Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities
Kohrs F, Wolter S, Benndorf D, Heyer R, Hoffmann M, Rapp E, Bremges A, Sczyrba A, Schlüter A, Reichl U (2015)
Proteomics 15(20): 3585-3589.
Zeitschriftenaufsatz
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Autor*in
Kohrs, Fabian;
Wolter, Sophie;
Benndorf, Dirk;
Heyer, Robert;
Hoffmann, Marcus;
Rapp, Erdmann;
Bremges, AndreasUniBi ;
Sczyrba, AlexanderUniBi ;
Schlüter, AndreasUniBi ;
Reichl, Udo
Einrichtung
Technische Fakultät > Computational Metagenomics
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Technische Fakultät > Int. Graduiertenkolleg DiDy (GRK 1906)
Centrum für Biotechnologie > Arbeitsgruppe A. Sczyrba
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Technische Fakultät > Int. Graduiertenkolleg DiDy (GRK 1906)
Centrum für Biotechnologie > Arbeitsgruppe A. Sczyrba
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Abstract / Bemerkung
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).
2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Stichworte
Metabolism;
Biogas plant;
Microbiology;
Microbial communities;
Metaproteomics;
Differential centrifugation
Erscheinungsjahr
2015
Zeitschriftentitel
Proteomics
Band
15
Ausgabe
20
Seite(n)
3585-3589
ISSN
1615-9853
eISSN
1615-9861
Page URI
https://pub.uni-bielefeld.de/record/2762833
Zitieren
Kohrs F, Wolter S, Benndorf D, et al. Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities. Proteomics. 2015;15(20):3585-3589.
Kohrs, F., Wolter, S., Benndorf, D., Heyer, R., Hoffmann, M., Rapp, E., Bremges, A., et al. (2015). Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities. Proteomics, 15(20), 3585-3589. doi:10.1002/pmic.201400557
Kohrs, Fabian, Wolter, Sophie, Benndorf, Dirk, Heyer, Robert, Hoffmann, Marcus, Rapp, Erdmann, Bremges, Andreas, Sczyrba, Alexander, Schlüter, Andreas, and Reichl, Udo. 2015. “Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities”. Proteomics 15 (20): 3585-3589.
Kohrs, F., Wolter, S., Benndorf, D., Heyer, R., Hoffmann, M., Rapp, E., Bremges, A., Sczyrba, A., Schlüter, A., and Reichl, U. (2015). Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities. Proteomics 15, 3585-3589.
Kohrs, F., et al., 2015. Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities. Proteomics, 15(20), p 3585-3589.
F. Kohrs, et al., “Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities”, Proteomics, vol. 15, 2015, pp. 3585-3589.
Kohrs, F., Wolter, S., Benndorf, D., Heyer, R., Hoffmann, M., Rapp, E., Bremges, A., Sczyrba, A., Schlüter, A., Reichl, U.: Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities. Proteomics. 15, 3585-3589 (2015).
Kohrs, Fabian, Wolter, Sophie, Benndorf, Dirk, Heyer, Robert, Hoffmann, Marcus, Rapp, Erdmann, Bremges, Andreas, Sczyrba, Alexander, Schlüter, Andreas, and Reichl, Udo. “Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities”. Proteomics 15.20 (2015): 3585-3589.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
4 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.
Blank C, Easterly C, Gruening B, Johnson J, Kolmeder CA, Kumar P, May D, Mehta S, Mesuere B, Brown Z, Elias JE, Hervey WJ, McGowan T, Muth T, Nunn B, Rudney J, Tanca A, Griffin TJ, Jagtap PD., Proteomes 6(1), 2018
PMID: 29385081
Blank C, Easterly C, Gruening B, Johnson J, Kolmeder CA, Kumar P, May D, Mehta S, Mesuere B, Brown Z, Elias JE, Hervey WJ, McGowan T, Muth T, Nunn B, Rudney J, Tanca A, Griffin TJ, Jagtap PD., Proteomes 6(1), 2018
PMID: 29385081
Metabolic Adaptation of Methanogens in Anaerobic Digesters Upon Trace Element Limitation.
Wintsche B, Jehmlich N, Popp D, Harms H, Kleinsteuber S., Front Microbiol 9(), 2018
PMID: 29593674
Wintsche B, Jehmlich N, Popp D, Harms H, Kleinsteuber S., Front Microbiol 9(), 2018
PMID: 29593674
Proteotyping of laboratory-scale biogas plants reveals multiple steady-states in community composition.
