title: Metaproteomics of activated sludge from a wastewater treatment plant - a pilot study.
abstract: In this study, the impact of protein fractionation techniques prior to LC/MS analysis was investigated on activated sludge samples derived at winter and summer condition from a full-scale wastewater treatment plant (WWTP). For reduction of the sample complexity, different fractionation techniques including RP-LC (1D-approach), SDS-PAGE and RP-LC (2D-approach) as well as RP-LC, SDS-PAGE and liquid IEF (3D-approach) were carried out before subsequent ion trap MS analysis. The derived spectra were identified by MASCOT search using a combination of the public UniProtKB/Swiss-Prot protein database and metagenome data from a WWTP. The results showed a significant increase of identified spectra, enabled by applying IEF and SDS-PAGE to the proteomic workflow. Based on meta-proteins, a core metaproteome and a corresponding taxonomic profile of the wastewater activated sludge were described. Functional aspects were analyzed using the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway library by plotting KEGG Orthology identifiers (KO numbers) of protein hits into pathway maps of the central carbon (map01200) and nitrogen metabolism (map00910). Using the 3D-approach, most proteins involved in glycolysis and citrate cycle and nearly all proteins of the nitrogen removal were identified, qualifying this approach as most promising for future studies. All MS data have been deposited in the ProteomeXchange with identifier PXD001547 (http://proteomecentral.proteomexchange.org/dataset/PXD001547).
authors.affiliation: Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Püttker
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: 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: Erdmann
authors.initials: E
authors.lastname: Rapp
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: D002853:Chromatography, Liquid; D030562:Databases, Protein; D006801:Humans; D054892:Metagenome; D020543:Proteome / Q000235:genetics*; D040901:Proteomics / Q000379:methods*; D012722:Sewage / Q000382:microbiology; D053719:Tandem Mass Spectrometry; D062065:Wastewater / Q000382:microbiology*
chemical_list: D020543:Proteome; D012722:Sewage; D062065:Wastewater
keywords: Activated sludge; MetaProteomeAnalyzer; Metaproteomics; Microbiology; Offgel isoelectric focusing; Wastewater treatment plant