The application of proteomic tools in ecology offers great promise, but methodological development is in an early stage. For example, one challenge unique to environmental proteomics is dealing with complex mixtures of unknown organisms. Our group has developed a proteomic approach to examine the response of complex microbial communities to stress. The response of a complex bacterial community to cadmium exposure was examined with 2DE, MALDI-TOF/TOF MS, and de novo peptide sequencing. Following cadmium exposure, community proteome responses were observed after 0.25, 1, 2, and 3 h of exposure, with more than 100 changes in protein expression at each time point. More than 100 unique differentially expressed proteins were identified through database searching and de novo sequencing, including ATPases, oxidoreductases, and transport proteins. A second challenge in environmental proteomics is the need for extraction and purification techniques suitable for downstream proteomic analyses. We developed a new extraction protocol, and examined the response of a semi-arid grassland soil and an Arctic tundra soil to freeze-thaw induced stress. Our hypothesis was that Arctic soil microbes are better adapted to deal with freeze-thaw stress, and would express a more diverse suite of proteins in response to freeze-thaw. Bulk soil proteins were extracted before and after freeze-thaw, and separated on polyacrylamide gels to detect up- and down- regulated proteins. Differential display revealed over 50 proteins that were responsive to freeze-thaw for both soils. Especially when combined with genomic approaches, these methods will help to link microbial community composition to functioning.