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.

doi:10.1038/s41467-019-10542-0

Title: Probing the active fraction of soil microbiomes using BONCAT-FACS

Journal Article · 24 June 2019 · Nature Communications

DOI: https://doi.org/10.1038/s41467-019-10542-0 · OSTI ID:1545190

^[1];

^[2]; Nath, Nandita ^[2];

^[3]; Bowen, Ben P. ^[2];

^[1]; Malmstrom, Rex R. ^[2];

^[4]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

The ability to link soil microbial diversity to soil processes requires technologies that differentiate active microbes from extracellular DNA and dormant cells. In this work, 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. In closing, it is evident that BONCAT-FACS is effective for interrogating the active fraction of soil microbiomes in situ and provides a new method for uncovering the links between soil processes and specific microbial groups.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725; AC02-05CH11231

OSTI ID:: 1545190

Alternate ID(s):: OSTI ID: 1545156

Journal Information:: Nature Communications, Vol. 10, Issue 1; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods Flynn, Jullien M.; Brown, Emily A.; Chain, Frédéric J. J. Ecology and Evolution, Vol. 5, Issue 11 https://doi.org/10.1002/ece3.1497	journal	May 2015
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Active microorganisms in soil: Critical review of estimation criteria and approaches Blagodatskaya, Evgenia; Kuzyakov, Yakov Soil Biology and Biochemistry, Vol. 67 https://doi.org/10.1016/j.soilbio.2013.08.024	journal	December 2013
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Embracing the unknown: disentangling the complexities of the soil microbiome Fierer, Noah Nature Reviews Microbiology, Vol. 15, Issue 10 https://doi.org/10.1038/nrmicro.2017.87	journal	August 2017
The diversity and biogeography of soil bacterial communities Fierer, N.; Jackson, R. B. Proceedings of the National Academy of Sciences, Vol. 103, Issue 3 https://doi.org/10.1073/pnas.0507535103	journal	January 2006
Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT) Dieterich, D. C.; Link, A. J.; Graumann, J. Proceedings of the National Academy of Sciences, Vol. 103, Issue 25 https://doi.org/10.1073/pnas.0601637103	journal	June 2006
Dormancy contributes to the maintenance of microbial diversity Jones, S. E.; Lennon, J. T. Proceedings of the National Academy of Sciences, Vol. 107, Issue 13 https://doi.org/10.1073/pnas.0912765107	journal	March 2010
Tracking heavy water (D ₂ O) incorporation for identifying and sorting active microbial cells Berry, David; Mader, Esther; Lee, Tae Kwon Proceedings of the National Academy of Sciences, Vol. 112, Issue 2 https://doi.org/10.1073/pnas.1420406112	journal	December 2014
Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia Hatzenpichler, Roland; Connon, Stephanie A.; Goudeau, Danielle Proceedings of the National Academy of Sciences, Vol. 113, Issue 28 https://doi.org/10.1073/pnas.1603757113	journal	June 2016
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers Walters, William A.; Caporaso, J. Gregory; Lauber, Christian L. Bioinformatics, Vol. 27, Issue 8 https://doi.org/10.1093/bioinformatics/btr087	journal	February 2011
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Predicting the responsiveness of soil biodiversity to deforestation: a cross-biome study Crowther, Thomas W.; Maynard, Daniel S.; Leff, Jonathan W. Global Change Biology, Vol. 20, Issue 9 https://doi.org/10.1111/gcb.12565	journal	April 2014
Effect of biological soil crusts on soil elemental concentrations: implications for biogeochemistry and as traceable biosignatures of ancient life on land Beraldi-Campesi, H.; Hartnett, H. E.; Anbar, A. Geobiology, Vol. 7, Issue 3 https://doi.org/10.1111/j.1472-4669.2009.00204.x	journal	June 2009
Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region Hansen, Martin Christian; Tolker-Nielsen, Tim; Givskov, Michael FEMS Microbiology Ecology, Vol. 26, Issue 2 https://doi.org/10.1111/j.1574-6941.1998.tb00500.x	journal	June 1998
A global atlas of the dominant bacteria found in soil Delgado-Baquerizo, Manuel; Oliverio, Angela M.; Brewer, Tess E. Science, Vol. 359, Issue 6373 https://doi.org/10.1126/science.aap9516	journal	January 2018
DNA Extraction from Soils: Old Bias for New Microbial Diversity Analysis Methods Martin-Laurent, F.; Philippot, L.; Hallet, S. Applied and Environmental Microbiology, Vol. 67, Issue 9 https://doi.org/10.1128/aem.67.9.4397-4397.2001	journal	September 2001
Use of Bromodeoxyuridine Immunocapture To Identify Active Bacteria Associated with Arbuscular Mycorrhizal Hyphae Artursson, V.; Jansson, J. K. Applied and Environmental Microbiology, Vol. 69, Issue 10 https://doi.org/10.1128/aem.69.10.6208-6215.2003	journal	October 2003
Toward a Census of Bacteria in Soil Schloss, Patrick D.; Handelsman, Jo PLoS Computational Biology, Vol. 2, Issue 7 https://doi.org/10.1371/journal.pcbi.0020092	journal	January 2006
Toward an Ecological Classification of soil Bacteria Fierer, Noah; Bradford, Mark A.; Jackson, Robert B. Ecology, Vol. 88, Issue 6 https://doi.org/10.1890/05-1839	journal	June 2007
Acid fumigation of soils to remove carbonates prior to total organic carbon or CARBON-13 isotopic analysis Harris, David; Horwáth, William R.; van Kessel, Chris Soil Science Society of America Journal, Vol. 65, Issue 6 https://doi.org/10.2136/sssaj2001.1853	journal	January 2001
Using Click-Chemistry for Visualizing in Situ Changes of Translational Activity in Planktonic Marine Bacteria Leizeaga, Ainara; Estrany, Margarita; Forn, Irene Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02360	journal	December 2017

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