Hermatypic Research Articles

Distinguishing Species Using GC Contents in Mixed DNA or RNA Sequences.

With the advent of whole transcriptome and genome analysis methods, classifying samples containing multiple origins has become a significant task. Nucleotide sequences can be allocated to a genome or transcriptome by aligning sequences to multiple target sequence sets, but this approach requires extensive computational resources and also depends on target sequence sets lacking contaminants, which is often not the case. Here, we demonstrate that raw sequences can be rapidly sorted into groups, in practice corresponding to genera, by exploiting differences in nucleotide GC content. To do so, we introduce GCSpeciesSorter, which uses classification, specifically Support Vector Machines (SVM) and the C4.5 decision tree generator, to differentiate sequences. It also implements a secondary BLAST feature to identify known outliers. In the test case presented, a hermatypic coral holobiont, the cnidarian host includes various endosymbionts. The best characterized and most common of these symbionts are zooxanthellae of the genus Symbiodinium. GCSpeciesSorter separates cnidarian from Symbiodinium sequences with a high degree of accuracy. We show that if the GC contents of the species differ enough, this method can be used to accurately distinguish the sequences of different species when using high-throughput sequencing technologies.

Ecological and functional diversity of gastropods associated with hermatypic corals of the Mexican tropical Pacific

This study used multi-scale models to evaluate spatial variation in the structure of the assemblage and functional groups of gastropods associated with hermatypic corals of the Mexican Tropical Pacific. A geographic model examined the spatial scales of the region, geographic position and sites, while an oceanographic model considered the oceanographic characteristics and sites. The relationship between gastropods and environmental and spatial variables was analyzed with additive partitions, based on canonical correspondence analysis. Both models coincide in that the greatest variation of gastropods was presented at quadrant (i.e., small-scale) and site (i.e., local-scale) levels, and the lowest variation to the scale of geographic position and oceanographic characteristics (i.e., medium-scale). Abundance and Shannon diversity presented greater variation at small and local-scales, while species richness presented greater variation at medium-scale. The functional groups varied to the greatest extent at medium-scale in the geographic model and at local-scale in the oceanographic model. The highest abundance, richness and diversity were found at: (1) Plataforma Pavonas and Tunel Amarradero, ~20°N (Northern region), influenced by the California Current and the Mexican Coastal Current; (2) Caleta de Chon and Morro Potosi, ~17°N (Southern region), affected by the Mexican Warm Pool; and (3) Salchi and Isla Montosa, where relatively high biological productivity occur mainly due to coastal upwelling, ~15°N (Southern region). The carnivorous epifauna was the most important functional group at all studied scales. The most important species in both models were the corallivore Coralliophila monodonta, the symbiont Muricopsis zeteki, Triphora hannai of sandy substrate and Vermicularia pellucida eburnea and Engina tabogaensis of hard substrate. Variation among sites was explained mainly by the coverage of sessile taxa (e.g., percentage of coverage of the coral Pocillopora spp., bryozoans, hydrozoans, octocorals and sponges) and proportion of substrates (e.g., sand, rock, dead coral and rubble). However, at upwelling sites, other variables such as primary productivity and phosphate concentration also contributed to local-scale variation. At medium-scale, oceanographic characteristics explain the variation of the assemblage and functional groups of gastropods.

Effects of coral-derived organic matter on the growth of bacterioplankton and heterotrophic nanoflagellates

Exudates derived from hermatypic corals were incubated with <2 µm filtered seawater containing heterotrophic bacteria and <10 µm filtered seawater containing bacteria and nanoflagellates (HNF) under dark conditions for 96 h to quantify the growth of both bacteria and HNF in response to coral-derived dissolved organic matter (DOM). The addition of coral-derived DOM caused significantly higher growth rates and production of bacteria and HNF compared to those in control seawater without coral exudates. During the incubation, HNF exhibited their peak in abundance 24–48 h after the peak abundance of bacteria. The growth efficiencies of both bacteria and HNF were significantly higher with coral-derived DOM, suggesting higher transfer efficiency from bacteria that is fueled by coral organic matter to HNF. Therefore, trophic transfer of coral-derived DOM from bacteria to HNF can contribute to efficient carbon flow through the microbial food web.

