PXD012479-3

PXD012479 is an original dataset announced via ProteomeXchange.

Title	microbiome of methane hydrate sediments: Hydrate Ridge
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.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:50:02.835.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Brook Nunn
SpeciesList	scientific name: sediment metagenome; NCBI TaxID: 749907;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-01-23 06:02:12	ID requested
1	2020-01-21 23:42:05	announced
2	2020-01-22 01:43:57	announced	2020-01-22: Updated publication reference for DOI(s): 10.1101/536078.
⏵ 3	2023-11-14 08:50:03	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: high-pressure, cold, hydrate-associated microbiome, bacteria,Atribacteria, metaproteomics

Brook L Nunn
contact affiliation	Univ of Washington Dept of Genome Sciences
contact email	brookh@uw.edu
lab head
Brook Nunn
contact affiliation	University of Washington
contact email	brookh@uw.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD012479

PRIDE project URI

• PRIDE
  1. PXD012479
     1. Label: PRIDE project
     2. Name: microbiome of methane hydrate sediments: Hydrate Ridge