Lehrstuhl für Bioprozesstechnik
 

Metaproteome Analysis of Complex Microbial Communities

Responsible:    Dirk Benndorf (PhD)
Contributors:    Robert Heyer (PhD student), Fabian Kohrs (PhD student),
                       Sebastian Püttker (PhD student), Kay Schallert (scientific coworker)
                       Erdmann Rapp (PhD, MPI Magdeburg)


Micro-organisms represent a significant proportion of biomass on earth and drive many natural cycles. Several analytical techniques allow the description of the structural and functional microbial diversity in ecosystems. Nucleic acids and phospholipid fatty acids are often used as biomarkers for microbial identity and metabolic potential in environmental samples. However, these approaches are not suitable to detect actual biological activities. In comparison to genes and lipids as biomarkers proteins are involved in metabolism and represent biological activities. Thus this project is devoted to establish the analysis of proteins extracted from natural [1,2] and technical [3] microbial communities. Protocols for extraction and gel-based (2D-electrophoresis) or gel-free (LC-MS/MS) analysis of proteins from wastewater treatment [3,12] and biogas [4,5,6,8,10,11,13] plants are currently improved.
A large scale proteotyping study separated biogas plants according to process temperature and reactor type [14]. These protocols will be applied to laboratory as well as industrial scale plants in order to screen for biomarkers that can be used to increase the performance of these systems.  Suitable software for the analysis of the incoming MS data (MetaProteomeAnalyzer) was simultaneously programmed [7,9]. The softwarwe is provided and continuously improved within de.NBI partner project MetProtServ.

Metaproteomics workflow
Collaborations:
  • Michael Klocke, Susanne Theuerl (Leibniz-Institut für Agrartechnik und Bioökonomie)
  • Ramona Kuhn (Brandenburgische Technische Universität, Cottbus)
  • Andreas Schlüter, Alexander Sczyrba (CeBiTec, Universität Bielefeld)
  • Anna Schnürer, Bettina Müller (Swedish University of Agricultural Sciences, Uppsala)
Funding:
  • Deutsche Bundesstiftung Umwelt e.V. (DBU), PhD grant for Robert Heyer (01.08.2011-31.07.2014): Prozesskontrolle und Optimierung der Biogasproduktion mittels Metaproteomanalyse.
  • BMELV, FNR, FKZ 22028811, Cooperative project (01.11.2011-31.10.2013): Prozessmikrobiologie in landwirtschaftlichen Biogasanlagen – Ermittlung der mikrobiellen Diversität in Biogasanlagen sowie von hauptsächlichen verfahrenstechnischen Einflussfaktoren auf die Mikroflora (BIOGAS-BIOCOENOSIS), workpackage: Ermittlung der hauptsächlich hydrolytisch bzw. methanogen aktiven Mikroorganismen durch Analyse des Metaproteoms.
  • MELV, FNR, FKZ 22404115, Cooperative project (01.12.2015-30.11.2018): Biogas-Messprogramm III, project 2: Systemmikrobiologie, workpackage 3: Enzymatische Biodiversittät.
  • JGI, CSP16 – 1945, Cooperative sequencing project (01.12.2015-30.11.2016): Anaerobic fungi and assessment of their potential for biogas production.
  • de.NBI - partner – project (01.11.2016-31.10.2019): „MetaProteomeAnalyzer Service“ (BMBF, PTJ, FKZ 031L0103).
  • DFG - project (01.10.2017 - 31.09.2018): InflammatorySystems-Microbiome: Systemdiagnostik des menschlichen Darmmikrobioms bei entzündungsbedingten Erkrankungen mittels Metaproteomeanalyse (DFG, HE 8077/1-1).
References:
  1. Benndorf, D., Balcke, G.U., Harms, H. and von Bergen, M. (2007). Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. The ISME Journal 1 , 224-234
  2. Benndorf, D., Vogt, C., Jehmlich, N., Schmidt, Y,. Thomas, H., Woffendin, G., Shevchenko, A., Richnow, H.H., von Bergen, M. (2009) Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments. Biodegradation 20, 737-750.PubMed
  3. Kuhn, R., Benndorf, D., Rapp, E., Reichl, U., Palese, L.L., Pollice, A. (2011) Metaproteome Analysis of Sewage Sludge from Membrane Bioreactors. Proteomics 11, 2738-44. PubMed
  4. Hanreich, A., Heyer, R., Benndorf, D., Rapp, E.,Pioch, M., Reichl, U., Klocke, M. (2012). Determination of the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass by metaproteome analysis. Can. J. Microbiol. 58, 917-922. PubMed
  5. Hanreich, A., Schimpf, U., Zakrzewski, M., Schlüter, A., Pühler, A., Benndorf, D., Rapp, E. Reichl, U., Heyer, R., Klocke, M. (2013). Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. Systematic and Applied Microbiology 36, 330-338. PubMed
  6. Heyer, R., Kohrs, F. , Benndorf, D., Rapp, E. , Kausmann, R. ,  Heiermann, M. , Klocke, M., Reichl, U. (2013). Metaproteome analysis of the microbial communities in agricultural biogas plants. New Biotechnology 30, 614-622. PubMed
  7. Muth, T., Benndorf, D., Reichl, U., Rapp, E., Martens, L. (2012). Searching for a needle in a stack of needles: challenges in metaproteomics data analysis. Mol. Biosyst. 9, 578-585. PubMed
  8. Kohrs, F., Heyer, R., Magnussen, A., Benndorf, D., Muth, T., Behne, A., Rapp, E., Kausmann, R., Heiermann, M., Klocke, M., Reichl, U. (2014). Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants. Anaerobe 29, 59-67. PubMed
  9. Muth, T., Behne, A., Heyer, R., Kohrs, F., Benndorf, D., Hoffmann, M., Lehtevä, M., Reichl, U., Martens, L., Rapp, E. (2015). The MetaProteomeAnalyzer: a powerful open-source software suite for metaproteomics data analysis and interpretation. J Proteome Res.14,1557-1565. PubMed
  10. Theuerl, S., Kohrs, F., Benndorf, D., Maus, I., Wibberg, D., Schlüter, A., Kausmann, R., Heiermann, M., Rapp, E., Reichl, U., Pühler, A., Klocke, M. (2015). Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome. Appl Microbiol Biotechnol., 99, 7791-7803. PubMed.
  11. Heyer, R., Kohrs, F., Reichl, U., Benndorf, D. (2015). Metaproteomics of complex microbial communities in biogas plants. Microb. Biotechnol., 8, 749–763. PubMed.
  12. Püttker, S., Kohrs, F., Benndorf, D., Heyer, R., Rapp, E., Reichl, U. (2015). Metaproteomics of activated sludge from a wastewater treatment plant - A pilot study. Proteomics 15, 3596-3601 . PubMed.
  13. Kohrs, F., Wolter, S., Benndorf, D., Heyer, R., Hoffmann, M., Rapp, E., Bremges, A., Sczyrba, A., Schlüter, A., Reichl, U. (2015). Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities. Proteomics 15, 3585-3589. PubMed.
  14. Heyer, R., Benndorf, D., Kohrs, F., De Vrieze, J., Boon, N., Hoffmann, M., Rapp, E.,Schlüter, A., Sczyrba, A., Reichl, U. (2016) Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type. Biotechnol Biofuels  9,155. PubMed