RT Journal Article
SR Electronic
T1 In situ single-cell activities of microbial populations revealed by spatial transcriptomics
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.02.24.432792
DO 10.1101/2021.02.24.432792
A1 Daniel Dar
A1 Nina Dar
A1 Long Cai
A1 Dianne K. Newman
YR 2021
UL http://biorxiv.org/content/early/2021/02/25/2021.02.24.432792.abstract
AB Microbial populations and communities are heterogeneous, yet capturing their diverse activities has proven challenging at the relevant spatiotemporal scales. Here we present par-seqFISH, a targeted transcriptome-imaging approach that records both gene-expression and spatial context within microscale assemblies at a single-cell and molecule resolution. We apply this approach to the opportunistic bacterial pathogen, Pseudomonas aeruginosa, analyzing ∼600,000 individuals across dozens of physiological conditions in planktonic and biofilm cultures. We explore the phenotypic landscape of this bacterium and identify metabolic and virulence related cell-states that emerge dynamically during growth. We chart the spatial context of biofilm-related processes including motility and kin-exclusion mechanisms and identify extensive and highly spatially-resolved metabolic heterogeneity. We find that distinct physiological states can co-exist within the same biofilm, just a few microns away, underscoring the importance of the microenvironment. Together, our results illustrate the complexity of microbial populations and present a new way of studying them at high-resolution.Competing Interest StatementThe authors have declared no competing interest.