New Approaches to the Assessment of Microbes in Groundwater: Application to Bioremediation and Detection of Pathogens

Objectives: 1) Development of molecular methods for the detection of a variety of bacteria in groundwater, including relevant pathogens 2) Development of molecular methods for the assessment of the population of methanotrophic bacteria in groundwater

Background: Because traditional culture-based methods of bacterial detection are of limited usefulness for environmental applications, molecular methods for the detection and quantification of bacteria are essential. This is relevant to the monitoring of bioremediation and of particular importance for pathogens, which may be may not be detected by culture-based methods. In earlier work, we applied Direct PCR (DPCR) to the detection of methanotrophic bacteria in environmental samples. In this work, this approach is extended to other bacteria, including pathogens.

To accurately predict the process of natural attenuation and to maximize the potential for bioremediation, it is necessary to understand the microbial processes at work. Ideally, it would be useful to know the composition of the bacterial population at a site and to be able to correlate particular microbes with reductions in the target chemical and with amendments of the site. This would lead to improved methods for monitoring and improved strategies for in situ bioremediation in which treatments of the site could be designed to stimulate the activity of those bacteria most effective in the degradation. In this research project, an approach to bacterial population analysis coupling DPCR to Single- Stranded Conformational Polymorphism (SSCP) was developed. This was applied to lab strains and natural populations of methanotrophic bacteria.