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Gierz SL, Forêt S, Leggat W. Transcriptomic Analysis of Thermally Stressed Symbiodinium Reveals Differential Expression of Stress and Metabolism Genes. FRONTIERS IN PLANT SCIENCE 2017; 8:271. [PMID: 28293249 PMCID: PMC5328969 DOI: 10.3389/fpls.2017.00271] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/14/2017] [Indexed: 05/29/2023]
Abstract
Endosymbioses between dinoflagellate algae (Symbiodinium sp.) and scleractinian coral species form the foundation of coral reef ecosystems. The coral symbiosis is highly susceptible to elevated temperatures, resulting in coral bleaching, where the algal symbiont is released from host cells. This experiment aimed to determine the transcriptional changes in cultured Symbiodinium, to better understand the response of cellular mechanisms under future temperature conditions. Cultures were exposed to elevated temperatures (average 31°C) or control conditions (24.5°C) for a period of 28 days. Whole transcriptome sequencing of Symbiodinium cells on days 4, 19, and 28 were used to identify differentially expressed genes under thermal stress. A large number of genes representing 37.01% of the transcriptome (∼23,654 unique genes, FDR < 0.05) with differential expression were detected at no less than one of the time points. Consistent with previous studies of Symbiodinium gene expression, fold changes across the transcriptome were low, with 92.49% differentially expressed genes at ≤2-fold change. The transcriptional response included differential expression of genes encoding stress response components such as the antioxidant network and molecular chaperones, cellular components such as core photosynthesis machinery, integral light-harvesting protein complexes and enzymes such as fatty acid desaturases. Differential expression of genes encoding glyoxylate cycle enzymes were also found, representing the first report of this in Symbiodinium. As photosynthate transfer from Symbiodinium to coral hosts provides up to 90% of a coral's daily energy requirements, the implications of altered metabolic processes from exposure to thermal stress found in this study on coral-Symbiodinium associations are unknown and should be considered when assessing the stability of the symbiotic relationship under future climate conditions.
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Affiliation(s)
- Sarah L. Gierz
- College of Public Health, Medical and Veterinary Sciences, James Cook University, TownsvilleQLD, Australia
- Comparative Genomics Centre, James Cook University, TownsvilleQLD, Australia
| | - Sylvain Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, TownsvilleQLD, Australia
- Evolution, Ecology and Genetics, Research School of Biology, Australian National University, CanberraACT, Australia
| | - William Leggat
- College of Public Health, Medical and Veterinary Sciences, James Cook University, TownsvilleQLD, Australia
- Comparative Genomics Centre, James Cook University, TownsvilleQLD, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, TownsvilleQLD, Australia
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102
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Reich HG, Robertson DL, Goodbody-Gringley G. Do the shuffle: Changes in Symbiodinium consortia throughout juvenile coral development. PLoS One 2017; 12:e0171768. [PMID: 28182684 PMCID: PMC5300206 DOI: 10.1371/journal.pone.0171768] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 01/25/2017] [Indexed: 11/18/2022] Open
Abstract
Previous studies of symbiotic associations between scleractinians corals and Symbiodinium have demonstrated that the consortium of symbionts can change in response to environmental conditions. However, less is known about symbiont shuffling during early coral development, particularly in brooding species. This study examined whether Symbiodinium consortia (1) varied in Porites astreoides on shallow (10m) and upper mesophotic (30m) reefs, (2) changed during coral development, and (3) influenced growth of juveniles in different environments. Symbiodinium ITS2 sequences were amplified using universal primers and analyzed using phylotype-specific primers designed for phylotypes A, B, and C. Adults from both depths were found to host only phylotype A, phylotypes A and B, or phylotypes A, B, and C and the frequency of the phylotype composition did not vary with depth. However, phylotype A was the dominant symbiont that was vertically transmitted to the planulae. The presence of phylotypes B and C was detected in the majority of juveniles when transplanted onto the shallow and upper mesophotic reefs whereas only phylotype A was detected in the majority of juveniles reared in outdoor aquaria. In addition, growth of juvenile P. astreoides harboring different combinations of Symbiodinium phylotypes did not vary when transplanted to different reef zones. However, juveniles reared in in situ reef environments grew faster than those reared in ex situ outdoor aquaria. These results show that Symbiodinium consortia change during development of P. astreoides and are influenced by environmental conditions.
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Affiliation(s)
- Hannah G. Reich
- Department of Biology, Clark University, Worcester, Massachusetts, United States of America
- * E-mail:
| | - Deborah L. Robertson
- Department of Biology, Clark University, Worcester, Massachusetts, United States of America
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103
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Levy O, Karako-Lampert S, Waldman Ben-Asher H, Zoccola D, Pagès G, Ferrier-Pagès C. Molecular assessment of the effect of light and heterotrophy in the scleractinian coral Stylophora pistillata. Proc Biol Sci 2017; 283:rspb.2015.3025. [PMID: 27122555 DOI: 10.1098/rspb.2015.3025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/31/2016] [Indexed: 12/18/2022] Open
Abstract
Corals acquire nutrients via the transfer of photosynthates by their endosymbionts (autotrophy), or via zooplankton predation by the animal (heterotrophy). During stress events, corals lose their endosymbionts, and undergo starvation, unless they increase their heterotrophic capacities. Molecular mechanisms by which heterotrophy sustains metabolism in stressed corals remain elusive. Here for the first time, to the best of our knowledge, we identified specific genes expressed in heterotrophically fed and unfed colonies of the scleractinian coral Stylophora pistillata, maintained under normal and light-stress conditions. Physiological parameters and gene expression profiling demonstrated that fed corals better resisted stress than unfed ones by exhibiting less oxidative damage and protein degradation. Processes affected in light-stressed unfed corals (HLU), were related to energy and metabolite supply, carbohydrate biosynthesis, ion and nutrient transport, oxidative stress, Ca(2+) homeostasis, metabolism and calcification (carbonic anhydrases, calcium-transporting ATPase, bone morphogenetic proteins). Two genes (cp2u1 and cp1a2), which belong to the cytochrome P450 superfamily, were also upregulated 249 and 10 times, respectively, in HLU corals. In contrast, few of these processes were affected in light-stressed fed corals (HLF) because feeding supplied antioxidants and energetic molecules, which help repair oxidative damage. Altogether, these results show that heterotrophy helps prevent the cascade of metabolic problems downstream of oxidative stress.
