Probing the active fraction of soil microbiomes using BONCAT-FACS

Nat Commun. 2019 Jun 24;10(1):2770. doi: 10.1038/s41467-019-10542-0.


The ability to link soil microbial diversity to soil processes requires technologies that differentiate active microbes from extracellular DNA and dormant cells. Here, we use BONCAT (bioorthogonal non-canonical amino acid tagging) to measure translationally active cells in soils. We compare the active population of two soil depths from Oak Ridge (Tennessee, USA) and find that a maximum of 25-70% of the extractable cells are active. Analysis of 16S rRNA sequences from BONCAT-positive cells recovered by fluorescence-activated cell sorting (FACS) reveals that the phylogenetic composition of the active fraction is distinct from the total population of extractable cells. Some members of the community are found to be active at both depths independently of their abundance rank, suggesting that the incubation conditions favor the activity of similar organisms. We conclude that BONCAT-FACS is effective for interrogating the active fraction of soil microbiomes in situ and provides a new approach for uncovering the links between soil processes and specific microbial groups.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acids / analysis
  • Amino Acids / chemistry
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Bacteria / metabolism
  • Flow Cytometry / methods*
  • Fluorescent Dyes / chemistry
  • Microbiota*
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • RNA, Ribosomal, 16S / isolation & purification
  • Soil Microbiology*
  • Staining and Labeling / methods


  • Amino Acids
  • Fluorescent Dyes
  • RNA, Ribosomal, 16S