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Circadian Cycles of Gene Expression in the Coral, Acropora millepora  [PDF]
Aisling K. Brady, Kevin A. Snyder, Peter D. Vize
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0025072
Abstract: Background Circadian rhythms regulate many physiological, behavioral and reproductive processes. These rhythms are often controlled by light, and daily cycles of solar illumination entrain many clock regulated processes. In scleractinian corals a number of different processes and behaviors are associated with specific periods of solar illumination or non-illumination—for example, skeletal deposition, feeding and both brooding and broadcast spawning. Methodology/Principal Findings We have undertaken an analysis of diurnal expression of the whole transcriptome and more focused studies on a number of candidate circadian genes in the coral Acropora millepora using deep RNA sequencing and quantitative PCR. Many examples of diurnal cycles of RNA abundance were identified, some of which are light responsive and damped quickly under constant darkness, for example, cryptochrome 1 and timeless, but others that continue to cycle in a robust manner when kept in constant darkness, for example, clock, cryptochrome 2, cycle and eyes absent, indicating that their transcription is regulated by an endogenous clock entrained to the light-dark cycle. Many other biological processes that varied between day and night were also identified by a clustering analysis of gene ontology annotations. Conclusions/Significance Corals exhibit diurnal patterns of gene expression that may participate in the regulation of circadian biological processes. Rhythmic cycles of gene expression occur under constant darkness in both populations of coral larvae that lack zooxanthellae and in individual adult tissue containing zooxanthellae, indicating that transcription is under the control of a biological clock. In addition to genes potentially involved in regulating circadian processes, many other pathways were found to display diel cycles of transcription.
Which Environmental Factors Predict Seasonal Variation in the Coral Health of Acropora digitifera and Acropora spicifera at Ningaloo Reef?  [PDF]
Saskia Hinrichs, Nicole L. Patten, Ming Feng, Daniel Strickland, Anya M. Waite
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0060830
Abstract: The impact of physico-chemical factors on percent coral cover and coral health was examined on a spatial basis for two dominant Acropora species, A. digitifera and A. spicifera, at Ningaloo Reef (north-western Australia) in the southeast Indian Ocean. Coral health was investigated by measuring metabolic indices (RNA/DNA ratio and protein concentration), energy levels (lipid ratio) and autotrophic indices (chlorophyll a (chl a) and zooxanthellae density) at six stations during typical seasons (austral autumn 2010 (March and April), austral winter 2010 (August)) and during an extreme La Ni?a event in summer 2011 (February). These indices were correlated with 15 physico-chemical factors (measured immediately following coral sampling) to identify predictors for health indices. Variations in metabolic indices (protein concentration and RNA/DNA ratio) for A. spicifera were mainly explained by nitrogen, temperature and zooplankton concentrations under typical conditions, while for A. digitifera, light as well as phytoplankton, in particular picoeukaryotes, were important, possibly due to higher energy requirement for lipid synthesis and storage in A. digitifera. Optimum metabolic values occurred for both Acropora species at 26–28°C when autotrophic indices (chl a and zooxanthellae density) were lowest. The extreme temperature during the La Ni?a event resulted in a shift of feeding modes, with an increased importance of water column plankton concentrations for metabolic rates of A. digitifera and light and plankton for A. spicifera. Our results suggest that impacts of high sea surface temperatures during extreme events such as La Ni?a may be mitigated via reduction on metabolic rates in coral host. The high water column plankton concentrations and associated low light levels resulted in a shift towards high symbiont densities, with lower metabolic rates and energy levels than the seasonal norm for the coral host.
