Development of an Inhibitor Resistant Genomic Assay for Environmental Samples

Abstract

Rapid identification and quantification of bacteria is beneficial for the environmental monitoring, such as water quality and site clean-up. However, existing bacteria quantification methods, such as colony counting or quantitative PCR (qPCR) assay, are limited because of their poor sensitivity and specificity, or vulnerable to inhibitors existing in the environment. A new genomic assay (referred as “NanoGene assay”) has been developed; it can quantify genes based on DNA hybridization using magnetic beads and quantum dot nanoparticles (Kim and Son 2010a). The NanoGene assay has shown high sensitivity and selectivity in quantifying a functional gene and has the potential to be resistant to inhibitors (Kim et al. 2011a; Kim et al. 2011b). The objective of this study is to further demonstrate the NanoGene assay for the inhibitor resistance in soils, to develop simple and rapid sample pretreatment for improving in situ applicability of the method, to identify and predict the effects of environmental factors to gene quantification and inhibition.