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 the biophysical mechanisms underlying biofilm development in three-dimensional confined environments in which the biofilm-dwelling cells must push against and even damage the surrounding environment to proliferate. Here, combining single-cell imaging, mutagenesis, and rheological measurement, we reveal the key morphogenesis steps of Vibrio cholerae biofilms embedded in hydrogels as they grow by four orders of magnitude from their initial size. We show that the morphodynamics and cell ordering in embedded biofilms are fundamentally different from those of biofilms on flat surfaces. Treating embedded biofilms as inclusions growing in an elastic medium, we quantitatively show that the stiffness contrast between the biofilm and its environment determines biofilm morphology and internal architecture, selecting between spherical biofilms with no cell ordering and oblate ellipsoidal biofilms with high cell ordering. When embedded in stiff gels, cells self-organize into a bipolar structure that resembles the molecular ordering in nematic liquid crystal droplets. In vitro biomechanical analysis shows that cell ordering arises from stress transmission across the biofilm–environment interface, mediated by specific matrix components. Our imaging technique and theoretical approach are generalizable to other biofilm-forming species and potentially to biofilms embedded in mucus or host tissues as during infection. Our results open an avenue to understand how confined cell communities grow by means of a compromise between their inherent developmental program and the mechanical constraints imposed by the environment.

We examine the full ‘life cycle’ of miscible viscous fingering from onset to shutdown with the aid of high-resolution numerical simulations. We study the injection of one fluid into a planar two-dimensional porous medium containing another, more viscous fluid. We find that the dynamics are distinguished by three regimes: an early-time linearly unstable regime, an intermediate-time nonlinear regime and a late-time single-finger exchange-flow regime. In the first regime, the flow can be linearly unstable to perturbations that grow exponentially. We identify, using linear stability theory and numerical simulations, a critical Péclet number below which the flow remains stable for all times. In the second regime, the flow is dominated by the nonlinear coalescence of fingers which form a mixing zone in which we observe that the convective mixing rate, characterized by a convective Nusselt number, exhibits power-law growth. In this second regime we derive a model for the transversely averaged concentration which shows good agreement with our numerical experiments and extends previous empirical models. Finally, we identify a new final exchange-flow regime in which a pair of counter-propagating diffusive fingers slow exponentially. We derive an analytic solution for this single-finger state which agrees well with numerical simulations. We demonstrate that the flow always evolves to this regime, irrespective of the viscosity ratio and Péclet number, in contrast to previous suggestions.

Fluid flowing through a deformable porous medium imparts viscous drag on the solid matrix, causing it to deform. This effect is investigated theoretically and experimentally in a one-dimensional configuration. The experiments consist of the downwards flow of water through a saturated pack of small, soft, hydrogel spheres, driven by a pressure head that can be increased or decreased. As the pressure head is increased, the effective permeability of the medium decreases and, in contrast to flow through a rigid medium, the flux of water is found to increase towards a finite upper bound such that it becomes insensitive to changes in the pressure head. Measurements of the internal deformation, extracted by particle tracking, show that the medium compacts differentially, with the porosity being lower at the base than at the upper free surface. A general theoretical model is derived, and the predictions of the model give good agreement with experimental measurements from a series of experiments in which the applied pressure head is sequentially increased. However, contrary to theory, all the experimental results display a distinct and repeatable hysteresis: the flux through the material for a particular applied pressure drop is appreciably lower when the pressure has been decreased to that value compared to when it has been increased to the same value.

In growing active matter systems, a large collection of engineered or living autonomous units metabolize free energy and create order at different length scales as they proliferate and migrate collectively. One such example is bacterial biofilms, surface-attached aggregates of bacterial cells embedded in an extracellular matrix that can exhibit community-scale orientational order. However, how bacterial growth coordinates with cell-surface interactions to create distinctive, long-range order during biofilm development remains elusive. Here we report a collective cell reorientation cascade in growing Vibrio cholerae biofilms that leads to a differentially ordered, spatiotemporally coupled core-rim structure reminiscent of a blooming aster. Cell verticalization in the core leads to a pattern of differential growth that drives radial alignment of the cells in the rim, while the growing rim generates compressive stresses that expand the verticalized core. Such self-patterning disappears in nonadherent mutants but can be restored through opto-manipulation of growth. Agent-based simulations and two-phase active nematic modeling jointly reveal the strong interdependence of the driving forces underlying the differential ordering. Our findings offer insight into the developmental processes that shape bacterial communities and provide ways to engineer phenotypes and functions in living active matter.