DNA extraction methodology for biochar-amended sand and clay

Abstract

Studies on the molecular ecology of microbial communities in soils amended with biochar are potentially biased by changes in soil DNA extraction efficiency caused by DNA adsorption to biochar. To examine the extent to which this might occur, we evaluated a kit-free method for soil DNA extraction as well as MoBio’s PowerSoil® commercial kit with and without phenol/chloroform/isoamyl (PCI) modification. DNA extraction efficiencies were quantified for soils amended with four biochar types that were added to either clay or sand soils at a rate of 3 % (w/w). Prior to extraction, all soil treatments were spiked with bacteria transformed with plasmids carrying a green fluorescent protein (gfp) gene, as a molecular marker. DNA purity and yield were assessed spectrophotometrically and fluorometrically. Quantitative PCR (qPCR) was utilized to enumerate gfp copy numbers extracted per gram soil. Results showed that qPCR-quality DNA could be efficiently extracted from biochar-amended soils using the PowerSoil® kit with or without PCI modification. However, the modified protocol resulted in an average of approximately 3 times greater yield than the provided protocol. Of the tested methods, none demonstrated reduced DNA extraction efficiency or purity when amended with the varying biochars.