Evaluation of Homogenization Methods for Extraction of Live Bacteria and Recombinant DNA in Soil

In many soil types, ubiquitous bacteria are present very in low quantities due to the inherent challenges of microorganism survival in environmental conditions. While, in some cases, only present in low quantity, soil microorganisms are a critical component of our ecosystem. Soil microbiome studies aim to characterize the microbial repertoire and to correlate the microbial population with soil and ecological functions. While many studies involve culturing and isolation of bacteria harvested from the soil, some organisms are hard to propagate in the laboratory or require the sample to be processed directly to maintain analyte integrity. In this study, the recovery and qPCR detection of a modified bacterium from spiked soil samples was evaluated to find a limit of detection with silica spin column purification methods for plasmids. Genetically modified Escherichia coli (E. coli) with green florescent protein (GFP) allowed the absolute subtraction of background signal originating from native organisms found in the soil samples.