Kohrs F, Heyer R, Bissinger T, Kottler R, Schallert K, Püttker S, Behne A, Rapp E, Benndorf D, Reichl U., Anaerobe 46(), 2017
PMID: 28189830
Kohrs F, Heyer R, Bissinger T, Kottler R, Schallert K, Püttker S, Behne A, Rapp E, Benndorf D, Reichl U., Anaerobe 46(), 2017
PMID: 28189830
Next-generation proteomics faces new challenges in environmental biotechnology.
Armengaud J., Curr Opin Biotechnol 38(), 2016
PMID: 26950175
Armengaud J., Curr Opin Biotechnol 38(), 2016
PMID: 26950175
12 References
Daten bereitgestellt von Europe PubMed Central.
The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms.
Wilmes P, Bond PL., Environ. Microbiol. 6(9), 2004
PMID: 15305916
Wilmes P, Bond PL., Environ. Microbiol. 6(9), 2004
PMID: 15305916
Functional metaproteome analysis of protein extracts from contaminated soil and groundwater.
Benndorf D, Balcke GU, Harms H, von Bergen M., ISME J 1(3), 2007
PMID: 18043633
Benndorf D, Balcke GU, Harms H, von Bergen M., ISME J 1(3), 2007
PMID: 18043633
Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass.
Hanreich A, Heyer R, Benndorf D, Rapp E, Pioch M, Reichl U, Klocke M., Can. J. Microbiol. 58(7), 2012
PMID: 22690648
Hanreich A, Heyer R, Benndorf D, Rapp E, Pioch M, Reichl U, Klocke M., Can. J. Microbiol. 58(7), 2012
PMID: 22690648
Proteomic tools for environmental microbiology--a roadmap from sample preparation to protein identification and quantification.
Wohlbrand L, Trautwein K, Rabus R., Proteomics 13(18-19), 2013
PMID: 23894077
Wohlbrand L, Trautwein K, Rabus R., Proteomics 13(18-19), 2013
PMID: 23894077
Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants.
Kohrs F, Heyer R, Magnussen A, Benndorf D, Muth T, Behne A, Rapp E, Kausmann R, Heiermann M, Klocke M, Reichl U., Anaerobe 29(), 2013
PMID: 24309213
Kohrs F, Heyer R, Magnussen A, Benndorf D, Muth T, Behne A, Rapp E, Kausmann R, Heiermann M, Klocke M, Reichl U., Anaerobe 29(), 2013
PMID: 24309213
Metaproteome analysis of the microbial communities in agricultural biogas plants.
Heyer R, Kohrs F, Benndorf D, Rapp E, Kausmann R, Heiermann M, Klocke M, Reichl U., N Biotechnol 30(6), 2013
PMID: 23369865
Heyer R, Kohrs F, Benndorf D, Rapp E, Kausmann R, Heiermann M, Klocke M, Reichl U., N Biotechnol 30(6), 2013
PMID: 23369865
The MetaProteomeAnalyzer: a powerful open-source software suite for metaproteomics data analysis and interpretation.
Muth T, Behne A, Heyer R, Kohrs F, Benndorf D, Hoffmann M, Lehteva M, Reichl U, Martens L, Rapp E., J. Proteome Res. 14(3), 2015
PMID: 25660940
Muth T, Behne A, Heyer R, Kohrs F, Benndorf D, Hoffmann M, Lehteva M, Reichl U, Martens L, Rapp E., J. Proteome Res. 14(3), 2015
PMID: 25660940
Comparative study of stability and half-life of enzymes and enzyme aggregates implemented in anaerobic biogas processes
Binner, Biomass Conv. Bioref. 1(), 2011
Binner, Biomass Conv. Bioref. 1(), 2011
KEGG: kyoto encyclopedia of genes and genomes.
Kanehisa M, Goto S., Nucleic Acids Res. 28(1), 2000
PMID: 10592173
Kanehisa M, Goto S., Nucleic Acids Res. 28(1), 2000
PMID: 10592173
AUTHOR UNKNOWN, 0
Microbial community analysis of a biogas-producing completely stirred tank reactor fed continuously with fodder beet silage as mono-substrate.
Klocke M, Mahnert P, Mundt K, Souidi K, Linke B., Syst. Appl. Microbiol. 30(2), 2006
PMID: 16697135
Klocke M, Mahnert P, Mundt K, Souidi K, Linke B., Syst. Appl. Microbiol. 30(2), 2006
PMID: 16697135
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.
Vizcaino JA, Cote RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Perez-Riverol Y, Reisinger F, Rios D, Wang R, Hermjakob H., Nucleic Acids Res. 41(Database issue), 2012
PMID: 23203882
Vizcaino JA, Cote RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Perez-Riverol Y, Reisinger F, Rios D, Wang R, Hermjakob H., Nucleic Acids Res. 41(Database issue), 2012
PMID: 23203882
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