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Probing the active fraction of soil microbiomes using BONCAT-FACS
Open accessAbstract
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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DADA2: High–resolution sample inference from Illumina amplicon data
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0209-9 · Cited by 23,742
The diversity and biogeography of soil bacterial communities
Fierer, N., & Jackson, R. B. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507535103 · Cited by 5,711
The importance of anabolism in microbial control over soil carbon storage
Liang, C., Schimel, J. P., & Jastrow, J. D. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2017.105 · Cited by 3,320
Using network analysis to explore co-occurrence patterns in soil microbial communities
Barberán, A., Bates, S. T., Casamayor, E. O., & Fierer, N. (2012) · The ISME Journal · doi:10.1038/ismej.2011.119 · Cited by 3,044
Dieterich, D. C., Link, A. J., Graumann, J., Tirrell, D. A., & Schuman, E. M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601637103 · Cited by 874
Cited by
Life and death in the soil microbiome: how ecological processes influence biogeochemistry
Sokol, N. W., Slessarev, E., Marschmann, G. L., Nicolas, A., Blazewicz, S. J., Brodie, E. L., Firestone, M. K., Foley, M. M., Hestrin, R., Hungate, B. A., et al. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00695-z · Cited by 1,179
Microbial functional diversity: From concepts to applications
Escalas, A., Hale, L., Voordeckers, J. W., Yang, Y., Firestone, M. K., Alvarez‐Cohen, L., & Zhou, J. (2019) · Ecology and Evolution · doi:10.1002/ece3.5670 · Cited by 265
Metadata
- Authors
- Couradeau, E., Sasse, J., Goudeau, D., Nath, N., Hazen, T. C., Bowen, B. P., Chakraborty, R., Malmstrom, R. R., & Northen, T. R.
- Venue
- Nature Communications
- Published
- 2019-06-24
- Volume
- 10
- Issue
- 1
- Pages
- 2770-2770
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2950422173
- Cited by
- 167
- References
- 6
- FWCI
- 10.69
- Type
- journal article
- Language
- en
- Open access
- gold
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- Couradeau, E., Sasse, J., Goudeau, D., Nath, N., Hazen, T. C., Bowen, B. P., Chakraborty, R., Malmstrom, R. R., & Northen, T. R. (2019). Probing the active fraction of soil microbiomes using BONCAT-FACS. Nature Communications. https://doi.org/10.1038/s41467-019-10542-0
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