Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1124250 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29449433_1.fastq.gz | Fastqsanger.gz | |||
| SRR29449433_2.fastq.gz | Fastqsanger.gz | |||
| SRR29449434_1.fastq.gz | Fastqsanger.gz | |||
| SRR29449434_2.fastq.gz | Fastqsanger.gz | |||
| SRR29449435_1.fastq.gz | Fastqsanger.gz |
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Project description:The Crown-of-Thorns starfish (COTS), Acanthaster planci, is a highly fecund predator of reef-building corals distributed throughout the Indo-Pacific. COTS population outbreaks cause substantial loss of coral cover, diminishing the integrity and resilience of the reef ecosystems thus increasing their susceptibility to climate change. We sequenced genomes of A. planci from the Great Barrier Reef, Australia (GBR) and Okinawa, Japan (OKI) to guide identification of species-specific peptide communication with potential applications in mitigation strategies. The genome-encoded proteins excreted and secreted into the surrounding seawater by COTS forming aggregations and by those escaping the predatory giant triton snail, Charonia tritonis, were identified LC-MS/MS.
2017-04-06 | PXD005409 | Pride
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>
2022-08-22 | MTBLS2855 | MetaboLights
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 identifies, quantifies, and compares metabolites released from common Caribbean benthic organisms and indicates that 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 uptake incubation assay</strong> is reported in the current study <strong>MTBLS3286</strong></p><p><strong>UPLC-MS Metabolite collection incubation assays</strong> are reported in <a href='https://www.ebi.ac.uk/metabolights/editor/study/MTBLS2855' rel='noopener noreferrer' target='_blank'><strong>MTBLS2855</strong></a></p>
2022-08-22 | MTBLS3286 | MetaboLights
Project description:Increasing seawater’s calcium concentration has shown to increase reef building (scleractinian) coral’s calcification rates. In this way the expression of the genes that are associated with the calcification process also altered and, thus can be identified. Needless to say that the overall gene repertoire that participate in the coral calcification process and its molecular mechanisms have not yet been revealed, although sporadic genes that are related to the process have been discovered and investigated. In this study, nubbins of the Red Sea scleractinian coral, Stylophora pistillata were treated with increased calcium concentrations seawater (addition of 100 gm/L) and the genes that have been up-regulated were compared to the genes expression profile of corals with natural seawater calcium concentration. Measurements of AT were taken at mid-day (11:00) and in nighttime (23:00), to record the calcification rates of coral individuals under normal and increased calcium seawater concentrations. In order to reveal the gene involved in the calcification process, S. pistillata fragments of normal and of increased calcium concentrations were sampled for microarray RNA transcriptional profiling at two time-points (mid-day and nighttime).Results of this study have revealed that Smad genes may play a role in the coral skeletal growth apparatus. This study show that the calcification molecular mechanism is conserved Among identified genes are large group of genes that are characterized in the TGF-b/BMP signal transduction pathways which have been revealed in other organisms to participate in bone and cartilage tissue development molecular processes.
2017-06-29 | GSE87159 | GEO
Project description:Coral disease is one of the major causes of reef degradation and therefore of concern to management and conservation efforts. Dark Spot Syndrome (DSS) was described in the early 1990’s as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease, since they can also be caused by physical injury in some species. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two geographic locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies with normal pigmentation and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip™ G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, however the amplicon pools were overwhelmed by coral 18S rRNA genes from S. siderea. Unlike a similar study on a white-plague-like disease, S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the healthy scleractinian coral S. siderea. 17 samples, coral tissue punches from healthy and also from dark-spot-affected Siderastrea Siderea coral in the Virgin Islands and the Dry Tortugas National Parks was collected for comparison of associated bacterial communities
2014-09-30 | E-GEOD-60622 | biostudies-arrayexpress
Project description:Background. Coral reef communities are undergoing marked declines due to a variety of stressors including climate change, eutrophication, sedimentation, and disease. The sea fan coral, Gorgonia ventalina, is a tractable study system to investigate the hypothesis that stressors compromise immunity and lead to onset of disease. Functional studies in Gorgonia ventalina immunity indicate that several key pathways and cellular responses are involved in response to natural microbial invaders, although to date the functional and regulatory pathways remain largely un-neffectors, the primary line of defense in invertebrates. This study used short-read sequencing (Illumina GAIIx) to identify genes involved in the response of G. ventalina to a naturally occurring Aplanochytrium spp. parasite. Results. De novo assembly of the G. ventalina transcriptome yielded 90,230 contigs of which 40, 142 were annotated. RNA-Seq analysis revealed 210 differentially expressed genes in