Understanding differential heat tolerance of the threatened mountainous star coral Orbicella faveolata from inshore and offshore reef sites in the Florida Keys using gene network analysis
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ABSTRACT:
ORGANISM(S): Orbicella faveolata
PROVIDER: GSE225085 | GEO | 2024/02/06
REPOSITORIES: GEO
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Project description:Thirty-five Orbicella faveolata (scleractinian coral) proteins were labeled with iTRAQ technology and analyzed across five runs ("batches") of nano-liquid chromatography followed by mass spectrometry on a Q Exactive instrument. The samples represent a mix of corals that either were or were not reciprocally transplanted across shelves (inshore vs. offshore) in the Upper Florida Keys prior to a laboratory thermal challenge (tank) experiment. The goal of this project was to determine the molecular basis of thermotolerance in this common reef-builder as well as attempt to understand why inshore genotypes are typically more stress-tolerant than closely related offshore conspecifics.
2023-07-08 | MSV000092379 | MassIVE
Project description:Given the overwhelming evidence that symbiont genotypes differentially affect host processes such as growth, bleaching susceptibility, and nutrient acquisition, we set out to measure gene expression differences in fragments of Montastraea faveolata harboring two different clades of Symbiodinium. On the reefs near Puerto Morelos, México, colonies of M. faveolata are known to shift algal symbiont clade with depth, often associating with clade A at the top, clade B in the middle, and clade C near the bottom of the colony. By measuring photosynthetic efficiency and gene expression in control and heat-stressed fragments containing either clade B, clade C, or a mix of both, we found that: 1) the algal response to thermal stress is due to both host and algal factors; 2) fragments of M. faveolata express different genes in response to sub-bleaching thermal stress depending on algal genotype; 3) the overall effect of heat stress on coral gene expression is less significant than the effect of housing different zooxanthellae types. Overall, we present convincing evidence that different Symbiodinium clades may be functionally distinct, which in turn, greatly influences host gene expression. Six fragments (9.5 ± 3.5cm2) from the top (2.7m), middle (3.7m), and bottom (5.2m) of one massive colony of Montastraea faveolata were collected with a hammer and chisel at âLa Bocanaâ reef near Puerto Morelos, Quintana Roo, Mexico on 31 July 2007. The fragments were divided evenly between two aquaria (50L) that received a constant flow of seawater (~0.64L/min). Each aquarium was fit with a water pump connected to a spray-bar to provide constant water movement and aeration. Both aquaria were placed in a common pond with flowing water to buffer diurnal temperature fluctuations, and both aquaria were exposed to shaded ambient light. All coral fragments were mounted on plasticene and kept at a depth of ~7cm. From 10 to 19 August 2007 (acclimation #1), both aquaria received an average water temperature of 27.9 ± 0.6oC (as recorded by HOBO Light/Temperature Data Loggers by Onset Corp.). Effective quantum yield (ÎF/Fmâ) measurements were taken at noon, and maximum quantum yield (Fv/Fm) measurements were taken at dusk for all 18 coral fragments using a DIVING-PAM (Walz) beginning on 11 August. Photosynthetically active radiation (PAR) was measured at noon and averaged 318 ± 129 umol/m2/sec. From 20 to 21 August 2007, all coral fragments were brought inside during the passage of Hurricane Dean. On 22 August, the experiment was reconstituted, and a second acclimation period began on 23 August and lasted until 1 September. During this time, both aquaria received water at an average temperature of 28.5 ± 0.8oC, and PAR at an average of 371 ± 169 umol/m2/sec. On the night of 1 September, one 200-Watt aquarium heater was turned on in the treatment aquarium, and a second heater was turned on 3 days later. During the thermal stress experiment, the control aquarium received an average water temperature of 28.8 ± 1.2oC; the heated aquarium, 31.5 ± 1.1oC. PAR present during the thermal stress experiment averaged 420 ± 152 uE. On the night of 7 September, all fragments were frozen in liquid nitrogen. Eighteen total microarray hybridizations were performed. A reference RNA sample was created by pooling RNA from all 18 prepâs. All control and heat-stressed samples were competitively hybridized against the reference RNA to the M. faveolata microarray (1,310 features).
