Ontology highlight
ABSTRACT:
PROVIDER: PRJNA778196 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16877400.fastq.gz | Fastqsanger.gz | |||
| SRR16877401_1.fastq.gz | Fastqsanger.gz | |||
| SRR16877401_2.fastq.gz | Fastqsanger.gz | |||
| SRR16877402.fastq.gz | Fastqsanger.gz | |||
| SRR16877398.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Marine cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity, yet little is known of the transcriptional response of marine Synechococcus to copper shock. Global transcriptional response to two levels of copper shock was assayed in both a coastal and an open ocean strain of marine Synechococcus using whole genome expression microarrays. Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability. This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus. The two strains additionally showed a reduction in photosynthetic gene transcripts. Contrastingly, the open ocean strain showed a typical stress response whereas the coastal strain exhibited a more specific oxidative or heavy metal type response. In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer. Thus, tolerance to copper shock in some marine Synechococcus may in part be a result of an increased ability to sense and respond in a more specialized manner.
2009-07-01 | GSE13910 | GEO
Project description:Atrazine is one of the most commonly used herbicide and has been frequently detected in estuarine and offshore waters worldwide. As a photosystem Ⅱ inhibitor, atrazine may inhibit phytoplankton from fixating of CO2 and alter its carbon metabolism, which will undoubtedly have negative effect on the primary productivity and carbon sequestration capacity of coastal waters. However, the existing reports mainly focused on agriculture and freshwater ecosystems and are mostly toxicity test with high-dose of atrazine, which have little concern about the negative effects of atrazine on the carbon metabolism of phytoplankton and can’t reflect the actual toxic situation in offshore water. Diatoms are widely distributed in freshwater and oceans and contribute at least 20% of the global CO2 assimilation, which is an ideal model group to assess the ecological risk of atrazine. Here we present a comprehensive analysis of the physiological and genome-wide gene expression characteristics of the diatom P. tricornutum Pt-1 (CCMP 2561) treated with environmental dose of atrazine at different stress stages.
2020-12-12 | GSE112478 | GEO
Project description:Marine cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity, yet little is known of the transcriptional response of marine Synechococcus to copper shock. Global transcriptional response to two levels of copper shock was assayed in both a coastal and an open ocean strain of marine Synechococcus using whole genome expression microarrays. Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability. This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus. The two strains additionally showed a reduction in photosynthetic gene transcripts. Contrastingly, the open ocean strain showed a typical stress response whereas the coastal strain exhibited a more specific oxidative or heavy metal type response. In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer. Thus, tolerance to copper shock in some marine Synechococcus may in part be a result of an increased ability to sense and respond in a more specialized manner. In this series four conditions have been analyzed. These are moderate copper shock for Synechococcus sp. WH8102 and CC9311 (pCu 11.1 and pCu 10.1, respectively), and high copper shock for WH8102 and CC9311 (pCu 10.1 and pCu 9.1, respectively). For each slide, an experimental RNA sample was labeled with Cy3 or Cy5 and was hybridized with a reference RNA from a non-copper-shocked sample labeled with the other Cy dye. There are six or eight slides per condition, each with two biological replicates. There are three or four technical replicates for each biological replicate including at least one flip-dye comparison. Each slide contains six replicate spots per gene.
2010-05-17 | E-GEOD-13910 | biostudies-arrayexpress
Project description:Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists of considerable proportions of polysaccharides, substantial parts of which are rapidly remineralized by heterotrophic bacteria. We analyzed the diversity, activity and functional potential of such polysaccharide-degrading bacteria in different size fractions during a diverse spring phytoplankton bloom at Helgoland Roads (southern North Sea) at high temporal resolution using microscopic, physicochemical, biodiversity, metagenome and metaproteome analyses.
2024-01-15 | PXD046705 | Pride
Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification This experiment is part of a much larger experiment. We have produced 4 454 metatranscriptomic datasets and 6 454 metagenomic datasets. These were derived from 4 samples. The experiment is an ocean acidification mesocosm set up in a Norwegian Fjord in 2006. We suspended 6 bags containing 11,000 L of sea water in a Coastal Fjord and then we bubbled CO2 through three of these bags to simulate ocean acidification conditions in the year 2100. The other three bags were bubbled with air. We then induced a phytoplankton bloom in all six bags and took measurements and performed analyses of phytoplankton, bacterioplankton and physiochemical characteristics over a 22 day period. We took water samples from the peak of the phytoplankton bloom and following the decline of the phytoplankton bloom to analyses using 454 metagenomics and 454 metatranscriptomics. Day 1, High CO2 Bag and Day 1, Present Day Bag, refer to the metatranscriptomes from the peak of the bloom. Day 2, High CO2 Bag and Day 2, Present Day Bag, refer to the metatranscriptomes following the decline of the bloom. Obviously High CO2 refers to the ocean acidification mesocosm and Present Day refers to the control mesocosm. Raw data for both the metagenomic and metatranscriptomic components are available at NCBI's Short Read Archive at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000101
2008-02-08 | E-GEOD-10119 | biostudies-arrayexpress
Project description:The project is aimed at the identification of conotoxins and conopeptides from the venom of marine cone snails found in the Indian coastal waters. Peptides of novel sequences will be further characterized in terms of structural and physico-chemical properties by NMR spectroscopy and other biophysical methods and will be studied for the abilities to elicit pharmacological responses against cellular targets.
2021-09-09 | PXD017882 | Pride
Project description:Metagenomic analysis of marine coastal waters
| PRJEB32650 | ENA
Project description:Although N2 fixation can occur in free-living cyanobacteria, the unicellular endosymbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is considered to be a dominant N2-fixing species in marine ecosystems. Four UCYN-A sublineages are known from partial nitrogenase (nifH) gene sequences. However, few studies have investigated their habitat preferences and regulation by their respective hosts in open-ocean versus coastal environments. Here, we compared UCYN-A transcriptomes from oligotrophic open-ocean versus nutrient-rich coastal waters. UCYN-A1 metabolism was more impacted by habitat changes than UCYN-A2. However, across habitats and sublineages genes for nitrogen fixation and energy production were highly transcribed. Curiously these genes, critical to the symbiosis for the exchange of fixed nitrogen for fixed carbon, maintained the same schedule of diel expression across habitats and UCYN-A sublineages, including UCYN-A3 in the open-ocean transcriptomes. Our results undersore the importance of nitrogen fixation in UCYN-A symbioses across habitats, with consequences for community interaction and global biogeochemical cycles.
2023-02-23 | GSE206403 | GEO
Project description:Phytoplankton communities in the shallow eastern Mediterranean coastal waters
| PRJNA670617 | ENA