The Use of DNA Microarrays for Bioremediation

Aaron D. Peacock (Haley & Aldrich, Inc.), Darrell Chandler (Akonni Biosystems, Inc.), Dora Ogles (Microbial Insights, Inc.), Phil Long (Pacific Northwest National Laboratory)

Microorganisms in the subsurface have a direct impact on the nature, extent, and fate of many contaminants.  Microorganisms can create conditions that decrease contaminant mobility or directly transform contaminants into innocuous or immobile forms.  However, there are presently very few readily available methods for assessing in situ microbial community structure, activity or remediation potential within a time frame that impacts treatment or remediation decisions. The objective of this effort was to develop and validate a simple-to-use, field-portable, microarray-based system for monitoring microbial community structure and dynamics in groundwater and subsurface environments. The system performance and efficacy was verified on 50 groundwater samples from an in situ Uranium bioremediation field experiment conducted at the Rifle, Colorado Integrated Field Research Center (IFRC).  Samples were collected over a 4 month period, representing site status before acetate injection, during the iron-reduction phase; during the transition from iron to sulfate reduction, and during the sulfate reduction phase. Sample-to-answer results for the field deployment were obtained in 4 hours and showed an expected onset of metal-reducer signatures within four days of acetate addition to the subsurface.  Retrospective analysis of all samples with the field portable system likewise showed the expected progression of microarray and microbial signatures from iron to sulfate reducers with changes in acetate amendment and in situ field conditions. Microarray results and S/N ratios were in concordance with quantitative PCR data sets and lipid profiles, indicating that the field-portable array is a reasonable and useful indicator of microbial presence and response to in situ remediation of a uranium-contaminated site.

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