Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
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Le résumé fourni par la source
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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Le contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
- Date Crossref
- 21/11/2019
- Éditeur
- Oxford University Press (OUP)
- Type
- journal-article
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.
Où se fait cette recherche
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Joint Genome Institute U.S. Department of Energy pays non établi dans la noticeStructure de recherche
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Lawrence Berkeley National Laboratory Environmental Genomics and Systems Biology Division pays non établi dans la noticeStructure de recherche
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Sandia National Laboratories California pays non établi dans la noticeStructure de recherche
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Joint BioEnergy Institute pays non établi dans la noticeStructure de recherche
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University of Wisconsin–Madison Department of Biochemistry pays non établi dans la noticeUniversité ou école supérieure
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Great Lakes Bioenergy Research Center pays non établi dans la noticeStructure de recherche
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University of Nevada pays non établi dans la noticeUniversité ou école supérieure
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University of California pays non établi dans la noticeUniversité ou école supérieure
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Department of Biotechnology and Bioengineering pays non établi dans la noticeInstitution
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School of Life Sciences pays non établi dans la noticeUniversité ou école supérieure
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School of Natural Sciences pays non établi dans la noticeUniversité ou école supérieure
U.S. Department of Energy — Joint Genome Institute, Environmental Genomics and Systems Biology Division — Lawrence Berkeley National Laboratory et Sandia National Laboratories California, avec 8 autres affiliations.
Une affiliation ne permet pas de déduire la nationalité d’un auteur.