Single-cell RNA sequencing suggests plasmids constrain bacterial heterogeneity and conjugation is subpopulation specific

Abstract Transcriptional heterogeneity is common within isogenic bacterial populations. Nonetheless, the interplay between conjugative plasmids and host subpopulation dynamics remains elusive. Here, the efficacy of microbial split-pool ligation transcriptomics in unraveling plasmid-host interactions was demonstrated through the generation of high-quality single-cell transcriptomic data. We found that transcription was impacted by growth state but also by plasmid carriage at the single-cell level, resulting in a reduction in subpopulations. Transcriptional heterogeneity among plasmid-encoded genes was also uncovered. This included core plasmid functions such as replication and maintenance fluctuations, likely associated with the cell cycle. Other key heterogeneously transcribed functions included tra genes revealing a subpopulation not engaging in conjugation and representing a possible plasmid strategy decreasing its burden at the population level. In sum, this study advances the understanding of plasmid-mediated subpopulation dynamics through a comprehensive single-cell transcriptomics approach, providing valuable insights into the intricate interplay between plasmids and bacteria.