Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution

Abstract

Spying on microbial communities, cell by cell Within any community of organisms, gene expression is heterogeneous, which can manifest in genetically identical individuals having a different phenotype. One has to look at individuals in context and analyze patterns in both space and time to see the full picture. Aiming to fill a gap in current methods, Dar et al . developed a transcriptome-imaging method named parallel sequential fluorescence in situ hybridization (par-seqFISH). They applied this technique to the opportunistic pathogen Pseudomonas aeruginosa , focusing on biofilms where growth conditions can change at microscopic scale. Development of these communities, as revealed by mRNA composition, were followed in space and time. The results revealed a heterogeneous phenotypic landscape, with oxygen availability shaping the metabolism at a spatial scale of microns within a single contiguous biofilm segment. This tool should be applicable to complex microbial communities in the environment and the human microbiome. —MAF