Sequential DNA extraction for soil microbiome study
The total DNA in soil consists of intracelullar DNA (i.e., DNA within intact cells) and extracellular DNA, which can be sequentially extracted. Extracellular DNA can further be classified into free DNA, tightly bound DNA and weakly bound DNA, based on its binding to soil colloids. In this study, we investigate the different variants of DNA in soil and how sequential DNA extraction can improve soil microbiome studies. We show that total DNA and intracellular DNA are similar in molecular weight and fragment length, but total DNA alone may underestimate the microbial diversity, while discriminating extra- and intracellular DNA can reveal additional taxa. This approach hightlights the importance of distinguishing between the different DNA types to enhance the resolution and interpretation of soil microbiome studies.