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

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Nature Microbiology

• Publication date

  2016-03-17

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1038/nmicrobiol.2016.242PMID 27991881
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  1991cited by this paper
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