A Functional Genomics Approach for Improving ....

Chlorinated Organic Bioremediation ProcessesDr. David R. JohnsonPostdoctoral ResearcherDepartment of Fundamental MicrobiologyUniversity of Laussane, SwitzerlandAbstract:Chlorinated organics are among the most prevalent contaminants of groundwater resources and pose a significant threat to human and ecological health. Remediating these resources with pump-and-treat strategies is technically challenging and costly. Fortunately, strategies that utilize microorganisms to degrade these pollutants in situ have been developed and applied with success. Of particular interest are members of the Dehalococcoides group of bacteria because of their ability to degrade a wide range of chlorinated organic pollutants. Although significant progress has been made, effective methods for optimizing and monitoring the performance of Dehalococcoides-based bioremediation systems are now needed.To begin to address these needs, this research applied functional genomics tools to improve our understanding of the model bacterium Dehalococcoides ethenogenes strain 195. Transcriptomics were analyzed by whole-genome microarrays while proteomics were analyzed by liquid chromatography coupled with tandem mass spectrometry. Active and non-active cultures were characterized and compared to identify factors that can potentially limit dechlorination performance. This approach successfully identified cobalamin (vitamin B12) as a key factor controlling dechlorination activity and revealed novel strategies for minimizing cobalamin deficiencies within bioremediation systems. In addition, these studies identified mRNA and peptide biomarkers that could be used to quantitatively assess the physiological state of strain 195 within uncharacterized systems. The results of this research demonstrate the utility of functional genomics approaches for accelerating our understanding of environmental biological systems. More collaborative efforts between the fields of genome sciences and environmental engineering are now needed to help address current and future environmental problems.

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