Ontology highlight
ABSTRACT:
PROVIDER: PRJNA816931 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18344400.fastq.gz | Fastqsanger.gz | |||
| SRR18344400_1.fastq.gz | Fastqsanger.gz | |||
| SRR18344400_2.fastq.gz | Fastqsanger.gz | |||
| SRR18344401.fastq.gz | Fastqsanger.gz | |||
| SRR18344401_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Corals are major sources of dimethylsulphoniopropionate (DMSP), a compound that plays a central role in the global sulphur cycle. While DMSP biosynthesis pathways have been investigated in plants and algae, the molecular basis for its production by corals is unknown. Given its potential role as an osmolyte, the effect of salinity stress on levels of DMSP was investigated in both adults and juveniles (lacking photosynthetic symbionts) of the coral Acropora millepora. This study used transcriptomic data to analyse the effects of salinity over the coral A. millepora and to identify coral genes likely to be involved in DMSP biosynthesis. Methods: Adults coral transcriptomic libraries were constructed from samples exposed during 1 and 24 hours of salinity treatment (25 PSU) and control (35 PSU) conditions (n=5 per condition). Juveniles coral transcriptomic libraries were constructed from samples exposed to 24 and 48 hours of salinity treatment (28 PSU) and control (35 PSU) conditions (n=6 per condition). All libraries were sequenced by 100 bp paired-end in a HiSeq 2000. Reads were mapped onto the Acropora millepora genome using TopHat2 to produce a count data gene expression matrix for subsequent gene expression analysis using DESeq2 package. Results: In adult coral samples, 5.5 - 10.2 million RNAseq reads were obtained for each treatment sampling time while 3.4 - 8.8 million reads were obtained for each juvenile coral sample. The count matrix of the 26,622 A. millepora gene predictions were generated using htseq-count workflow. BlastP analysis of the A. millepora gene predictions led to the identification of coral members of gene families implicated in DMSP biosynthesis in other organisms, while RNA-seq data was used to identify the differentially expressed ones in response to hyposaline stress and on this basis were considered to be candidates for roles in DMSP biosynthesis in corals. Conclusions: Hyposaline stress increased DMSP production in both adults and aposymbiotic juvenile corals, and transcriptomic analyses highlighted the potential involvement of specific candidate genes in the production of DMSP via an alga-like pathway. The biochemistry of DMSP production is not well established for any eukaryotic system and, as the first animals in which it has been demonstrated, this is particularly true in the case of corals. Our RNA-seq results enabled the identification of candidates for roles in DMSP biosynthesis in corals but, given its critical roles in diverse biological processes, a thorough investigation of the molecular mechanisms leading to its production by corals is required.
2017-08-20 | GSE96916 | GEO
Project description:Marine phytoplankton produce ~109 tons of dimethylsulfoniopropionate (DMSP) per year, an estimated 10% of which is catabolized by bacteria through the DMSP cleavage pathway to the climatically active gas dimethyl sulfide (DMS). SAR11 Alphaproteobacteria (order Pelagibacterales), the most abundant chemoorganotrophic bacteria in the oceans, have been shown to assimilate DMSP into biomass, thereby supplying this cell’s unusual requirement for reduced sulfur. Here we report that Pelagibacter HTCC1062 produces the gas methanethiol (MeSH) and that simultaneously a second DMSP catabolic pathway, mediated by a DMSP lyase, shunts as much as 59% of DMSP uptake to DMS production. We propose a model in which the allocation of DMSP between these pathways is kinetically controlled to release DMS when the supply of DMSP exceeds cellular sulfur demands for biosynthesis. These findings suggest that DMSP supply and demand relationships can significantly control rates of oceanic DMS production.
2017-12-08 | PXD001717 | Pride
Project description:Coral bleaching and coral reef degradation become severe as the surface seawater temperature rises. Much research to date has focused on the bacterial community composition properties within the coral holobiont, but less attention has been paid to the interactions of bacteria and corals under thermal stress. We investigated the changes of coral symbiotic bacteria and metabolites under thermal stress, and analyzed the internal relationship between bacteria and metabolites as well as their relationship with coral health. We found obvious signs of coral bleaching after heating treatment, and the interaction within symbiotic bacterial community became closer. The coral symbiotic bacterial community and metabolites changed significantly under thermal stress, and bacteria such as Flavobacterium, Shewanella and Psychrobacter increased significantly. Bacteria associated with stress tolerance, biofilm formation and mobile elements decreased, and bacterial DMSP metabolism increased slightly after heating treatment. Differential metabolites in corals after heating treatment were associated with cell cycle regulation and antioxidant. This study revealed the correlation between differential metabolites and bacterial community composition changes in corals under thermal stress, and providing valuable insight on metabolomics research of corals.
2022-10-27 | MTBLS5272 | MetaboLights
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:The fraction of dissolved dimethylsulfoniopropionate (DMSPd) converted by marine bacterioplankton into the climate-active gas dimethylsulfide (DMS) varies widely in the ocean, with the factors that determine this value still largely unknown. One current hypothesis is that the ratio of DMS formation:DMSP demethylation is determined by DMSP availability, with 'availability' in both an absolute sense (i.e., concentration in seawater) and in a relative sense (i.e., proportionally to other labile organic S compounds) being proposed as the critical factor. We investigated these models during an experimentally-induced phytoplankton bloom using an environmental microarray targeting DMSP-related gene expression in the Roseobacter group, a taxon of marine bacteria known to play an important role in the surface ocean sulfur cycle. The array consisted of 1,578 probes to 431 genes, including those previously linked to DMSP degradation as well as core genes common in sequenced Roseobacter genomes. The prevailing pattern of Roseobacter gene expression showed depletion of DMSP-related transcripts during the peak of the bloom, despite the fact that absolute concentrations and flux of DMSP-related compounds were increasing. A likely interpretation is that DMSPd was assimilated by Roseobacter populations in proportion to its relative abundance in the organic matter pool (the “relative sense” hypothesis), and that it is not taken up in preference to other sources of labile organic sulfur or carbon produced during the bloom. The relative investment of the Roseobacter community in DMSP demethylation did not predict the fractional conversion of DMSP to DMS, however, suggesting a complex regulatory process that may involve multiple fates of DMSPd.
2010-08-05 | GSE21325 | 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.
2014-09-30 | GSE60622 | GEO