Microbiome dynamics of coral reefs, Stony Coral Tissue Loss Disease, and reef fish
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA986867 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25022300_1.fastq.gz | Fastqsanger.gz | |||
| SRR25022300_2.fastq.gz | Fastqsanger.gz | |||
| SRR25022400_1.fastq.gz | Fastqsanger.gz | |||
| SRR25022400_2.fastq.gz | Fastqsanger.gz | |||
| SRR25022301_1.fastq.gz | Fastqsanger.gz |
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Project description:Florida’s coral reefs are currently experiencing a multi-year disease-related mortality event, that has resulted in massive die-offs in multiple coral species. Approximately 21 species of coral, including both Endangered Species Act-listed and the primary reef-building species, have displayed tissue loss lesions which often result in whole colony mortality [Stony Coral Tissue Loss Disease (SCTLD)]. Determining the causative agent(s) of coral disease relies on a multidisciplinary approach since the causation may be a combination of abiotic, microbial or viral agents. Metaproteomics was used to survey changes in the molecular landscape in the coral holobiont with the goal of providing useful information not only in diagnosis, but for prediction and prognosis. Specifically, in the case of SCTLD, defining molecular changes in the coral holobiont will help define disease progression and aid in identifying the causative agent by clearly defining traits of disease progression shared across affected species. Using samples from nine coral species (46 samples total; those appearing healthy, n = 23, and diseased, n = 23), analysis of the coral and its associated microbiome were performed using bottom-up proteomics. Ongoing analysis (including improving coral holobiont genome-based search space) will demonstrate the utility of this approach and help define improved future experiments.
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Project description:Florida’s coral reefs are currently experiencing a multi-year disease-related mortality event, that has resulted in massive die-offs in multiple coral species. Coral monitoring data and disease prevention/treatment efforts from recent years have identified individual Orbicella faveolata that possess high, moderate, or low resistance to stony coral tissue loss disease (SCTLD). Ninety samples of high, moderate, or low SCTLD resistance were collected from 3 reefs for bottom-up LC-MS/MS analysis (n=30 for each resistance category).
2022-01-13 | PXD030923 | Pride
Project description:Transcriptional profiling of gene responses in liver in the coral reef fish Pomacentrus moluccensis in response to different types of environmental stress: cold, heat, hypoxic and hyposmotic shock. Goal was to determine the common effects of different types of environmental stress on gene expression as well as responses unique to different stressors. Abstract from Kassahn et al. BMC Genomics (2007) 8:358 Background While our understanding of the importance of transcriptional regulation for biological function is continuously growing, we still know comparatively little about how environmentally-induced stress affects gene expression in vertebrates and how consistent transcriptional stress responses are across different types of environmental stress. Results In this study, we looked for a genetic measure of environmental stress and used a multi-stressor approach to identify components of a common stress response as well as components unique to different types of environmental stress. We exposed individuals of the coral reef fish Pomacentrus moluccensis to hypoxic, hyposmotic, cold and heat shock and measured the responses of approximately 16,000 genes in liver. We also compared winter and summer responses to heat shock to examine the capacity for such responses to vary with acclimation to different ambient temperatures. We identified a series of gene functions that were consistently involved in all stress responses examined here, suggesting common effects of stress on biological function. These common responses were achieved by the regulation of largely independent sets of genes and the responses of individual genes varied greatly across different stress types. However, we were able to identify groups of co-regulated genes, the genes within which shared similar functions. Given current estimates of climatic change, we were particularly interested in the response to prolonged heat exposure. In total, 324 gene loci were differentially expressed following exposure to heat over five days. The functions of these heat-responsive genes suggest that prolonged heat stress leads to oxidative stress and protein damage, challenge of the immune system, and a re-allocation of energy sources. Conclusion This is the first environmental genomic study to measure gene regulation in response to different environmental stressors in a natural population of a warm-adapted ectothermic vertebrate. This study offers insight into the effects of environmental stress on biological function and sheds light on the expected sensitivity of coral reef fishes to elevated temperatures in the future. Keywords: Stress response
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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.
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Project description:Coral Reef Stony Coral Tissue Loss Disease Microbiomes in Coral Tissue and Near-Coral Seawater
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Project description:Construction of a comprehensive spectral library for the coral reef fish, Acanthochromis polyacanthus, from both DIA and DDA MS runs. The spectral library was then used to quantify proteomes of individual fish exposed to different environmental conditions including ocean acidification and ocean warming. Proteomes were measured for both liver and brain tissue and differential expression between environmental conditions was analyzed.
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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.
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Project description:<p>Benthic organisms sustain coral reefs through their growth and metabolism, but less is known about how their released metabolites influence reef seawater microorganisms. To investigate metabolite composition of benthic exudates and their ecological significance for reef microbial communities, we harvested exudates from six species of Caribbean benthic organisms including stony corals, octocorals, and an invasive encrusting algae, and subjected these exudates to untargeted and targeted metabolomics approaches using liquid chromatography-mass spectrometry. Incubations with reef seawater microorganisms were conducted to monitor changes in microbial community composition using 16S rRNA gene sequencing and abundance in relation to exudate source and three specific metabolites. Exudates tended to be enriched in amino acids, nucleosides, and vitamins, indicating that benthic organisms contribute labile organic matter to reefs. The phytohormone indole-3-acetic acid was detected in octocoral exudates, suggesting that this metabolite facilitates microbial interactions within and outside of benthic organisms. Exudate compositions were species-specific and significantly enriched in the indole class of metabolites. Microbial abundances and specific microbial taxa responded differently in relation to exudates from stony corals and octocorals, demonstrating the link between benthic organismal composition, metabolite exudates, and microbial growth. Conversely, microbial communities did not respond to additions of the individual metabolites, suggesting that reef microorganisms likely provide diverse metabolite pools that support microbial growth. This work provides novel information about the metabolites released from common Caribbean benthic organisms and indicates that the recent shifts in benthic composition from stony to octocorals alter exudate composition and likely impact microbial community composition and function on coral reefs.</p><p><br></p><p><strong>UPLC-MS Metabolite collection incubation assays</strong> are reported in the current study <strong>MTBLS2855</strong></p><p><strong>UPLC-MS Metabolite uptake incubation assay</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/editor/study/MTBLS3286' rel='noopener noreferrer' target='_blank'><strong>MTBLS3286</strong></a></p>
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