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Affiliation(s)
- Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Sarit Karako-Lampert
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Hiba Waldman Ben-Asher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 quai Antoine 1er, 98000 Monaco, Monaco
| | - Gilles Pagès
- Université de Nice-Sophia Antipolis, Institut de Recherche sur le Cancer et le Veillissement, IRCAN, CNRS-UMR 7284, INSERM U1081, Nice, France
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104
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Kitchen SA, Weis VM. The sphingosine rheostat is involved in the cnidarian heat stress response but not necessarily in bleaching. J Exp Biol 2017; 220:1709-1720. [DOI: 10.1242/jeb.153858] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 02/16/2017] [Indexed: 12/17/2022]
Abstract
Sphingolipids play important roles in mitigating cellular heat and oxidative stress by altering membrane fluidity, receptor clustering and gene expression. Accumulation of signaling sphingolipids that comprise the sphingosine rheostat, pro-apoptotic sphingosine (Sph) and pro-survival sphingosine-1-phosphate (S1P), is key to determining cell fate. Reef-building corals and other symbiotic cnidarians living in shallow tropical waters can experience elevated seawater temperature and high UV irradiance, two stressors that are increasing in frequency and severity with climate change. In symbiotic cnidarians, these stressors disrupt the photosynthetic machinery of the endosymbiont and ultimately result in the collapse of the partnership (dysbiosis), known as cnidarian bleaching. In a previous study, exogenously applied sphingolipids altered heat-induced bleaching in the symbiotic anemone Aiptasia pallida, but endogenous regulation of these lipids is unknown. Here, we characterized the role of the rheostat in the cnidarian heat stress response (HSR) and in dysbiosis. Gene expression of rheostat enzymes sphingosine kinase (AP-SPHK) and S1P phosphatase (AP-SGPP), and concentrations of sphingolipids were quantified from anemones incubated at elevated temperatures. We observed a biphasic HSR in A. pallida. At early exposure, rheostat gene expression and lipid levels were suppressed while gene expression of a heat stress biomarker increased and 40% of symbionts were lost. After longer incubations at the highest temperature, AP-SGPP and then Sph levels both increased. These results indicate that the sphingosine rheostat in A. pallida does not participate in initiation of dysbiosis, but instead functions in the chronic response to prolonged heat stress that promotes host survival.
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Affiliation(s)
- Sheila A. Kitchen
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA
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105
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Louis YD, Bhagooli R, Kenkel CD, Baker AC, Dyall SD. Gene expression biomarkers of heat stress in scleractinian corals: Promises and limitations. Comp Biochem Physiol C Toxicol Pharmacol 2017; 191:63-77. [PMID: 27585119 DOI: 10.1016/j.cbpc.2016.08.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 08/02/2016] [Accepted: 08/21/2016] [Indexed: 12/13/2022]
Abstract
Gene expression biomarkers (GEBs) are emerging as powerful diagnostic tools for identifying and characterizing coral stress. Their capacity to detect sublethal stress prior to the onset of signs at the organismal level that might already indicate significant damage makes them more precise and proactive compared to traditional monitoring techniques. A high number of candidate GEBs, including certain heat shock protein genes, metabolic genes, oxidative stress genes, immune response genes, ion transport genes, and structural genes have been investigated, and some genes, including hsp16, Cacna1, MnSOD, SLC26, and Nf-kB, are already showing excellent potential as reliable indicators of thermal stress in corals. In this mini-review, we synthesize the current state of knowledge of scleractinian coral GEBs and highlight gaps in our understanding that identify directions for future work. We also address the underlying sources of variation that have sometimes led to contrasting results between studies, such as differences in experimental set-up and approach, intrinsic variation in the expression profiles of different experimental organisms (such as between different colonies or their algal symbionts), diel cycles, varying thermal history, and different expression thresholds. Despite advances in our understanding there is still no universally accepted biomarker of thermal stress, the molecular response of corals to heat stress is still unclear, and biomarker research in Symbiodinium still lags behind that of the host. These gaps should be addressed in future work.
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Affiliation(s)
- Yohan D Louis
- Department of Biosciences, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius
| | - Ranjeet Bhagooli
- Department of Marine & Ocean Science, Fisheries & Mariculture, Faculty of Ocean Studies, University of Mauritius, Réduit 80837, Mauritius.
| | - Carly D Kenkel
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, QLD 4810, Australia
| | - Andrew C Baker
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Cswy., Miami, FL, USA
| | - Sabrina D Dyall
- Department of Biosciences, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius
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106
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Gene expression plasticity as a mechanism of coral adaptation to a variable environment. Nat Ecol Evol 2016; 1:14. [PMID: 28812568 DOI: 10.1038/s41559-016-0014] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/07/2016] [Indexed: 02/07/2023]
Abstract
Local adaptation is ubiquitous, but the molecular mechanisms that give rise to this ecological phenomenon remain largely unknown. A year-long reciprocal transplant of mustard hill coral (Porites astreoides) between a highly environmentally variable inshore habitat and a more stable offshore habitat demonstrated that populations exhibit phenotypic signatures that are consistent with local adaptation. We characterized the genomic basis of this adaptation in both coral hosts and their intracellular symbionts (Symbiodinium sp.) using genome-wide gene expression profiling. Populations differed primarily in their capacity for plasticity: following transplantation to a novel environment, inshore-origin coral expression profiles became significantly more similar to the local population's profiles than those in offshore-origin corals. Furthermore, elevated plasticity of the environmental stress response expression was correlated with lower susceptibility to a natural summer bleaching event, suggesting that plasticity is adaptive in the inshore environment. Our results reveal a novel genomic mechanism of resilience to a variable environment, demonstrating that corals are capable of a more diverse molecular response to stress than previously thought.
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107
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Guzman C, Conaco C. Gene Expression Dynamics Accompanying the Sponge Thermal Stress Response. PLoS One 2016; 11:e0165368. [PMID: 27788197 PMCID: PMC5082814 DOI: 10.1371/journal.pone.0165368] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/11/2016] [Indexed: 12/13/2022] Open
Abstract
Marine sponges are important members of coral reef ecosystems. Thus, their responses to changes in ocean chemistry and environmental conditions, particularly to higher seawater temperatures, will have potential impacts on the future of these reefs. To better understand the sponge thermal stress response, we investigated gene expression dynamics in the shallow water sponge, Haliclona tubifera (order Haplosclerida, class Demospongiae), subjected to elevated temperature. Using high-throughput transcriptome sequencing, we show that these conditions result in the activation of various processes that interact to maintain cellular homeostasis. Short-term thermal stress resulted in the induction of heat shock proteins, antioxidants, and genes involved in signal transduction and innate immunity pathways. Prolonged exposure to thermal stress affected the expression of genes involved in cellular damage repair, apoptosis, signaling and transcription. Interestingly, exposure to sublethal temperatures may improve the ability of the sponge to mitigate cellular damage under more extreme stress conditions. These insights into the potential mechanisms of adaptation and resilience of sponges contribute to a better understanding of sponge conservation status and the prediction of ecosystem trajectories under future climate conditions.
