Coral-associated bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA527938 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8751250_1.fastq.gz | Fastqsanger.gz | |||
| SRR8751250_2.fastq.gz | Fastqsanger.gz | |||
| SRR8751260_1.fastq.gz | Fastqsanger.gz | |||
| SRR8751260_2.fastq.gz | Fastqsanger.gz | |||
| SRR8751270_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Bacteria associated with early life stages of the coral Acropora tenuis
| PRJNA517286 | ENA
Project description:Purpose: There is a dearth of knowledge regarding the molecular pathology of growth anomaly in corals. We investigated the gene expression profile of Montipora capitata metatranscriptomes from healthy and diseased (growth anomaly) coral colonies to elucidate differentially expressed genes. Methods: mRNA profiles of coral tissue (including symbionts) were generated from three different tissue states: healthy, affected and unaffected. Healthy tissue was collected from coral colonies not affected by growth anomaly. Affected tissue was collected from coral growth anomaly lesions. Unaffected tissue was collected from coral colonies affected by growth anomaly.
2017-06-20 | GSE97888 | GEO
Project description:Coral reefs are declining globally. Temperature anomalies disrupt coral-algal symbioses at the molecular level, causing bleaching and mortality events. In terrestrial mutualisms, diversity in pairings of host and symbiont individuals (genotypes) results in ecologically and evolutionarily relevant stress response differences. The extent to which such intraspecific diversity provides functional variation in coral-algal systems is unknown. Here we assessed functional diversity among unique pairings of coral and algal individuals (holobionts). We targeted six genetically distinct Acropora palmata coral colonies that all associated with a single, clonal Symbiodinium ‘fitti’ strain in a natural common garden. No other species of algae or other strains of S. ‘fitti’ could be detected in host tissues. When colony branches were experimentally exposed to cold stress, host genotype influenced the photochemical efficiency of the symbiont strain, buffering the stress response to varying degrees. Gene expression differences among host individuals with buffered vs. non-buffered symbiont responses included biochemical pathways that mediate iron availability and oxygen stress signaling—critical components of molecular interactions with photosynthetic symbionts. Spawning patterns among hosts reflected symbiont performance differences under stress. These data are some of the first to indicate that genetic interactions below the species level affect coral holobiont performance. Intraspecific diversity serves as an important but overlooked source of physiological variation in this system, contributing raw material available to natural selection. Note: in the final publication, only ambient and cold treatments are discussed, but there was an additional hot treatment for each genotype at 34C. Most colonies expired after 6 hours, so PAM data could not be collected. The microarray data from 3.5 hours are included here.
2015-10-01 | GSE50926 | GEO
Project description:Publication Abstract: As climate changes, sea surface temperature anomalies that negatively impact coral reef organisms continue to increase in frequency and intensity. Yet, despite widespread coral mortality, genetic diversity remains high even in those coral species listed as threatened. While this is good news in many ways it presents a challenge for the development of biomarkers that can identify resilient or vulnerable genotypes. Taking advantage of three coral restoration nurseries in Florida that serve as long-term common garden experiments, we exposed over thirty genetically distinct Acropora cervicornis colonies to hot and cold temperature shocks seasonally and measured pooled gene expression responses using RNAseq. Targeting a subset of twenty genes, we designed a high-throughput qPCR array to quantify expression in all individuals separately under each treatment with the goal of identifying predictive and/or diagnostic thermal stress biomarkers. We observed extensive transcriptional variation in the population, suggesting abundant raw material is available for adaptation via natural selection. However, this high variation made it difficult to correlate gene expression changes with colony performance metrics such as growth, mortality, and bleaching susceptibility. Nevertheless, we identified several promising diagnostic biomarkers for acute thermal stress that may improve coral restoration and climate change mitigation efforts in the future.
2017-12-21 | GSE108338 | GEO
Project description:This experiment assessed the natural gene expression variation present between colonies of the Indo-Pacific reef-building coral Acropora millepora, and additionally explored whether gene expression differed between two different intron haplotypes according to intron 4-500 in a carbonic anhydrase homolog. This study found no correspondence between host genotype and transcriptional state, but found significant intercolony variation, detecting 488 representing unique genes or 17% of the total genes analyzed. Such transcriptomic variation could be the basis upon which natural selection can act. Underlying variation could potentially allow reef corals to respond to different environments. Whether this source of variation and the genetic responses of corals and its symbionts will allow coral reefs to cope to the rapid pace of global change remains unknown. A. millepora colonies were brought to a common garden in the reef lagoon, i.e. under the same environmental conditions. This common garden combined with acclimatization removes environmental effects on the physiology of the coral colonies. For the comparison of the two intron haplotypes, we applied a multiple dye-swap microarray design for the two groups of coral colonies (N=3 per group) defined based on the two genotypes resolved with the use of intron 4-500 (Fig. 1). To also examine the intra-haplotype variation we added a loop design nested to the above multiple dye-swap design, where three samples per colony were included. Colonies 1, 2, and 3 are of intron 4-500 haplotype 1; colonies 4, 5, and 6 are haplotype 2.
