Cargando…
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...
Autores principales: | , , , , , , , , , , , , , , , |
---|---|
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 |
_version_ | 1783499394968977408 |
---|---|
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. |
format | Online Article Text |
id | pubmed-7031533 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT douddevinfr functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT bowersrobertm functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT schulzfrederik functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT deraadmarkus functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT dengkai functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT tarverangela functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT glasgowevan functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT vandermeulenkirk functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT foxbrian functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT deutschsam functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT yoshikuniyasuo functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT northentrent functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT hedlundbrianp functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT singerstevenw functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT ivanovanatalia functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere AT woyketanja functiondrivensinglecellgenomicsuncoverscellulosedegradingbacteriafromtherarebiosphere |