecedented temporal scales that require large-scale synoptic coverage and monitoring of coral reefs. A variety of sensors and analyses have been employed for monitoring coral reefs: this study applied a spectrum-matching and look-up-table methodology to the analysis of hyperspectral imagery of a shallow coral reef in the Bahamas. In unconstrained retrievals the retrieved bathymetry was on average within 5% of that measured acoustically, and 92% of pixels had retrieved depths within 25% of the acoustic depth. Retrieved absorption coefficients had less than 20% errors observed at blue wavelengths. The reef scale benthic classification derived by analysis of the imagery was consistent with the percent cover of specific coral reef habitat classes obtained by conventional line transects over the reef, and the inversions were robust as the results were similar when the benthic classification retrieval was constrained by measurements of bathymetry or water column optical properties. These results support the use of calibrated hyperspectral imagery for the rapid determination of bathymetry, water optical properties, and the classification of important habitat classes common to coral reefs.     

珊瑚礁生态系统病毒研究进展

病毒对珊瑚礁生态系统中的生物进化、生物地球化学循环、珊瑚疾病等方面具有重要的生态影响。随着珊瑚礁的全球性退化,病毒在珊瑚礁生态系统中的功能与危害日益显现。综述了珊瑚礁生态系统中病毒的研究现状与进展,包括：（1）珊瑚礁病毒的多样性与分布特征（水体、宿主、核心病毒组）;（2）珊瑚礁病毒的生态功能（感染方式、促进生物进化、生物地球化学循环）;（3）珊瑚礁病毒对全球气候变化的响应（热压力、珊瑚疾病）。总体而言,珊瑚礁生态系统具有极高的病毒多样性,所发现的60个科占已知所有病毒科数量的58%。珊瑚的核心病毒组主要由双链DNA病毒、单链DNA病毒、单链逆转录病毒所组成,珊瑚黏液层对病毒具有富集作用。"Piggyback-the-Winner"（依附-胜利）是病毒在珊瑚礁中主要的生物动力学模式,其可通过水平基因迁移的方式促进礁区生物进化。病毒可通过裂解细菌与浮游藻类的途径参与珊瑚礁的生物地球化学循环,尤其是碳循环与氮循环过程。此外,病毒还具有介导珊瑚热白化与直接引发珊瑚疾病的能力,这会影响珊瑚礁生态系统应对气候变化的适应性与恢复力。基于国际上的研究进展综述,结合南海珊瑚礁生态现状提出以下研究方向,以期促进我国珊瑚礁病毒学的发展：（1）开展南海珊瑚礁中病毒多样性的识别及其时-空分布特征研究;（2）探索病毒对南海珊瑚热白化、珊瑚疾病的介导作用及其与气候变化的关系;（3）揭示病毒对南海珊瑚礁生物地球化学循环的贡献。     

Coral and sea urchin assemblage structure and interrelationships in Kenyan reef lagoons

Patterns of hard coral and sea urchin assemblage structure (species richness, diversity, and abundance) were studied in Kenyan coral reef lagoons which experienced different types of human resource use. Two protected reefs (Malindi and Watamu Marine National Parks) were protected from fishing and coral collection, but exposed to heavy tourist use. One reef (Mombasa MNP) received protection from fishermen for one year and was exploited for fish and corals prior to protection and was defined as a transitional reef. Three reefs (Vipingo, Kanamai, and Diani) were unprotected and experienced heavy fishing and some coral collection. Protected and unprotected reefs were distinct in terms of their assemblage structure with the transitional reef grouping with unprotected reefs based on relative and absolute abundance of coral genera. Protected reefs had slightly higher (p<0.01) coral cover (23.6 ± 8.3 % ± S.D.) than unprotected reefs (16.7 ± 8.5), but the transitional reef had the highest coral cover (30.8 ± 6.4) which increased by 250% since measured in 1987: largely attributable to a large increase inPorites nigrescens cover. Protected reefs had higher coral species richness and diversity and a greater relative abundance ofAcropora, Montipora andGalaxea than unprotected reefs. The transitional reef had high species richness, but lower diversity due to the high dominance ofPorites. Sea urchins showed the opposite pattern with highest diversity in most unprotected reefs. Coral cover, species richness, and diversity were negatively associated with sea urchin abundance, but the relative abundance ofPorites increased with sea urchin abundance to the point wherePorites composed >90% of the coral cover at sites with the highest sea urchin abundance. Effects of coral overcollection was only likely for the genusAcropora (staghorn corals). A combination of direct and indirect effects of human resource use may reduce diversity, species richness, and abundance of corals while increasing the absolute abundance of sea urchins and the relative cover ofPorites.     

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.