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Affiliation(s)
- Christine Guzman
- Marine Science Institute, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
| | - Cecilia Conaco
- Marine Science Institute, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
- * E-mail:
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108
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Mansour TA, Rosenthal JJC, Brown CT, Roberson LM. Transcriptome of the Caribbean stony coral Porites astreoides from three developmental stages. Gigascience 2016; 5:33. [PMID: 27485233 PMCID: PMC4969664 DOI: 10.1186/s13742-016-0138-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 07/14/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Porites astreoides is a ubiquitous species of coral on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most other coral species. We assembled and annotated a transcriptome from this coral using Illumina sequences from three different developmental stages collected over several years: free-swimming larvae, newly settled larvae, and adults (>10 cm in diameter). This resource will aid understanding of coral calcification, larval settlement, and host-symbiont interactions. FINDINGS A de novo transcriptome for the P. astreoides holobiont (coral plus algal symbiont) was assembled using 594 Mbp of raw Illumina sequencing data generated from five age-specific cDNA libraries. The new transcriptome consists of 867 255 transcript elements with an average length of 685 bases. The isolated P. astreoides assembly consists of 129 718 transcript elements with an average length of 811 bases, and the isolated Symbiodinium sp. assembly had 186 177 transcript elements with an average length of 1105 bases. CONCLUSIONS This contribution to coral transcriptome data provides a valuable resource for researchers studying the ontogeny of gene expression patterns within both the coral and its dinoflagellate symbiont.
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Affiliation(s)
- Tamer A. Mansour
- Department of Population Health and Reproduction, University of California, Davis, California USA
- Department of Clinical Pathology, College of Medicine, Mansoura University, Mansoura, Egypt
| | - Joshua J. C. Rosenthal
- Marine Biological Laboratory, Woods Hole, Massachusetts USA
- Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico USA
| | - C. Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, California USA
| | - Loretta M. Roberson
- Marine Biological Laboratory, Woods Hole, Massachusetts USA
- Department of Environmental Science, University of Puerto Rico Río Piedras, San Juan, Puerto Rico USA
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109
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Howells EJ, Abrego D, Meyer E, Kirk NL, Burt JA. Host adaptation and unexpected symbiont partners enable reef-building corals to tolerate extreme temperatures. GLOBAL CHANGE BIOLOGY 2016; 22:2702-14. [PMID: 26864257 DOI: 10.1111/gcb.13250] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 02/02/2016] [Accepted: 02/02/2016] [Indexed: 05/18/2023]
Abstract
Understanding the potential for coral adaptation to warming seas is complicated by interactions between symbiotic partners that define stress responses and the difficulties of tracking selection in natural populations. To overcome these challenges, we characterized the contribution of both animal host and symbiotic algae to thermal tolerance in corals that have already experienced considerable warming on par with end-of-century projections for most coral reefs. Thermal responses in Platygyra daedalea corals from the hot Persian Gulf where summer temperatures reach 36°C were compared with conspecifics from the milder Sea of Oman. Persian Gulf corals had higher rates of survival at elevated temperatures (33 and 36°C) in both the nonsymbiotic larval stage (32-49% higher) and the symbiotic adult life stage (51% higher). Additionally, Persian Gulf hosts had fixed greater potential to mitigate oxidative stress (31-49% higher) and their Symbiodinium partners had better retention of photosynthetic performance under elevated temperature (up to 161% higher). Superior thermal tolerance of Persian Gulf vs. Sea of Oman corals was maintained after 6-month acclimatization to a common ambient environment and was underpinned by genetic divergence in both the coral host and symbiotic algae. In P. daedalea host samples, genomewide SNP variation clustered into two discrete groups corresponding with Persian Gulf and Sea of Oman sites. Symbiodinium within host tissues predominantly belonged to ITS2 rDNA type C3 in the Persian Gulf and type D1a in the Sea of Oman contradicting patterns of Symbiodinium thermal tolerance from other regions. Our findings provide evidence that genetic adaptation of both host and Symbiodinium has enabled corals to cope with extreme temperatures in the Persian Gulf. Thus, the persistence of coral populations under continued warming will likely be determined by evolutionary rates in both, rather than single, symbiotic partners.
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Affiliation(s)
- Emily J Howells
- Center for Genomics and Systems Biology, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - David Abrego
- Department of Natural Science and Public Health, Zayed University, P.O. Box 144534, Abu Dhabi, United Arab Emirates
| | - Eli Meyer
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA
| | - Nathan L Kirk
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA
| | - John A Burt
- Center for Genomics and Systems Biology, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
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110
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Coral Carbonic Anhydrases: Regulation by Ocean Acidification. Mar Drugs 2016; 14:md14060109. [PMID: 27271641 PMCID: PMC4926068 DOI: 10.3390/md14060109] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/09/2016] [Accepted: 05/30/2016] [Indexed: 11/17/2022] Open
Abstract
Global change is a major threat to the oceans, as it implies temperature increase and acidification. Ocean acidification (OA) involving decreasing pH and changes in seawater carbonate chemistry challenges the capacity of corals to form their skeletons. Despite the large number of studies that have investigated how rates of calcification respond to ocean acidification scenarios, comparatively few studies tackle how ocean acidification impacts the physiological mechanisms that drive calcification itself. The aim of our paper was to determine how the carbonic anhydrases, which play a major role in calcification, are potentially regulated by ocean acidification. For this we measured the effect of pH on enzyme activity of two carbonic anhydrase isoforms that have been previously characterized in the scleractinian coral Stylophora pistillata. In addition we looked at gene expression of these enzymes in vivo. For both isoforms, our results show (1) a change in gene expression under OA (2) an effect of OA and temperature on carbonic anhydrase activity. We suggest that temperature increase could counterbalance the effect of OA on enzyme activity. Finally we point out that caution must, thus, be taken when interpreting transcriptomic data on carbonic anhydrases in ocean acidification and temperature stress experiments, as the effect of these stressors on the physiological function of CA will depend both on gene expression and enzyme activity.
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111
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Recent Advances in Understanding the Effects of Climate Change on Coral Reefs. DIVERSITY-BASEL 2016. [DOI: 10.3390/d8020012] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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112
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Abstract
Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein-coding sequences is particularly puzzling, because methylation causes cytosine hypermutability and hence is likely to produce deleterious amino acid substitutions. We investigate this enigma using an evolutionarily basal group of Metazoa, the stony corals (order Scleractinia, class Anthozoa, phylum Cnidaria). We show that patterns of coral gbM are similar to other invertebrate species, predicting wide and active transcription and slower sequence evolution. We also find a strong correlation between gbM and codon bias, resulting from systematic replacement of CpG bearing codons. We conclude that gbM has strong effects on codon evolution and speculate that this may influence establishment of optimal codons.
