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Probing the active fraction of soil microbiomes using BONCAT-FACS

Author

Listed:
  • Estelle Couradeau

    (Lawrence Berkeley National Laboratory)

  • Joelle Sasse

    (Lawrence Berkeley National Laboratory)

  • Danielle Goudeau

    (Joint Genome Institute, Department of Energy)

  • Nandita Nath

    (Joint Genome Institute, Department of Energy)

  • Terry C. Hazen

    (University of Tennessee, Oak Ridge National Laboratory)

  • Ben P. Bowen

    (Joint Genome Institute, Department of Energy)

  • Romy Chakraborty

    (Lawrence Berkeley National Laboratory)

  • Rex R. Malmstrom

    (Joint Genome Institute, Department of Energy)

  • Trent R. Northen

    (Lawrence Berkeley National Laboratory
    Joint Genome Institute, Department of Energy)

Abstract

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.

Suggested Citation

  • Estelle Couradeau & Joelle Sasse & Danielle Goudeau & Nandita Nath & Terry C. Hazen & Ben P. Bowen & Romy Chakraborty & Rex R. Malmstrom & Trent R. Northen, 2019. "Probing the active fraction of soil microbiomes using BONCAT-FACS," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10542-0
    DOI: 10.1038/s41467-019-10542-0
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    Cited by:

    1. Dennis Metze & Jörg Schnecker & Alberto Canarini & Lucia Fuchslueger & Benjamin J. Koch & Bram W. Stone & Bruce A. Hungate & Bela Hausmann & Hannes Schmidt & Andreas Schaumberger & Michael Bahn & Chri, 2023. "Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    2. Tilman Schmider & Anne Grethe Hestnes & Julia Brzykcy & Hannes Schmidt & Arno Schintlmeister & Benjamin R. K. Roller & Ezequiel Jesús Teran & Andrea Söllinger & Oliver Schmidt & Martin F. Polz & Andre, 2024. "Physiological basis for atmospheric methane oxidation and methanotrophic growth on air," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Alexa M. Nicolas & Ella T. Sieradzki & Jennifer Pett-Ridge & Jillian F. Banfield & Michiko E. Taga & Mary K. Firestone & Steven J. Blazewicz, 2023. "A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Stefanie Imminger & Dimitri V. Meier & Arno Schintlmeister & Anton Legin & Jörg Schnecker & Andreas Richter & Osnat Gillor & Stephanie A. Eichorst & Dagmar Woebken, 2024. "Survival and rapid resuscitation permit limited productivity in desert microbial communities," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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