Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution
Daniel Dar, Nina Dar, Long Cai, Dianne K. Newman
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