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 · Mon Jun 24 00:00:00 EDT 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. 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.

View Accepted Manuscript (DOE)

Cite

Export

Save

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

Citation Metrics:

Cited by: 51 works

Citation information provided by
Web of Science

References (42)

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
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
Biological crusts as a model system for examining the biodiversity–ecosystem function relationship in soils Bowker, Matthew A.; Maestre, Fernando T.; Escolar, Cristina Soil Biology and Biochemistry, Vol. 42, Issue 3 https://doi.org/10.1016/j.soilbio.2009.10.025	journal	March 2010
Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases Yao, Yushu; Sun, Terence; Wang, Tony Metabolites, Vol. 5, Issue 3 https://doi.org/10.3390/metabo5030431	journal	July 2015
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
Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities Verastegui, Y.; Cheng, J.; Engel, K. mBio, Vol. 5, Issue 4 https://doi.org/10.1128/mBio.01157-14	journal	July 2014
In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry : Visualizing new proteins in microbes by click chemistry Hatzenpichler, Roland; Scheller, Silvan; Tavormina, Patricia L. Environmental Microbiology, Vol. 16, Issue 8 https://doi.org/10.1111/1462-2920.12436	journal	April 2014
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
DNA stable-isotope probing Neufeld, Josh D.; Vohra, Jyotsna; Dumont, Marc G. Nature Protocols, Vol. 2, Issue 4 https://doi.org/10.1038/nprot.2007.109	journal	April 2007
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
Belowground biodiversity and ecosystem functioning Bardgett, Richard D.; van der Putten, Wim H. Nature, Vol. 515, Issue 7528 https://doi.org/10.1038/nature13855	journal	November 2014
Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils Eichorst, Stephanie A.; Strasser, Florian; Woyke, Tanja FEMS Microbiology Ecology, Vol. 91, Issue 10 https://doi.org/10.1093/femsec/fiv106	journal	August 2015
Microbial diversity and function in soil: from genes to ecosystems Torsvik, Vigdis; Øvreås, Lise Current Opinion in Microbiology, Vol. 5, Issue 3, p. 240-245 https://doi.org/10.1016/S1369-5274(02)00324-7	journal	June 2002
Global drivers and patterns of microbial abundance in soil: Global patterns of soil microbial biomass Serna-Chavez, Hector M.; Fierer, Noah; van Bodegom, Peter M. Global Ecology and Biogeography, Vol. 22, Issue 10 https://doi.org/10.1111/geb.12070	journal	June 2013
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
Identification of active oxalotrophic bacteria by Bromodeoxyuridine DNA labeling in a microcosm soil experiments Bravo, Daniel; Martin, Gaëtan; David, Maude M. FEMS Microbiology Letters, Vol. 348, Issue 2 https://doi.org/10.1111/1574-6968.12244	journal	September 2013
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
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
Transfer of Defluvibacter lusatiensis to the genus Aquamicrobium as Aquamicrobium lusatiense comb. nov. and description of Aquamicrobium aerolatum sp. nov. Kampfer, P.; Martin, E.; Lodders, N. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 10 https://doi.org/10.1099/ijs.0.008730-0	journal	July 2009
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 5 https://doi.org/10.1128/AEM.67.5.2354-2359.2001	journal	May 2001
Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S. mBio, Vol. 6, Issue 3 https://doi.org/10.1128/mBio.00326-15	journal	May 2015
Formalin-induced infidelity in PCR-amplified DNA fragments De Giorgi, Carla; Sialer, Mariella Finetti; Lamberti, Franco Molecular and Cellular Probes, Vol. 8, Issue 6 https://doi.org/10.1006/mcpr.1994.1065	journal	December 1994
Characterization of Aquamicrobium defluvii gen. nov. sp. nov., a thiophene-2-carboxylate-metabolizing bacterium from activated sludge Bambauer, Andreas; Rainey, Fred A.; Stackebrandt, Erko Archives of Microbiology, Vol. 169, Issue 4 https://doi.org/10.1007/s002030050575	journal	April 1998
Using stable isotopes to explore root-microbe-mineral interactions in soil Pett-Ridge, Jennifer; Firestone, Mary K. Rhizosphere, Vol. 3 https://doi.org/10.1016/j.rhisph.2017.04.016	journal	June 2017
Using network analysis to explore co-occurrence patterns in soil microbial communities Barberán, Albert; Bates, Scott T.; Casamayor, Emilio O. The ISME Journal, Vol. 6, Issue 2 https://doi.org/10.1038/ismej.2011.119	journal	September 2011
Capturing the genetic makeup of the active microbiome in situ Singer, Esther; Wagner, Michael; Woyke, Tanja The ISME Journal, Vol. 11, Issue 9 https://doi.org/10.1038/ismej.2017.59	journal	June 2017
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
Microbial ecology of chlorinated solvent biodegradation: Microbial ecology of PCE degradation David, Maude M.; Cecillon, Sebastien; Warne, Brett M. Environmental Microbiology, Vol. 17, Issue 12 https://doi.org/10.1111/1462-2920.12413	journal	March 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
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
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
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
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
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
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
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
Toward a census of bacteria in soil Schloss, Patrick David; Handelsman, Jo PLoS Computational Biology, Vol. preprint, Issue 2006 https://doi.org/10.1371/journal.pcbi.0020092.eor	journal	January 2005
Single-cell bacterial transcription measurements reveal the importance of dimethylsulfoniopropionate (DMSP) hotspots in ocean sulfur cycling Gao, Cherry; Fernandez, Vicente I.; Lee, Kang S. ETH Zurich https://doi.org/10.3929/ethz-b-000412734	text	January 2020
Erratum: Using network analysis to explore co-occurrence patterns in soil microbial communities Barberán, Albert; Bates, Scott T.; Casamayor, Emilio O. The ISME Journal, Vol. 8, Issue 4 https://doi.org/10.1038/ismej.2013.236	journal	March 2014
Evaluation and Optimization of DNA Extraction and Purification Procedures for Soil and Sediment Samples Miller, D. N.; Bryant, J. E.; Madsen, E. L. Applied and Environmental Microbiology, Vol. 65, Issue 11 https://doi.org/10.1128/aem.65.11.4715-4724.1999	journal	November 1999
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

