Single-cell genomics based on Raman sorting reveals novel carotenoid-containing bacteria in the Red Sea

Yizhi Song; Anne-Kristin Kaster; John Vollmers; Yanqing Song; Paul A. Davison; Martinique Frentrup; Gail M. Preston; Ian P. Thompson; J. Colin Murrell; Huabing Yin; C. Neil Hunter; Wei E. Huang

doi:10.1111/1751-7915.12420

Single-cell genomics based on Raman sorting reveals novel carotenoid-containing bacteria in the Red Sea

Yizhi Song, Anne-Kristin Kaster, John Vollmers, Yanqing Song, Paul A. Davison, Martinique Frentrup, Gail M. Preston, Ian P. Thompson, J. Colin Murrell, Huabing Yin, C. Neil Hunter, Wei E. Huang

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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.

Original language	English
Pages (from-to)	125–137
Journal	Microbial Biotechnology
Volume	10
Issue number	1
Early online date	17 Oct 2016
DOIs	https://doi.org/10.1111/1751-7915.12420
Publication status	Published - Jan 2017

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10.1111/1751-7915.12420

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© 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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http://doi.wiley.com/10.1111/1751-7915.12420Licence: CC BY

Functional Metagenomics and Stable Isoptope Probing of Marine Methylotrophs
Murrell, C. & Chen, Y.
Gordon & Betty Moore Foundation
1/06/12 → 31/10/16
Project: Research

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@article{f6f35c22edf9483aac65f22ee34c8685,

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 {\textquoteleft}dark matter{\textquoteright}. Single-cell Raman spectra (SCRSs) are label-free biochemical {\textquoteleft}fingerprints{\textquoteright} 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.",

author = "Yizhi Song and Anne-Kristin Kaster and John Vollmers and Yanqing Song and Davison, {Paul A.} and Martinique Frentrup and Preston, {Gail M.} and Thompson, {Ian P.} and Murrell, {J. Colin} and Huabing Yin and Hunter, {C. Neil} and Huang, {Wei E.}",

note = " {\textcopyright} 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.",

year = "2017",

month = jan,

doi = "10.1111/1751-7915.12420",

language = "English",

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pages = "125–137",

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AU - Song, Yizhi

AU - Kaster, Anne-Kristin

AU - Vollmers, John

AU - Song, Yanqing

AU - Davison, Paul A.

AU - Frentrup, Martinique

AU - Preston, Gail M.

AU - Thompson, Ian P.

AU - Murrell, J. Colin

AU - Yin, Huabing

AU - Hunter, C. Neil

AU - Huang, Wei E.

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AB - 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.

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SN - 1751-7915

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ER -

Single-cell genomics based on Raman sorting reveals novel carotenoid-containing bacteria in the Red Sea

Abstract

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Projects

Functional Metagenomics and Stable Isoptope Probing of Marine Methylotrophs

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