The Study of Species Richness in Coral Communities of Vietnam

Dynamics of biodiversity research traced reef-building scleractinian on the reefs of Vietnam for more than 35 years. Found 376 corals species, pertaining to 80 genera (including nine ahermatypic corals), of which 153 species, belonging to 28 genera, were not previously known for that region, and 16 species from six genera were described for the first time. As in most Indo-Pacific reefs, the species diversity of Vietnam's reefs consists mainly of the members of five families: Acroporidae (98 species), Faviidae (42 species), Fungiidae (32 species), Poritidae (31 species), and Dendrophylliidae (26 species), making up altogether 64.48% of the total scleractinian species composition. The species composition and high diversity of Vietnam's coral fauna, as well as its close similarity to the Southwest Pacific coral fauna, allow one to refer it to the Indonesia-Polynesian center of origin of the coral faunas of the tropical Indo-Pacific. The whole Vietnam coast, from the Gulf of Tonkin to the Gulf of Siam, is a biogeographically single whole and is part of the Indo-Polynesian Province of the Indo-Pacific Area.

Localised hydrodynamics influence vulnerability of coral communities to environmental disturbances

The movement of water can have a significant influence on the vulnerability of hermatypic corals to environmental disturbances such as cyclone damage, heat stress and anoxia. Here, we explore the relationship between small reef-scale water circulation patterns and measured differences in the abundance, composition and vulnerability of coral assemblages over decades. Changes in coral cover and community structure within Bill’s Bay (Ningaloo Reef, Western Australia) over a 22-yr period, during which multiple disturbance events (including mass bleaching, anoxia, and tropical cyclones) have impacted the area, were compared with spatial variation in water residence times (WRT). We found that reef sites associated with longer water residence times (WRT >15 h) experienced higher rates of coral mortality during acute environmental disturbances compared to reef sites with shorter WRT. Shifts in coral community composition from acroporid to faviid-dominated assemblages were also more prominent at sites with long WRT compared to reef sites with shorter WRT, although shifts in community composition were also observed at sites close to shore. Interestingly, these same long-WRT sites also tended to have the fastest recovery rates so that coral cover was returned to original levels of approximately 20% over two decades. This study provides empirical evidence that spatial patterns in water circulation and flushing can influence the resilience of coral communities, thus identifying areas sensitive to emerging threats associated with global climate change.

Multi-scale analysis of hermatypic coral assemblages at Mexican Central Pacific

The Mexican Central Pacific is located in a zone of oceanographic transition between two biogeographic provinces with particular conditions that affect the associated fauna. The objective of this study was to evaluate the variation of hermatypic coral assemblages in this region and to determine their relationship with the heterogeneity of the benthonic habitat and spatial variables. A total of 156 transects were carried out at 41 sites in the years 2010 and 2011. The sampling effort returned 96.7% of the coral richness expected for the area, with a total of 15 species recorded. The results showed that richness, diversity and cover of corals varied only at the site and state scales. However, the composition and coverage of all coral species, as well as the benthonic habitat structure, differed significantly across the study scales (i.e. sites, zones and states). Canonical redundancy analysis showed that variation in the richness, diversity and assemblages of corals was explained by the cover of live corals, articulated calcareous algae, sandy substrate, sponges and fleshy macroalgae. This study suggests that local scale (i.e. site) variation in the coral assemblages of the Mexican Central Pacific is the result of the heterogeneity of the benthonic habitat, while geomorphological and oceanographic characteristics play a greater role at regional scale.

Substrate selection of Christmas tree worms (Spirobranchusspp.) in the Gulf of Eilat, Red Sea

Christmas tree worms (Spirobranchusspp.) are prominent sessile organisms inhabiting hermatypic corals in tropical and sub-tropical reefs. Until recently, most of the largerSpirobranchusspecies were considered to be in obligatory associations with live hermatypic corals. However, recent studies indicate that someSpirobranchusspecies can build tubes on artificial substrate as well and that others may show preferences for using specific species of corals and hydrozoans as substrates. In the present study, we conducted a survey ofSpirobranchusspp. substrate preference in the Gulf of Eilat. We found seven morphotaxa ofSpirobranchus, of which two may be a single new species. We show thatSpirobranchustaxa differ not only in their morphology, but also in their substrate use. Our results demonstrate that the ecological niche ofSpirobranchusis species-specific, and a putative innate preference exists for some substrates.

