Methods for DNA extraction from various soils: a comparison

Abstract

Seven methods for bacterial DNA extraction and purification from soil samples were compared. Holben’s direct lysis method recovered significantly greater amounts of DNA than the other methods tested, while CsCl-ethidium bromide density gradient ultracentrifugation was better than gel filtration at removing humic acid from crude DNA isolated from soil. When both these methods were combined, 5·94 μg of DNA (A260/280 ratio around 1·754) was yielded g−1 oven-dried sandstone shale alluvial soil; similarly satisfactory yields were obtained from Taiwan clay, and sandstone shale and slate alluvial soil managed under different farming practices. DNA obtained by these methods was readily digested by EcoR I and Hind III. When soil samples were stored for 3 weeks at 4 °C, the fraction of high-molecular-weight DNA was reduced significantly. Thus, DNA extraction should be carried out as soon as possible after a soil sample has been collected from the field. When hyphae of Pythium aphanidermatum and Fusarium solani were subjected to the above lysis method, DNA could not be detected in the extract.