Spatial organization of different sigma factor activities and c-di-GMP signalling within the three-dimensional landscape of a bacterial biofilm

Open Biol. 2018 Aug;8(8):180066. doi: 10.1098/rsob.180066.


Bacterial biofilms are large aggregates of cells embedded in an extracellular matrix of self-produced polymers. In macrocolony biofilms of Escherichia coli, this matrix is generated in the upper biofilm layer only and shows a surprisingly complex supracellular architecture. Stratified matrix production follows the vertical nutrient gradient and requires the stationary phase σS (RpoS) subunit of RNA polymerase and the second messenger c-di-GMP. By visualizing global gene expression patterns with a newly designed fingerprint set of Gfp reporter fusions, our study reveals the spatial order of differential sigma factor activities, stringent control of ribosomal gene expression and c-di-GMP signalling in vertically cryosectioned macrocolony biofilms. Long-range physiological stratification shows a duplication of the growth-to-stationary phase pattern that integrates nutrient and oxygen gradients. In addition, distinct short-range heterogeneity occurs within specific biofilm strata and correlates with visually different zones of the refined matrix architecture. These results introduce a new conceptual framework for the control of biofilm formation and demonstrate that the intriguing extracellular matrix architecture, which determines the emergent physiological and biomechanical properties of biofilms, results from the spatial interplay of global gene regulation and microenvironmental conditions. Overall, mature bacterial macrocolony biofilms thus resemble the highly organized tissues of multicellular organisms.

Keywords: RpoS; bacterial second messenger; biofilm; c-di-GMP; sigma factor.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biofilms
  • Cyclic GMP / analogs & derivatives*
  • Cyclic GMP / metabolism
  • Escherichia coli / genetics
  • Escherichia coli / growth & development*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / metabolism
  • Gene Expression Regulation, Bacterial
  • Green Fluorescent Proteins / genetics
  • Green Fluorescent Proteins / metabolism
  • Sigma Factor / genetics
  • Sigma Factor / metabolism*
  • Signal Transduction


  • Escherichia coli Proteins
  • Sigma Factor
  • Green Fluorescent Proteins
  • bis(3',5')-cyclic diguanylic acid
  • Cyclic GMP