Bacterial biofilms

Functional states in a small aggregate biofilm of Pseudomonas aeruginosa

Biofilms are structured bacterial communities that represent the most prevalent bacterial life form. During biofilm formation, bacteria differentiate into phenotypically distinct subpopulations with specialized roles. The transcriptional states inside of a biofilm may represent both stochastically induced gene expression programs, and the adaptations to different physicochemical conditions within multiple microscale environmental niches. Despite decades of studies, there are still open questions about the extent and roles of transcriptional heterogeneity within the developing biofilm. What specialized phenotypic subpopulations emerge at different stages of biofilm development? In this project, we aim to create a single-cell gene expression map of the surface-attached and suspended-aggregate biofilms of a pathogen Pseudomonas aeruginosa by a combination of single-cell RNA sequencing and fluorescence imaging. Using microSPLiT, a bacterial single-cell RNA sequencing method optimized for the biofilm, we are finding heterogeneity in metabolic strategies between branched amino acids or succinate, fatty acid synthesis or degradation, expression of motility or virulence genes, and a population of cells exhibiting stress responses. In addition, we detect heterogeneous subpopulations of cells expressing diverse small RNA which provide an additional layer of gene regulation.

Led by: Stephen Fedak