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Environmental Proteomics: Methods development and characterization of proteinaceous compounds in environmental samples

Final Report Summary - ENVIPRO (Environmental Proteomics: Methods development and characterization of proteinaceous compounds in environmental samples)

To date, substantial effort has been devoted to characterize the microbial communities in environmental samples, to understand the role of individual microbes and to unravel the key processes controlling the functioning of various ecosystems. Several culture-based methods and culture-independent DNA-based techniques have been developed for the assessment of microbial diversity, but these have some serious disadvantages (inefficient, laborious, slow, not informative about microorganisms function). Although these approaches enable the phylogenetic analysis of microbial communities, they do not necessary tell us what individual microorganisms can do and if they play any role in ecosystem functioning. The analysis of messenger-RNA has been suggested as an alternative approach for the retrieval of useful information about the cell’s major activities, but mRNA molecules degrade very rapidly and their analysis is usually problematic.

In the last few years, there has been increasing interest in the potential applications of proteomics in the fields of environmental chemistry and ecology. Recently, proteomics opened a new avenue for the study of microorganisms in the different environmental compartments and the elucidation of their role in biogeochemical processes. Considering that proteins are the end products of gene expression, the identification characterization of proteinaceous molecules in environmental matrices can provide information not only for the processes taking place, but also for the identity of the active microbial species. The key goal of ENVIPRO project was to establish an appropriate proteomic workflow that will be properly tailored toward mass-spectrometry based characterization of proteins/peptides in environmental matrices and to enable the investigation of bacteria functioning under challenging environmental conditions.

The main objectives of the ENVIPRO project can be summarized as follows:
- To offer extensive hands-on training in modern proteomic techniques to the Marie-Curie fellow
- To select specific “model” environmental samples and evaluate the efficiency of the different sample treatment steps involved in the extraction, purification and analysis of proteins
- To integrate the most efficient analytical steps and establish a proteomic workflow that will be best-suited for the application of proteomics in environmental samples
- To evaluate the applicability of the developed method in a number of easily accessible environmental samples, such as soils.
- To evaluate the applicability of proteomics in aerosol samples.