MIOCENE SCLERACTINIAN CORALS OF GAVDOS ISLAND, SOUTHERN GREECE: IMPLICATIONS FOR TECTONIC CONTROL AND SEA-LEVEL CHANGES

Low-diversity scleractinian patch reefs that have been developed, during Early to Middle Tortonian, in Gavdos island are studied, aiming in a better understanding of the time and space relationships of the reef development and the associated basin fill evolution. Gavdos island consists part of a tectonically active setting constituting the southernmost extension of the Hellenic arc (Eastern Mediterranean). A representative Tortonian section (Bo section), located in the northwest part of the island, which hosts a mass occurrence of hermatypic corals, is studied. Scleractinian samples were collected from the upper 12 m of the section, which is characterized by interchanges of marly limestone and compact marls. The reefs are represented by the coral species Heliastraea oligophylla, Porites maicientensis, Thegioastraea roasendai and Porites collegniana. The microfacies analysis showed that the mediumto-thin-bedded carbonates of the limestone-marl alternations comprise patch reefs (boundstones-framestones, SMF 16, sensu Wilson, 1975, FZ 7-8, sensu Flügel 1982) consisted of screractinian corals. Corals are associated with corallinacean algae. Patch reefs are associated by bioclastic packstones-floatstones, characterized by benthic foraminifera, calcareous algae, spines of echinoids, gastropods and molluscs. Reefs are laterally associated by a bioclastic limestone rich in planktonic forams, associated by detrital material (fragments of quartz, feldspars, quartzites and cherts). The studied reef facies have been dolomitized and cemented in the meteoric realm. In places pseudomorphs after evaporites have been observed, tending to occlude cavities resulted after dissolution. The depositional environment corresponds to a moderate to high-energy inner platform setting, experiencing open-ocean influences. The pattern of coralgal reef development during Miocene, in the tectonically controlled Gavdos island, represents a complex interaction of tectonic activity and global sea-level changes.

Skeletal dissolution kinetics and mechanical tests in response to morphology among coral genera

Ocean acidification is widely accepted as a primary threat to coral reef populations. Negative physiological effects include decreased calcification rates, heightened metabolic energy expenditure, and increased dissolution of coral skeletons. However, studies on the dissolution of coral skeletons structures under ocean acidification conditions and their implications on sediments remain scarce. In this work, we examined skeletal dissolution kinetics from four of the most representative hermatypic corals of the Eastern Pacific coasts (Pocillopora, Porites, Pavona, and Psammocora). Samples were treated with a highly acidic solution for defined periods of time, and measurements of dissolved calcium ([Ca+2]) were used to evaluate the kinetics of coral skeleton dissolution. All genera tests except Porites showed a zero reaction rate. Porites exhibited a first-order reaction and a faster reaction rate than other genera. Compression strength tests and skeletal density did not correlate with reaction rate. Pavona showed greater structural strength. Porites were the most susceptible to acidic dissolution compared to other genera tested due to their morphology, i.e., possession of the largest surface area, suggesting a high vulnerability under low-pH conditions. The hierarchical response in dissolution kinetics among coral genera tested suggests that the most soluble coral might act as a buffer under ocean acidification conditions.

Miocene to Pleistocene transatlantic dispersal of Ceratoconcha coral-dwelling barnacles and North Atlantic island biogeography

Coral-dwelling pyrgomatid barnacles (subfamily Ceratoconchinae) were widely dispersed throughout the Paratethys and Mediterranean seas as well as the Atlantic Ocean during the Neogene, but today are limited to the Western Atlantic. Herein, the paleobiogeographic origin and dispersal of the genus Ceratoconcha is studied based on a combination of field, taxonomic, and literature studies. The first confirmed appearances of Ceratoconcha occur in lower Miocene strata (Burdigalian) with two closely related species on both sides of the Atlantic in western France and Florida. Fossils from the Miocene of Lanzarote in the Canary Islands and Pleistocene of Maio in the Cape Verde islands extend the known geographical and temporal range of the Ceratoconcha barnacles in the eastern Atlantic. During the Neogene, dispersal of marine taxa was a two-way process due to tectonic changes both influencing oceanic circulation and appearance and disappearance of oceanic islands. During the early Miocene, gyre formation was weak and the Atlantic Ocean mid-latitudes were warmer than today. This resulted in increased hurricane activity and the expansion of hermatypic coral hosts farther north in the North Atlantic. Normal ocean circulation transported barnacle larvae from east to west, but currents generated by hurricanes may have transported them in the opposite direction towards the margins of the northeastern Atlantic. Islands in between abetted barnacle contact and dispersal. The temporal range for Ceratoconcha is extended considerably in the eastern Atlantic from the early Pliocene to the Pleistocene. The hermatypic host corals of Ceratoconcha suffered a severe decline in the eastern Atlantic and the Mediterranean after the Miocene. Corals were present during the Pliocene and Pleistocene in the Cape Verde Islands. This suggests that the southernmost oceanic islands acted as a tropical refuge for host corals and their likely barnacle symbionts.

