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.

The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment

“…Previous metaproteome studies provided detailed phylogenetic information of the microbial composition [12,14] and helped to provide important insights about ecological equilibrium between microbial populations. Crude-spiking increased the abundance of the proteobacterialassociated proteins with impacts at the taxonomic level of the order.…”

“…However, these approaches cannot easily link phylogenetic and functionalities in the microbial community. Nowadays, a definitive linkage between functional and taxonomic relationships of the microbial populations inhabiting hydrocarbon-polluted soils is feasible due to the recent advance in the field of environmental [11,12] and, particularly in soil [13,14] metaproteomics.…”

RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes

“…Protein-SIP, the youngest amongst the different strategies to detect biomarker labelling, allows for the most direct indication of specific metabolic activities by a given microbial population [10]. However, it requires a considerable depth of à-priori (meta)genomic information in order to phylogenetically place labelled peptide sequences.…”

MetaProSIP: Automated Inference of Stable Isotope Incorporation Rates in Proteins for Functional Metaproteomics

“…The use of stable isotopelabeled substrates can verify metabolic active key players as well as elemental fluxes. Because these fluxes can be quantified and phylogenetically resolved through protein-SIP, detailed insights into the community can be obtained 6 . The relative isotope abundance (RIA) reflects the heavy isotope incorporation into the proteins, and the labeling ratio (LR) reflects the ratio of the labeled to the unlabeled peptide.…”

“…This results in increased peptide identification and a concomitant larger coverage of phylogenetic and functional information. 6 The first part of the workflow identifies unlabeled peptides. In the case of unlabeled reference samples, prior map alignment is performed to compensate for retention time shifts.…”