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Doud DFR, Bowers RM, Schulz F, De Raad M, Deng K, Tarver A, Glasgow E, Vander Meulen K, Fox B, Deutsch S, Yoshikuni Y, Northen T, Hedlund BP, Singer SW, Ivanova N, Woyke T. Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere. ISME J 2019; 14:659-675. [PMID: 31754206 PMCID: PMC7031533 DOI: 10.1038/s41396-019-0557-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/04/2019] [Accepted: 11/08/2019] [Indexed: 11/09/2022]
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.
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Affiliation(s)
- Devin F R Doud
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Robert M Bowers
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Frederik Schulz
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Markus De Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Angela Tarver
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Evan Glasgow
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kirk Vander Meulen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Brian Fox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sam Deutsch
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Yasuo Yoshikuni
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent Northen
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Natalia Ivanova
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Tanja Woyke
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA. .,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA.
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Wang G, Zhao Z, Ke J, Engel Y, Shi YM, Robinson D, Bingol K, Zhang Z, Bowen B, Louie K, Wang B, Evans R, Miyamoto Y, Cheng K, Kosina S, De Raad M, Silva L, Luhrs A, Lubbe A, Hoyt DW, Francavilla C, Otani H, Deutsch S, Washton NM, Rubin EM, Mouncey NJ, Visel A, Northen T, Cheng JF, Bode HB, Yoshikuni Y. CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria. Nat Microbiol 2019; 4:2498-2510. [PMID: 31611640 DOI: 10.1038/s41564-019-0573-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 08/27/2019] [Indexed: 12/11/2022]
Abstract
It is generally believed that exchange of secondary metabolite biosynthetic gene clusters (BGCs) among closely related bacteria is an important driver of BGC evolution and diversification. Applying this idea may help researchers efficiently connect many BGCs to their products and characterize the products' roles in various environments. However, existing genetic tools support only a small fraction of these efforts. Here, we present the development of chassis-independent recombinase-assisted genome engineering (CRAGE), which enables single-step integration of large, complex BGC constructs directly into the chromosomes of diverse bacteria with high accuracy and efficiency. To demonstrate the efficacy of CRAGE, we expressed three known and six previously identified but experimentally elusive non-ribosomal peptide synthetase (NRPS) and NRPS-polyketide synthase (PKS) hybrid BGCs from Photorhabdus luminescens in 25 diverse γ-Proteobacteria species. Successful activation of six BGCs identified 22 products for which diversity and yield were greater when the BGCs were expressed in strains closely related to the native strain than when they were expressed in either native or more distantly related strains. Activation of these BGCs demonstrates the feasibility of exploiting their underlying catalytic activity and plasticity, and provides evidence that systematic approaches based on CRAGE will be useful for discovering and identifying previously uncharacterized metabolites.
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Affiliation(s)
- Gaoyan Wang
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Zhiying Zhao
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Jing Ke
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Yvonne Engel
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Yi-Ming Shi
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - David Robinson
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Kerem Bingol
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Zheyun Zhang
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Benjamin Bowen
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine Louie
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Bing Wang
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Robert Evans
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Yu Miyamoto
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Kelly Cheng
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Suzanne Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Markus De Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Leslie Silva
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | | | - David W Hoyt
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Hiroshi Otani
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Samuel Deutsch
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nancy M Washton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Edward M Rubin
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Nigel J Mouncey
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Axel Visel
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent Northen
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Helge B Bode
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany.
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL, USA. .,Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido, Japan.
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Abstract
Surface-assisted laser desorption ionization (SALDI) is an approach for gas-phase ion generation for mass spectrometry using laser excitation on typically conductive or semiconductive nanostructures. Here, we introduce insulator nanostructure desorption ionization mass spectrometry (INDI-MS), a nanostructured polymer substrate for SALDI-MS analysis of small molecules and peptides. INDI-MS surfaces are produced through the self-assembly of a perfluoroalkyl silsesquioxane nanostructures in a single chemical vapor deposition silanization-step. We find that surfaces formed from the perfluorooctyltrichlorosilane monomer assemble semielliptical features with a 10 nm height, diameters between 10 and 50 nm, and have attomole-femtomole sensitivities for selected analytes. Surfaces prepared with silanes that either lack the trichloro or perfluoro groups, lack sensitivity. Further, we demonstrate that hydrophobic INDI regions can be micropatterned onto hydrophilic surfaces to perform on-chip self-desalting in an array format.
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Affiliation(s)
- Todd A Duncombe
- DOE Joint BioEnergy Institute , 5885 Hollis Street , Emeryville , California 94608 , United States.,Sandia National Laboratories , Livermore , California 94550 , United States
| | - Markus De Raad
- Environmental Genomics and Systems Biology, Biosciences , Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
| | - Benjamin P Bowen
- Joint Genome Institute , Department of Energy , 2800 Mitchell Drive , Walnut Creek , California 94598 , United States.,Environmental Genomics and Systems Biology, Biosciences , Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
| | - Anup K Singh
- DOE Joint BioEnergy Institute , 5885 Hollis Street , Emeryville , California 94608 , United States.,Sandia National Laboratories , Livermore , California 94550 , United States
| | - Trent R Northen
- DOE Joint BioEnergy Institute , 5885 Hollis Street , Emeryville , California 94608 , United States.,Joint Genome Institute , Department of Energy , 2800 Mitchell Drive , Walnut Creek , California 94598 , United States.,Environmental Genomics and Systems Biology, Biosciences , Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
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