2013-04-08 | E-GEOD-42684 | biostudies-arrayexpress
Project description:Corals continuously adjust to short term variation in light availability on shallow reefs. Long-term light alterations can also occur due to natural and anthropogenic stressors, as well as management interventions such as coral transplantation. Although short term photophysiological responses are relatively well-understood in corals, little information is available regarding photoacclimation dynamics over weeks of altered light availability. We coupled photophysiology and metabolomic profiling to explore changes that accompany longer-term photoacclimation in a key Great Barrier Reef coral species (Acropora muricata). High (HL) and low light (LL) acclimated corals were collected from the reef and reciprocally exposed to high and low light ex situ. Rapid light curves using Pulse Amplitude Modulation (PAM) fluorometry revealed photophysiological acclimation of LL to HL and HL to LL shifted corals within 21 days. A subset of colonies sampled at 7 and 21 days for untargeted LC-MS and GC-MS metabolomic profiling revealed metabolic reorganization before acclimation was detected using PAM fluorometry. Metabolomic shifts were more pronounced for LL to HL treated corals than their HL to LL counterparts. Compounds driving metabolomic separation between HL-exposed and LL control colonies included amino acids, organic acids, fatty acids and sterols. Reduced glycerol and campesterol suggest decreased translocation of photosynthetic products from symbiont to host in LL to HL shifted corals, with concurrent increases in fatty acid abundance indicating reliance on stored lipids for energy. We discuss how these data provide novel insight into environmental regulation of metabolism and implications for management strategies that drive rapid changes in light availability.
2019-04-11 | MTBLS768 | MetaboLights
Project description:The emergence of genomic tools for reef-building corals and symbiotic anemones comes at a time when alarming losses in coral cover are being observed worldwide. These tools hold great promise in elucidating novel and unforeseen cellular processes underlying the successful mutualism between corals and their algal endosymbionts (Symbiodinium spp.). Since thermal stress triggers a breakdown in the symbiosis (coral bleaching), measuring the transcriptomic response to thermal stress-induced bleaching offers an extraordinary view of the cellular processes specific to coral-algal symbioses. In the present study, we utilized a cDNA microarray containing 2,059 genes of the Caribbean Elkhorn coral Acropora palmata to identify genes differentially expressed upon thermal stress. Fragments from four separate colonies were exposed to elevated temperature (3˚C increase) for two days, and samples were frozen for microarray analysis after 24 and 48 hours. Fragments experienced a 60% reduction in algal cell density after two days. 204 genes were differentially expressed in samples collected one day after thermal stress; in samples collected after two days, 104 genes. Annotations of the differentially expressed genes indicate a conserved cellular stress response in A. palmata involving: 1) growth arrest; 2) chaperone activity; 3) nucleic acid stabilization and repair; and 4) the removal of damaged macromolecules. Other differentially expressed processes include sensory perception, metabolite transfer between host and symbiont, nitric oxide signaling, and modifications to the actin cytoskeleton and extracellular matrix. The results are also compared to those from a previous coral microarray study of thermal stress in Montastraea faveolata.
2009-10-31 | GSE16151 | GEO
Project description:Similar to many marine invertebrates, scleractinian corals experience a dramatic morphological transformation, as well as a habitat switch, upon settlement and metamorphosis. At this time, planula larvae transform from non-calcifying, demersal, motile organisms into sessile, calcifying, benthic juvenile polyps. We performed a gene expression microarray analysis between planulae, aposymbiotic primary polyps, and symbiotic adult tissue to elucidate the molecular mechanisms underlying coral metamorphosis and early stages of calcification in the Robust/Short clade scleractinian coral Montastraea faveolata. Among the annotated genes, the most abundant upregulated transcripts in the planula stage are involved in protein synthesis, chromatin assembly and mitochondrial metabolism; the polyp stage, morphogenesis, protein catabolism and organic matrix synthesis; and the adult stage, sexual reproduction, stress response and symbiosis. Additionally, our results indicate that metamorphosis in M. faveolata planulae is likely regulated by: 1) a mechanism that resembles that described for hydrozoan cnidarians involving the neuropeptide LWamide; and 2) conserved cell adhesion and apoptosis mechanisms. Our results also suggest that calicoblast differentiation pathways may be regulated by transforming growth factors from the BMP family and Notch signalling pathway. We also present evidence showing that the planula and adult transcriptomes are more similar to each other than to the polyp trancriptome. Lastly, our results point to a large number of uncharacterized adult coral-specific genes likely involved in coral-specific functions such as symbiosis and calcification.
2009-05-06 | GSE15962 | 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