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Nat Microbiol. 2016 Dec 19;2:16242. doi: 10.1038/nmicrobiol.2016.242.

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

Author information

1
Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, USA.
2
Department of Chemistry, Metropolitan State University of Denver, Denver, Colorado 80217, USA.
3
Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA.
4
Department of Biological Sciences, Virginia Tech University, Blacksburg, Virginia 24061, USA.

Abstract

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.

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