PXD012699

PXD012699 is an original dataset announced via ProteomeXchange.

Title	Establishment of a metaproteomics pipeline for marine particle associated microbial communities
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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:18:55.389.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Daniela Zuehlke
SpeciesList	scientific name: Candidatus Pelagibacter sp.; NCBI TaxID: 2024849;
ModificationList	monohydroxylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2019-02-13 23:49:56	ID requested
1	2021-02-14 23:41:51	announced
⏵ 2	2024-10-22 05:18:55	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: metaproteomics, spring phytoplankton bloom, marine snow

Katharina Riedel
contact affiliation	university of Greifswald, institute of microbiology, department of microbial physiology and molecular biology
contact email	riedela@uni-greifswald.de
lab head
Daniela Zuehlke
contact affiliation	University of Greifswald, Institute of Microbiology
contact email	zuehlke@uni-greifswald.de
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/2021/02/PXD012699

PRIDE project URI

• PRIDE
  1. PXD012699
     1. Label: PRIDE project
     2. Name: Establishment of a metaproteomics pipeline for marine particle associated microbial communities