Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sediment metagenome

ABSTRACT: Amplicon sequencing of Psb A gene for phytoplankton assemblages in surface sediments in the Tohoku (north-eastern Honshu) coast of Japan

PROVIDER: PRJDB15989 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR483964_1.fastq.gz	Fastqsanger.gz
	DRR483964_2.fastq.gz	Fastqsanger.gz
	DRR483965_1.fastq.gz	Fastqsanger.gz
	DRR483965_2.fastq.gz	Fastqsanger.gz
	DRR483966_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 142

Similar Datasets

microbiome of methane hydrate sediments: Hydrate Ridge

Project description:Gas hydrates, also known as clathrates, are cages of ice-like water crystals encasing gas molecules such as methane (CH4). Despite the global importance of gas hydrates, their microbiomes remain mysterious. Microbial cells are physically associated with hydrates, and the taxonomy of these hydrate-associated microbiomes is distinct from non-hydrate-bearing sites. Global 16S rRNA gene surveys show that members of sub-clade JS-1 of the uncultivated bacterial candidate phylum Atribacteria are the dominant taxa in gas hydrates. The Atribacteria phylogeny is highly diverse, suggesting the potential for wide functional variation and niche specialization. Here, we examined the distribution, phylogeny, and metabolic potential of uncultivated Atribacteria in cold, salty, and high-pressure sediments beneath Hydrate Ridge, off the coast of Oregon, USA, using a combination of 16S rRNA gene amplicon, metagenomic, and metaproteomic analysis. Methods were developed to extract bacterial cellular protein from these sediments, as outlined below. Sample Description Three sediments samples were collected from beneath Hydrate Ridge, off the coast of Oregon, USA. Sediments were cored at ODP site 1244 (44°35.1784´N; 125°7.1902´W; 895 m water depth) on the eastern flank of Hydrate Ridge ~3 km northeast of the southern summit on ODP Leg 204 in 2002 and stored at -80°C at the IODP Gulf Coast Repository. E10H5 sediment is from 68.5 meters below sediment surface interface C1H2 sediment is from 2 meters below sediment surface interface. C3H4 sediment is from 21 meters below sediment surface interface.

2020-01-22 | PXD012479 | Pride

The ProteOMZ Expedition: Investigating Life Without Oxygen in the Pacific Ocean

Project description:Untargeted proteomics from a 5,000 km+ transect across the central Pacific Ocean from Hawaii to Tahiti. The expedition crossed multiple biogeochemical provinces, inlcuding the oligotrophic North Pacific Subtropical Gyre, the extremety of the Eastern Tropical North Pacific Oxygen Deficient Zone, and the relatively productive equatorial region associated with upwelling. This dataset focuses on the microbial fraction (0.2-3.0 micrometer filter size) and the microbial community dynamics across these biogeochemical provinces, from the surface oceance to the mesopelagic (1,250 m depth maximum).

2022-08-31 | PXD030684 | Pride

Protistan metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling

Project description:An Autonomous Underwater Vehicle (AUV) and large volume underwater pumps were used to collect microbial biomass from offshore waters of the Sargasso Sea, from surface waters and into the deep ocean. Seawater collection was performed along a transect in the western North Atlantic Ocean beginning near Bermuda and ending off the coast of Massachusetts, capturing metabolic signatures from oligotrophic, continental margin, and productive coastal ecosystems.

2023-10-25 | PXD045395 | Pride

Proteomics of Gammarus fossarum A individuals sampled from the wild

Project description:Next-generation proteomics of Gammarus fossarum A animals sampled from the Seebach river in north-eastern France.

2020-04-17 | PXD014166 | Pride

marine sediment metagenome

Project description:Amplicon sequencing of phytoplankton assemblages in sediment cores in Onagawa Bay

| PRJDB8175 | ENA

Phytoplankton assemblage during the North Atlantic spring bloom assessed from functional gene analysis

Project description:The spring bloom in the North Atlantic develops over a few weeks in response to the physical stabilization of the nutrient replete water column and is one of the biggest biological signals on earth. The composition of the phytoplankton assemblage during the spring bloom of 2008 was evaluated, using a microarray, on the basis of functional genes that encode key enzymes in nitrogen and carbon assimilation in eukaryotic and prokaryotic phytoplankton. Oligonucleotide archetype probes representing RuBisCO, nitrate reductase and nitrate transporter genes from major phytoplankton classes detected a diverse assemblage. For RuBisCO, the archetypes with strongest signals represented known phytoplankton groups, but for the nitrate related genes, the major signals were not closely related to any known phytoplankton sequences. Most of the assemblage's components exhibited consistent temporal/spatial patterns. Yet, the strongest archetype signals often showed quite different patterns, indicating different ecological responses by the main players. The most abundant phytoplankton genera identified previously by microscopy, however, were not well represented on the microarray. The lack of sequence data for well-studied species, and the inability to identify organisms associated with functional gene sequences in the environment, still limits our understanding of phytoplankton ecology even in this relatively well-studied system.

2016-05-11 | GSE81262 | GEO

marine sediment metagenome

Project description:Microbial communities in deep eastern Mediterranean Sea surface sediments

| PRJNA270910 | ENA

Project description:Monterey Bay & North-Eastern Pacific V1V2 Amplicon Sequencing

| PRJNA1107937 | ENA

sediment metagenome

Project description:Amplicon sequencing of phytoplankton assemblages in a sediment core in Onagawa Bay

| PRJDB14150 | ENA

eukaryotic plankton metagenome

Project description:Amplicon sequencing of phytoplankton assemblages in a sediment core in Ofunato Bay

| PRJDB14151 | ENA