Comparative Analysis of Soil DNA Extraction Methods to Study Various Ammonium-Oxidizing Bacteria and Archaeaby PCR-DGGE

摘要

A comparative analysis of five methods of extraction and purification of soil DNA, including a modification of the authors, was performed for the further molecular investigation of various ammonium-oxidizing bacteria and archaea in soils. Experimentsusing soil samples from natural ecosystems and agroec-osystems of the European area of Russia established that the amount of DNA extracted by different methods depended significantly on the type of soil. The subsequent molecular analysis (PCR—DGGE) of ribosomal (16S rRNA) and functional (amoA) genes demonstrated significant differences in the community structure of ammonium oxidizers depending on the method of DNA extraction. The best results were obtained for acidic soil (soddy-podzolic and gray forest soils) when using the method of Griffiths et al. [4] with our own modification. On the other hand, application of commercial DNA extraction kits was most efficient for soils with a high content of humus (black and chestnut soils). According to the results obtained, molecular analysis of soil microbe communities required selection of optimum conditions for DNA extraction, especially for soils with high contents of organic compounds and clay minerals at different pH levels.