Recognizing diversity in coral symbiotic dinoflagellate communities

A detailed understanding of how diversity in endosymbiotic dinoflagellate communities maps onto the physiological range of coral hosts is critical to predicting how coral reef ecosystems will respond to climate change. Species-level taxonomy of the dinoflagellate genus Symbiodinium has been predominantly examined using the internal transcribed spacer (ITS) region of the nuclear ribosomal array (rDNA ITS2) and downstream screening for dominant types using denaturing gradient gel electrophoresis (DGGE). Here, ITS2 diversity in the communities of Symbiodinium harboured by two Hawaiian coral species was explored using direct sequencing of clone libraries. We resolved sixfold to eightfold greater diversity per coral species than previously reported, the majority of which corresponds to a novel and distinct phylogenetic lineage. We evaluated how these sequences migrate in DGGE and demonstrate that this method does not effectively resolve this diversity. We conclude that the Porites spp. examined here harbour diverse assemblages of novel Symbiodinium types and that cloning and sequencing is an effective methodological approach for resolving the complexity of endosymbiotic dinoflagellate communities harboured by reef corals.     

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.     

High diversity of microplankton surrounds deep-water coral reef in the Norwegian Sea

Coral reefs that exist in the depths of the oceans are surrounded by Eukarya, Archaea and bacterial communities that may play an important role in the nutrition and health of the reef. The first interdomain community structure of planktonic organisms in seawater from a deep-water coral reef is described. Community profiling and analysis of ribosomal RNA gene sequences from a coral reef system at 350?m depth in the Norwegian Sea revealed a rich diversity of Eukarya and Bacteria and a moderate diversity of Archaea. Most sequences affiliated with marine microplankton from deep-sea to cold-surface regions, with many sequences being similar to those described in studies of mesopelagic and oxygen minimum zones. Dominant phylotypes belonged to the Alveolata (group I, II, dinoflagellates), Stramenopiles (silicoflagellates), Alphaproteobacteria (Pelagibacter ubique), Gammaproteobacteria (ARCTIC96BD-19), Bacteroidetes (Flavobacteria) and mesophilic Crenarchaeota (Nitrosopumilus maritimus). Several rare and novel members of the community fell into distinct phylogenetic groups. The inferred function of dominant community members suggested autotrophs that utilise light, ammonium or sulphide, and lifestyles based on host associations. The high diversity reflected a microplankton community structure, which is significantly different from that of microplankton collected at the same depth at a pelagic station away from reefs.     

Disturbance and the structure of coral reef fish communities on the reef slope

Three levels of physical disturbance were applied to corals in permanent 10x10 m quadrats along a section of fringing reef at Lizard Island on the Great Barrier Reef to investigate the response of fish assemblages. Tabular and corymbose corals were overturned and left in situ, reducing total hard coral cover from ˜55% to ˜47%, ˜43%, and ˜34%. Despite pre-existing associations with benthic cover, all fish groups examined (pomacentrids, labrids, chaetodontids, and acanthurids) were resistent to benthic disturbances at the level and scale at which they were applied. Partial Mantel's tests, in combination with partial Canonical Correspondence Analysis enabled spatial and temporal variation to be factored out from experimental effects. Most of the variation in the fish community could be assigned to spatio-temporal variables, indicating that spatial structure over the reef landscape may moderate localised disturbance effects. This study indicates that coral reef fish assemblages may be more resistant to disturbance than many correlative studies would suggest, and highlights a need for further information on levels and scales of natural habitat disturbance in order to apply a structured approach to the experimental investigation of the importance of habitat in structuring coral-reef fish assemblages.     

Fine-scale diversity and specificity in the most prevalent lineage of symbiotic dinoflagellates (Symbiodinium, Dinophyceae) of the Caribbean

The success of coral reefs is due to obligate mutualistic symbioses involving invertebrates and photosynthetic dinoflagellate symbionts belonging to the genus Symbiodinium. In the Caribbean, the vast majority of octocorals and other invertebrate hosts associate with Symbiodinium clade B, and more selectively, with a single lineage of this clade, Symbiodinium B1/B184. Although B1/B184 represents the most prevalent Symbiodinium in the Caribbean, there is little evidence supporting fine-scale diversity and host-alga specificity within this lineage. We explored simultaneously the questions of diversity and specificity in Symbiodinium B1/B184 by sequencing the flanking regions of two polymorphic microsatellites from a series of Symbiodinium clade B cultures along with Symbiodinium B1/B184 populations of the octocorals Pseudopterogorgia elisabethae, P. bipinnata and Gorgonia ventalina. Seven unique sequence variants were identified based on concatenation of the two loci. Phylogenetic analyses of these variants, which we refer to as phylotypes, recognized five as belonging to B1/B184, thus providing the first evidence of distinct taxa within this Symbiodinium lineage. Furthermore, sympatric P. elisabethae and P. bipinnata at San Salvador in the Bahamas were found to harbour distinct Symbiodinium B1/B184 phylotypes, demonstrating unequivocally the existence of fine-scale specificity between Caribbean octocorals and these algae. Taken together, this study exemplifies the complex nature of Symbiodinium biodiversity and specificity.     

