Bacterial assembleges in corals
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA729083 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14636700.fastq.gz | Fastqsanger.gz | |||
| SRR14636701.fastq.gz | Fastqsanger.gz | |||
| SRR14636702.fastq.gz | Fastqsanger.gz | |||
| SRR14636703.fastq.gz | Fastqsanger.gz | |||
| SRR14636704.fastq.gz | Fastqsanger.gz |
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Project description:Scleractinian corals acquire autotrophic nutrients via the photosynthetic activity of their symbionts and the subsequent transfer of photosynthates. Zooplankton predation by the animal (heterotrophy) is an additional food source. Under stress events, corals loose their symbionts, a phenomena known as bleaching, which eventually leads to starvation, unless corals increase their heterotrophic capacities. Molecular mechanisms by which heterotrophy sustains metabolism in stressed corals remain elusive. Here for the first time, we identify specific genes expressed in heterotrophically fed and unfed corals maintained under normal and light-stress conditions inducing bleaching. Physiological parameters and gene expression profiling showed ominously that fed corals better resisted the stress than unfed corals, by presenting less oxidative damage and protein/DNA degradation. Light stressed and unfed/starved corals (HLS) up-regulated by 140 and 13 times two genes (CP2U1 and CP1A2), which belong to the Cytochrome P450 superfamily, while these genes remained almost unchanged in fed corals (HLF). Other genes of redox regulation, DNA damage response, molecular chaperones, and protein degradation were also up-regulated in HLS corals, presenting higher bleaching, and strong decrease of the photosynthesis performance compared to HLF corals. Several pivotal genes associated with the calcification apparatus such as carbonic anhydrases, calcium-transporting ATPase, calcium channel subunit, and bone morphogenetic proteins (BMPs), were significantly down-regulated only in HLS corals. A parallel decrease in the calcification rates of these later corals was also observed. All together, these results show clearly that heterotrophy helps preventing oxidative stress in corals, and thus avoid the cascade of metabolic problems downstream this stress.
2016-05-04 | GSE53661 | GEO
Project description:Corals especially the reef-building species are very important to marine ecosystems. Proteomics has been used for researches on coral diseases, bleaching and responses to the environment change. Corals especially the reef-building species are very important to marine ecosystems. Proteomics has been used for researches on coral diseases, bleaching and responses to the environment change. In the present study, five protocols were compared for protein extraction from stony corals.
2022-07-24 | PXD006334 | Pride
Project description:stony corals metagenome Raw sequence reads
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Project description:Background Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH) with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization). Results Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate. Conclusions The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than nuclear encoded genes in robust corals. Accordingly, this needs to be taken into account when using mitochondrial markers for scleractinian phylogenies.
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Project description:Bacterial and fungal composition of corals in Vietnam
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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:Genome-wide association studies (GWAS) have revolutionized the field of genetics, providing numerous associations between human SNPs and health traits. Likewise, metagenome-wide association studies (MWAS) between bacterial SNPs and human traits can suggest mechanistic links between the microbiota and its host. However, very few such studies have been done to date, in part due to the large number of samples required to address the variable coverage of bacteria across samples and the fact that most bacteria are present in only a subset of the population. Here, we devised an MWAS framework to detect SNPs and associate them with host phenotypes systematically. We recruited and obtained gut metagenomic samples from a cohort of 7,190 healthy individuals and discovered 1,358 statistically significant associations between a bacterial SNP and host body mass index (BMI). To address the possible effects of population structure and linkage disequilibrium, we applied a clumping procedure, and found 40 independent associations between SNPs and host BMI. We uncovered BMI-associated SNPs in the genomes of 27 bacterial species, even though the relative abundance of 12 of these species was not associated with the phenotype. We separated genome-wide sub-species variations from local associations in individual SNPs, and demonstrated how this framework can highlight specific bacterial functions of interest. Our results demonstrate the importance of considering nucleotide-level diversity in microbiome studies and pave the way toward a better understanding of interpersonal gut microbiome differences and their health implications.
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Project description:Bacterial communities associated with several solitary bee species
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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.
2014-09-30 | GSE60622 | GEO