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

Abstract

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. Measures of microbial activity based on various techniques including DNA labelling have suggested that most cells in soils are inactive, a fact that has been difficult to reconcile with observed high levels of bulk soil activities. We hypothesized that measures of in situ DNA synthesis may be missing the soil microbes that are metabolically active but not replicating, and we therefore applied BONCAT (Bioorthogonal Non Canonical Amino Acid Tagging) i.e. a proxy for activity that does not rely on cell division, to measure translationally active cells in soils. We compared the active population of two soil depths from Oak Ridge (TN) incubated under the same conditions 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 type, which is an order of magnitude higher than previous estimates. The BONCAT positive cell fraction was recovered by fluorescence activated cell sorting (FACS) and identified by 16S rDNA amplicon sequencing. The diversity of the active fraction was a selected subset ofmore » 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 on soil microbiomes provides evidence that a large portion of the soil microbes can be active simultaneously. We conclude that BONCAT coupled to FACS and sequencing is effective for interrogating the active fraction of soil microbiomes in situ and provides new perspectives to link metabolic capacity to overall soil ecological traits and processes.« less

Authors:
; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1545140
DOE Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
biorxiv.or Repository
Additional Journal Information:
Journal Volume: 2018; Journal ID: ISSN 9999-0031
Publisher:
Cold Springs Harbor Laboratory
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 58 GEOSCIENCES

Citation Formats

Couradeau, Estelle, Sasse, Joelle, Goudeau, Danille, Nath, Nandita, Hazen, Terry C., Bowen, Benjamin P., Malmstrom, Rex R., and Northen, Trent R. Study of Oak Ridge soils using BONCAT-FACS-Seq reveals that a large fraction of the soil microbiome is active. United States: N. p., 2018. Web. doi:10.1101/404087.
Couradeau, Estelle, Sasse, Joelle, Goudeau, Danille, Nath, Nandita, Hazen, Terry C., Bowen, Benjamin P., Malmstrom, Rex R., & Northen, Trent R. Study of Oak Ridge soils using BONCAT-FACS-Seq reveals that a large fraction of the soil microbiome is active. United States. doi:10.1101/404087.
Couradeau, Estelle, Sasse, Joelle, Goudeau, Danille, Nath, Nandita, Hazen, Terry C., Bowen, Benjamin P., Malmstrom, Rex R., and Northen, Trent R. Thu . "Study of Oak Ridge soils using BONCAT-FACS-Seq reveals that a large fraction of the soil microbiome is active". United States. doi:10.1101/404087. https://www.osti.gov/servlets/purl/1545140.
@article{osti_1545140,
title = {Study of Oak Ridge soils using BONCAT-FACS-Seq reveals that a large fraction of the soil microbiome is active},
author = {Couradeau, Estelle and Sasse, Joelle and Goudeau, Danille and Nath, Nandita and Hazen, Terry C. and Bowen, Benjamin P. and Malmstrom, Rex R. and Northen, Trent R.},
abstractNote = {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. Measures of microbial activity based on various techniques including DNA labelling have suggested that most cells in soils are inactive, a fact that has been difficult to reconcile with observed high levels of bulk soil activities. We hypothesized that measures of in situ DNA synthesis may be missing the soil microbes that are metabolically active but not replicating, and we therefore applied BONCAT (Bioorthogonal Non Canonical Amino Acid Tagging) i.e. a proxy for activity that does not rely on cell division, to measure translationally active cells in soils. We compared the active population of two soil depths from Oak Ridge (TN) incubated under the same conditions 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 type, which is an order of magnitude higher than previous estimates. The BONCAT positive cell fraction was recovered by fluorescence activated cell sorting (FACS) and identified by 16S 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 on soil microbiomes provides evidence that a large portion of the soil microbes can be active simultaneously. We conclude that BONCAT coupled to FACS and sequencing is effective for interrogating the active fraction of soil microbiomes in situ and provides new perspectives to link metabolic capacity to overall soil ecological traits and processes.},
doi = {10.1101/404087},
journal = {biorxiv.or Repository},
issn = {9999-0031},
number = ,
volume = 2018,
place = {United States},
year = {2018},
month = {8}
}

Works referenced in this record:

Microbial diversity and function in soil: from genes to ecosystems
journal, June 2002