Environmental metaproteomics: Identifying the protein machinery that impact the activities and interactions of microbes in isolation or communities

The availability of complete genome sequences for many cultured microbes, as well as some consortia and even communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, proteomic, and metabolomic information. This provides a unique opportunity to begin to characterize the molecular activities of these microbial systems (and their interactions) at a comprehensive level never before possible. Such information would not only provide details about the organizational, functional, and metabolic activities of such systems, but also the untapped reserve of molecular activities that might be invoked under certain environmental conditions (i.e. bacteria could be tailored to degrade specific metallic contaminants or produce copious amounts of bioenergy-related products). Environmental proteomics has as its goal the comprehensive identification of the complete suite of functional proteins in a natural environmental sample. Key developments in experimental (in particular mass spectrometry) and computational (in particular high performance computing) technologies have enabled the pursuit of this previously elusive goal by providing a powerful approach that can be sufficiently scaled to provide the high-throughput measurements needed. Not only has this facilitated the characterization of the functional activities of microbial isolates, but also has opened the door to the study of more complex microbial consortia and communities from natural environmental samples, such as the human microbiome and soil communities. This chapter will provide a description of the overall scope and goals of environmental proteomics, with emphasis on the experimental approach and its inherent caveats, instrumentation, informatics, and biological outputs. Additionally, examples of proteomic measurements from a variety of environmental samples, such as ocean water, soils, and even human gut microbiomes, will be featured and described. Finally, an outlook section will be presented to highlight the biological deliverables provided by this experimental approach, as well as discuss new and emerging developments in this area.