Cited By (3)

Microbial functional diversity: From concepts to applications Escalas, Arthur; Hale, Lauren; Voordeckers, James W. Ecology and Evolution, Vol. 9, Issue 20 https://doi.org/10.1002/ece3.5670	journal	September 2019
Next-generation physiology approaches to study microbiome function at single cell level Hatzenpichler, Roland; Krukenberg, Viola; Spietz, Rachel L. Nature Reviews Microbiology, Vol. 18, Issue 4 https://doi.org/10.1038/s41579-020-0323-1	journal	February 2020
Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry Rubbens, Peter; Schmidt, Marian L.; Props, Ruben mSystems, Vol. 4, Issue 5 https://doi.org/10.1128/msystems.00093-19	journal	September 2019

Similar Records

Study of Oak Ridge soils using BONCAT-FACS-Seq reveals that a large fraction of the soil microbiome is active

Journal Article · Thu Aug 30 00:00:00 EDT 2018 · OSTI ID:1545190

Couradeau, Estelle; Sasse, Joelle; Goudeau, Danielle; +5 more

BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event

Journal Article · Mon Jun 26 00:00:00 EDT 2023 · Frontiers in Microbiology · OSTI ID:1545190

Trexler, Ryan V.; Van Goethem, Marc W.; Goudeau, Danielle; +4 more

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

Journal Article · Tue Jun 28 00:00:00 EDT 2016 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1545190

Hatzenpichler, Roland; Connon, Stephanie A.; Goudeau, Danielle; +3 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

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

Citation Formats

References (42)

Cited By (3)

Similar Records

Related Subjects