Soil metaproteomics: a review of an emerging environmental science. Significance, methodology and perspectives

Abstract

SummarySoil is a dynamic system in which microorganisms perform important tasks in organic matter transformations and nutrient cycles. Recently, some studies have started to focus on soil metaproteomics as a tool for understanding the function and the role of members of the microbial community. The aim of our work was to provide a review of soil proteomics by looking at the methodologies used in order to illustrate the challenges and gaps in this field, and to provide a broad perspective about the use and meaning of soil metaproteomics. The development of soil metaproteomics is influenced strongly by the extraction methods. Several methods are available but only a few provide an identification of soil proteins, while others extract proteins and are able to separate them by electrophoresis but do not provide an identification. The extraction of humic compounds together with proteins interferes with the latter's separation and identification, although some methods can avoid these chemical interferences. Nevertheless, the major problems regarding protein identification reside in the fact that soil is a poor source of proteins and that there is not enough sequencedatabase information for the identification of proteins by mass spectrometric analysis. Once these pitfalls have been solved, the identification of soil proteins may provide information about the biogeochemical potential of soils and pollutant degradation and act as an indicator of soil quality, identifying which proteins and microorganisms are affected by a degradation process. The development of soil metaproteomics opens the way to proteomic studies in other complex substrates, such as organic wastes. These studies can be a source of knowledge about the possibility of driven soil restoration in polluted and degraded areas with low organic matter content and even for the identification of enzymes and proteins with a potential biotechnological value.

The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes

“…1). As with metagenomics and metatranscriptomics, there has been a steady evolution of the methodology for the extraction and analysis of proteins from soils (Bastida et al, 2009;Hettich et al, 2012;Siggins et al, 2012). Nonetheless, the extraction of proteins lags behind that of nucleic acids, in part because of the strong interactions between proteins and other organic molecules and inorganic minerals in soils (Adamczyk et al, 2008; Kleber et al, 2007).…”

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

“…Metaproteomic studies of rhizosphere samples are still at its beginning and first reports were only published very recently Wu et al, 2011). In those studies, proteins were directly extracted from rhizosphere samples (without a preceding physical enrichment step of microbial cells; Bastida et al, 2009), separated by twodimensional gel electrophoresis and identified by MALDI-TOF/TOF. The studies revealed that a direct protein extraction method restricted microbial protein identification in the rhizosphere samples by the high recovery of plant proteins (475% from 120 different identified proteins).…”

The Influence of Polychlorinated Biphenyls Contamination on Soil Protein Expression

“…Furthermore, the changes in protein pattern might indicate that the community structure of soil microorganisms and their physiological activities were modified significantly under pollutants stress [15]. These low molecular weight proteins could be related to the presence of PCBs and could be a microbial response to organic pollutants.…”

“…Currently, the emergence of soil proteomics could offer us a new perspective to solve the problem [15]. Proteins are the major actors in organism metabolism process, and they fall into a variety of categories; for example, enzymes are proteins with a catalytic function.…”