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dc.contributor.authorGéron, Augustinen_UK
dc.contributor.authorWerner, Johannesen_UK
dc.contributor.authorWattiez, Ruddyen_UK
dc.contributor.authorLebaron, Philippeen_UK
dc.contributor.authorMatallana-Surget, Sabineen_UK
dc.description.abstractUnraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotype–genotype linkages. Despite its rapid development, this technology has faced many technical challenges that still hamper its potential power. How to maximize the number of protein identification, improve quality of protein annotation, and provide reliable ecological interpretation are questions of immediate urgency. In our study, we used a robust metaproteomic workflow combining two protein fractionation approaches (gel-based versus gel-free) and four protein search databases derived from the same metagenome to analyze the same seawater sample. The resulting eight metaproteomes provided different outcomes in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. The characterization and/or representativeness of numerous proteins from ecologically relevant taxa such as Pelagibacterales, Rhodobacterales, and Synechococcales, as well as crucial environmental processes, such as nutrient uptake, nitrogen assimilation, light harvesting, and oxidative stress response, were found to be particularly affected by the methodology. Our results provide clear evidences that the use of different protein search databases significantly alters the biological conclusions in both gel-free and gel-based approaches. Our findings emphasize the importance of diversifying the experimental workflow for a comprehensive metaproteomic study.en_UK
dc.publisherFrontiers Media SAen_UK
dc.relationGéron A, Werner J, Wattiez R, Lebaron P & Matallana-Surget S (2019) Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics. Frontiers in Microbiology, 10, Art. No.: 2395.
dc.rights© 2019 Géron, Werner, Wattiez, Lebaron and Matallana-Surget. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY - The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.en_UK
dc.subjectmass spectrometryen_UK
dc.subjectmicrobial ecologyen_UK
dc.titleDeciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomicsen_UK
dc.typeJournal Articleen_UK
dc.citation.jtitleFrontiers in Microbiologyen_UK
dc.type.statusVoR - Version of Recorden_UK
dc.contributor.funderRoyal Societyen_UK
dc.contributor.affiliationBiological and Environmental Sciencesen_UK
dc.contributor.affiliationLeibniz Institute of Baltic Sea Research, Warnemündeen_UK
dc.contributor.affiliationUniversity of Monsen_UK
dc.contributor.affiliationSorbonne Universityen_UK
dc.contributor.affiliationBiological and Environmental Sciencesen_UK
dc.description.refREF Compliant by Deposit in Stirling's Repositoryen_UK
dc.relation.funderprojectOCEANCLOCK: Light/dark cycle in picoplankton in response to environmental changeen_UK
Appears in Collections:Biological and Environmental Sciences Journal Articles

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