Morphological instability and roughening of growing 3D bacterial colonies

Scale-dependent sharpening of interfacial fluctuations in shape-based models of dense cellular sheets

The properties of tissue interfaces - between separate populations of cells, or between a group of cells and its environment - has attracted intense theoretical, computational, and experimental study. Recent work on shape-based models inspired by dense epithelia have suggested a possible "topological sharpening" effect, by which four-fold vertices spatially coordinated along a cellular interface lead to a cusp-like restoring force acting on cells at the interface, which in turn greatly suppresses interfacial fluctuations. We revisit these interfacial fluctuations, focusing on the distinction between short length scale reduction of interfacial fluctuations and long length scale renormalized surface tension. To do this, we implement a spectrally resolved analysis of fluctuations over extremely long simulation times. This leads to more quantitative information on the topological sharpening effect, in which the degree of sharpening depends on the length scale over which it is measured. We compare our findings with a Brownian bridge model of the interface, and close by analyzing existing experimental data in support of the role of short-length-scale topological sharpening effects in real biological systems.

Cell shape affects bacterial colony growth under physical confinement

Evidence from homogeneous liquid or flat-plate cultures indicates that biochemical cues are the primary modes of bacterial interaction with their microenvironment. However, these systems fail to capture the effect of physical confinement on bacteria in their natural habitats. Bacterial niches like the pores of soil, mucus, and infected tissues are disordered microenvironments with material properties defined by their internal pore sizes and shear moduli. Here, we use three-dimensional matrices that match the viscoelastic properties of gut mucus to test how altering the physical properties of their microenvironment influences the growth of bacteria under confinement. We find that low aspect ratio (spherical) bacteria form compact, spherical colonies under confinement while high aspect ratio (rod-shaped) bacteria push their progenies further outwards to create elongated colonies with a higher surface area, enabling increased access to nutrients. As a result, the population growth of high aspect ratio bacteria is, under the tested conditions, more robust to increased physical confinement compared to that of low aspect ratio bacteria. Thus, our experimental evidence supports that environmental physical constraints can play a selective role in bacterial growth based on cell shape.

Mechanics and Morphology of Proliferating Cell Collectives with Self-Inhibiting Growth

We study the dynamics of proliferating cell collectives whose microscopic constituents' growth is inhibited by macroscopic growth-induced stress. Discrete particle simulations of a growing collective show the emergence of concentric-ring patterns in cell size whose spatiotemporal structure is closely tied to the individual cell's stress response. Motivated by these observations, we derive a multiscale continuum theory whose parameters map directly to the discrete model. Analytical solutions of this theory show the concentric patterns arise from anisotropically accumulated resistance to growth over many cell cycles. This Letter shows how purely mechanical processes can affect the internal patterning and morphology of cell collectives, and provides a concise theoretical framework for connecting the micro- to macroscopic dynamics of proliferating matter.

Facile Physicochemical Reprogramming of PEG-Dithiolane Microgels

Granular biomaterials have found widespread applications in tissue engineering, in part because of their inherent porosity, tunable properties, injectability, and 3D printability. However, the assembly of granular hydrogels typically relies on spherical microparticles and more complex particle geometries have been limited in scope, often requiring templating of individual microgels by microfluidics or in-mold polymerization. Here, we use dithiolane-functionalized synthetic macromolecules to fabricate photopolymerized microgels via batch emulsion, and then harness the dynamic disulfide crosslinks to rearrange the network. Through unconfined compression between parallel plates in the presence of photoinitiated radicals, we transform the isotropic microgels are transformed into disks. Characterizing this process, we find that the areas of the microgel surface in contact with the compressive plates are flattened while the curvature of the uncompressed microgel boundaries increases. When cultured with C2C12 myoblasts, cells localize to regions of higher curvature on the disk-shaped microgel surfaces. This altered localization affects cell-driven construction of large supraparticle scaffold assemblies, with spherical particles assembling without specific junction structure while disk microgels assemble preferentially on their curved surfaces. These results represent a unique spatiotemporal process for rapid reprocessing of microgels into anisotropic shapes, providing new opportunities to study shape-driven mechanobiological cues during and after granular hydrogel assembly.

