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ISME J. 2019 Nov 21. doi: 10.1038/s41396-019-0557-y. [Epub ahead of print]

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

Author information

1
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
2
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
3
Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
4
Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA, 94551, USA.
5
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
6
Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA.
7
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
8
School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA.
9
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA. twoyke@lbl.gov.
10
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. twoyke@lbl.gov.
11
School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA. twoyke@lbl.gov.

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 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.

PMID:
31754206
DOI:
10.1038/s41396-019-0557-y

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