Evaluation of the commercial kits for the extraction of extracellular DNA in soil

Abstract

Five commercial DNA extraction kits for microbial DNA in soil were evaluated in terms of the extraction e‹ciencies of artiˆcially-spiked extracellular DNA in soil. Commercially-available puriˆed DNA derived from the sperm of Clupea harengus (Atlantic herring) was homogeneously premixed in blank soil samples and extracted using the kits. The spiked DNA in each of the extracts was quantitated by real-time PCR to evaluate extraction e‹ciency using a speciˆc primer set for the mitochondrial 16S rRNA gene of Clupea harengus. Only the Extrap Soil DNA Kit could extract the DNA from all types of soils spiked at 10 mg/g soil (vegetable garden soil 0.85, courtyard soil 0.30 and virgin andosol 0.027), whereas other kits (Nucleospin Soil, Power Soil DNA Isolation Kit, ISOIL and ISOIL for Beads Beating) could not extract the DNA larger than the quantitation limit (0.020) from the courtyard soil and the virgin andosol which exhibited high phosphate absorption coe‹cient. Skim milk concentration and bead-beating time using the Extrap Soil DNA Kit were optimized for 20 mg/g soil and 30 s, respectively. Signiˆcant PCR inhibition was not observed under the optimized condition.