A Model for Mechanical Stress Limited Bacterial Growth and Resporulation in Confinement

In this study, we propose a self-limiting growth model forBacillus subtilisspores confined within porous polyacrylamide (PA) hydrogels. We observed thatB. subtilisspores germinate into vegetative cells within the hydrogel matrix, forming spherical colonies. These colonies expand until the mechanical stress they exert on their environment surpasses the yield stress of the hydrogel, leading to formation of a nonpermeable layer that halts nutrient diffusion and forces the bacteria to resporulate. These novel observations suggest a model to explain why bacterial growth in confined environments and material interfaces may be limited, providing insight for natural phenomena and biotechnological applications involving bacterial encapsulation.

Engineered Bacteria as Living Biosensors in Dermal Tattoos

Dermal tattoo biosensors are promising platforms for real-time monitoring of biomarkers, with skin used as a diagnostic interface. Traditional tattoo sensors have utilized small molecules as biosensing elements. However, the rise of synthetic biology has enabled the potential employment of engineered bacteria as living analytical tools. Exploiting engineered bacterial sensors will allow for potentially more sensitive detection across a broad biomarker range, with advanced processing and sense/response functionalities using genetic circuits. Here, the interfacing of bacterial biosensors as living analytics in tattoos is shown. Engineered bacteria are encapsulated into micron-scale hydrogel beads prepared through scalable microfluidics. These biosensors can sense both biochemical cues (model biomarkers) and biophysical cues (temperature changes, using RNA thermometers), with fluorescent readouts. By tattooing beads into skin models and confirming sensor activity post-tattooing, our study establishes a foundation for integrating bacteria as living biosensing entities in tattoos.

Metabolically-driven flows enable exponential growth in macroscopic multicellular yeast

The ecological and evolutionary success of multicellular lineages is due in no small part to their increased size relative to unicellular ancestors. However, large size also poses biophysical challenges, especially regarding the transport of nutrients to all cells; these constraints are typically overcome through multicellular innovations (e.g., a circulatory system). Here we show that an emergent biophysical mechanism - spontaneous fluid flows arising from metabolically-generated density gradients - can alleviate constraints on nutrient transport, enabling exponential growth in nascent multicellular clusters of yeast lacking any multicellular adaptations for nutrient transport or fluid flow. Surprisingly, beyond a threshold size, the metabolic activity of experimentally-evolved snowflake yeast clusters drives large-scale fluid flows that transport nutrients throughout the cluster at speeds comparable to those generated by the cilia of extant multicellular organisms. These flows support exponential growth at macroscopic sizes that theory predicts should be diffusion limited. This work demonstrates how simple physical mechanisms can act as a 'biophysical scaffold' to support the evolution of multicellularity by opening up phenotypic possibilities prior to genetically-encoded innovations. More broadly, our findings highlight how co-option of conserved physical processes is a crucial but underappreciated facet of evolutionary innovation across scales.

Design approaches for 3D cell culture and 3D bioprinting platforms

The natural habitat of most cells consists of complex and disordered 3D microenvironments with spatiotemporally dynamic material properties. However, prevalent methods of in vitro culture study cells under poorly biomimetic 2D confinement or homogeneous conditions that often neglect critical topographical cues and mechanical stimuli. It has also become increasingly apparent that cells in a 3D conformation exhibit dramatically altered morphological and phenotypical states. In response, efforts toward designing biomaterial platforms for 3D cell culture have taken centerstage over the past few decades. Herein, we present a broad overview of biomaterials for 3D cell culture and 3D bioprinting, spanning both monolithic and granular systems. We first critically evaluate conventional monolithic hydrogel networks, with an emphasis on specific experimental requirements. Building on this, we document the recent emergence of microgel-based 3D growth media as a promising biomaterial platform enabling interrogation of cells within porous and granular scaffolds. We also explore how jammed microgel systems have been leveraged to spatially design and manipulate cellular structures using 3D bioprinting. The advent of these techniques heralds an unprecedented ability to experimentally model complex physiological niches, with important implications for tissue bioengineering and biomedical applications.

