Abstract

In nature, bacteria are not necessarily free in their environment but rather they navigate through complex topologies such as porous materials, rough surfaces or wounds. When doing so, they may give place to living liquid crystals due to the cell-cell alignment. In this study, we use a mutant of Bacillus subtilis that lack flagella as a model organism to study bacteria assembly and liquid crystal formation in extreme confinement. The confinement is micropatterned using an adaptation of a soft lithography-based method. The desired patterns are situated at the bottom of a deep well which acts as a reservoir for a solution containing the immotile bacteria. These bacteria precipitate over time, forming a dense liquid crystalline layer at the bottom of the well. The patterning of bacteria leads to the formation of complex nematic phases whose topological defects depend on the geometry of the confinement and can be resolved at single cell resolution. This characterization allows the comparison with more simple systems of hard rod-shaped colloidal particles and of soft fd rod-shaped viruses which, unlike bacteria, do not undergo cell replication. We discovered that the patterns formed by the bacteria resemble those in other nematic phases made by silica rods or fd viruses and predicted by theoretical studies.