The role of herbivorous fishes and urchins in coral reef communities

Synopsis Herbivorous fishes and invertebrates are conspicious elements of coral reef communities where they predominate both in numbers and biomass. Herbivores and the coral reef algae on which they feed represent a co-evolved system of defense and counter-defense. Algal species have developed toxic, structural, spatial and temporal defense or escape mechanisms, while the herbivores employ strategies that involve anatomical, physiological and behavioral adaptations. Current research demonstrates that many reef fishes are highly selective in the algae they consume. Food selection in these fishes may be correlated with their morphological and digestive capabilities to rupture algal cell walls. Sea urchins select more in accordance with relative abundance, although certain algal species are clearly avoided.The determinants of community structure on coral reefs have yet to be established but evidence indicates a strong influence by herbivores. Reef herbivores may reduce the abundance of certain competitively superior algae, thus allowing corals and cementing coralline algae to survive. We discuss how the foraging activities of tropical marine herbivores affect the distribution and abundance of algae and how these activities contribute to the development of coral reef structure and the fish assemblages which are intimately associated with reef structure.This paper forms a part of the proceedings of a mini-symposium convened at Cornell University, Ithaca, N.Y., 18–19 May 1976, entitled Patterns of Community Structure in Fishes (G. S. Helfman, ed.).     

Disturbance,coral reef communities,and changing ecological paradigms

We examine changing ecological theory regarding the role of disturbance in natural communities and relate past and emerging paradigms to coral reefs. We explore the elements of this theory, including patterns (diversity, distribution, and abundance) and processes (competition, succession, and disturbance), using currently evolving notions concerning matters of scale (temporal and spatial), local versus regional species richness, and the equilibrium versus nonequilibrium controversy. We conclude that any attempt to categorize coral reef communities with respect to disturbance regimes will depend on the question being asked and the desired level of resolution: local assemblage versus regional species pool, successional versus geological time, and on the taxonomic and tropic affinities of species included in the study. As with many communities in nature, coral reefs will prove to be mosaics of species assemblages with equilibrial and nonequilibrial dynamics.     

Larval mortality and the composition of coral reef fish communities

Research over the past decade shows that fish populations on coral reefs can vary enormously, both spatially and temporally. Nonetheless, predictable patterns in structure are present at both small and regional scales. These have usually been interpreted as resulting from processes acting after settlement of fishes from the plankton. However, current research now suggests that planktonic processes could also result in deterministic patterns of community structure.     

Multi-spectral mapping of reef bathymetry and coral cover; Kailua Bay,Hawaii

We used high-resolution, airborne, digital, multi-spectral imagery to map bathymetry and the percent of living coral in the nearshore marine environment of Kailua Bay, Oahu, Hawai'i. Three spectral bands, with centers at 488, 551, and 577 nm (each with a full-width half maximum of 10 nm), were selected for good water transmission and good coral/sand/algae discrimination. However, the third band (577 nm) was not used in the depth and bottom-type solutions. The spatial resolution of 1 m per pixel was selected to balance resolution with the size of the total data set. A radiative transfer model accounting for the optical effects of the atmosphere, ocean surface, water, and reflection off the ocean bottom substrates was applied to the multi-spectral images, normalizing multiple images to one another for a mosaic that spans the bay. Atmospheric parameters in the radiative transfer model were estimated from published values measured for similar environments. Water-attenuation coefficients for the model were determined from the observed spectral data values over the sand bottom type in the bay. Relative depth and bottom-type coefficients were derived by a method most simply described as the "differencing" of two spectral bands. Accuracy exceeding 85% in predicted depth was achieved to a depth of 25 m. Depth prediction errors were assessed with comparison to hydrographic survey data. Classification of bottom-type coefficients into seven "percent living coral" categories results in 77% overall accuracy tested by diver-obtained line-intercept transect data (ground truth). Bottom-type coefficients derived by the model were corrected for atmospheric and ocean conditions on the date of collection, so spatial changes in bathymetry and "percent living coral" through time can be analyzed and related to environmental factors. The radiative transfer model and the "differencing" method used to solve for depth and "percent living coral" can be applied to any airborne, passive remote sensing digital data with appropriate spectral bands.     

Spatial scales of bacterial diversity in cold-water coral reef ecosystems

Background

Cold-water coral reef ecosystems are recognized as biodiversity hotspots in the deep sea, but insights into their associated bacterial communities are still limited. Deciphering principle patterns of bacterial community variation over multiple spatial scales may however prove critical for a better understanding of factors contributing to cold-water coral reef stability and functioning.

Methodology/Principal Findings

Bacterial community structure, as determined by Automated Ribosomal Intergenic Spacer Analysis (ARISA), was investigated with respect to (i) microbial habitat type and (ii) coral species and color, as well as the three spatial components (iii) geomorphologic reef zoning, (iv) reef boundary, and (v) reef location. Communities revealed fundamental differences between coral-generated (branch surface, mucus) and ambient microbial habitats (seawater, sediments). This habitat specificity appeared pivotal for determining bacterial community shifts over all other study levels investigated. Coral-derived surfaces showed species-specific patterns, differing significantly between Lophelia pertusa and Madrepora oculata, but not between L. pertusa color types. Within the reef center, no community distinction corresponded to geomorphologic reef zoning for both coral-generated and ambient microbial habitats. Beyond the reef center, however, bacterial communities varied considerably from local to regional scales, with marked shifts toward the reef periphery as well as between different in- and offshore reef sites, suggesting significant biogeographic imprinting but weak microbe-host specificity.