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Affiliation(s)
- Groves B Dixon
- Institute for Cell and Molecular Biology, University of Texas
| | - Line K Bay
- Australian Institute of Marine Science, Townsville, QLD, Australia ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
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113
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Maor-Landaw K, Levy O. Gene expression profiles during short-term heat stress; branching vs. massive Scleractinian corals of the Red Sea. PeerJ 2016; 4:e1814. [PMID: 27069783 PMCID: PMC4824894 DOI: 10.7717/peerj.1814] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/24/2016] [Indexed: 11/20/2022] Open
Abstract
It is well-established that there is a hierarchy of susceptibilities amongst coral genera during heat-stress. However, molecular mechanisms governing these differences are still poorly understood. Here we explored if specific corals possessing different morphologies and different susceptibilities to heat stress may manifest varied gene expression patterns. We examined expression patterns of seven genes in the branching corals Stylophora pistillata and Acropora eurystoma and additionally in the massive robust coral, Porites sp. The tested genes are representatives of key cellular processes occurring during heat-stress in Cnidaria: oxidative stress, ER stress, energy metabolism, DNA repair and apoptosis. Varied response to the heat-stress, in terms of visual coral paling, algal maximum quantum yield and host gene expression was evident in the different growth forms. The two branching corals exhibited similar overall responses that differed from that of the massive coral. A. eurystoma that is considered as a susceptible species did not bleach in our experiment, but tissue sloughing was evident at 34 °C. Interestingly, in this species redox regulation genes were up-regulated at the very onset of the thermal challenge. In S. pistillata, bleaching was evident at 34 °C and most of the stress markers were already up-regulated at 32 °C, either remaining highly expressed or decreasing when temperatures reached 34 °C. The massive Porites species displayed severe bleaching at 32 °C but stress marker genes were only significantly elevated at 34 °C. We postulate that by expelling the algal symbionts from Porites tissues, oxidation damages are reduced and stress genes are activated only at a progressed stage. The differential gene expression responses exhibited here can be correlated with the literature well-documented hierarchy of susceptibilities amongst coral morphologies and genera in Eilat’s coral reef.
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Affiliation(s)
- Keren Maor-Landaw
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat Gan , Israel
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat Gan , Israel
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114
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Ding JY, Shiu JH, Chen WM, Chiang YR, Tang SL. Genomic Insight into the Host-Endosymbiont Relationship of Endozoicomonas montiporae CL-33(T) with its Coral Host. Front Microbiol 2016; 7:251. [PMID: 27014194 PMCID: PMC4781883 DOI: 10.3389/fmicb.2016.00251] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/15/2016] [Indexed: 11/13/2022] Open
Abstract
The bacterial genus Endozoicomonas was commonly detected in healthy corals in many coral-associated bacteria studies in the past decade. Although, it is likely to be a core member of coral microbiota, little is known about its ecological roles. To decipher potential interactions between bacteria and their coral hosts, we sequenced and investigated the first culturable endozoicomonal bacterium from coral, the E. montiporae CL-33(T). Its genome had potential sign of ongoing genome erosion and gene exchange with its host. Testosterone degradation and type III secretion system are commonly present in Endozoicomonas and may have roles to recognize and deliver effectors to their hosts. Moreover, genes of eukaryotic ephrin ligand B2 are present in its genome; presumably, this bacterium could move into coral cells via endocytosis after binding to coral's Eph receptors. In addition, 7,8-dihydro-8-oxoguanine triphosphatase and isocitrate lyase are possible type III secretion effectors that might help coral to prevent mitochondrial dysfunction and promote gluconeogenesis, especially under stress conditions. Based on all these findings, we inferred that E. montiporae was a facultative endosymbiont that can recognize, translocate, communicate and modulate its coral host.
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Affiliation(s)
- Jiun-Yan Ding
- Biodiversity Research Center, Academia Sinica Taipei, Taiwan
| | - Jia-Ho Shiu
- Biodiversity Research Center, Academia Sinica Taipei, Taiwan
| | - Wen-Ming Chen
- Department of Seafood Science, Laboratory of Microbiology, National Kaohsiung Marine University Kaohsiung, Taiwan
| | - Yin-Ru Chiang
- Biodiversity Research Center, Academia Sinica Taipei, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica Taipei, Taiwan
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115
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Dimond JL, Roberts SB. Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change. Mol Ecol 2016; 25:1895-904. [DOI: 10.1111/mec.13414] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/26/2015] [Accepted: 10/01/2015] [Indexed: 12/27/2022]
Affiliation(s)
- James L. Dimond
- School of Aquatic and Fishery Sciences; University of Washington; 1122 Boat Street Seattle WA 98105 USA
| | - Steven B. Roberts
- School of Aquatic and Fishery Sciences; University of Washington; 1122 Boat Street Seattle WA 98105 USA
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Anderson DA, Walz ME, Weil E, Tonellato P, Smith MC. RNA-Seq of the Caribbean reef-building coral Orbicella faveolata (Scleractinia-Merulinidae) under bleaching and disease stress expands models of coral innate immunity. PeerJ 2016; 4:e1616. [PMID: 26925311 PMCID: PMC4768675 DOI: 10.7717/peerj.1616] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 01/01/2016] [Indexed: 12/16/2022] Open
Abstract
Climate change-driven coral disease outbreaks have led to widespread declines in coral populations. Early work on coral genomics established that corals have a complex innate immune system, and whole-transcriptome gene expression studies have revealed mechanisms by which the coral immune system responds to stress and disease. The present investigation expands bioinformatic data available to study coral molecular physiology through the assembly and annotation of a reference transcriptome of the Caribbean reef-building coral, Orbicella faveolata. Samples were collected during a warm water thermal anomaly, coral bleaching event and Caribbean yellow band disease outbreak in 2010 in Puerto Rico. Multiplex sequencing of RNA on the Illumina GAIIx platform and de novo transcriptome assembly by Trinity produced 70,745,177 raw short-sequence reads and 32,463 O. faveolata transcripts, respectively. The reference transcriptome was annotated with gene ontologies, mapped to KEGG pathways, and a predicted proteome of 20,488 sequences was generated. Protein families and signaling pathways that are essential in the regulation of innate immunity across Phyla were investigated in-depth. Results were used to develop models of evolutionarily conserved Wnt, Notch, Rig-like receptor, Nod-like receptor, and Dicer signaling. O. faveolata is a coral species that has been studied widely under climate-driven stress and disease, and the present investigation provides new data on the genes that putatively regulate its immune system.
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Affiliation(s)
- David A Anderson
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Marine Sciences, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico, United States of America
| | - Marcus E Walz
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin , United States of America
| | - Ernesto Weil
- Department of Marine Sciences, University of Puerto Rico at Mayagüez , Mayagüez, Puerto Rico , United States of America
| | - Peter Tonellato
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America; Department of Biomedical Informatics, Harvard Medical School, Harvard University, Boston, Massachusetts, United States of America
| | - Matthew C Smith
- School of Freshwater Sciences, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin , United States of America
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Rose NH, Seneca FO, Palumbi SR. Gene Networks in the Wild: Identifying Transcriptional Modules that Mediate Coral Resistance to Experimental Heat Stress. Genome Biol Evol 2015; 8:243-52. [PMID: 26710855 PMCID: PMC4758253 DOI: 10.1093/gbe/evv258] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Organisms respond to environmental variation partly through changes in gene expression, which underlie both homeostatic and acclimatory responses to environmental stress. In some cases, so many genes change in expression in response to different influences that understanding expression patterns for all these individual genes becomes difficult. To reduce this problem, we use a systems genetics approach to show that variation in the expression of thousands of genes of reef-building corals can be explained as variation in the expression of a small number of coexpressed “modules.” Modules were often enriched for specific cellular functions and varied predictably among individuals, experimental treatments, and physiological state. We describe two transcriptional modules for which expression levels immediately after heat stress predict bleaching a day later. One of these early “bleaching modules” is enriched for sequence-specific DNA-binding proteins, particularly E26 transformation-specific (ETS)-family transcription factors. The other module is enriched for extracellular matrix proteins. These classes of bleaching response genes are clear in the modular gene expression analysis we conduct but are much more difficult to discern in single gene analyses. Furthermore, the ETS-family module shows repeated differences in expression among coral colonies grown in the same common garden environment, suggesting a heritable genetic or epigenetic basis for these expression polymorphisms. This finding suggests that these corals harbor high levels of gene-network variation, which could facilitate rapid evolution in the face of environmental change.
