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How, When, and Where Relic DNA Affects Microbial Diversity.

J T Lennon1, M E Muscarella2, S A Placella3

  • 1Department of Biology, Indiana University, Bloomington, Indiana, USA lennonj@indiana.edu.

Mbio
|June 21, 2018
PubMed
Summary

Extracellular DNA, or relic DNA, is abundant in environments. This study shows that large relic DNA pools do not automatically bias microbial diversity estimates, contrary to expectations.

Keywords:
biodiversityecologyextracellular DNAmathematical modelingphylogenetic analysissampling theory

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Area of Science:

  • Microbial Ecology
  • Environmental DNA (eDNA)
  • Molecular Biology

Background:

  • Extracellular DNA (relic DNA) is a significant nucleic acid pool in the biosphere.
  • Relic DNA can impact ecological processes and microbial abundance/diversity estimates.
  • Understanding relic DNA's influence is crucial for environmental, engineered, and host-associated ecosystems.

Purpose of the Study:

  • To develop models predicting relic DNA pool size and composition.
  • To identify conditions leading to biased biodiversity estimates.
  • To empirically assess relic DNA's effect on microbial diversity.

Main Methods:

  • Developed theoretical models of relic DNA dynamics.
  • Quantified relic DNA abundance across diverse ecosystems (soil, sediment, water, gut).
  • Analyzed bacterial diversity using 16S rRNA gene sequencing.

Main Results:

  • Relic DNA constituted 33% of total DNA on average, exceeding 80% in some samples.
  • Despite abundance, relic DNA minimally affected taxonomic and phylogenetic diversity estimates.
  • Bias was minimal even in ecosystems with high relic DNA and physical protection.

Conclusions:

  • Large relic DNA pools do not inherently bias microbial diversity estimates.
  • Bias is contingent on distinct species abundance distributions between relic and intact DNA.
  • Relic DNA's impact is minimal if degradation rates are equal across taxa.