Metaproteomics; marine sediment; protein extraction; Microbiology
Abstract :
[en] Marine sediments harbor extremely diverse microbial communities that contribute to global biodiversity and play an essential role in the functioning of ecosystems. However, the metaproteome of marine sediments is still poorly understood. The extraction of proteins from environmental samples is still a challenge, especially from marine sediments, due to the complexity of the matrix. Therefore, methods for protein extraction from marine sediments need to be improved. To develop an effective workflow for protein extraction for clayey sediments, we compared, combined and enhanced different protein extraction methods. The workflow presented here includes blocking of protein binding sites on sediment particles with high concentrations of amino acids, effective cell lysis by ultrasonic capture, electro-elution, and simultaneous fractionation of proteins. To test the protocol's efficacy, we added Escherichia coli cells to sediment samples before protein extraction. By using our refined workflow, we were able to identify a comparable number of E. coli proteins from the supplemented sediment to those from pure E. coli cultures. This new protocol will enable future studies to identify active players in clay-rich marine sediments and accurately determine functional biodiversity based on their respective protein complements.
Disciplines :
Microbiology
Author, co-author :
Ostrzinski, Anne; Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
KUNATH, Benoît ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine > Systems Ecology > Team Paul WILMES
Soares, André Rodrigues; Department of Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
LACZNY, Cedric Christian ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
HALDER, Rashi ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Scientific Central Services > Sequencing Platform
Kallmeyer, Jens; Subsurface Geochemistry, Section Geomicrobiology, GFZ Helmholtz Centre for Geoscience, 14473 Potsdam, Germany
di Primio, Rolando; Exploration Manager Play Analysis and Access, Aker BP, 1366 Lysaker, Norway
WILMES, Paul ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
Probst, Alexander J; Department of Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
Trautwein-Schult, Anke; Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
Becher, Dörte; Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
External co-authors :
yes
Language :
English
Title :
Systematic evaluation of protein extraction for metaproteomic analysis of marine sediment with high clay content.
H2020 - 899667 - PROSPECTOMICS - Using Omics Techniques for Hydrocarbon Prospecting
FnR Project :
FNR13684739 - metaPUF - The Dark Metaproteome: Identifying Proteins Of Unknown Function In The Human Gut Microbiome, 2019 (01/04/2020-31/03/2022) - Paul Wilmes
Funders :
European Union’s Horizon 2020 research and innovation program Luxembourg National Research Fund European Union
Funding text :
This work has received funding from the European Union\u2019s Horizon 2020 research and innovation program under grant agreement n\u00B0 899667. This project benefitted through funding from the Luxembourg National Research Fund (CORE/19/13684739) to PW.
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