期刊
NATURE MICROBIOLOGY
卷 2, 期 3, 页码 -出版社
NATURE PORTFOLIO
DOI: 10.1038/nmicrobiol.2016.242
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资金
- National Science Foundation [DEB 0953331, EAR 1331828, DUE 1259336, EAR 1461281]
- Visiting Postdoctoral Fellowship award
- Cooperative Institute for Research in Environmental Sciences
- Division Of Earth Sciences
- Directorate For Geosciences [1461281] Funding Source: National Science Foundation
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 DNAintercalating 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.
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