Human Pathogen Shown to Cause Disease in the Threatened Eklhorn Coral Acropora palmata  [PDF]
Kathryn Patterson Sutherland, Sameera Shaban, Jessica L. Joyner, James W. Porter, Erin K. Lipp
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0023468
Abstract: Coral reefs are in severe decline. Infections by the human pathogen Serratia marcescens have contributed to precipitous losses in the common Caribbean elkhorn coral, Acropora palmata, culminating in its listing under the United States Endangered Species Act. During a 2003 outbreak of this coral disease, called acroporid serratiosis (APS), a unique strain of the pathogen, Serratia marcescens strain PDR60, was identified from diseased A. palmata, human wastewater, the non-host coral Siderastrea siderea and the corallivorous snail Coralliophila abbreviata. In order to examine humans as a source and other marine invertebrates as vectors and/or reservoirs of the APS pathogen, challenge experiments were conducted with A. palmata maintained in closed aquaria to determine infectivity of strain PDR60 from reef and wastewater sources. Strain PDR60 from wastewater and diseased A. palmata caused disease signs in elkhorn coral in as little as four and five days, respectively, demonstrating that wastewater is a definitive source of APS and identifying human strain PDR60 as a coral pathogen through fulfillment of Koch's postulates. A. palmata inoculated with strain PDR60 from C. abbreviata showed limited virulence, with one of three inoculated fragments developing APS signs within 13 days. Strain PDR60 from non-host coral S. siderea showed a delayed pathogenic effect, with disease signs developing within an average of 20 days. These results suggest that C. abbreviata and non-host corals may function as reservoirs or vectors of the APS pathogen. Our results provide the first example of a marine “reverse zoonosis” involving the transmission of a human pathogen (S. marcescens) to a marine invertebrate (A. palmata). These findings underscore the interaction between public health practices and environmental health indices such as coral reef survival.
Genetic Diversity and Connectivity in the Threatened Staghorn Coral (Acropora cervicornis) in Florida  [PDF]
Elizabeth M. Hemond,Steven V. Vollmer
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0008652
Abstract: Over the past three decades, populations of the dominant shallow water Caribbean corals, Acropora cervicornis and A. palmata, have been devastated by white-band disease (WBD), resulting in the listing of both species as threatened under the U.S. Endangered Species Act. A key to conserving these threatened corals is understanding how their populations are genetically interconnected throughout the greater Caribbean. Genetic research has demonstrated that gene flow is regionally restricted across the Caribbean in both species. Yet, despite being an important site of coral reef research, little genetic data has been available for the Florida Acropora, especially for the staghorn coral, A. cervicornis. In this study, we present new mitochondrial DNA sequence data from 52 A. cervicornis individuals from 22 sites spread across the upper and lower Florida Keys, which suggest that Florida's A. cervicornis populations are highly genetically interconnected (FST = ?0.081). Comparison between Florida and existing mtDNA data from six regional Caribbean populations indicates that Florida possesses high levels of standing genetic diversity (h = 0.824) relative to the rest of the greater Caribbean (h = 0.701±0.043). We find that the contemporary level of gene flow across the greater Caribbean, including Florida, is restricted ( = 0.117), but evidence from shared haplotypes suggests the Western Caribbean has historically been a source of genetic variation for Florida. Despite the current patchiness of A. cervicornis in Florida, the relatively high genetic diversity and connectivity within Florida suggest that this population may have sufficient genetic variation to be viable and resilient to environmental perturbation and disease. Limited genetic exchange across regional populations of the greater Caribbean, including Florida, indicates that conservation efforts for A. cervicornis should focus on maintaining and managing populations locally rather than relying on larval inputs from elsewhere.
The Skeleton of the Staghorn Coral Acropora millepora: Molecular and Structural Characterization  [PDF]
Paula Ramos-Silva, Jaap Kaandorp, Frédéric Herbst, Laurent Plasseraud, Gérard Alcaraz, Christine Stern, Marion Corneillat, Nathalie Guichard, Christophe Durlet, Gilles Luquet, Frédéric Marin
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0097454
Abstract: The scleractinian coral Acropora millepora is one of the most studied species from the Great Barrier Reef. This species has been used to understand evolutionary, immune and developmental processes in cnidarians. It has also been subject of several ecological studies in order to elucidate reef responses to environmental changes such as temperature rise and ocean acidification (OA). In these contexts, several nucleic acid resources were made available. When combined to a recent proteomic analysis of the coral skeletal organic matrix (SOM), they enabled the identification of several skeletal matrix proteins, making A. millepora into an emerging model for biomineralization studies. Here we describe the skeletal microstructure of A. millepora skeleton, together with a functional and biochemical characterization of its occluded SOM that focuses on the protein and saccharidic moieties. The skeletal matrix proteins show a large range of isoelectric points, compositional patterns and signatures. Besides secreted proteins, there are a significant number of proteins with membrane attachment sites such as transmembrane domains and GPI anchors as well as proteins with integrin binding sites. These features show that the skeletal proteins must have strong adhesion properties in order to function in the calcifying space. Moreover this data suggest a molecular connection between the calcifying epithelium and the skeletal tissue during biocalcification. In terms of sugar moieties, the enrichment of the SOM in arabinose is striking, and the monosaccharide composition exhibits the same signature as that of mucus of acroporid corals. Finally, we observe that the interaction of the acetic acid soluble SOM on the morphology of in vitro grown CaCO3 crystals is very pronounced when compared with the calcifying matrices of some mollusks. In light of these results, we wish to commend Acropora millepora as a model for biocalcification studies in scleractinians, from molecular and structural viewpoints.
