Single-Cell Genomics of Microbial Dark Matter

  • Christian RinkeEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1849)


Single-cell genomics allows bypassing the culturing step and to directly access environmental microbes one cell at a time. The method has been successfully applied to explore archaeal and bacterial candidate phyla, referred to as microbial dark matter. Here I summarize the single-cell genomics workflow, including sample preparation and preservation, high-throughput fluorescence-activated cell sorting, cell lysis and amplification of environmental samples. Furthermore I describe phylogenetic screening based on 16S rRNA genes and suggest a suitable library preparation and sequencing approach.

Key words

Single-cell genomics Microbial dark matter Fluorescence-activated cell sorting FACS Multiple genome amplification 16S rRNA gene ILLUMINA Nextera XT libraries Biofilm Sludge Sediment 



The work was conducted at the Australian Centre for Ecogenomics (ACE) at UQ, and was supported by the ARC Discovery Project DP160103811. I would like to thank the ACE team for support, especially Dr. Michael Nefedov and Alexander Baker.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Australian Centre for EcogenomicsUniversity of QueenslandBrisbaneAustralia

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