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Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere

Assigning a functional role to a microorganism has historically relied on cultivation of isolates or detection of environmental genome-based biomarkers using a posteriori knowledge of function. However, the emerging field of function-driven single-cell genomics aims to expand this paradigm by identi...

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Autores principales: Doud, Devin F. R., Bowers, Robert M., Schulz, Frederik, De Raad, Markus, Deng, Kai, Tarver, Angela, Glasgow, Evan, Vander Meulen, Kirk, Fox, Brian, Deutsch, Sam, Yoshikuni, Yasuo, Northen, Trent, Hedlund, Brian P., Singer, Steven W., Ivanova, Natalia, Woyke, Tanja
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7031533/
https://www.ncbi.nlm.nih.gov/pubmed/31754206
http://dx.doi.org/10.1038/s41396-019-0557-y
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author Doud, Devin F. R.
Bowers, Robert M.
Schulz, Frederik
De Raad, Markus
Deng, Kai
Tarver, Angela
Glasgow, Evan
Vander Meulen, Kirk
Fox, Brian
Deutsch, Sam
Yoshikuni, Yasuo
Northen, Trent
Hedlund, Brian P.
Singer, Steven W.
Ivanova, Natalia
Woyke, Tanja
author_facet Doud, Devin F. R.
Bowers, Robert M.
Schulz, Frederik
De Raad, Markus
Deng, Kai
Tarver, Angela
Glasgow, Evan
Vander Meulen, Kirk
Fox, Brian
Deutsch, Sam
Yoshikuni, Yasuo
Northen, Trent
Hedlund, Brian P.
Singer, Steven W.
Ivanova, Natalia
Woyke, Tanja
author_sort Doud, Devin F. R.
collection PubMed
description Assigning a functional role to a microorganism has historically relied on cultivation of isolates or detection of environmental genome-based biomarkers using a posteriori knowledge of function. However, the emerging field of function-driven single-cell genomics aims to expand this paradigm by identifying and capturing individual microbes based on their in situ functions or traits. To identify and characterize yet uncultivated microbial taxa involved in cellulose degradation, we developed and benchmarked a function-driven single-cell screen, which we applied to a microbial community inhabiting the Great Boiling Spring (GBS) Geothermal Field, northwest Nevada. Our approach involved recruiting microbes to fluorescently labeled cellulose particles, and then isolating single microbe-bound particles via fluorescence-activated cell sorting. The microbial community profiles prior to sorting were determined via bulk sample 16S rRNA gene amplicon sequencing. The flow-sorted cellulose-bound microbes were subjected to whole genome amplification and shotgun sequencing, followed by phylogenetic placement. Next, putative cellulase genes were identified, expressed and tested for activity against derivatives of cellulose and xylose. Alongside typical cellulose degraders, including members of the Actinobacteria, Bacteroidetes, and Chloroflexi, we found divergent cellulases encoded in the genome of a recently described candidate phylum from the rare biosphere, Goldbacteria, and validated their cellulase activity. As this genome represents a species-level organism with novel and phylogenetically distinct cellulolytic activity, we propose the name Candidatus ‘Cellulosimonas argentiregionis’. We expect that this function-driven single-cell approach can be extended to a broad range of substrates, linking microbial taxonomy directly to in situ function.
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spelling pubmed-70315332020-03-04 Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere Doud, Devin F. R. Bowers, Robert M. Schulz, Frederik De Raad, Markus Deng, Kai Tarver, Angela Glasgow, Evan Vander Meulen, Kirk Fox, Brian Deutsch, Sam Yoshikuni, Yasuo Northen, Trent Hedlund, Brian P. Singer, Steven W. Ivanova, Natalia Woyke, Tanja ISME J Article Assigning a functional role to a microorganism has historically relied on cultivation of isolates or detection of environmental genome-based biomarkers using a posteriori knowledge of function. However, the emerging field of function-driven single-cell genomics aims to expand this paradigm by identifying and capturing individual microbes based on their in situ functions or traits. To identify and characterize yet uncultivated microbial taxa involved in cellulose degradation, we developed and benchmarked a function-driven single-cell screen, which we applied to a microbial community inhabiting the Great Boiling Spring (GBS) Geothermal Field, northwest Nevada. Our approach involved recruiting microbes to fluorescently labeled cellulose particles, and then isolating single microbe-bound particles via fluorescence-activated cell sorting. The microbial community profiles prior to sorting were determined via bulk sample 16S rRNA gene amplicon sequencing. The flow-sorted cellulose-bound microbes were subjected to whole genome amplification and shotgun sequencing, followed by phylogenetic placement. Next, putative cellulase genes were identified, expressed and tested for activity against derivatives of cellulose and xylose. Alongside typical cellulose degraders, including members of the Actinobacteria, Bacteroidetes, and Chloroflexi, we found divergent cellulases encoded in the genome of a recently described candidate phylum from the rare biosphere, Goldbacteria, and validated their cellulase activity. As this genome represents a species-level organism with novel and phylogenetically distinct cellulolytic activity, we propose the name Candidatus ‘Cellulosimonas argentiregionis’. We expect that this function-driven single-cell approach can be extended to a broad range of substrates, linking microbial taxonomy directly to in situ function. Nature Publishing Group UK 2019-11-21 2020-03 /pmc/articles/PMC7031533/ /pubmed/31754206 http://dx.doi.org/10.1038/s41396-019-0557-y Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Doud, Devin F. R.
Bowers, Robert M.
Schulz, Frederik
De Raad, Markus
Deng, Kai
Tarver, Angela
Glasgow, Evan
Vander Meulen, Kirk
Fox, Brian
Deutsch, Sam
Yoshikuni, Yasuo
Northen, Trent
Hedlund, Brian P.
Singer, Steven W.
Ivanova, Natalia
Woyke, Tanja
Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
title Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
title_full Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
title_fullStr Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
title_full_unstemmed Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
title_short Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
title_sort function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7031533/
https://www.ncbi.nlm.nih.gov/pubmed/31754206
http://dx.doi.org/10.1038/s41396-019-0557-y
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