PXD005624

PXD005624 is an original dataset announced via ProteomeXchange.

Title	Fermentative Spirochaetes drive nutrient cycling by a subsurface microbial loop in hydrocarbon-contaminated habitats
Description	Members of the bacterial phylum Spirochaetes are primarily studied for their commensal and pathogenic roles in animal hosts. However, Spirochaetes are also frequently detected in anoxic hydrocarbon-contaminated environments but their ecological role in such ecosystems has so far remained unclear. Here we provide a functional trait to these frequently detected organisms with an example of a sulfate-reducing, naphthalene-degrading enrichment culture consisting of a sulfate-reducing deltaproteobacterium Desulfobacterium naphthalenivorans and a novel spirochete Rectinema cohabitans. Using a combination of genomic, proteomic, and physiological studies we show that R. cohabitans grows by fermentation of organic compounds derived from biomass from dead cells (necromass). It recycles the derived electrons in the form of H2 to the sulfate-reducing D. naphthalenivorans, thereby supporting naphthalene degradation and forming a simple microbial loop. We provide metagenomic evidence that equivalent associations between Spirochaetes and hydrocarbon-degrading microorganisms are of general importance in hydrocarbon- and organohalide-contaminated ecosystems. We propose that environmental Spirochaetes form a critical component of a microbial loop central to nutrient cycling in subsurface environments. This emphasizes the importance of necromass and H2-cycling in highly toxic contaminated subsurface habitats such as hydrocarbon-polluted aquifers.
HostingRepository	PRIDE
AnnounceDate	2018-05-17
AnnouncementXML	Submission_2018-06-06_00:03:03.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Farnusch Kaschani
SpeciesList	scientific name: Treponema; NCBI TaxID: 157; scientific name: uncultured Desulfobacterium sp.; NCBI TaxID: 201089;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2016-12-22 05:18:36	ID requested
1	2018-05-17 02:54:47	announced
⏵ 2	2018-06-06 00:03:04	announced	Updated publication reference for PubMed record(s): 29849169.

Dong X, Greening C, Br, ü, ls T, Conrad R, Guo K, Blaskowski S, Kaschani F, Kaiser M, Laban NA, Meckenstock RU, Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats. ISME J, 12(8):2039-2050(2018) [pubmed]

curator keyword: Biological

submitter keyword: Desulfobacterium naphthalenivorans, Rectinema cohabitans, label free quantification MS

Farnusch Kaschani
contact affiliation	Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany
contact email	farnusch.kaschani@uni-due.de
lab head
Farnusch Kaschani
contact affiliation	University Duisburg-Essen
contact email	farnusch.kaschani@uni-due.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/2018/05/PXD005624

PRIDE project URI

• PRIDE
  1. PXD005624
     1. Label: PRIDE project
     2. Name: Fermentative Spirochaetes drive nutrient cycling by a subsurface microbial loop in hydrocarbon-contaminated habitats