Quantification, base composition, and fate of extracellular DNA in marine sediments

The discovery of high concentrations of DNA in marine sediments unaccounted for by living biomass suggests the presence of a large fraction of extracellular DNA, which might play an important role in gene transfer via natural transformation as well as in phosphorous biogeochemical cycling. But a universally accepted procedure for extracellular DNA extraction is not available yet. In this study, we developed a new nuclease-based procedure to extract extracellular DNA from marine sediments. Coastal sand and deep-sea mud samples were collected to test the efficiency of extracellular DNA removal from different sediment types. Extracellular DNA concentrations were quantified at six sediment depths, and changes in base composition were investigated to gather information on extracellular DNA fate. The extraction procedure was highly specific and only extracellular DNA was hydrolyzed after nuclease treatment. Hydrolyzable DNA accounted for <10 to >70% of the total DNA pool, suggesting that extracellular DNA can only be partially degraded. Base composition changed vertically with depth in the sediment as deoxycytidine content increased and deoxyadenosine decreased with increasing depth. Integrating our results for the top 15 cm of the sediment, we calculate that more than 50% of extracellular DNA was recalcitrant to enzymatic degradation. This finding might explain why DNA accumulates in surface sediments and suggests that DNA, might play a nonnegligible role in P biogeochemical cycle.