RNA-seq Profiles of Immune Related Genes in the Staghorn Coral Acropora cervicornis Infected with White Band Disease  [PDF]
Silvia Libro, Stefan T. Kaluziak, Steven V. Vollmer
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0081821
Abstract: Coral diseases are among the most serious threats to coral reefs worldwide, yet most coral diseases remain poorly understood. How the coral host responds to pathogen infection is an area where very little is known. Here we used next-generation RNA-sequencing (RNA-seq) to produce a transcriptome-wide profile of the immune response of the Staghorn coral Acropora cervicornis to White Band Disease (WBD) by comparing infected versus healthy (asymptomatic) coral tissues. The transcriptome of A. cervicornis was assembled de novo from A-tail selected Illumina mRNA-seq data from whole coral tissues, and parsed bioinformatically into coral and non-coral transcripts using existing Acropora genomes in order to identify putative coral transcripts. Differentially expressed transcripts were identified in the coral and non-coral datasets to identify genes that were up- and down-regulated due to disease infection. RNA-seq analyses indicate that infected corals exhibited significant changes in gene expression across 4% (1,805 out of 47,748 transcripts) of the coral transcriptome. The primary response to infection included transcripts involved in macrophage-mediated pathogen recognition and ROS production, two hallmarks of phagocytosis, as well as key mediators of apoptosis and calcium homeostasis. The strong up-regulation of the enzyme allene oxide synthase-lipoxygenase suggests a key role of the allene oxide pathway in coral immunity. Interestingly, none of the three primary innate immune pathways - Toll-like receptors (TLR), Complement, and prophenoloxydase pathways, were strongly associated with the response of A. cervicornis to infection. Five-hundred and fifty differentially expressed non-coral transcripts were classified as metazoan (n = 84), algal or plant (n = 52), fungi (n = 24) and protozoans (n = 13). None of the 52 putative Symbiodinium or algal transcript had any clear immune functions indicating that the immune response is driven by the coral host, and not its algal symbionts.
Gene Discovery in the Threatened Elkhorn Coral: 454 Sequencing of the Acropora palmata Transcriptome  [PDF]
Nicholas R. Polato, J. Cristobal Vera, Iliana B. Baums
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0028634
Abstract: Background Cnidarians, including corals and anemones, offer unique insights into metazoan evolution because they harbor genetic similarities with vertebrates beyond that found in model invertebrates and retain genes known only from non-metazoans. Cataloging genes expressed in Acropora palmata, a foundation-species of reefs in the Caribbean and western Atlantic, will advance our understanding of the genetic basis of ecologically important traits in corals and comes at a time when sequencing efforts in other cnidarians allow for multi-species comparisons. Results A cDNA library from a sample enriched for symbiont free larval tissue was sequenced on the 454 GS-FLX platform. Over 960,000 reads were obtained and assembled into 42,630 contigs. Annotation data was acquired for 57% of the assembled sequences. Analysis of the assembled sequences indicated that 83–100% of all A. palmata transcripts were tagged, and provided a rough estimate of the total number genes expressed in our samples (~18,000–20,000). The coral annotation data contained many of the same molecular components as in the Bilateria, particularly in pathways associated with oxidative stress and DNA damage repair, and provided evidence that homologs of p53, a key player in DNA repair pathways, has experienced selection along the branch separating Cnidaria and Bilateria. Transcriptome wide screens of paralog groups and transition/transversion ratios highlighted genes including: green fluorescent proteins, carbonic anhydrase, and oxidative stress proteins; and functional groups involved in protein and nucleic acid metabolism, and the formation of structural molecules. These results provide a starting point for study of adaptive evolution in corals. Conclusions Currently available transcriptome data now make comparative studies of the mechanisms underlying coral's evolutionary success possible. Here we identified candidate genes that enable corals to maintain genomic integrity despite considerable exposure to genotoxic stress over long life spans, and showed conservation of important physiological pathways between corals and bilaterians.
