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

View ORCID ProfilePaul Carini, Patrick J. Marsden, Jonathan W. Leff, Emily E. Morgan, Michael S. Strickland, View ORCID ProfileNoah Fierer
doi: https://doi.org/10.1101/043372
Paul Carini
1Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309
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  • For correspondence: Paul.Carini@gmail.com Noah.Fierer@colorado.edu
Patrick J. Marsden
2Department of Chemistry, Metropolitan State University of Denver, Denver, CO 80217
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Jonathan W. Leff
1Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309
3Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
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Emily E. Morgan
1Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309
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Michael S. Strickland
4Department of Biological Sciences, Virginia Tech University, Blacksburg, VA 24061
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Noah Fierer
1Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309
3Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
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  • ORCID record for Noah Fierer
  • For correspondence: Paul.Carini@gmail.com Noah.Fierer@colorado.edu
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Abstract

It is implicitly assumed that the microbial DNA recovered from soil originates from living cells. However, because relic DNA (DNA from dead cells) can persist in soil for weeks to years, it could impact DNA-based analyses of microbial diversity. We examined a wide range of soils and found that, on average, 40% of prokaryotic and fungal DNA was derived from the relic DNA pool. Relic DNA inflated the observed prokaryotic and fungal diversity by as much as 55%, and caused misestimation of taxon abundances, including taxa integral to key ecosystem processes. These findings imply that relic DNA can obscure treatment effects, spatiotemporal patterns, and relationships between taxa and environmental conditions. Moreover, relic DNA may represent a historical record of microbes formerly living in soil.

One Sentence Summary Soils can harbor substantial amounts of DNA from dead microbial cells; this ‘relic’ DNA inflates estimates of microbial diversity and obscures assessments of community structure.

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Posted March 17, 2016.
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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
bioRxiv 043372; doi: https://doi.org/10.1101/043372
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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
bioRxiv 043372; doi: https://doi.org/10.1101/043372

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