Field Portable Gel Element Arrays for Microbial Community Profiling in Subsurface Sediments and Groundwater

In order to implement effective, safe, and scientifically-based approaches to the remediation of contaminated sites, such as some in the DOE complex, engineers and policy makers require fundamental information on microorganisms in the subsurface. In particular, information is needed to identify: factors that affect specific changes in contaminant speciation and mobility; how microbial populations respond to natural or engineered changes; and how shifts in population structure are related to or constitute signatures of bioremediation effectiveness. This project will develop technology for a field-deployable, facile, near-real-time analysis system that will provide the information needed to monitor microbial activity and composition in the subsurface. Phase I will: (1) automate a metal-, sulfate-, and nitrate-reducer gel element array sub-circuit for direct rRNA hybridization and detection, with the option of performing on-card thermal dissociation analysis; (2) demonstrate the on-card identification of Geobacter chapellei rRNA and natural microbiota from nucleic acids processed (off-card) from subsurface sediment; and (3) develop and test a prototype sample preparation sub-circuit for rRNA purification. Commercial Applications and Other Benefits as described by the applicant: The technology should enable the near real-time, direct identification of in situ contaminant transformation, thereby improving the management of onsite cleanup efforts. As a result, the public would be better protected from the re-mobilization of heavy metals and radionuclides in aquifers, which might occur over time due to changing subsurface conditions. In addition, the basic technology platform could be expanded to monitor other microorganisms capable of transforming DOE contaminants of concern, including chlorinated solvents and aromatic hydrocarbons.