Experimental investigation into the preservation and recovery of degraded DNA from sediments

Controlled experiments were used to recover DNA from sediments in order to understand DNA preservation in sediments and to examine the effectiveness of different DNA recovery methods. Known quantities of DNA were added to different sediment samples and artificially degraded through heat exposure. DNA extraction techniques included a chloroform/octanol and silica-spin column method. Standard and quantitative PCR were employed to assess the quantity of mtDNA recovered. The results demonstrate that DNA can be preserved in sediment, with successful DNA detection after exposure to 120ºC for up to 70 hours. It was also shown that the silica-spin column method recovered significantly more DNA than the other method but PCR inhibition was a consistent problem, with at least 25X sample dilution required for successful amplification. Technical improvements are needed to advance sediment DNA research; however, the data from this study support the notion that degraded DNA can be recovered directly from sediments.