In the Microbiology unit, we are currently assessing the viability and metabolic capacity of the bacterial population that is present in the Boom Clay layer that was selected for the disposal of radioactive waste. One way of elucidating this population’s characteristics is to look at its phylogenetic and functional genes, which requires the extraction of the total microbial DNA (the metagenome). The extraction of metagenomic DNA from an environmental sample like a geological clay layer however poses several challenges. The microbial cell concentration in subsurface soil environmental samples is sometimes extremely low, which stresses the need for a highly efficient extraction protocol. The presence of clay and organic matter reduces extraction efficiency by adsorbing DNA after cell lysis or by interfering with extraction reagentia.In this thesis project, different steps in our customized DNA extraction protocol were evaluated one by one to finally develop the most efficient protocol for subsoil clay samples. To improve cell lysis, the composition and storage of the lysis buffer was scrutinised. Within the purification of DNA from the lysing solution, the impact of different DNA precipitation methods was investigated. In the end, crucial recommendations for optimization of the customized protocol for DNA extraction were made.
|Place of Publication
|Published - 29 Aug 2012