Microbial single-cell RNA sequencing by split-pool barcoding of Pseudomonas putida KT2440/pKJK5

microSPLiT is a high-throughput single-cell RNA-sequencing method that we applied to Pseudomonas putida KT2440 with or without the pKJK5 plasmid sampled at 2 growth stages, to unraveling plasmid biology at the subpopulation level. We performed a microSPLiT experiment with blind cell assignation or using the first barcode as a sample identifier. microSPLiT results were compared to bulk transcriptomics.We find that chromosomal gene transcription was impacted by plasmid carriage mainly at the single cell level, resulting in a reduction of transcriptional subpopulations. A large degree of transcriptional heterogeneity was seen among plasmid-encoded genes.