title: Single-cell genomics based on Raman sorting reveals novel carotenoid-containing bacteria in the Red Sea.
abstract: Cell sorting coupled with single-cell genomics is a powerful tool to circumvent cultivation of microorganisms and reveal microbial 'dark matter'. Single-cell Raman spectra (SCRSs) are label-free biochemical 'fingerprints' of individual cells, which can link the sorted cells to their phenotypic information and ecological functions. We employed a novel Raman-activated cell ejection (RACE) approach to sort single bacterial cells from a water sample in the Red Sea based on SCRS. Carotenoids are highly diverse pigments and play an important role in phototrophic bacteria, giving strong and distinctive Raman spectra. Here, we showed that individual carotenoid-containing cells from a Red Sea sample were isolated based on the characteristic SCRS. RACE-based single-cell genomics revealed putative novel functional genes related to carotenoid and isoprenoid biosynthesis, as well as previously unknown phototrophic microorganisms including an unculturable Cyanobacteria spp. The potential of Raman sorting coupled to single-cell genomics has been demonstrated.
authors.affiliation: Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
authors.forename: Yizhi
authors.initials: Y
authors.lastname: Song
authors.affiliation: Leibniz Institute DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany.
authors.forename: Anne-Kristin
authors.initials: AK
authors.lastname: Kaster
authors.affiliation: Leibniz Institute DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany.
authors.forename: John
authors.initials: J
authors.lastname: Vollmers
authors.affiliation: Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK.
authors.forename: Yanqing
authors.initials: Y
authors.lastname: Song
authors.affiliation: Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Davison
authors.affiliation: Leibniz Institute DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany.
authors.forename: Martinique
authors.initials: M
authors.lastname: Frentrup
authors.affiliation: Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
authors.forename: Gail M
authors.initials: GM
authors.lastname: Preston
authors.affiliation: Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
authors.forename: Ian P
authors.initials: IP
authors.lastname: Thompson
authors.affiliation: School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
authors.forename: J Colin
authors.initials: JC
authors.lastname: Murrell
authors.affiliation: Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK.
authors.forename: Huabing
authors.initials: H
authors.lastname: Yin
authors.affiliation: Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK.
authors.forename: C Neil
authors.initials: CN
authors.lastname: Hunter
authors.affiliation: Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
authors.forename: Wei E
authors.initials: WE
authors.lastname: Huang
mesh_terms: D002338:Carotenoids / Q000032:analysis*; D000458:Cyanobacteria / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification*; D016680:Genome, Bacterial; D019156:Indian Ocean; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis / Q000379:methods*; D013059:Spectrum Analysis, Raman
chemical_list: D002338:Carotenoids