2010-05-18 | E-GEOD-12809 | biostudies-arrayexpress
Project description:Given the overwhelming evidence that symbiont genotypes differentially affect host processes such as growth, bleaching susceptibility, and nutrient acquisition, we set out to measure gene expression differences in fragments of Montastraea faveolata harboring two different clades of Symbiodinium. On the reefs near Puerto Morelos, México, colonies of M. faveolata are known to shift algal symbiont clade with depth, often associating with clade A at the top, clade B in the middle, and clade C near the bottom of the colony. By measuring photosynthetic efficiency and gene expression in control and heat-stressed fragments containing either clade B, clade C, or a mix of both, we found that: 1) the algal response to thermal stress is due to both host and algal factors; 2) fragments of M. faveolata express different genes in response to sub-bleaching thermal stress depending on algal genotype; 3) the overall effect of heat stress on coral gene expression is less significant than the effect of housing different zooxanthellae types. Overall, we present convincing evidence that different Symbiodinium clades may be functionally distinct, which in turn, greatly influences host gene expression.
2009-05-31 | GSE12809 | GEO
Project description:In this work, I took a proteome profiling approach to characterize the cellular biology of 16 coral samples from a laboratory-based thermal stress experiment. The specific goal of this work was to uncover proteins involved in the high-temperature response of the Caribbean reef coral Orbicella faveolata. Coral colonies from two inshore (Cheeca Rocks [UKI] & The Rocks [UKI2]) and one offshore reef (Little Conch [UKO2]) were cored in situ, with cores later brought to the “Experimental Reef Laboratory” housed at the University of Miami’s Rosenstiel School of Marine and Atmospheric Sciences (RSMAS). After laboratory acclimation, the samples were exposed to either 33°C for 5 days or 32°C days for 31 days, with control corals maintained at 30°C. Proteins were extracted from a subset of samples representing multiple coral genotypes exposed to the experimental treatment conditions for 5 or 31 days and sequenced with nano-liquid chromatography followed by mass spectrometry. In this submission, I have uploaded 16 RAW files generated by the mass spectrometer, 16 MZML (open-access mass spectrometry mass peak data) files, 16 MZID (open-access mass spectrometry results) files, and a tab-delineated file that describes which samples were analyzed ("Mayfield et al. online supplemental data file"). I have also uploaded the supplemental material that accompanies the Mayfield et al. (2021) article since that is what readers interested in the specifics of the proteomic analysis pipeline should consult. The peak data were queried against both conceptually translated Orbicella faveolata and Symbiodiniaceae dinoflagellate transcriptomes; both fasta files have been uploaded.
| MSV000086098 | MassIVE
Project description:Corals rely on a symbiosis with dinoflagellate algae (Symbiodinium spp.) to thrive in nutrient poor tropical oceans. However, the coral-algal symbiosis can break down during bleaching events, potentially leading to coral death. While genome-wide expression studies have shown the genes associated with the breakdown of this partnership, the full conglomerate of genes responsible for the establishment and maintenance of a healthy symbiosis remains unknown. Results from previous studies suggested little transcriptomic change associated with the establishment of symbiosis. In order to elucidate the transcriptomic response of the coral host in the presence of its associated symbiont, we utilized a comparative framework. Post-metamorphic aposymbiotic coral polyps of Orbicella faveolata were compared to symbiotic coral polyps 9 days after metamorphosis and the subsequent differential gene expression between control and treatment was quantified using cDNA microarray technology. Coral polyps exhibited differential expression of genes associated with nutrient metabolism and development, providing insight into pathways turned as a result of symbiosis driving early polyp growth. Furthermore, genes associated with lysosomal fusion were also upregulated, suggesting host regulation of symbiont densities soon after infection.
2016-12-22 | GSE92695 | GEO
Project description:The declining health of coral reefs worldwide is likely to intensify in response to continued anthropogenic disturbance from coastal development, pollution, and climate change. In response to these stresses, reef-building corals may exhibit bleaching, which marks the breakdown in symbiosis between coral and zooxanthellae. Mass coral bleaching due to elevated water temperature can devastate coral reefs on a large geographic scale. In order to understand the molecular and cellular basis of bleaching in corals, we have measured gene expression changes associated with thermal stress and bleaching using a cDNA microarray containing 1,310 genes of the Caribbean coral Montastraea faveolata. In a first experiment, we identified differentially expressed genes by comparing experimentally bleached M. faveolata fragments to control non-heat-stressed fragments. We also identified differentially expressed genes during a time course experiment with four time points across nine days. Results suggest that thermal stress and bleaching in M. faveolata affect the following processes: oxidative stress, Ca2+ homeostasis, cytoskeletal organization, cell death, calcification, metabolism, protein synthesis, heat shock protein activity, and transposon activity. These results represent the first large-scale transcriptomic study focused on revealing the cellular foundation of thermal stress-induced coral bleaching. We postulate that oxidative stress in thermal-stressed corals causes a disruption of Ca2+ homeostasis, which in turn leads to cytoskeletal and cell adhesion changes, decreased calcification, and the initiation of cell death via apoptosis and necrosis. Keywords: thermal stress response; coral bleaching 5 control and 5 heat-stressed RNA samples were hybridized in a 5-replicate dye-swap design (10 total hyb's).
