A practical guide to studying the microbiology of karst aquifers

Abstract

Examination of microbial communities within karst aquifers is an important aspect of determining the quality of the drinking water obtained from groundwater. While past work has been based on culture-based assays, a more complete view of the microbial community within karst aquifers can be achieved using molecular approaches based on DNA sequencing. Due to a reduced cell number when compared to surface environments, collecting sufficient microbial cells for analysis in karst aquifers can be problematic. In addition to issues of cell density, particulates due to the geologic location, technological limitations of equipment that can be hand-carried and work for extended periods underground, and even the physical access to some of these subsurface sites, all contribute to making examination of the microbiology in karst aquifers a challenge. This chapter highlights some of the approaches we have used to successfully isolate microbial cells for DNA extraction from an aquifer accessed in a remote cave location. The methods we developed can aid other researchers to evaluate the microbiology of similar isolated karst aquifers.