Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia

Application of DNA fingerprinting methods enables the detection of diverse members of soil bacterial consortia, even including those bacteria not yet cultivated. However, extraction and purification of DNA from soil samples w ithout bias is difficult. We compared five different DNA isolation methods and three purification methods for rhizosphere soil samples. Purified DNA e xtracts were amplified in PCR using universal bacterial primers and the PCR products were analysed with denaturing gradient gel electrophoresis (DGGE) for the visualisation of DNA bands representing dominant bacterial species . Both the isolation and purification methods affected the apparent bacteri al community structure of the samples. (C) 2001 Elsevier Science B.V. All r ights reserved.