Soil washing improves the recovery of total community DNA from polluted and high organic content sediments

Treatment of soil with surfactants and chelating agents is used in bioremediation studies to desorb and solubilize contaminants to increase their bioavalability to microorganisms. In the same way that pollutants are made more bioavailable to microorganisms, the procedure can be used to remove potential interfering materials from soil prior to cell lysis and extraction of DNA from indigenous microorganisms. The effect of soil washing was evaluated by extracting DNA from sediments of an intertidal freshwater wetland contaminated with hydrocarbons and from highly contaminated marine sediments from Sydney Harbour, Nova Scotia, Canada. Sediment samples had total organic carbon (TOC) contents that varied between 0.2% and 13%. The chemical lysis technique was also examined by comparison of an ammonium acetate precipitation of proteins and humic acids with a hexadecyltrimethylammonium bromide (CTAB) incubation and phenol:chloroform extraction. In this study, the incorporation of soil washing steps facilitated the desorption of contaminants from sediment surfaces and improved the recovery of DNA of amplifiable quality from both freshwater and marine sediments. CTAB contributed only slightly to the recovery of DNA of higher quality in the most contaminated sample from Sydney Harbour and was concomitant with a decrease in DNA yield in both sediment types. The incorporation of a soil washing step prior to the extraction of DNA from polluted environments may be important to solubilize and remove contaminants when high-quality DNA is required for subsequent analyses.