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

Paul Carini, Patrick J. Marsden, Jonathan W. Leff, Emily E. Morgan, Michael S. Strickland, Noah Fierer

Research output: Contribution to journalArticlepeer-review

391 Scopus citations

Abstract

Extracellular DNA from dead microorganisms can persist in soil for weeks to years 1-3. 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 monoazide 4. 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.

Original languageEnglish (US)
Article number16242
JournalNature Microbiology
Volume2
DOIs
StatePublished - Dec 19 2016
Externally publishedYes

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Applied Microbiology and Biotechnology
  • Genetics
  • Microbiology (medical)
  • Cell Biology

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