sea fans exposed to the Aplanochytrium parasite. Differentially expressed genes involved in immunity include pattern recognition molecules, anti-microbial peptides, wound repair, and reactive oxygen species. Gene enrichment analysis indicated eight biological processes were enriched representing 36 genes, largely involved with protein translation and energy production. Conclusions. This is the first report using high-throughput sequencing to characterize the host response of a coral to a natural pathogen. Furthermore, we have generated the first transcriptome for a soft coral species. G. ventalina is a non-model species for which few sequences had been previously described, and we were able to annotate a large number of genes and describe their potential roles in immune function. Expression analysis revealed genes important in invertebrate innate immune pathways, as well as those whose role is previously un-described in cnidarians. This resource will be valuable in characterizing G. ventalina immune response to infection and co-infection of pathogens in the context of environmental change. RNA seq experiment using Illumina GAIIx to compare sea fans exposed to an Aplanochytrium species compared to controls
2012-08-17 | E-GEOD-40169 | biostudies-arrayexpress
Project description:Background. Coral reef communities are undergoing marked declines due to a variety of stressors including climate change, eutrophication, sedimentation, and disease. The sea fan coral, Gorgonia ventalina, is a tractable study system to investigate the hypothesis that stressors compromise immunity and lead to onset of disease. Functional studies in Gorgonia ventalina immunity indicate that several key pathways and cellular responses are involved in response to natural microbial invaders, although to date the functional and regulatory pathways remain largely un-neffectors, the primary line of defense in invertebrates. This study used short-read sequencing (Illumina GAIIx) to identify genes involved in the response of G. ventalina to a naturally occurring Aplanochytrium spp. parasite. Results. De novo assembly of the G. ventalina transcriptome yielded 90,230 contigs of which 40, 142 were annotated. RNA-Seq analysis revealed 210 differentially expressed genes in sea fans exposed to the Aplanochytrium parasite. Differentially expressed genes involved in immunity include pattern recognition molecules, anti-microbial peptides, wound repair, and reactive oxygen species. Gene enrichment analysis indicated eight biological processes were enriched representing 36 genes, largely involved with protein translation and energy production. Conclusions. This is the first report using high-throughput sequencing to characterize the host response of a coral to a natural pathogen. Furthermore, we have generated the first transcriptome for a soft coral species. G. ventalina is a non-model species for which few sequences had been previously described, and we were able to annotate a large number of genes and describe their potential roles in immune function. Expression analysis revealed genes important in invertebrate innate immune pathways, as well as those whose role is previously un-described in cnidarians. This resource will be valuable in characterizing G. ventalina immune response to infection and co-infection of pathogens in the context of environmental change.
2012-08-17 | GSE40169 | GEO
Project description:Sponges are efficient filter feeders, removing significant portions of particulate and dissolved organic matter (POM, DOM) from the water column. While the assimilation and respiration of POM and DOM by sponges and their abundant microbial symbiont communities have received much attention, there is virtually no information on the impact of sponge holobiont metabolism on the composition of DOM at a molecular-level. We applied untargeted and targeted metabolomics techniques to characterize DOM in seawater samples prior to entering the sponge (inhalant reef water), in samples exiting the sponge (exhalent seawater), and in samples collected just outside the reef area (off reef seawater). Samples were collected from two sponge species, Ircinia campana and Spheciospongia vesparium, on a near-shore hard bottom reef in the Florida Keys. Metabolic profiles generated from untargeted metabolomics analysis indicated that many more compounds were enhanced in the exhalent samples than in the inhalant samples. Targeted metabolomics analysis revealed differences in diversity and concentration of metabolites between exhalent and off reef seawater. For example, most of the nucleosides were enriched in the exhalent seawater, while the aromatic amino acids, caffeine and the nucleoside xanthosine were elevated in the off reef water samples. Although the metabolic profile of the exhalent seawater was unique, the impact of sponge metabolism on the overall reef DOM profile was spatially limited in our study. There were also no significant differences in the metabolic profiles of exhalent water between the two sponge species, potentially indicating that there is a characteristic DOM profile in the exhalent seawater of Caribbean sponges. Additional work is needed to determine whether the impact of sponge DOM is greater in habitats with higher sponge cover and diversity. This work provides the first insight into the molecular-level impact of sponge holobiont metabolism on reef DOM and establishes a foundation for future experimental studies addressing the influence of sponge-derived DOM on chemical and ecological processes in coral reef ecosystems.
2016-02-01 | MTBLS281 | MetaboLights
Project description:Coral microbial communities in experimental coral reef mesocosms
| PRJNA262618 | ENA