PXD023357-2

PXD023357 is an original dataset announced via ProteomeXchange.

Title	Metaproteogenomic profiling of chemosynthetic microbial biofilms reveals metabolic flexibility during colonization of a shallow-water gas vent
Description	Tor Caldara is a shallow-water gas vent located in the Mediterranean Sea, with active venting of CO 2 , H 2 S. At Tor Caldara, filamentous microbial biofilms, mainly composed of Epsilon- and Gammaproteobacteria, grow on substrates exposed to the gas venting. In this study, we took a metaproteogenomic approach to identify the metabolic potential and in situ expression of central metabolic pathways at two stages of biofilm maturation. Our findings indicate that inorganic reduced sulfur species are the main electron donors and CO 2 the main carbon source for the filamentous biofilms, which conserve energy by oxygen and nitrate respiration, fix dinitrogen gas and detoxify heavy metals. Three metagenome-assembled genomes (MAGs), representative of key members in the biofilm community, were also recovered. Metaproteomic data show that metabolically active chemoautotrophic sulfide-oxidizing members of the Epsilonproteobacteria dominated the young microbial biofilms, while Gammaproteobacteria become prevalent in the established community. The co-expression of different pathways for sulfide oxidation by these two classes of bacteria suggests exposure to different sulfide concentrations within the biofilms, as well as fine-tuned adaptations of the enzymatic complexes. Taken together, our findings demonstrate a shift in the taxonomic composition and associated metabolic activity of these biofilms in the course of the colonization process.
HostingRepository	PRIDE
AnnounceDate	2021-01-25
AnnouncementXML	Submission_2021-01-25_01:17:18.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	francesco smedile
SpeciesList	scientific name: microbial mat metagenome; NCBI TaxID: 527640;
ModificationList	No PTMs are included in the dataset
Instrument	6220 Time-of-Flight LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-04 01:29:48	ID requested
1	2021-01-24 22:59:27	announced
⏵ 2	2021-01-25 01:17:18	announced	2021-01-25: Updated publication reference for DOI(s): 10.1101/2020.10.15.340729.
3	2023-11-14 08:52:01	announced	2023-11-14: Updated project metadata.

10.1101/2020.10.15.340729;

submitter keyword: shallow-water gas vent, Mediterranean Sea, Tor Caldara, microbial filaments, biofilms, metaproteome, metagenome, metabolic profile, Epsilonproteobacteria, Gammaproteobacteria

Costantino Vetriani
contact affiliation	Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
contact email	vetriani@marine.rutgers.edu
lab head
francesco smedile
contact affiliation	CNR italy
contact email	francesco.smedile@cnr.it
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/2021/01/PXD023357

PRIDE project URI

• PRIDE
  1. PXD023357
     1. Label: PRIDE project
     2. Name: Metaproteogenomic profiling of chemosynthetic microbial biofilms reveals metabolic flexibility during colonization of a shallow-water gas vent