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Affiliation(s)
- Noah H Rose
- Biology Department, Stanford University, Hopkins Marine Station
| | - Francois O Seneca
- Biology Department, Stanford University, Hopkins Marine Station Present address: Kewalo Marine Lab, University of Hawaii, Honolulu, HI
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118
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DeBiasse MB, Kelly MW. Plastic and Evolved Responses to Global Change: What Can We Learn from Comparative Transcriptomics?: Table 1. J Hered 2015; 107:71-81. [DOI: 10.1093/jhered/esv073] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 08/06/2015] [Indexed: 01/02/2023] Open
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119
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Intraspecific diversity among partners drives functional variation in coral symbioses. Sci Rep 2015; 5:15667. [PMID: 26497873 PMCID: PMC4620489 DOI: 10.1038/srep15667] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 09/29/2015] [Indexed: 11/25/2022] Open
Abstract
The capacity of coral-dinoflagellate mutualisms to adapt to a changing climate relies in part on standing variation in host and symbiont populations, but rarely have the interactions between symbiotic partners been considered at the level of individuals. Here, we tested the importance of inter-individual variation with respect to the physiology of coral holobionts. We identified six genetically distinct Acropora palmata coral colonies that all shared the same isoclonal Symbiodinium ‘fitti’ dinoflagellate strain. No other Symbiodinium could be detected in host tissues. We exposed fragments of each colony to extreme cold and found that the stress-induced change in symbiont photochemical efficiency varied up to 3.6-fold depending on host genetic background. The S. ‘fitti’ strain was least stressed when associating with hosts that significantly altered the expression of 184 genes under cold shock; it was most stressed in hosts that only adjusted 14 genes. Key expression differences among hosts were related to redox signaling and iron availability pathways. Fine-scale interactions among unique host colonies and symbiont strains provide an underappreciated source of raw material for natural selection in coral symbioses.
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120
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De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes. G3-GENES GENOMES GENETICS 2015; 5:2441-52. [PMID: 26384772 PMCID: PMC4632063 DOI: 10.1534/g3.115.020164] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Many nonmodel species exemplify important biological questions but lack the sequence resources required to study the genes and genomic regions underlying traits of interest. Reef-building corals are famously sensitive to rising seawater temperatures, motivating ongoing research into their stress responses and long-term prospects in a changing climate. A comprehensive understanding of these processes will require extending beyond the sequenced coral genome (Acropora digitifera) to encompass diverse coral species and related anthozoans. Toward that end, we have assembled and annotated reference transcriptomes to develop catalogs of gene sequences for three scleractinian corals (Fungia scutaria, Montastraea cavernosa, Seriatopora hystrix) and a temperate anemone (Anthopleura elegantissima). High-throughput sequencing of cDNA libraries produced ~20-30 million reads per sample, and de novo assembly of these reads produced ~75,000-110,000 transcripts from each sample with size distributions (mean ~1.4 kb, N50 ~2 kb), comparable to the distribution of gene models from the coral genome (mean ~1.7 kb, N50 ~2.2 kb). Each assembly includes matches for more than half the gene models from A. digitifera (54-67%) and many reasonably complete transcripts (~5300-6700) spanning nearly the entire gene (ortholog hit ratios ≥0.75). The catalogs of gene sequences developed in this study made it possible to identify hundreds to thousands of orthologs across diverse scleractinian species and related taxa. We used these sequences for phylogenetic inference, recovering known relationships and demonstrating superior performance over phylogenetic trees constructed using single mitochondrial loci. The resources developed in this study provide gene sequences and genetic markers for several anthozoan species. To enhance the utility of these resources for the research community, we developed searchable databases enabling researchers to rapidly recover sequences for genes of interest. Our analysis of de novo assembly quality highlights metrics that we expect will be useful for evaluating the relative quality of other de novo transcriptome assemblies. The identification of orthologous sequences and phylogenetic reconstruction demonstrates the feasibility of these methods for clarifying the substantial uncertainties in the existing scleractinian phylogeny.
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121
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Shikina S, Chiu YL, Lee YH, Chang CF. From Somatic Cells to Oocytes: A Novel Yolk Protein Produced by Ovarian Somatic Cells in a Stony Coral, Euphyllia ancora1. Biol Reprod 2015; 93:57. [DOI: 10.1095/biolreprod.115.129643] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 07/07/2015] [Indexed: 11/01/2022] Open
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122
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Rocker MM, Noonan S, Humphrey C, Moya A, Willis BL, Bay LK. Expression of calcification and metabolism-related genes in response to elevated pCO2 and temperature in the reef-building coral Acropora millepora. Mar Genomics 2015; 24 Pt 3:313-8. [PMID: 26275825 DOI: 10.1016/j.margen.2015.08.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 08/05/2015] [Accepted: 08/05/2015] [Indexed: 02/07/2023]
Abstract
Declining health of scleractinian corals in response to deteriorating environmental conditions is widely acknowledged, however links between physiological and functional genomic responses of corals are less well understood. Here we explore growth and the expression of 20 target genes with putative roles in metabolism and calcification in the branching coral, Acropora millepora, in two separate experiments: 1) elevated pCO2 (464, 822, 1187 and 1638 μatm) and ambient temperature (27°C), and 2) elevated pCO2 (490 and 822 μatm) and temperature (28 and 31 °C). After 14 days of exposure to elevated pCO2 and ambient temperatures, no evidence of differential expression of either calcification or metabolism genes was detected between control and elevated pCO2 treatments. After 37 days of exposure to control and elevated pCO2, Ubiquinol-Cytochrome-C Reductase Subunit 2 gene (QCR2; a gene involved in complex III of the electron chain transport within the mitochondria and critical for generation of ATP) was significantly down-regulated in the elevated pCO2 treatment in both ambient and elevated temperature treatments. Overall, the general absence of a strong response to elevated pCO2 and temperature by the other 19 targeted calcification and metabolism genes suggests that corals may not be affected by these stressors on longer time scales (37 days). These results also highlight the potential for QCR2 to act as a biomarker of coral genomic responses to changing environments.
