Proteomic Analysis of a Bacterial Consortium during Biodegradation of Chemical Mixtures (TSE-03N)

Colorado State University, Fort Collins CO

Investigators

Abstract

Kenneth F Reardon Colorado State University 0329514 Assessment of Proteomics as a Tool to Improve Performance of Biological Waste Treatment Processes (TSE03-N; Exploratory Proposal) Engineered environmental bioprocesses (e.g., wastewater treatment, in situ bioremediation) rely almost exclusively on microbial communities. However, the complexity of these communities can make it very difficult to appropriately design, control, and trouble-shoot those processes based on microbial parameters; instead, observed chemical changes must be monitored and biological factors inferred from them. This can lead to poor control and fault diagnosis, and does not allow optimization of the microbial consortium involved. Over the past 20 years, the use of nucleic acid-based methods has proven to be valuable to understand certain aspects of microbial communities. Nonetheless, these methods have significant limitations, primarily because ribosomal DNA analysis reveals an organism's phylogeny instead of its function, and the latter is far more important for engineering applications. The goal of this exploratory project is to obtain initial evidence of the type and utility of data that can be obtained by a proteomics analysis of a model waste treatment bioreactor. Specific objectives are (1) to demonstrate the ability to obtain 2-dimensional electrophoresis images from mixed culture samples, (2) to use pattern recognition techniques from computer science to determine whether protein markers of significant process changes can be identified, and (3) to compare these proteomic data with 16S rDNA population analysis and chemical concentrations. The project objectives will be achieved by analyzing samples from a model bio treatment system: a mixed-culture bioreactor degrading a mixture of organics that is subjected to different environmental perturbations (feed composition, pH, and toxin), and samples analyzed for proteome profiles, population composition, and organic chemical composition. This research is of significance and intellectual merit because it would produce the first evaluation of a new approach to analysis of environmental bioprocesses, with potential to reveal new information on the function of a microbial consortium with which to improve a bioprocess.