Electroelution to remove humic compounds from soil DNA and RNA extracts

The application of nucleic acid techniques to detect, identify, and monitor specific genes or organisms in soils or sediments is often complicated by the inhibitory effects of humic compounds that copurify with nucleic acids. A rapid electroelution technique was developed to separate inhibitory compounds from extracts of soil DNA and RNA. This technique was used in conjunction with PCR to detect nifH, terrestrial ammonia-oxidizer (TAO) 16S rRNA genes and TAO 16S rRNA from a variety of surface soils and contaminated sediments. After electroelution of crude nucleic acid extracts, PCR sensitivity was increased up to a factor of 10(4) relative to DNA templates that had not been electroeluted. Without electroelution of crude DNA extracts, target genes often remained undetected. Likewise, electroelution of crude RNA extracts increased RT-PCR sensitivity (for TAO 16S rRNA) by a factor of 10(3) relative to RNA extracts that had not been further purified. The electroelution technique will therefore be useful for rendering environmental nucleic acids extracted from soil and sediment more amenable to PCR methods and nucleic acid analysis.