Conclusions/Significance

This study presents the first multi-scale survey of bacterial diversity in cold-water coral reefs, spanning a total of five observational levels including three spatial scales. It demonstrates that bacterial communities in cold-water coral reefs are structured by multiple factors acting at different spatial scales, which has fundamental implications for the monitoring of microbial diversity and function in those ecosystems.     

Fatty acid variations in symbiotic dinoflagellates from Okinawan corals

The fatty acid composition of polar lipids and triacylglycerols was determined in different morphophysiological types of symbiotic dinoflagellates (SD) isolated from the hydrocoral Millepora intricata and the scleractinian corals Pocillopora damicornis, Seriatopora caliendrum, Seriatopora hystrix and Stylophora pistillata from a fringing reef of Sesoko Island, Okinawa, Japan. The distribution of the fatty acids among the morphophysiologically distinct types of SD reported in these corals makes it possible to readily distinguish one type of SD from the other. Moreover, differences were found both in polar lipids and triacylglycerols. The polar lipids of SD from M. intricata showed a very distinctive fatty acid profile. A combination of large proportions of 18:4 (n-3), 18:5 (n-3), 22:5 (n-6), and 22:6 (n-3) and negligible amounts of 20:4 (n-6), and 20:5 (n-3) in SD from M. intricata was particularly noteworthy. The fatty acid profiles of SD from P. damicornis and SD isolated from S. caliendrum and S. hystrix differed in the proportion of 18:4 (n-3) and 22:6 (n-3). It is suggested that fatty acids might provide useful information on possible taxonomic differences among symbiotic dinoflagellates. It is assumed that biochemical differences can reflect the genetic diversity of the morphophysiological types of SD associated with several species of hermatypic corals from this region.     

Functional significance of genetically different symbiotic algae Symbiodinium in a coral reef symbiosis

The giant sea anemone Condylactis gigantea associates with members of two clades of the dinoflagellate alga Symbiodinium, either singly or in mixed infection, as revealed by clade-specific quantitative polymerase chain reaction of large subunit ribosomal DNA. To explore the functional significance of this molecular variation, the fate of photosynthetically fixed carbon was investigated by (14)C radiotracer experiments. Symbioses with algae of clades A and B released ca. 30-40% of fixed carbon to the animal tissues. Incorporation into the lipid fraction and the low molecular weight fraction dominated by amino acids was significantly higher in symbioses with algae of clade A than of clade B, suggesting that the genetically different algae in C. gigantea are not functionally equivalent. Symbioses with mixed infections yielded intermediate values, such that this functional trait of the symbiosis can be predicted from the traits of the contributing algae. Coral and sea anemone symbioses with Symbiodinium break down at elevated temperature, a process known as 'coral bleaching'. The functional response of the C. gigantea symbiosis to heat stress varied between the algae of clades A and B, with particularly depressed incorporation of photosynthetic carbon into lipid of the clade B algae, which are more susceptible to high temperature than the algae of clade A. This study provides a first exploration of how the core symbiotic function of photosynthate transfer to the host varies with the genotype of Symbiodinium, an algal symbiont which underpins corals and, hence, coral reef ecosystems.     

Hyperspectral discrimination of coral reef benthic communities in the western Caribbean

Determining a subset of wavelengths that best discriminates reef benthic habitats and their associated communities is essential for the development of remote sensing techniques to monitor them. This study measured spectral reflectance from 17 species of western Caribbean reef biota including coral, algae, seagrasses, and sediments, as well as healthy and diseased coral. It sought to extend the spectral library of reef-associated species found in the literature and to test the spectral discrimination of a hierarchy of habitats, community groups, and species. We compared results from hyperspectral reflectance and derivative datasets to those simulated for the three visible multispectral wavebands of the IKONOS sensor. The best discriminating subset of wavelengths was identified by multivariate stepwise selection procedure (discriminant function analysis). Best discrimination at all levels was obtained using the derivative dataset based on 6–15 non-contiguous wavebands depending on the level of the classification, followed by the hyperspectral reflectance dataset which was based on as few as 2–4 non-contiguous wavebands. IKONOS wavebands performed worst. The best discriminating subset of wavelengths in the three classification resolutions, and particularly those of the medium resolution, was in agreement with those identified by Hochberg and Atkinson (2003) and Hochberg et al. (2003) for reef communities worldwide. At all levels of classification, reflectance wavebands selected by the analysis were similar to those reported in recent studies carried out elsewhere, confirming their applicability in different biogeographical regions. However the greater accuracies achieved using the derivative datasets suggests that hyperspectral data is required for the most accurate classification of reef biotic systems.