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

Author

Listed:
  • Valentine Cyriaque

    (University of Copenhagen
    UMONS)

  • Rodrigo Ibarra-Chávez

    (University of Copenhagen)

  • Anna Kuchina

    (Institute for Systems Biology
    University of Washington
    University of Washington)

  • Georg Seelig

    (University of Washington
    University of Washington)

  • Joseph Nesme

    (University of Copenhagen)

  • Jonas Stenløkke Madsen

    (University of Copenhagen)

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.

Suggested Citation

  • Valentine Cyriaque & Rodrigo Ibarra-Chávez & Anna Kuchina & Georg Seelig & Joseph Nesme & Jonas Stenløkke Madsen, 2024. "Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49793-x
    DOI: 10.1038/s41467-024-49793-x
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    References listed on IDEAS

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    1. Elena Perrin & Veronica Ghini & Michele Giovannini & Francesca Di Patti & Barbara Cardazzo & Lisa Carraro & Camilla Fagorzi & Paola Turano & Renato Fani & Marco Fondi, 2020. "Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
    2. Suzanne Humphrey & Álvaro San Millán & Macarena Toll-Riera & John Connolly & Alejandra Flor-Duro & John Chen & Carles Ubeda & R. Craig MacLean & José R. Penadés, 2021. "Staphylococcal phages and pathogenicity islands drive plasmid evolution," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    3. Ziye Xu & Yuting Wang & Kuanwei Sheng & Raoul Rosenthal & Nan Liu & Xiaoting Hua & Tianyu Zhang & Jiaye Chen & Mengdi Song & Yuexiao Lv & Shunji Zhang & Yingjuan Huang & Zhaolun Wang & Ting Cao & Yife, 2023. "Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
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