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Probing the active fraction of soil microbiomes using BONCAT-FACS

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 acti...

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Autores principales: Couradeau, Estelle, Sasse, Joelle, Goudeau, Danielle, Nath, Nandita, Hazen, Terry C., Bowen, Ben P., Chakraborty, Romy, Malmstrom, Rex R., Northen, Trent R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591230/
https://www.ncbi.nlm.nih.gov/pubmed/31235780
http://dx.doi.org/10.1038/s41467-019-10542-0
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author Couradeau, Estelle
Sasse, Joelle
Goudeau, Danielle
Nath, Nandita
Hazen, Terry C.
Bowen, Ben P.
Chakraborty, Romy
Malmstrom, Rex R.
Northen, Trent R.
author_facet Couradeau, Estelle
Sasse, Joelle
Goudeau, Danielle
Nath, Nandita
Hazen, Terry C.
Bowen, Ben P.
Chakraborty, Romy
Malmstrom, Rex R.
Northen, Trent R.
author_sort Couradeau, Estelle
collection PubMed
description 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.
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spelling pubmed-65912302019-06-26 Probing the active fraction of soil microbiomes using BONCAT-FACS Couradeau, Estelle Sasse, Joelle Goudeau, Danielle Nath, Nandita Hazen, Terry C. Bowen, Ben P. Chakraborty, Romy Malmstrom, Rex R. Northen, Trent R. Nat Commun Article 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. Nature Publishing Group UK 2019-06-24 /pmc/articles/PMC6591230/ /pubmed/31235780 http://dx.doi.org/10.1038/s41467-019-10542-0 Text en © This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Couradeau, Estelle
Sasse, Joelle
Goudeau, Danielle
Nath, Nandita
Hazen, Terry C.
Bowen, Ben P.
Chakraborty, Romy
Malmstrom, Rex R.
Northen, Trent R.
Probing the active fraction of soil microbiomes using BONCAT-FACS
title Probing the active fraction of soil microbiomes using BONCAT-FACS
title_full Probing the active fraction of soil microbiomes using BONCAT-FACS
title_fullStr Probing the active fraction of soil microbiomes using BONCAT-FACS
title_full_unstemmed Probing the active fraction of soil microbiomes using BONCAT-FACS
title_short Probing the active fraction of soil microbiomes using BONCAT-FACS
title_sort probing the active fraction of soil microbiomes using boncat-facs
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591230/
https://www.ncbi.nlm.nih.gov/pubmed/31235780
http://dx.doi.org/10.1038/s41467-019-10542-0
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