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Affiliation(s)
- Melissa M Rocker
- Australian Institute of Marine Science, PMB #3, Townsville MC, QLD 4810, Australia; AIMS@JCU, Australian Institute of Marine Science, James Cook University, Townsville, QLD 4811, Australia; College of Marine and Environmental Sciences, James Cook University, Townsville, QLD 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia.
| | - Sam Noonan
- Australian Institute of Marine Science, PMB #3, Townsville MC, QLD 4810, Australia
| | - Craig Humphrey
- Australian Institute of Marine Science, PMB #3, Townsville MC, QLD 4810, Australia
| | - Aurelie Moya
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Bette L Willis
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Line K Bay
- Australian Institute of Marine Science, PMB #3, Townsville MC, QLD 4810, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
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123
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Heritable differences in fitness-related traits among populations of the mustard hill coral, Porites astreoides. Heredity (Edinb) 2015; 115:509-16. [PMID: 26081798 DOI: 10.1038/hdy.2015.52] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 04/07/2015] [Accepted: 04/21/2015] [Indexed: 11/08/2022] Open
Abstract
A population's potential for rapid evolutionary adaptation can be estimated from the amount of genetic variation in fitness-related traits. Inshore populations of the mustard hill coral (Porites astreoides) have been shown to be more tolerant to thermal stress than offshore populations, but it is unclear whether this difference is due to long-term physiological acclimatization or genetic adaptation. Here, we evaluated variation in growth rate and survival among 38 families of juvenile recruits of P. astreoides spawned by colonies originating from inshore and offshore locations. Recruits were reared in a common garden for 5 weeks and then subjected to two thermal treatments (28 and 31 °C) for 2.5 weeks. The most significant effects were detected during the first 5 weeks, before thermal stress was applied: 27-30% of variance in growth and 94% of variance in recruit survival was attributable to parental effects. Genotyping of eight microsatellite loci indicated that the high early mortality of some of the recruit families was not due to higher inbreeding. Post treatment, parental effects diminished such that only 10-15% of variance in growth rate was explained, which most likely reflects the dissipation of maternal effects. However, offshore-origin recruits still grew significantly less under elevated temperature compared with inshore-origin recruits. These differences observed in naive juvenile corals suggest that population-level variation in fitness in response to different thermal environments has a genetic basis and could represent raw material for natural selection in times of climate change.
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124
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Hopkinson BM, Tansik AL, Fitt WK. Internal carbonic anhydrase activity in the tissue of scleractinian corals is sufficient to support proposed roles in photosynthesis and calcification. ACTA ACUST UNITED AC 2015; 218:2039-48. [PMID: 25908060 DOI: 10.1242/jeb.118182] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/20/2015] [Indexed: 11/20/2022]
Abstract
Reef-building corals import inorganic carbon (Ci) to build their calcium carbonate skeletons and to support photosynthesis by the symbiotic algae that reside in their tissue. The internal pathways that deliver Ci for both photosynthesis and calcification are known to involve the enzyme carbonic anhydrase (CA), which interconverts CO2 and HCO3 (-). We have developed a method for absolute quantification of internal CA (iCA) activity in coral tissue based on the rate of (18)O-removal from labeled Ci. The method was applied to three Caribbean corals (Orbicella faveolata, Porites astreoides and Siderastrea radians) and showed that these species have similar iCA activities per unit surface area, but that S. radians has ∼10-fold higher iCA activity per unit tissue volume. A model of coral Ci processing shows that the measured iCA activity is sufficient to support the proposed roles for iCA in Ci transport for photosynthesis and calcification. This is the case even when iCA activity is homogeneously distributed throughout the coral, but the model indicates that it would be advantageous to concentrate iCA in the spaces where calcification (the calcifying fluid) and photosynthesis (the oral endoderm) take place. We argue that because the rates of photosynthesis and calcification per unit surface area are similar among the corals studied here, the areal iCA activity used to deliver Ci for these reactions should also be similar. The elevated iCA activity per unit volume of S. radians compared with that of the other species is probably due to the thinner effective tissue thickness in this species.
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Affiliation(s)
- Brian M Hopkinson
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| | - Anna L Tansik
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| | - William K Fitt
- School of Ecology, University of Georgia, Athens, GA 30602, USA
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125
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Porcelli D, Butlin RK, Gaston KJ, Joly D, Snook RR. The environmental genomics of metazoan thermal adaptation. Heredity (Edinb) 2015; 114:502-14. [PMID: 25735594 PMCID: PMC4815515 DOI: 10.1038/hdy.2014.119] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 11/06/2014] [Accepted: 11/11/2014] [Indexed: 01/07/2023] Open
Abstract
Continued and accelerating change in the thermal environment places an ever-greater priority on understanding how organisms are going to respond. The paradigm of ‘move, adapt or die', regarding ways in which organisms can respond to environmental stressors, stimulates intense efforts to predict the future of biodiversity. Assuming that extinction is an unpalatable outcome, researchers have focussed attention on how organisms can shift in their distribution to stay in the same thermal conditions or can stay in the same place by adapting to a changing thermal environment. How likely these respective outcomes might be depends on the answer to a fundamental evolutionary question, namely what genetic changes underpin adaptation to the thermal environment. The increasing access to and decreasing costs of next-generation sequencing (NGS) technologies, which can be applied to both model and non-model systems, provide a much-needed tool for understanding thermal adaptation. Here we consider broadly what is already known from non-NGS studies about thermal adaptation, then discuss the benefits and challenges of different NGS methodologies to add to this knowledge base. We then review published NGS genomics and transcriptomics studies of thermal adaptation to heat stress in metazoans and compare these results with previous non-NGS patterns. We conclude by summarising emerging patterns of genetic response and discussing future directions using these increasingly common techniques.
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Affiliation(s)
- D Porcelli
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - R K Butlin
- 1] Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK [2] Sven Lovén Centre-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - K J Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn, UK
| | - D Joly
- 1] Laboratoire Evolution, Génomes et Spéciation, CNRS-UPR 9034, Gif sur Yvette, France [2] Université Paris-Sud, Orsay, France
| | - R R Snook
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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126
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Studivan MS, Hatch WI, Mitchelmore CL. Responses of the soft coral Xenia elongata following acute exposure to a chemical dispersant. SPRINGERPLUS 2015; 4:80. [PMID: 25713766 PMCID: PMC4332917 DOI: 10.1186/s40064-015-0844-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 01/22/2015] [Indexed: 11/10/2022]
Abstract
Limited toxicology data are available regarding oil dispersant exposure to coral species. Corexit® EC9500A (Corexit) is a commonly applied dispersant most well known for its use after the Deepwater Horizon spill in April, 2010. There is limited evidence that Corexit can cause a bleaching response in corals. The aims of the study were: (1) to determine the extent of bleaching after acute 24 h and 72 h exposures of sublethal concentrations (0-50 ppm) of Corexit to the pulsing soft coral Xenia elongata and (2) to investigate a percent symbiont loss calculation using zooxanthellae density. The percent symbiont loss calculation was compared to a traditional metric of normalizing zooxanthellae density to soluble protein content. Percent symbiont loss was an effective measure of coral stress in acute Corexit exposures, while protein normalized zooxanthellae density was more variable. The bleaching data suggest a positive relationship between dispersant concentration and percent symbiont loss, culminating in excessive tissue necrosis and coral mortality within 72 h in high concentration exposures (p < 0.001). Percent beaching ranged from 25% in 5 ppm exposures to 100% in 50 ppm exposures. Corexit also caused a significant decrease in pulse activity (p < 0.0001) and relative oxygen saturation (p < 0.001), possibly indicating a reduction in photosynthetic efficiency. This study and other similar research indicate that dispersant exposure is highly damaging to marine organisms, including ecologically important coral species.
