Challenges in quantifying microbial gene expression in soil using quantitative reverse transcription real-time PCR

The quantification of microbial gene expression in diverse soil samples via quantitative reverse transcription real time polymerase chain reaction (qRT-PCR) has numerous challenges including total RNA extraction, sample preparation, qRT-PCR optimization and the correlation of gene expression with function. Despite these challenges, microbial gene expression has been successfully quantified in soil microorganisms, and will yield valuable information on soil functions and expression of genes in soil samples. In this perspective we discuss challenges of measuring microbial gene expression and highlight recent applications using qRT-PCR to research gene function in soil.