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scMAR-Seq: a novel workflow for targeted single-cell genomics of microorganisms using radioactive labeling

Lo, Hao-Yu 1; Wink, Konstantin; Nitz, Henrike; Kästner, Matthias; Belder, Detlev; Müller, Jochen A. ORCID iD icon 1; Kaster, Anne-Kristin 1; Hess, Matthias [Hrsg.]
1 Institut für Biologische Grenzflächen (IBG), Karlsruher Institut für Technologie (KIT)

Abstract:

Current methods for the identification of specific microorganisms based on an in situ metabolism are often hampered by insufficient sensitivity and habitat complexity. Here, we present a novel approach for identifying and sequencing single microbial cells metabolizing a specific organic compound with high sensitivity and without prior knowledge of the microbial community. The workflow consists of labeling individual cells with a [$^{14}$C] substrate based on their metabolic activity, followed by encapsulating cells in alginate with nuclear emulsion by using microfluidics. We here adapted the concept of microautoradiography to visually distinguish between encapsulated labeled and non-labeled cells, which are then sorted via flow cytometry for single cell genomics. As a proof-of-concept, we labeled, separated, lysed, and sequenced single cells of the benzene degrader Pseudomonas veronii from mock microbial communities. The cells of P. veronii were isolated with 100% specificity. Single-cell microautoradiography and genome sequencing is an innovative method for elucidating microbial identity, activity, and function in diverse habitats, contributing to elucidate novel taxa and genes with potential for biotechnological applications such as bioremediation.


Verlagsausgabe §
DOI: 10.5445/IR/1000165518
Veröffentlicht am 11.12.2023
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Biologische Grenzflächen (IBG)
Publikationstyp Zeitschriftenaufsatz
Publikationsjahr 2023
Sprache Englisch
Identifikator ISSN: 2379-5077
KITopen-ID: 1000165518
HGF-Programm 43.33.11 (POF IV, LK 01) Adaptive and Bioinstructive Materials Systems
Erschienen in mSystems
Verlag American Society for Microbiology
Band 8
Heft 6
Seiten e00998-23
Bemerkung zur Veröffentlichung Gefördert durch den KIT-Publikationsfonds
Vorab online veröffentlicht am 20.11.2023
Nachgewiesen in Dimensions
Web of Science
Scopus
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