title: Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities.
abstract: With the development of high resolving mass spectrometers, metaproteomics evolved as a powerful tool to elucidate metabolic activity of microbial communities derived from full-scale biogas plants. Due to the vast complexity of these microbiomes, application of suitable fractionation methods are indispensable, but often turn out to be time and cost intense, depending on the method used for protein separation. In this study, centrifugal fractionation has been applied for fractionation of two biogas sludge samples to analyze proteins extracted from (i) crude fibers, (ii) suspended microorganisms, and (iii) secreted proteins in the supernatant using a gel-based approach followed by LC-MS/MS identification. This fast and easy method turned out to be beneficial to both the quality of SDS-PAGE and the identification of peptides and proteins compared to untreated samples. Additionally, a high functional metabolic pathway coverage was achieved by combining protein hits found exclusively in distinct fractions. Sample preparation using centrifugal fractionation influenced significantly the number and the types of proteins identified in the microbial metaproteomes. Thereby, comparing results from different proteomic or genomic studies, the impact of sample preparation should be considered. All MS data have been deposited in the ProteomeXchange with identifier PXD001508 (http://proteomecentral.proteomexchange.org/dataset/PXD001508).
authors.affiliation: Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Kohrs
authors.affiliation: Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany.
authors.forename: Sophie
authors.initials: S
authors.lastname: Wolter
authors.affiliation: Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany.
authors.forename: Dirk
authors.initials: D
authors.lastname: Benndorf
authors.affiliation: Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany.
authors.forename: Robert
authors.initials: R
authors.lastname: Heyer
authors.affiliation: Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
authors.forename: Marcus
authors.initials: M
authors.lastname: Hoffmann
authors.affiliation: Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
authors.forename: Erdmann
authors.initials: E
authors.lastname: Rapp
authors.affiliation: Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Bremges
authors.affiliation: Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Sczyrba
authors.affiliation: Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Schlüter
authors.affiliation: Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany.|Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
authors.forename: Udo
authors.initials: U
authors.lastname: Reichl
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics*; D056804:Biofuels; D010455:Peptides / Q000737:chemistry / Q000235:genetics*; D010944:Plants / Q000737:chemistry / Q000235:genetics; D020543:Proteome / Q000235:genetics*; D040901:Proteomics; D012722:Sewage; D053719:Tandem Mass Spectrometry
chemical_list: D001426:Bacterial Proteins; D056804:Biofuels; D010455:Peptides; D020543:Proteome; D012722:Sewage
keywords: Biogas plant; Differential centrifugation; Metabolism; Metaproteomics; Microbial communities; Microbiology