Probing the active fraction of soil microbiomes using BONCAT-FACS

• Published in: Nature communications 2019-06, Vol.10 (1), p.2770-10, Article 2770
• Main Authors: Couradeau, Estelle, Sasse, Joelle, Goudeau, Danielle, Nath, Nandita, Hazen, Terry C., Bowen, Ben P., Chakraborty, Romy, Malmstrom, Rex R., Northen, Trent R.
• Format: Article
• Language: English
• Subjects: 45; 45/22; 45/77; 49/31; 631/326/171/1818; 704/158/855; Amino acids; Amino Acids - analysis; Amino Acids - chemistry; Bacteria - genetics; Bacteria - isolation & purification; Bacteria - metabolism; BASIC BIOLOGICAL SCIENCES; Cell division; Deoxyribonucleic acid; DNA; Flow cytometry; Flow Cytometry - methods; Fluorescence; Fluorescent Dyes - chemistry; Humanities and Social Sciences; Laboratories; Microbiomes; Microbiota; Microorganisms; multidisciplinary; Phylogenetics; Phylogeny; RNA, Ribosomal, 16S - genetics; RNA, Ribosomal, 16S - isolation & purification; rRNA 16S; Science; Science (multidisciplinary); Soil Microbiology; Soils; Staining and Labeling - methods
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-10542-0

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. Standard DNA-based analyses of microbial communities cannot distinguish between active microbes and dead or dormant cells. Here, Couradeau et al. use BONCAT (bioorthogonal non-canonical amino acid tagging), flow cytometry, and 16S rRNA gene amplicon sequencing to identify active microbial cells in soils.