Metagenomic comparison of direct and indirect soil DNA extraction approaches

Full pyrosequencing runs of both direct-extracted (high yield, low DNA size) and indirect-extracted DNA (low yield, high DNA size) from the same prairie soil show that the sequence distribution of the majority of the metabolic functions and species detected were statistically similar. Although some microbial functions differed at the 95% confidence interval in bootstrap analyses, the overall functional diversity was the same.

► Indirect and direct DNA extraction access similar levels of microbial biodiversity.
► Indirect and direct DNA extractions do not access exactly the same microbial populations.
► Differences in microbial populations targeted by the two approaches reflect the stringency of the extraction method.
► Indirect DNA extraction is less stringent and produces longer DNA fragments.