Challenging our view of the active fraction of soil microbiomes using BONCAT-FACS-Seq

Estelle Couradeau, Joelle Sasse, Danielle Goudeau, Nandita Nath, Terry C. Hazen, Ben Bowen, Rex R. Malmstrom, Trent Northen

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Oct 05, 2018
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Received Date: 25th September 2018

The ability to link soil microbial diversity to soil processes requires technologies that differentiate active subpopulations of microbes from so-called relic DNA and dormant cells. Here, we describe the first application of BONCAT (Biorthogonal Non Canonical Amino Acid Tagging) to measure translationally active cells in soils. We compared the active population of two soil depths from Oak Ridge (TN) incubated in the same condition for up to seven days. Depending on the soil, a maximum of 25 – 70% of the cells were active, accounting for 3-4 million cells per gram of soil. The BONCAT positive cell fraction was recovered by fluorescence activated cell sorting (FACS) and identified by16S rDNA amplicon sequencing. The diversity of the active fraction was a selected subset of the bulk soil community. Excitingly, some of the same members of the community were recruited at both depths independently from their abundance rank. On average, 86% of sequence reads recovered from the active community shared >97% sequence similarity with cultured isolates from the field site. Our observations are in line with a recent report that, of the few taxa that are both abundant and ubiquitous in soil, 45% are also cultured – and indeed some of these ubiquitous microorganisms were found to be translationally active. The use of BONCAT in soil challenges the common view that soils microbiomes consist of scattered cells that are mostly inactive. We conclude that BONCAT coupled to FACS and sequencing is effective for interrogating the active fraction of soil microbiomes in situ and will unlock new perspectives to link metabolic capacity to overall soil ecological traits and processes.

Read in full at bioRxiv.

This is an abstract of a preprint hosted on an independent third party site. It has not been peer reviewed but is currently under consideration at Nature Communications.

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