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

Abstract

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 genomemore » 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.« less

Authors:
 [1];  [1]; ORCiD logo [1];  [2];  [3];  [1];  [4];  [4]; ORCiD logo [4];  [1]; ORCiD logo [5]; ORCiD logo [5]; ORCiD logo [6]; ORCiD logo [7]; ORCiD logo [5]; ORCiD logo [8]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
  4. Univ. of Wisconsin, Madison, WI (United States)
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. Univ. of Nevada, Las Vegas, NV (United States)
  7. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  8. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Merced, CA (United States)
Publication Date:
Research Org.:
Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1579340
Grant/Contract Number:  
SC0018409; FC02- 07ER64494; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Name: The ISME Journal; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English

Citation Formats

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, and Woyke, Tanja. Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere. United States: N. p., 2019. Web. doi:10.1038/s41396-019-0557-y.
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. United States. doi:10.1038/s41396-019-0557-y.
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, and Woyke, Tanja. Thu . "Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere". United States. doi:10.1038/s41396-019-0557-y. https://www.osti.gov/servlets/purl/1579340.
@article{osti_1579340,
title = {Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere},
author = {Doud, Devin F. R. and Bowers, Robert M. and Schulz, Frederik and De Raad, Markus and Deng, Kai and Tarver, Angela and Glasgow, Evan and Vander Meulen, Kirk and Fox, Brian and Deutsch, Sam and Yoshikuni, Yasuo and Northen, Trent and Hedlund, Brian P. and Singer, Steven W. and Ivanova, Natalia and Woyke, Tanja},
abstractNote = {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.},
doi = {10.1038/s41396-019-0557-y},
journal = {The ISME Journal},
number = ,
volume = ,
place = {United States},
year = {2019},
month = {11}
}

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