Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation

Valentine Cyriaque (), Rodrigo Ibarra-Chávez, Anna Kuchina, Georg Seelig, Joseph Nesme and Jonas Stenløkke Madsen ()
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Valentine Cyriaque: University of Copenhagen
Rodrigo Ibarra-Chávez: University of Copenhagen
Anna Kuchina: Institute for Systems Biology
Georg Seelig: University of Washington
Joseph Nesme: University of Copenhagen
Jonas Stenløkke Madsen: University of Copenhagen

Nature Communications, 2024, vol. 15, issue 1, 1-10

Abstract: Abstract Transcriptional heterogeneity in isogenic bacterial populations can play various roles in bacterial evolution, but its detection remains technically challenging. Here, we use microbial split-pool ligation transcriptomics to study the relationship between bacterial subpopulation formation and plasmid-host interactions at the single-cell level. We find that single-cell transcript abundances are influenced by bacterial growth state and plasmid carriage. Moreover, plasmid carriage constrains the formation of bacterial subpopulations. Plasmid genes, including those with core functions such as replication and maintenance, exhibit transcriptional heterogeneity associated with cell activity. Notably, we identify a cell subpopulation that does not transcribe conjugal plasmid transfer genes, which may help reduce plasmid burden on a subset of cells. Our study advances the understanding of plasmid-mediated subpopulation dynamics and provides insights into the plasmid-bacteria interplay.

Date: 2024
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DOI: 10.1038/s41467-024-49793-x

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