Evaluation of commercial RNA extraction kits for the isolation of viral MS2 RNA from soil

Abstract

Nucleic acid extraction is a critical step in the detection of an unknown biological agent. However, success can vary depending on the isolation and identification methods chosen and the difficulty of extraction from environmental matrices. In this work, bacteriophage MS2 RNA was extracted from three soil matrices, sand, clay, and loam, using five commercially available kits: the PowerSoil™ Total RNA Isolation, E.Z.N.A. ® Soil RNA, FastRNA ® Pro Soil-Direct, FastRNA ® Pro Soil-Indirect, and IT 1-2-3 Platinum Path™ kits. Success of the isolation was determined using an MS2-specific RT-PCR assay. The reproducibility and sensitivity of each method in the hands of both experienced and novice users were assessed and compared. Cost, operator time, and storage conditions were also considered in the evaluation. The RNA isolation method that yielded the best results, as defined by reproducibility and sensitivity, was the E.Z.N.A. ® Soil RNA kit for sand, the IT 1-2-3 Platinum Path™ Sample Purification kit for clay, and the FastRNA ® Pro Soil-Indirect kit for loam. However, if time and storage conditions are important considerations, the IT 1-2-3 Platinum Path™ kit may be appropriate for use with all soils since the kit has the shortest processing time and fewest temperature requirements.