Rapid method for direct extraction of mRNA from seeded soils

Abstract

A protocol for direct extraction of mRNA from soil samples was developed. Soil samples (10 g) were washed twice with 120 mM phosphate buffer (pH 5.2). The lysis of cells, fixation of RNA, and hydrolysis of DNA were achieved by vigorously shaking the washed soil in a 4 M guanidine thiocyanate solution containing 25 mM sodium citrate, 0.5% sarcosyl, and 0.1 M 2-mercaptoethanol. The pH of the homogenized mixture was adjusted with 2 M sodium acetate (pH 4.0); the mRNA was then extracted with phenol and chloroform. Total RNA was precipitated with isopropanol. This method extracts up to 17 mug of total RNA per g (wet weight) of soil containing 8.0 x 10 cells of Pseudomonas aeruginosa PU21, and mRNA has been detected in 160-ng total RNA fractions. This method has been used for the detection of mRNA transcribed from specific biodegradative genes, including the nah and mer operons, in contaminated soils. This extraction method can be completed within a few hours and has tremendous potential for ecological studies of in situ gene expression among soil microbiotas.