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Briefings in Functional Genomics and Proteomics Advance Access published online on March 11, 2009
Briefings in Functional Genomics and Proteomics, doi:10.1093/bfgp/elp005
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© The Author 2009. Published by Oxford University Press. For permissions, please email: journals.permissions@oxfordjournals.org

Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology

Carla M. R. Lacerda and Kenneth F. Reardon

Corresponding author. Kenneth F. Reardon, Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1370, USA. Tel: +1 970 491 6505; Fax: +1 970 491 7369; E-mail: kenneth.reardon{at}colostate.edu

In this review, we present the use of proteomics to advance knowledge in the field of environmental biotechnology, including studies of bacterial physiology, metabolism and ecology. Bacteria are widely applied in environmental biotechnology for their ability to catalyze dehalogenation, methanogenesis, denitrification and sulfate reduction, among others. Their tolerance to radiation and toxic compounds is also of importance. Proteomics has an important role in helping uncover the pathways behind these cellular processes. Environmental samples are often highly complex, which makes proteome studies in this field especially challenging. Some of these challenges are the lack of genome sequences for the vast majority of environmental bacteria, difficulties in isolating bacteria and proteins from certain environments, and the presence of complex microbial communities. Despite these challenges, proteomics offers a unique dynamic view into cellular function. We present examples of environmental proteomics of model organisms, and then discuss metaproteomics (microbial community proteomics), which has the potential to provide insights into the function of a community without isolating organisms. Finally, the environmental proteomics literature is summarized as it pertains to the specific application areas of wastewater treatment, metabolic engineering, microbial ecology and environmental stress responses.

Keywords: environmental microbiology, metaproteomics, microbial community


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