2008-05-31 | E-GEOD-10630 | biostudies-arrayexpress
Project description:The declining health of coral reefs worldwide is likely to intensify in response to continued anthropogenic disturbance from coastal development, pollution, and climate change. In response to these stresses, reef-building corals may exhibit bleaching, which marks the breakdown in symbiosis between coral and zooxanthellae. Mass coral bleaching due to elevated water temperature can devastate coral reefs on a large geographic scale. In order to understand the molecular and cellular basis of bleaching in corals, we have measured gene expression changes associated with thermal stress and bleaching using a cDNA microarray containing 1,310 genes of the Caribbean coral Montastraea faveolata. In a first experiment, we identified differentially expressed genes by comparing experimentally bleached M. faveolata fragments to control non-heat-stressed fragments. We also identified differentially expressed genes during a time course experiment with four time points across nine days. Results suggest that thermal stress and bleaching in M. faveolata affect the following processes: oxidative stress, Ca2+ homeostasis, cytoskeletal organization, cell death, calcification, metabolism, protein synthesis, heat shock protein activity, and transposon activity. These results represent the first large-scale transcriptomic study focused on revealing the cellular foundation of thermal stress-induced coral bleaching. We postulate that oxidative stress in thermal-stressed corals causes a disruption of Ca2+ homeostasis, which in turn leads to cytoskeletal and cell adhesion changes, decreased calcification, and the initiation of cell death via apoptosis and necrosis. Keywords: thermal stress response, time course, coral bleaching Time course with 4 time points and 4 biological replicates per time point. Each biological replicate at each time point was hybridized to a pooled reference control sample containing RNA from all control non-heat-stressed coral fragments.
2008-05-31 | E-GEOD-10632 | biostudies-arrayexpress
Project description:The declining health of coral reefs worldwide is likely to intensify in response to continued anthropogenic disturbance from coastal development, pollution, and climate change. In response to these stresses, reef-building corals may exhibit bleaching, which marks the breakdown in symbiosis between coral and zooxanthellae. Mass coral bleaching due to elevated water temperature can devastate coral reefs on a large geographic scale. In order to understand the molecular and cellular basis of bleaching in corals, we have measured gene expression changes associated with thermal stress and bleaching using a cDNA microarray containing 1,310 genes of the Caribbean coral Montastraea faveolata. In a first experiment, we identified differentially expressed genes by comparing experimentally bleached M. faveolata fragments to control non-heat-stressed fragments. We also identified differentially expressed genes during a time course experiment with four time points across nine days. Results suggest that thermal stress and bleaching in M. faveolata affect the following processes: oxidative stress, Ca2+ homeostasis, cytoskeletal organization, cell death, calcification, metabolism, protein synthesis, heat shock protein activity, and transposon activity. These results represent the first large-scale transcriptomic study focused on revealing the cellular foundation of thermal stress-induced coral bleaching. We postulate that oxidative stress in thermal-stressed corals causes a disruption of Ca2+ homeostasis, which in turn leads to cytoskeletal and cell adhesion changes, decreased calcification, and the initiation of cell death via apoptosis and necrosis. Keywords: thermal stress response; coral bleaching
2008-05-31 | GSE10630 | GEO
Project description:The declining health of coral reefs worldwide is likely to intensify in response to continued anthropogenic disturbance from coastal development, pollution, and climate change. In response to these stresses, reef-building corals may exhibit bleaching, which marks the breakdown in symbiosis between coral and zooxanthellae. Mass coral bleaching due to elevated water temperature can devastate coral reefs on a large geographic scale. In order to understand the molecular and cellular basis of bleaching in corals, we have measured gene expression changes associated with thermal stress and bleaching using a cDNA microarray containing 1,310 genes of the Caribbean coral Montastraea faveolata. In a first experiment, we identified differentially expressed genes by comparing experimentally bleached M. faveolata fragments to control non-heat-stressed fragments. We also identified differentially expressed