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Affiliation(s)
- Michael S Studivan
- />Department of Biology, St. Mary’s College of Maryland, 18952 E. Fisher Rd, 20686 St. Mary’s City, MD USA
- />Present Address: Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 N US Highway 1, 34946 Fort Pierce, FL USA
| | - Walter I Hatch
- />Department of Biology, St. Mary’s College of Maryland, 18952 E. Fisher Rd, 20686 St. Mary’s City, MD USA
| | - Carys L Mitchelmore
- />Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, PO Box 38, 20688 Solomons, MD USA
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127
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Abstract
Reef-building corals are vulnerable to heat stress and are facing widespread losses due to climate change. A new study shows that coral heat tolerance can result from selection on a suite of genes to maintain genetic flexibility.
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Affiliation(s)
- Andrew C Baker
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA.
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128
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Dixon GB, Bay LK, Matz MV. Bimodal signatures of germline methylation are linked with gene expression plasticity in the coral Acropora millepora. BMC Genomics 2014; 15:1109. [PMID: 25511458 PMCID: PMC4378018 DOI: 10.1186/1471-2164-15-1109] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/10/2014] [Indexed: 11/24/2022] Open
Abstract
Background In invertebrates, genes belonging to dynamically regulated functional categories appear to be less methylated than “housekeeping” genes, suggesting that DNA methylation may modulate gene expression plasticity. To date, however, experimental evidence to support this hypothesis across different natural habitats has been lacking. Results Gene expression profiles were generated from 30 pairs of genetically identical fragments of coral Acropora millepora reciprocally transplanted between distinct natural habitats for 3 months. Gene expression was analyzed in the context of normalized CpG content, a well-established signature of historical germline DNA methylation. Genes with weak methylation signatures were more likely to demonstrate differential expression based on both transplant environment and population of origin than genes with strong methylation signatures. Moreover, the magnitude of expression differences due to environment and population were greater for genes with weak methylation signatures. Conclusions Our results support a connection between differential germline methylation and gene expression flexibility across environments and populations. Studies of phylogenetically basal invertebrates such as corals will further elucidate the fundamental functional aspects of gene body methylation in Metazoa. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1109) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Groves B Dixon
- Institute for Cell and Molecular Biology, University of Texas Austin, Austin, USA.
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129
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Rosic N, Kaniewska P, Chan CKK, Ling EYS, Edwards D, Dove S, Hoegh-Guldberg O. Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 2014; 15:1052. [PMID: 25467196 PMCID: PMC4301396 DOI: 10.1186/1471-2164-15-1052] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 11/12/2014] [Indexed: 11/10/2022] Open
Abstract
Background Changes to the environment as a result of human activities can result in a range of impacts on reef building corals that include coral bleaching (reduced concentrations of algal symbionts), decreased coral growth and calcification, and increased incidence of diseases and mortality. Understanding how elevated temperatures and nutrient concentration affect early transcriptional changes in corals and their algal endosymbionts is critically important for evaluating the responses of coral reefs to global changes happening in the environment. Here, we investigated the expression of genes in colonies of the reef-building coral Acropora aspera exposed to short-term sub-lethal levels of thermal (+6°C) and nutrient stress (ammonium-enrichment: 20 μM). Results The RNA-Seq data provided hundreds of differentially expressed genes (DEGs) corresponding to various stress regimes, with 115 up- and 78 down-regulated genes common to all stress regimes. A list of DEGs included up-regulated coral genes like cytochrome c oxidase and NADH-ubiquinone oxidoreductase and up-regulated photosynthetic genes of algal origin, whereas coral GFP-like fluorescent chromoprotein and sodium/potassium-transporting ATPase showed reduced transcript levels. Taxonomic analyses of the coral holobiont disclosed the dominant presence of transcripts from coral (~70%) and Symbiodinium (~10-12%), as well as ~15-20% of unknown sequences which lacked sequence identity to known genes. Gene ontology analyses revealed enriched pathways, which led to changes in the dynamics of protein networks affecting growth, cellular processes, and energy requirement. Conclusions In corals with preserved symbiont physiological performance (based on Fv/Fm, photo-pigment and symbiont density), transcriptomic changes and DEGs provided important insight into early stages of the stress response in the coral holobiont. Although there were no signs of coral bleaching after exposure to short-term thermal and nutrient stress conditions, we managed to detect oxidative stress and apoptotic changes on a molecular level and provide a list of prospective stress biomarkers for both partners in symbiosis. Consequently, our findings are important for understanding and anticipating impacts of anthropogenic global climate change on coral reefs. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1052) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nedeljka Rosic
- School of Biological Sciences, The University of Queensland, Brisbane Qld 4072, Australia.
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130
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Maor-Landaw K, Karako-Lampert S, Waldman Ben-Asher H, Goffredo S, Falini G, Dubinsky Z, Levy O. Gene expression profiles during short-term heat stress in the red sea coral Stylophora pistillata. GLOBAL CHANGE BIOLOGY 2014; 20:3026-35. [PMID: 24706387 DOI: 10.1111/gcb.12592] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 02/09/2014] [Accepted: 02/10/2014] [Indexed: 05/21/2023]
Abstract
During the past several decades, corals worldwide have been affected by severe bleaching events leading to wide-spread coral mortality triggered by global warming. The symbiotic Red Sea coral Stylophora pistillata from the Gulf of Eilat is considered an opportunistic 'r' strategist. It can thrive in relatively unstable environments and is considered a stress-tolerant species. Here, we used a S. pistillata custom microarray to examine gene expression patterns and cellular pathways during short-term (13-day) heat stress. The results allowed us to identify a two-step reaction to heat stress, which intensified significantly as the temperature was raised to a 32 °C threshold, beyond which, coping strategies failed at 34 °C. We identified potential 'early warning genes' and 'severe heat-related genes'. Our findings suggest that during short-term heat stress, S. pistillata may divert cellular energy into mechanisms such as the ER-unfolded protein response (UPR) and ER-associated degradation (ERAD) at the expense of growth and biomineralization processes in an effort to survive and subsequently recover from the stress. We suggest a mechanistic theory for the heat stress responses that may explain the success of some species which can thrive under a wider range of temperatures relative to others.