Light effects on the isotopic fractionation of skeletal oxygen and carbon in the cultured zooxanthellate coral, Acropora: implications for coral-growth rates
A. Juillet-Leclerc,S. Reynaud
Biogeosciences (BG) & Discussions (BGD) , 2010,
Abstract: Skeletal isotopic and metabolic measurements of the branching coral Acropora cultured in constant conditions and subjected to two light intensities were revisited. We individually compared the data recorded at low light (LL) and high light (HL) for 24 colonies, all derived from the same parent colony. Metabolic and isotopic responses to the different light levels were highly variable. High light led to productivity enhancement, reduction of surface extension, doubling of aragonite deposited weight and increased δ18O levels in all nubbins; responses in respiration and δ13C were not clear. The partitioning of the colonies cultured at HL into two groups, one showing a δ13C enrichment and the other a δ13C decrease revealed common behaviors. Samples showing an increase in δ13C were associated with the co-variation of low surface extension and high productivity while samples showing a decrease in δ13C were associated with the co-variation of higher surface extension and limited productivity. This experiment, which allowed for the separation of temperature and light effects on the coral, highlighted the significant light influences on both skeletal δ18O and δ13C. The high scattering of inter-colony δ18O observed at one site could be due to the differing photosynthetic responses of symbiotic algal assemblages. We compared our results with observations by Gladfelter on Acropora cervicornis (1982). Both set of results highlight the relationships between coral-growth rates, micro-structures and photosynthetic activity. It appears that extension growth and skeleton thickening are two separate growth modes, and thickening is light-enhanced while extension is light-suppressed. There are multiple consequences of these findings for paleoclimatic reconstructions involving corals.
Light effects on the isotopic fractionation of skeletal oxygen and carbon in the cultured zooxanthellate coral, Acropora: implications for coral-growth rates  [PDF]
A. Juillet-Leclerc,S. Reynaud
Biogeosciences Discussions , 2009,
Abstract: Skeletal isotopic and metabolic measurements of the branching coral Acropora cultured in constant conditions and subjected to two light intensities were revisited. We individually compared the data recorded at low light (LL) and high light (HL) for 24 colonies, all derived from the same parent colony. Metabolic and isotopic responses to the different light levels were highly variable. High light led to productivity enhancement, reduction of surface extension, doubling of aragonite deposited weight and increased δ18O levels in all nubbins; responses in respiration and δ13C were not clear. The partitioning of the colonies into two groups, one showing a δ13C increase and the other a δ13C decrease with increased light, revealed common behaviors. Samples showing an increase in δ13C were associated with the co-variation of low surface extension and high productivity while samples showing a decrease in δ13C were associated with the co-variation of higher surface extension and limited productivity. This experiment, which allowed for the separation of temperature and light effects on the coral, highlighted the significant light influences on both skeletal δ18O and δ13C. The high scattering of inter-colony δ18O observed at one site could be due to the differing photosynthetic responses of symbiotic algal assemblages. The δ13C responses could also be related to differing algal distributions in different skeletal portions. Our results were compared to observations by Gladfelter on Acropora cervicornis (1982). Both set of results highlight the relationships between coral-growth rates, micro-structures and photosynthetic activity. It appears that extension growth and accretion are two separate growth modes, and accretion is light-enhanced while extension is light-repressed. There are multiple consequences of these findings for paleoclimatic reconstructions involving corals.
Cryptobiota associated to dead Acropora palmata (Scleractinia: Acroporidae) coral, Isla Grande, Colombian Caribbean
Moreno-Forero,Silvia K.; Navas S.,Gabriel R.; Solano,O.David;
Revista de Biología Tropical , 1998,
Abstract: cryptobiota of dead fragments of five branches in live position and five fallen pieces of the coral acropora palmata each one of approximate 1dm3, covered by filamentous algae were extracted from the north reef crest of isla grande (colombian caribbean), in april 1991. there were three groups of organisms according to size and position (on and within the coral): 1) mobile epibenthos, mainly microcrustaceans that live among the filamentous algae 2) boring microcryptobiota, located in the layer between the epilithic organisms and the coral skeleton itself and, 3) perforating macrocryptobionts that bore and penetrate the coral skeleton. polychaetes, sipuncu-lids, mollusks and crustaceans were most abundant in the last group. there were no differences in macrocryptobiont composition between standing dead branches and fallen fragments. there was a large variation in total biomass and type and density of macro-cryptobionts, possibly associated to stochastic factors such as placement and thickness of branches and small scale variations in recruitment
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