Coral reef fish assemblages at Clipperton Atoll (Eastern Tropical Pacific) and their relationship with coral cover

Clipperton Atoll, one of the most isolated coral reefs worldwide, is of great scientific interest due to its geomorphology and high levels of endemism. This study explored the reef fish assemblage structure of Clipperton Atoll and its relationship with live coral cover. Nine stations were sampled at three sites and three depths (6, 12 and 20 m) around the reef, measuring fish species richness and biomass and hermatypic coral cover (at genus level). We evaluated variation in species richness, biomass and diversity of fish assemblages among sites and depths, as well as the relationship between the entire fish assemblage composition and live coral cover. The results showed that species richness and biomass were similar among sites, but differed across depths, increasing with depth. In contrast, diversity differed among sites but not among depths. Multivariate analyses indicated that fish assemblage composition differed among sites and depths in relation to changes in cover of coral of the genera Pocillopora, Porites, Pavona and Leptoseris, which dominate at different depths. The results showed that fish species richness and diversity were low at Clipperton Atoll and that, in isolated coral reefs with a low habitat heterogeneity and low human disturbance, live coral cover has a significant influence on the spatial variation of the reef fish assemblages. This study highlights the importance of coral habitat structure in shaping coral reef fish assemblages.

Calcification of the main reef-building coral species on the Pacific coast of southern Mexico

Global warming and ocean acidification affect coral calcification. Nevertheless, there is not enough information regarding the growth parameters of the main reef-building coral species in marginal growth areas such as the Pacific coast of southern Mexico. In order to fill this gap, coral growth parameters of 8 hermatypic coral species (massive species: Porites panamensis, Porites lobata, Pavona gigantea, and Pavona varians; branching species: Pocillopora meandrina, Pocillopora damicornis, Pocillopora verrucosa, and Pocillopora capitata) were estimated in 2 areas of the southern Mexican Pacific. Branching coral species had a higher calcification rate (2.99–5.23 g CaCO3 cm–2 yr–1) than massive species (0.34–1.13 g CaCO3 cm–2 yr–1). A significant relation between sea surface temperature (SST) and skeletal density was observed in all massive coral species. Also, 2 massive species (P. gigantea and P. varians) showed a significant relation between SST and calcification rate. Upwelling in the Gulf of Tehuantepec transports deep water with low pH and low aragonite saturation, and may be affecting the calcification rate of stony corals in the studied area.

First deep screening of bacterial assemblages associated with corals of the Tropical Eastern Pacific.

Bacterial assemblages associated with the hermatypic corals Pocillopora damicornis and P. verrucosa, the surrounding seawater and the sediment at six coral reef sites in the north section of the Tropical Eastern Pacific were assessed using MiSeq Illumina sequencing of the V4 region of the 16S rDNA. The bacterial microbiota in both coral species, seawater and sediment were stable to seasonal variations. Bacterial assemblages between the same substrates were not significantly different from each other in the six sites sampled. Interestingly, the bacterial composition between substrates within the same site was significantly different, or not, depending on the conservation status of the site. Moreover, we found species-specific bacterial OTUs in both coral species. Analyzing the relationship between bacterial composition and environmental variables revealed a positive correlation between bacterial assemblages and dissolved oxygen, ammonium and silicate.

Evolution of symbiosis in hermatypic corals: A model of the past, present, and future

This work can be considered a prequel to our previous paper on coral bleaching induced by global warming. We once again investigate, using Finsler geometry, dynamical energy budget theory and nonlinear modular mechanics, the origin of endosymbiosis, between reef-building corals and the algae. We assume their relationship starts out as entosymbiosis, with the algal organism living on the external surfaces of host coral exoskeleton, but with both gradually adapting to each other over evolutionary time-scales. Our main conclusion is that such an evolutionary conversion is possible and indeed is quite likely.

Decapod crustaceans from the Paleocene (Danian) of the Paris Basin (Vigny stratotype and allied localities) and a limpet palaeoassociation

As the lowermost stage of the Palaeogene, the Danian is a key period for ecosystems which followed the K–Pg boundary. The Vigny quarry (Val d'Oise, France) is a co-stratotype of the Danian stage, along with the well-known one of Fakse (Denmark). The Vigny ecosystem (Bois-des-Roches site at Vigny and allied Danian localities) is the only known Cenozoic reef of the Paris Basin and is formed by hermatypic corals, unlike reefs at Fakse. Well studied by scientists, including d'Orbigny, for almost two centuries, the decapod crustacean fauna of Vigny has been much less documented than that of Fakse. Here, we describe new material of decapod crustaceans from the Danian of the Paris Basin, based on material in the Muséum national d'Histoire naturelle (Paris). This material (six carapaces and 14 isolated claws) constitutes anomurans, brachyurans and, for the first time, axiideans in the Danian of the Paris Basin. Among brachyurans, it includes the paleoxanthopsid crab Jakobsenius cretaceus is described and the dynomenid Dromiopsis mosae. Two new brachyuran species are described from Vigny: Titanocarcinus schweitzerae sp. nov. (Tumidocarcinidae) and Dromilites montenati sp. nov. (Dromiidae). The latter is the oldest representative of its genus. The Danian decapod crustaceans of the Paris Basin are revised and their diversity is compared to that at Fakse. The enigmatic association of a limpet (Patella herbetiana) attached to a crab carapace is described and interpreted. Based on a small number of available specimens, this study reveals some specificity of the Vigny brachyuran fauna and recognizes the Paris Basin as an important region for knowledge of Danian decapod crustaceans.http://zoobank.org/urn:lsid:zoobank.org:pub:2813A14B-AE65-4296-9C3C-2B10B9C5DC6B

