Freshwater metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA176929 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2177750.fastq.gz | Fastqsanger.gz | |||
| SRR2177780.fastq.gz | Fastqsanger.gz | |||
| SRR2177790.fastq.gz | Fastqsanger.gz | |||
| SRR2177800.fastq.gz | Fastqsanger.gz | |||
| SRR2179960_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 59 |
Similar Datasets
Project description:Eutrophication can lead to an uncontrollable increase in algal biomass, which has repercussions for the entire microbial and pelagic community. Studies have shown how nutrient enrichment affects microbial species succession, however details regarding the impact on community functionality are rare. Here, we applied a metaproteomic approach to investigate the functional changes to algal and bacterial communities, over time, in oligotrophic and eutrophic conditions, in freshwater microcosms. Samples were taken early during algal and cyanobacterial dominance and later under bacterial dominance. 1048 proteins, from the two treatments and two timepoints, were identified and quantified by their exponentially modified protein abundance index. In oligotrophic conditions, Bacteroidetes express extracellular hydrolases and Ton-B dependent receptors to degrade and transport high molecular weight compounds captured while attached to the phycosphere. Alpha- and Beta-proteobacteria were found to capture different substrates from algal exudate (carbohydrates and amino acids, respectively) suggesting resource partitioning to avoid direct competition. In eutrophic conditions, environmental adaptation proteins from cyanobacteria suggested better resilience compared to algae in a low carbon nutrient enriched environment. This study provides insight into differences in functional microbial processes between oligo- and eutrophic conditions at different timepoints and highlights how primary producers control bacterial resources in freshwater environments.
2016-08-01 | PXD004592 | Pride
Project description:Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment. This is the RNA-seq experiment, DNA methylation data (bisulfite-seq) is provided under accession number GSE82310.
2021-11-03 | GSE186925 | GEO
Project description:Cyanobacteria produce various cyanotoxins, which can cause severe effects to other organisms. Microcystins, one group of such toxins, primarily produced by species of Microcystis, are strong hepatotoxins and inhibit potently protein phosphatases 1 and 2A. Microcystin is the most studied cyanotoxin, however, others are not investigated. Eutrophication of water bodies promotes the occurrence of toxic algal blooms and since a anthropogenic caused increase in eutrophication events can be observed, it is becoming increasingly important to study the consequences and to increase the knowledge on toxins associated with algal blooms. Recently a new cyanobacteria toxin from a Microcystis strain, CP1020, was described. CP1020 belongs to the class of cyanopeptolins and its toxicity was shown to be comparable to that of microcystin (Gademann et al., 2009). It is a strong protease inhibitor inhibiting trypsin in the picomolar range (IC50 = 670 pM) and effects survival of the freshwater crustacean Thamnocephalus platyurus (LC50) 8.8 μM (Gademann et al., 2009). Nothing is known, however, about the toxicity of CP1020 to fish. Furthermore, no information is available on the toxic modes of action, in addition to the proteinase activity. Consequently our study has the aim to elucidate the modes of action of CP1020 on zebrafish eleuthero-embryos. By using a microarray technique, we will analyse alterations of global gene expression by CP1020 at two different concentrations. Thereby, we hope to elucidate the whole array of affected biological pathways to elucidate the mechanisms by which CP1020 affect fish.
2014-03-31 | GSE50139 | GEO
Project description:Chlorella sp. HS2 is a halotolerant microalga exhibiting relatively high biomass productivity and substantially high lipid accumulation in marine growth media, which suggests this alga as an important crop for industrial algal cultivation systems. To determine pathways leading to HS2's acclimation responses to salt stress, we performed RNA-seq analysis with triplicated cultures grown in freshwater and marine media at both exponential and stationary growth phases. We then run de novo assembly to obtain HS2 transcriptome, which in turn was annotated and processed to extract dysregulated pathways. Results showed a large proportion of down-regulated genes, for instance photosynthesis and TCA pathways. Photosynthesis appeared, however, to recover at the stationary phase, while the general down-regulation pattern was maintained.
2020-03-12 | GSE146789 | GEO
Project description:Cyanobacteria produce various cyanotoxins, which can cause severe effects to other organisms. Microcystins, one group of such toxins, primarily produced by species of Microcystis, are strong hepatotoxins and inhibit potently protein phosphatases 1 and 2A. Microcystin is the most studied cyanotoxin, however, others are not investigated. Eutrophication of water bodies promotes the occurrence of toxic algal blooms and since a anthropogenic caused increase in eutrophication events can be observed, it is becoming increasingly important to study the consequences and to increase the knowledge on toxins associated with algal blooms. Recently a new cyanobacteria toxin from a Microcystis strain, CP1020, was described. CP1020 belongs to the class of cyanopeptolins and its toxicity was shown to be comparable to that of microcystin (Gademann et al., 2009). It is a strong protease inhibitor inhibiting trypsin in the picomolar range (IC50 = 670 pM) and effects survival of the freshwater crustacean Thamnocephalus platyurus (LC50) 8.8 M-NM-<M (Gademann et al., 2009). Nothing is known, however, about the toxicity of CP1020 to fish. Furthermore, no information is available on the toxic modes of action, in addition to the proteinase activity. Consequently our study has the aim to elucidate the modes of action of CP1020 on zebrafish eleuthero-embryos. By using a microarray technique, we will analyse alterations of global gene expression by CP1020 at two different concentrations. Thereby, we hope to elucidate the whole array of affected biological pathways to elucidate the mechanisms by which CP1020 affect fish. Gene expression in zebrafish eleuthero-embryos was measured after exposure for 96h to 100 ug/L and 1000 ug/L CP1020 or to the respective controls. A total of 12 arrays (Agilent 4 M-CM-^W 44 K Zebrafish microarray) were used, including four for the solvent control group, four for the 100 M-NM-<g/L and four for the 1000 M-NM-<g/L CP1020 dose group.
2014-03-31 | E-GEOD-50139 | biostudies-arrayexpress
Project description:Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment.
2017-05-30 | GSE82310 | GEO
Project description:Metagenomics of freshwater microbial community in secondary cooling water system
| PRJNA451386 | ENA
Project description:Nanoscale zero valent iron (nZVI) is used to remediate aquifers polluted by organochlorines or heavy metals and was also suggested to eliminate harmful algal blooms. nZVI can therefore affect microorganisms in the vicinity of the application area, including microalgae. However, studies on early transcriptomic effects of microalgae after exposure to nZVI are rare. Here, we described the early physiological and transcriptomic response of the freshwater ecological indicator green microalga, Raphidocelis subcapitata ATCC 22662, to 100 mg/L of reactive nZVI and non-reactive nano-magnetite (nFe3O4). The combined effect of shading and the release of total iron from nZVI posed a short-term inhibition effect leading to 15 % of deformed cells and cytosol leakage, while cells viability increased after 24 h. nZVI triggered a more pronounced transcriptomic response with (7380 differentially expressed genes [DEGs]) compared to nFe3O4 (4601 DEGs) after 1 h. nZVI, but not nFe3O4 increased the expression of genes function in DNA repair and replication, while deactivated carbohydrate-energy metabolisms, mitochondria signaling, and transmembrane ion transport. This study highlights an early fate assessment of algal cells under nZVI and nFe3O4 exposure using next-generation risk assessment methods and will serve as valuable information for safe and sustainable application of nZVI in water remediation.
2023-06-06 | GSE234088 | GEO