genes during a time course experiment with four time points across nine days. Results suggest that thermal stress and bleaching in M. faveolata affect the following processes: oxidative stress, Ca2+ homeostasis, cytoskeletal organization, cell death, calcification, metabolism, protein synthesis, heat shock protein activity, and transposon activity. These results represent the first large-scale transcriptomic study focused on revealing the cellular foundation of thermal stress-induced coral bleaching. We postulate that oxidative stress in thermal-stressed corals causes a disruption of Ca2+ homeostasis, which in turn leads to cytoskeletal and cell adhesion changes, decreased calcification, and the initiation of cell death via apoptosis and necrosis. Keywords: thermal stress response, time course, coral bleaching
2008-05-31 | GSE10632 | GEO
Project description:A mutualistic relationship between reef-building corals and endosymbiotic algae (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. If, and to what extent, differences in algal symbiont clade contents can exert effects on the coral host transcriptome is currently unknown. In this study, we monitored algal physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered coral fragments using a custom cDNA gene expression microarray. Combining these analyses with results from algal and host genotyping revealed a striking symbiont effect on both the acclimated coral host transcriptome and the magnitude of the thermal stress response. This is the first study that links coral host transcriptomic patterns to the clade content of their algal symbiont community. Our data provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-algal partnerships. Sample Collection and Tank Experiment. On July 31 2007, six replicate fragments (9.5 ± 3.5cm2) were collected using hammer and chisel from the upper sun-exposed surface of five different, healthy-looking Montastraea faveolata colonies near Puerto Morelos, Quintana Roo, México (20o52â28.77âN and 86o51â04.53âW). The fragments were transported to the institute within 1 h and divided evenly between two 50 L aquaria (i.e., 3 fragments from each colony were placed into each tank) that received a constant flow of seawater (0.6 L/min). Each aquarium was fit with a water pump connected to a spray-bar to provide constant water movement and aeration. Both aquaria were placed in a common pond with flowing water to buffer diurnal temperature fluctuations, and both aquaria were acclimated to the same shaded ambient light condition. All coral fragments were mounted on plasticene and kept at a depth of 7 cm. From 10 to 19 August 2007, both aquaria received an average water temperature of 27.9 ± 0.6oC (as recorded by HOBO Light/Temperature Data Loggers, Onset Corp.). Beginning on 11 August, dark-adapted maximum quantum yields for charge separation (Fv/Fm) were measured at dusk for all coral fragments using a DIVING-Pulse Amplitude Modulated (PAM) fluorometer (Walz, Germany). Photosynthetically active radiation (PAR) was measured at noon and averaged 318 ± 129 µmol m-2 s-1. From 20 to 21 August 2007, all coral fragments were brought inside during the passage of Hurricane Dean. On 22 August, the experiment was reconstituted, and acclimation continued on 23 August and lasted until 1 September. During this time, both aquaria received a mean water temperature of 28.5 ± 0.8oC, and mean PAR of 371 ± 169 µmol m-2 s-1. On the night of 1 September, control time point samples from five different colonies were collected from each tank (Figure 1), before one 200-Watt aquarium heater was turned on in the treatment aquarium. A second heater was turned on 3 days later. During the thermal stress experiment, the control aquarium received mean water temperature of 28.8 ± 1.2oC; the heated aquarium, 31.5 ± 1.1oC. During the thermal stress experiment, tanks received mean PAR of 420 ± 152 µmol m-2 s-1. On 11 September, and 19 October, one sample each from five different colonies was collected from each tank for the bleaching and recovery time point, respectively. Microarray Gene Expression Analysis of Coral Host Gene Expression. For the biologically replicated time series experiment, a pool of RNA from all control tank fragments was used as a reference RNA sample, against which each sample from the treatment tank was competitively hybridized. All control and heat-stressed samples were competitively hybridized against the reference RNA. Dye swaps were not performed, as any dye bias present is equal in all comparisons to the reference. Note: Samples VALUEs used for statistical analysis of differential expression. GSE15253_shini_cbr_matrix2_norm.txt used for hierarchical clustering.
2010-05-18 | E-GEOD-15253 | biostudies-arrayexpress