Mechanical stress determines morphogenesis and cell ordering in confined bacterial biofilms

Biofilms are aggregates of bacterial cells surrounded by an extracellular matrix. Much progress has been made in studying biofilm growth on solid substrates; however, little is known about how biofilms develop in three-dimensional confined environments. Here, combining single-cell imaging, continuum mechanical modeling, and mutagenesis, we reveal the key morphogenesis steps of Vibrio cholerae biofilms embedded in hydrogels. We demonstrate how mechanical stress determines the global morphology and gives rise to bipolar cell ordering in confined biofilms. Our analysis shows that cell ordering arises from stress transmission across the biofilm-environment interface, mediated by specific matrix components. Our results open an avenue to understand how organisms grow within complex environments by means of a compromise between their inherent developmental program and the constraints imposed by the environment. One sentence summaryEmbedded biofilms mechanically interact with the confining environment, leading to the emergence of an anisotropic architecture and a precise cell organization.