title: Relic DNA is abundant in soil and obscures estimates of soil microbial diversity.
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.
authors.affiliation: Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, USA.
authors.forename: Paul
authors.identifier: http://orcid.org/0000-0002-9653-7309
authors.initials: P
authors.lastname: Carini
authors.affiliation: Department of Chemistry, Metropolitan State University of Denver, Denver, Colorado 80217, USA.
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Marsden
authors.affiliation: Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, USA.|Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA.
authors.forename: Jonathan W
authors.initials: JW
authors.lastname: Leff
authors.affiliation: Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, USA.
authors.forename: Emily E
authors.initials: EE
authors.lastname: Morgan
authors.affiliation: Department of Biological Sciences, Virginia Tech University, Blacksburg, Virginia 24061, USA.
authors.forename: Michael S
authors.identifier: http://orcid.org/0000-0001-5349-0363
authors.initials: MS
authors.lastname: Strickland
authors.affiliation: Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, USA.|Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA.
authors.forename: Noah
authors.initials: N
authors.lastname: Fierer