title: Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.
abstract: The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.
authors.affiliation: 1] Department of Proteomics, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany [2] Department of Metabolomics, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany [3] Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark.
authors.forename: Martin
authors.initials: M
authors.lastname: von Bergen
authors.forename: Nico
authors.initials: N
authors.lastname: Jehmlich
authors.forename: Martin
authors.initials: M
authors.lastname: Taubert
authors.forename: Carsten
authors.initials: C
authors.lastname: Vogt
authors.forename: Felipe
authors.initials: F
authors.lastname: Bastida
authors.forename: Florian-Alexander
authors.initials: FA
authors.lastname: Herbst
authors.forename: Frank
authors.initials: F
authors.lastname: Schmidt
authors.forename: Hans-Hermann
authors.initials: HH
authors.lastname: Richnow
authors.forename: Jana
authors.initials: J
authors.lastname: Seifert
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000378:metabolism*; D002247:Carbon Isotopes / Q000378:metabolism; D004463:Ecology / Q000379:methods*; D006801:Humans; D007553:Isotope Labeling; D064307:Microbiota / Q000235:genetics / Q000502:physiology*; D009587:Nitrogen Isotopes / Q000378:metabolism; D040901:Proteomics
chemical_list: D001426:Bacterial Proteins; D002247:Carbon Isotopes; D009587:Nitrogen Isotopes