PXD009349

PXD009349 is an original dataset announced via ProteomeXchange.

Title	Biogas Plant Survey Magdeburg 2014-2016
Description	Biogas plants (BGPs) produce methane and carbon dioxide through the anaerobic digestion of agricultural waste. Identification of strategies for more stable biogas plant operation and increased biogas yields require better knowledge about the individual degradation steps and the interactions within the microbial communities. The metaprotein profiles of ten agricultural BGPs and one laboratory reactor were investigated using a metaproteomics pipeline. Fractionation of samples using SDS-PAGE was combined with a high resolution Orbitrap mass spectrometer, metagenome sequences specific for BGPs, and the MetaProteomeAnalyzer software. This enabled us to achieve a high coverage of the metaproteome of the BGP microbial communities. The investigation revealed approx. 17,000 protein groups (metaproteins), covering the majority of the expected metabolic networks of the biogas process such as hydrolysis, transport, fermentation processes, amino acid metabolism, methanogenesis and bacterial C1-metabolism. Biological functions could be linked with the taxonomic composition. Two different types of BGPs were classified by the abundance of the acetoclastic methanogenesis and by abundance of enzymes implicating syntrophic acetate oxidation. Linking of the identified metaproteins with the process steps of the Anaerobic Digestion Model 1 proved the main model assumptions but indicated also some improvements such as considering syntrophic acetate oxidation. Beside the syntrophic interactions, the microbial communities in BGPs are also shaped by competition for substrates and host-phage interactions causing cell lysis. In particular, larger amounts of Bacteriophages for the bacterial families Bacillaceae, Enterobacteriaceae and Clostridiaceae, exceeding the cell number of the Bacteria by approximately four-fold. In contrast, less Bacteriophages were found for Archaea, but more CRISPR proteins were detected. On the one hand, the virus induced turnover of biomass might cause slow degradation of complex biomass in BGP. On the other hand, the lysis of bacterial cells allows cycling of essential nutrients.
HostingRepository	PRIDE
AnnounceDate	2019-05-03
AnnouncementXML	Submission_2019-05-03_09:04:34.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kay Schallert
SpeciesList	scientific name: environmental samples ; NCBI TaxID: 95920;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-03-28 00:24:51	ID requested
⏵ 1	2019-05-03 09:04:36	announced

Heyer R, Schallert K, Siewert C, Kohrs F, Greve J, Maus I, Klang J, Klocke M, Heiermann M, Hoffmann M, P, ü, ttker S, Calusinska M, Zoun R, Saake G, Benndorf D, Reichl U, Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants. Microbiome, 7(1):69(2019) [pubmed]

curator keyword: Technical

submitter keyword: microbial communities, metaproteomics, MetaProteomeAnalyzer, bacteriophages, anaerobic digestion, biogas process, syntrophy, competition, Anaerobic Digestion Model 1, host-phage interactions

Dirk Benndorf
contact affiliation	Bioprocess Engeneering, IVT, Otto-von-Guericke University, Magdeburg, Germany
contact email	benndorf@mpi-magdeburg.mpg.de
lab head
Kay Schallert
contact affiliation	Otto-von-Guericke University Magdeburg
contact email	kay.schallert@ovgu.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/2019/05/PXD009349

PRIDE project URI

• PRIDE
  1. PXD009349
     1. Label: PRIDE project
     2. Name: Biogas Plant Survey Magdeburg 2014-2016