Active nematics are the nonequilibrium analog of passive liquid crystals in which anisotropic units consume free energy to drive emergent behavior. Similar to liquid crystal (LC) molecules in displays, ordering and dynamics in active nematics are sensitive to boundary conditions; however, unlike passive liquid crystals, active nematics, such as those composed of living matter, have the potential to regulate their boundaries through self-generated stresses.  Here, using bacterial biofilms confined by a hydrogel as a model system, we show how a three-dimensional, living nematic can actively shape itself and its boundary in order to regulate its internal architecture through growth-induced stresses. We show that biofilms exhibit a sharp transition in shape from domes to lenses upon changing environmental stiffness or cell-substrate friction, which is explained by a theoretical model considering the competition between confinement and interfacial forces. The growth mode defines the progression of the boundary, which in turn determines the trajectories and spatial distribution of cell lineages. We further demonstrate that the evolving boundary defines the orientational ordering of cells and the emergence of topological defects in the interior of the biofilm. Our findings reveal novel self-organization phenomena in confined active matter and provide strategies for guiding the development of programmed microbial consortia with emergent material properties.

The dataset was acquired using a Yokogawa CSU-W1 spinning-disk confocal scanning unit mounted on a Nikon Ti2-E microscope body, using the Nikon perfect focus system and images were acquired using Nikon Elements 5.20. For high-resolution, single-cell level imaging, a 100× silicon oil immersion objective (Lambda S 100XC Sil, numerical aperture = 1.35) was used. A z-step size of 0.195 μm was used. The green mNeonGreen fluorophore was excited using a 488 nm laser. For time course imaging, cells were incubated in a Tokai-Hit stage-top incubator at a temperature of 30°C. Provided here are raw data without any postprocessing.

The dataset was aqcuired and can be opened with Nikon Elements 5.20. Alternatively, free software such as FIJI can also open it (https://imagej.net/software/fiji/).