Skeletal extension, density and calcification rates of massive free-living coral Porites lobata Dana, 1846

Hermatypic corals are an important sessile group in the benthic structure of tropical coral reef communities. Many organisms, in response to the environmental conditions, have developed different strategies of growth by modifying their morphologies and reproduction mode, as is the case of free-living colonies called coralliths. So far, important parameters such as calcification, growth rates and their relation with biotic and abiotic factors on coralliths have not been described. This study represents the first record of a corallith form of Porites lobata and provides information on its sclerochronology. Coral growth parameters of different coralliths were compared by measuring extension rate (cmy−1), skeletal density (gcm−3), calcification rate (gcm−2y−1), average age (yr) and sphericity (S). The influence of the environment on corallith growth was assessed using water temperature as an abiotic factor and bioturbation by fish as a biotic factor. Analysis of annual density bands using X-ray densitometry provided a mean extension rate of 0.47±0.23cmy−1, skeletal density of 1.08±0.14gcm−3, and calcification rate of 0.51±0.26gcm−2y−1. The results reveal differences in growth parameters between coralliths including a strong relationship of calcification rate with seawater temperature. In addition, direct and indirect bioturbations promoted the colony rotation resulting in a hemispherical form. Hence, the evidence suggests that scleractinian corals have developed an important growth strategy that allows the species to form new colonies and maintain successful coral reef communities through free-living corallith growth.

Light Enhanced Calcification in Hermatypic Corals: New Insights from Light Spectral Responses

Light enhanced calcification (LEC) is a well documented phenomenon in reef-building corals. The main mechanism proposed for LEC is that photosynthetic CO2 uptake by the algal symbionts elevates the pH and thus enhances calcification. We evaluated the role of light and of photosynthesis on calcification by assessing the response of the corals Porites lutea and Acropora variabilis to different components of the light spectrum. Calcification and photosynthesis of both species decreased under “lagoon” blue, green and red light (peaks at 500, 550 and 600nm respectively). However, blue light (peak at 455nm) enhanced calcification rates of P. lutea and A. variabilis (up to 4.1 and 10.5 fold of dark values, respectively) reaching levels comparable to those measured under full spectrum illumination. However, contrary to our expectations, photosynthetic oxygen production was considerably reduced under blue light, to the extent that it remained below the compensation point even under illumination as high as 400µmol photons m-2 s-1. It is the first time that a direct effect of light not mediated by the photosynthetic process has been demonstrated to trigger LEC in corals. We propose that blue light signaling, and animal receptors thereof may be involved in the enhancement of calcification by hermatypic corals.

Reproductive Synchrony of the Hermatypic Corals, Acropora hemperchii and Pocillopora verrucosa, along the Egyptian Red Sea Offshore and Onshore Reefs: Environmental Constraints

Reproductive Synchrony of the Hermatypic Corals, Acropora hemperchii and Pocillopora verrucosa, along the Egyptian Red Sea Offshore and Onshore Reefs: Environmental Constraints

Particular Qualities Of Identification And Taxonomy Of Some Scleractinian (Scleractinia: Astrocoeniina) Family Acroporidae Verrill, 1903

Brief history of taxonomy and identification of one of the diverse groups of the hermatypic coral family Acroporidae. Drawn attention to the difficulties and errors that have occurred in their taxonomy. Describes the terminology and morphological characteristics that can be successful identification and description of corals of the family.

Particular Qualities of Identification and Taxonomy of Some Scleractinian (Scleractinia: Faviina), Faviidae Gregory, 1900

It is a brief history of taxonomy and identification of one of the most interesting groups of massive hermatypic corals family Faviidae, characterized by placoid, cerioid and meandroid forms of corallum and having with Acroporidae and Fungiidae the greatest number of genera and species diversity among all hermatypic Scleractinian. Describes terminology and morphological signs under the definition and description of corals of the family.