Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

Extracellular DNA from dead microorganisms can persist in soil for weeks to years1–3. Although it is implicitly assumed that the microbial DNA recovered from soil predominantly represents intact cells, it is unclear how extracellular DNA affects molecular analyses of microbial diversity. We examined a wide range of soils using viability PCR based on the photoreactive DNA-intercalating dye propidium monoazide4. We found that, on average, 40% of both prokaryotic and fungal DNA was extracellular or from cells that were no longer intact. Extracellular DNA inflated the observed prokaryotic and fungal richness by up to 55% and caused significant misestimation of taxon relative abundances, including the relative abundances of taxa integral to key ecosystem processes. Extracellular DNA was not found in measurable amounts in all soils; it was more likely to be present in soils with low exchangeable base cation concentrations, and the effect of its removal on microbial community structure was more profound in high-pH soils. Together, these findings imply that this ‘relic DNA’ remaining in soil after cell death can obscure treatment effects, spatiotemporal patterns and relationships between microbial taxa and environmental conditions. Viability polymerase chain reaction based on the photoreactive DNA-intercalating dye propidium monoazide revealed that on average 40% of prokaryotic and fungal DNA in soil is extracellular, or from cells no longer intact, confounding estimates of richness and taxon relative abundance.