Optimisation of Protein Extraction Methods for Metaproteomics of Freshwater Microbial Communities

Recent developments in the molecular biology toolbox allow access to the genetic structure and diversity of microbial communities. More specifically, the advances in metaproteomics allow us to identify the functional expression of the genome and link this information to the biogeochemical processes of an ecosystem. One of the challenges, in this field, is the optimisation of protein extraction methods from environmental samples where protein concentrations can be low and the presence of interfering substances high. Experiments were conducted by extracting proteins from freshwater microbial communities utilising an array of physical and chemical methods. We used protein yield and 1D SDS-PAGE resolution as deciding factors. Liquid N2 grinding and freeze-thaw cycles resulted, after purification, in an enhanced resolution and protein yield. Furthermore, regarding sample purification, the use of detergent removal columns resulted in higher yields but literature indicates that acetone precipitation is more efficient in removing interfering substances.