The mere study of individual genes and their regulation, which has been well developed in the recent years, is not sufficient to fully understand microbial adaptation strategies in soil ecosystems. The aim of this research is to investigate at a molecular level the proteins released by a complex microbial consortia in soil. These proteins are particularly interesting for their ecological functions and biotechnological potential applications. They can be considered functional bioindicators to monitor dynamics and sustainability of environmental quality. The proteomic technologies will allow to revisit microbial ecology concepts by linking genetic and functional diversity in microbial communities and relating taxonomic and functional diversity to ecosystem stability.
Our research group is continuing the development of the method for the soil proteomic studies. The heterogeneity of soil, associated complex microbial communities, and presence of interfering compounds (e.g. phenolic substances, humic acids) make the extraction of protein from soil a technical challenge. We have developed a protocol for extracting environmental extracellular proteins (secretome) from soil. This is a reproducible, dialysis filtration-based, three-phase extraction applicable to a variety of soil types. The protein extracts have been analyzed on conventional SDS-PAGE gels and coomassie stained. The procedure has been successfully applied to soils with different origin selected on the basis of the main characteristics that could interfere with the secretome extraction procedure such as organic carbon content and texture (Fig.1).
Moreover, differences in protein pattern on SDS-page could be useful to identify the effects of pollutants on protein composition. For example, in a bioremediation experiment, preliminary protein SDS-page results, have permitted the identification of proteins that have been recovered in phytoremediated soil with respect to an untreated soil (Fig.2); this may become a basic tool for improving the biogeochemical status of soil during the decontamination. In addition, the combination of mass spectrometry and protein database could identify the microbial populations that are active in soil decontamination.