Aquatic metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA230876 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1049760.fastq.gz | Fastqsanger.gz | |||
| SRR1049761.fastq.gz | Fastqsanger.gz | |||
| SRR1049762.fastq.gz | Fastqsanger.gz | |||
| SRR1049763.fastq.gz | Fastqsanger.gz | |||
| SRR1049764.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 10 |
Similar Datasets
Project description:Individual metagenomes of selected red sea deep brine pools interface layers
| PRJNA219363 | ENA
Project description:Metagenomes of Sediments from Red Sea Atlantis II and Discovery Deep Brine Pools
| PRJNA248772 | ENA
Project description:Metagenomes of Sediments from Red Sea Atlantis II, Discovery and Chain Deep Brine Pools
| PRJNA299097 | ENA
Project description:Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.
2024-11-24 | GSE263620 | GEO
Project description:Marine snow plays a central role in carbon cycling. It consists of organic particles and particle-associated (PA) microbMarine snow plays a central role in carbon cycling. It consists of organic particles and particle-associated (PA) microbial communities that are embedded in a sugary matrix. Metaproteomic analysis offers the unique opportunity to gain unprecedented insight into the microbial community composition and biomolecular activity of environmental samples. In order to realize this potential for marine PA microbial communities, new methods of protein extraction must be developed. In this study, we used 1D-SDS-PAGEs and LC-MS/MS to compare the efficiency of six established protein extraction protocols for their applicability of metaproteomic analyses of the PA microbial community in the North Sea. A combination of SDS-buffer extraction and bead beating resulted in the greatest number of identified protein groups. As expected, a metagenomic database of the same environmental sample increased the number of protein identification by approximately 50%. To demonstrate the application of our established protocol, particulate bacterioplankton samples collected during spring phytoplankton bloom in 2009 near the island Helgoland, were analysed by a GeLC-MS/MS-based metaproteomic approach. Our results indicated that there are only slight differences in the taxonomical distribution between free-living (FL) and PA bacteria but that the abundance of protein groups involved in polysaccharide degradation, motility and particle specific stress (oxygen limitation, nutrient limitation, heavy metal stress) is higher in the PA fractions. ial communities that are embedded in a sugary matrix. Metaproteomic analysis offers the unique opportunity to gain unprecedented insight into the microbial community composition and biomolecular activity of environmental samples. In order to realize this potential for marine PA microbial communities, new methods of protein extraction must be developed. In this study, we used 1D-SDS-PAGEs and LC-MS/MS to compare the efficiency of six established protein extraction protocols for the their applicability of metaproteomic analyses of the PA microbial community in the North Sea. A combination of SDS-buffer extraction and bead beating resulted in the greatest number of identified protein groups. As expected, a metagenomic database of the same environmental sample increased the number of protein identification by approximately 50%. To demonstrate the application of our established protocol, particulate bacterioplankton samples collected during spring phytoplankton bloom in 2009 near the island Helgoland, were analysed by a GeLC-MS/MS-based metaproteomic approach. Our results indicated that there are only slight differences in the taxonomical distribution between free-living (FL) and PA bacteria but that the abundance of protein groups involved in polysaccharide degradation, motility and particle specific stress (oxygen limitation, nutrient limitation, heavy metal stress) is higher in the PA fractions.
2021-02-15 | PXD012699 | Pride
Project description:Proteomic measurements from cyanobacteria colonies picked from the Gulf of Aqaba (Red Sea); analyzed to reveal interaction of cyanobacteria Trichodesmium and its taxonomically diverse microbial community partners. Samples were digested with trypsin, fractionated, and analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline against a metagenomics FASTA file sequenced at JGI.
2023-03-06 | MSV000091416 | MassIVE
Project description:Seawater viral communities from deep brine pools at the bottom of the Mediterranean Sea - Kryos Brine metagenome
| PRJNA539655 | ENA
Project description:Seawater viral communities from deep brine pools at the bottom of the Mediterranean Sea - LS2A Brine metagenome
| PRJNA539648 | ENA
Project description:Seawater viral communities from deep brine pools at the bottom of the Mediterranean Sea - Urania Brine metagenome
| PRJNA539659 | ENA