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Affiliation(s)
- Keren Maor-Landaw
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
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131
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Shinzato C, Mungpakdee S, Satoh N, Shoguchi E. A genomic approach to coral-dinoflagellate symbiosis: studies of Acropora digitifera and Symbiodinium minutum. Front Microbiol 2014; 5:336. [PMID: 25071748 PMCID: PMC4083563 DOI: 10.3389/fmicb.2014.00336] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/17/2014] [Indexed: 12/16/2022] Open
Abstract
Far more intimate knowledge of scleractinian coral biology is essential in order to understand how diverse coral-symbiont endosymbioses have been established. In particular, molecular and cellular mechanisms enabling the establishment and maintenance of obligate endosymbiosis with photosynthetic dinoflagellates require further clarification. By extension, such understanding may also shed light upon environmental conditions that promote the collapse of this mutualism. Genomic data undergird studies of all symbiotic processes. Here we review recent genomic data derived from the scleractinian coral, Acropora digitifera, and the endosymbiotic dinoflagellate, Symbiodinium minutum. We discuss Acropora genes involved in calcification, embryonic development, innate immunity, apoptosis, autophagy, UV resistance, fluorescence, photoreceptors, circadian clocks, etc. We also detail gene loss in amino acid metabolism that may explain at least part of the Acropora stress-response. Characteristic features of the Symbiodinium genome are also reviewed, focusing on the expansion of certain gene families, the molecular basis for permanently condensed chromatin, unique spliceosomal splicing, and unusual gene arrangement. Salient features of the Symbiodinium plastid and mitochondrial genomes are also illuminated. Although many questions regarding these interdependent genomes remain, we summarize information necessary for future studies of coral-dinoflagellate endosymbiosis.
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Affiliation(s)
- Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan
| | - Sutada Mungpakdee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan
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132
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Wang J, Qi H, Li L, Que H, Wang D, Zhang G. Discovery and validation of genic single nucleotide polymorphisms in the Pacific oyster Crassostrea gigas. Mol Ecol Resour 2014; 15:123-35. [PMID: 24823694 DOI: 10.1111/1755-0998.12278] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 05/09/2014] [Accepted: 05/09/2014] [Indexed: 12/01/2022]
Abstract
The economic and ecological importance of the oyster necessitates further research on the molecular mechanisms, which both regulate the commercially important traits of the oyster and help it to survive in the variable marine environment. Single nucleotide polymorphisms (SNPs) have been widely used to assess genetic variation and identify genes underlying target traits. In addition, high-resolution melting (HRM) analysis is a potentially powerful method for validating candidate SNPs. In this study, we adopted a rapid and efficient pipeline for the screening and validation of SNPs in the genic region of Crassostrea gigas based on transcriptome sequencing and HRM analysis. Transcriptomes of three wild oyster populations were sequenced using Illumina sequencing technology. In total, 50-60 million short reads, corresponding to 4.5-5.4 Gbp, from each population were aligned to the oyster genome, and 5.8 × 10(5) SNPs were putatively identified, resulting in a predicted SNP every 47 nucleotides on average. The putative SNPs were unevenly distributed in the genome and high-density (≥2%), nonsynonymous coding SNPs were enriched in genes related to apoptosis and responses to biotic stimuli. Subsequently, 1,671 loci were detected by HRM analysis, accounting for 64.7% of the total selected candidate primers, and finally, 1,301 polymorphic SNP markers were developed based on HRM analysis. All of the validated SNPs were distributed into 897 genes and located in 672 scaffolds, and 275 of these genes were stress inducible under unfavourable salinity, temperature, and exposure to air and heavy metals. The validated SNPs in this study provide valuable molecular markers for genetic mapping and characterization of important traits in oysters.
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Affiliation(s)
- Jiafeng Wang
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Affiliated Hospital of Guangdong Medical College, Guangdong, 524001, China
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133
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Kenkel CD, Sheridan C, Leal MC, Bhagooli R, Castillo KD, Kurata N, McGinty E, Goulet TL, Matz MV. Diagnostic gene expression biomarkers of coral thermal stress. Mol Ecol Resour 2014; 14:667-78. [PMID: 24354729 DOI: 10.1111/1755-0998.12218] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/13/2013] [Accepted: 12/14/2013] [Indexed: 11/29/2022]
Abstract
Gene expression biomarkers can enable rapid assessment of physiological conditions in situ, providing a valuable tool for reef managers interested in linking organism physiology with large-scale climatic conditions. Here, we assessed the ability of quantitative PCR (qPCR)-based gene expression biomarkers to evaluate (i) the immediate cellular stress response (CSR) of Porites astreoides to incremental thermal stress and (ii) the magnitude of CSR and cellular homeostasis response (CHR) during a natural bleaching event. Expression levels largely scaled with treatment temperature, with the strongest responses occurring in heat-shock proteins. This is the first demonstration of a 'tiered' CSR in a coral, where the magnitude of expression change is proportional to stress intensity. Analysis of a natural bleaching event revealed no signature of an acute CSR in normal or bleached corals, indicating that the bleaching stressor(s) had abated by the day of sampling. Another long-term stress CHR-based indicator assay was significantly elevated in bleached corals, although assay values overall were low, suggesting good prospects for recovery. This study represents the first step in linking variation in gene expression biomarkers to stress tolerance and bleaching thresholds in situ by quantifying the severity of ongoing thermal stress and its accumulated long-term impacts.
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Affiliation(s)
- C D Kenkel
- Section of Integrative Biology, The University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA
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134
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Kenkel CD, Goodbody-Gringley G, Caillaud D, Davies SW, Bartels E, Matz MV. Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides) from different reef environments. Mol Ecol 2013; 22:4335-4348. [PMID: 23906315 DOI: 10.1111/mec.12391] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 05/06/2013] [Accepted: 05/08/2013] [Indexed: 11/27/2022]
Abstract
Studying the mechanisms that enable coral populations to inhabit spatially varying thermal environments can help evaluate how they will respond in time to the effects of global climate change and elucidate the evolutionary forces that enable or constrain adaptation. Inshore reefs in the Florida Keys experience higher temperatures than offshore reefs for prolonged periods during the summer. We conducted a common garden experiment with heat stress as our selective agent to test for local thermal adaptation in corals from inshore and offshore reefs. We show that inshore corals are more tolerant of a 6-week temperature stress than offshore corals. Compared with inshore corals, offshore corals in the 31 °C treatment showed significantly elevated bleaching levels concomitant with a tendency towards reduced growth. In addition, dinoflagellate symbionts (Symbiodinium sp.) of offshore corals exhibited reduced photosynthetic efficiency. We did not detect differences in the frequencies of major (>5%) haplotypes comprising Symbiodinium communities hosted by inshore and offshore corals, nor did we observe frequency shifts ('shuffling') in response to thermal stress. Instead, coral host populations showed significant genetic divergence between inshore and offshore reefs, suggesting that in Porites astreoides, the coral host might play a prominent role in holobiont thermotolerance. Our results demonstrate that coral populations inhabiting reefs <10-km apart can exhibit substantial differences in their physiological response to thermal stress, which could impact their population dynamics under climate change.
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Affiliation(s)
- C D Kenkel
- Section of Integrative Biology, The University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA
| | - G Goodbody-Gringley
- Bermuda Institute of Ocean Sciences, 17 Biological Lane, St. George, GE01, Bermuda.,Mote Marine Laboratory, 24244 Overseas Highway, Summerland Key, FL, 33042, USA
| | - D Caillaud
- Section of Integrative Biology, The University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA.,Dian Fossey Gorilla Fund International, 800 Cherokee Avenue, Atlanta, GA, 30315, USA
| | - S W Davies
- Section of Integrative Biology, The University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA
| | - E Bartels
- Mote Marine Laboratory, 24244 Overseas Highway, Summerland Key, FL, 33042, USA
| | - M V Matz
- Section of Integrative Biology, The University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA
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