Dissecting Gut-Microbial Community Interactions using a Gut Microbiome-on-a-Chip

While the human gut microbiota has a significant impact on gut health and disease, understanding of the roles of gut microbes, interactions, and collective impact of gut microbes on various aspects of human gut health is limited by the lack of suitable in vitro model system that can accurately replicate gut-like environment and enable the close visualization on causal and mechanistic relationships between microbial constitutents and the gut. , In this study, we present a scalable Gut Microbiome-on-a-Chip (GMoC) with great imaging capability and scalability, providing a physiologically relevant dynamic gut-microbes interfaces. This chip features a reproducible 3D stratified gut epithelium derived from Caco-2 cells (µGut), mimicking key intestinal architecture, functions, and cellular complexity, providing a physiolocially relevant gut environment for microbes residing in the gut. Incorporating tumorigenic bacteria, enterotoxigenic Bacteroides fragilis (ETBF), into the GMoC enable the observation of pathogenic behaviors of ETBF, leading to µGut disruption and pro-tumorigenic signaling activations. Pre-treating the µGut with a beneficial gut microbe Lactobacillus spp., effectively prevent ETBF-mediated gut pathogenesis, preserving the healthy state of the µGut through competition-mediated colonization resistance. The GMoC holds potential as a valuable tool for exploring unknown roles of gut microbes in microbe-induced pathogenesis and microbe-based therapeutic development.

Interplay between environmental yielding and dynamic forcing modulates bacterial growth

Many bacterial habitats-ranging from gels and tissues in the body to cell-secreted exopolysaccharides in biofilms-are rheologically complex, undergo dynamic external forcing, and have unevenly distributed nutrients. How do these features jointly influence how the resident cells grow and proliferate? Here, we address this question by studying the growth of Escherichia coli dispersed in granular hydrogel matrices with defined and highly tunable structural and rheological properties, under different amounts of external forcing imposed by mechanical shaking, and in both aerobic and anaerobic conditions. Our experiments establish a general principle: that the balance between the yield stress of the environment that the cells inhabit, σy, and the external stress imposed on the environment, σ, modulates bacterial growth by altering transport of essential nutrients to the cells. In particular, when σy<σ, the environment is easily fluidized and mixed over large scales, providing nutrients to the cells and sustaining complete cellular growth. By contrast, when σy>σ, the elasticity of the environment suppresses large-scale fluid mixing, limiting nutrient availability and arresting cellular growth. Our work thus reveals a new mechanism, beyond effects that change cellular behavior via local forcing, by which the rheology of the environment may modulate microbial physiology in diverse natural and industrial settings.

Marangoni spreading on liquid substrates in new media art

With the advent of new media art, artists have harnessed fluid dynamics to create captivating visual narratives. A striking technique known as dendritic painting employs mixtures of ink and isopropanol atop paint, yielding intricate tree-like patterns. To unravel the intricacies of that technique, we examine the spread of ink/alcohol droplets over liquid substrates with diverse rheological properties. On Newtonian substrates, the droplet size evolution exhibits two power laws, suggesting an underlying interplay between viscous and Marangoni forces. The leading edge of the droplet spreads as a precursor film with an exponent of 3/8, while its main body spreads with an exponent of 1/4. For a weakly shear-thinning acrylic resin substrate, the same power laws persist, but dendritic structures emerge, and the texture of the precursor film roughens. The observed roughness and growth exponents (3/4 and 3/5) suggest a connection to the quenched Kardar-Parisi-Zhang universality class, hinting at the existence of quenched disorder in the liquid substrate. Mixing the resin with acrylic paint renders it more viscous and shear-thinning, refining the dendrite edges and further roughening the precursor film. At larger paint concentrations, the substrate becomes a power-law fluid. The roughness and growth exponents then approach 1/2 and 3/4, respectively, deviating from known universality classes. The ensuing structures have a fractal dimension of 1.68, characteristic of diffusion-limited aggregation. These findings underscore how the nonlinear rheological properties of the liquid substrate, coupled with the Laplacian nature of Marangoni spreading, can overshadow the local kinetic roughening of the droplet interface.

Spatial structure, chemotaxis and quorum sensing shape bacterial biomass accumulation in complex porous media

Biological tissues, sediments, or engineered systems are spatially structured media with a tortuous and porous structure that host the flow of fluids. Such complex environments can influence the spatial and temporal colonization patterns of bacteria by controlling the transport of individual bacterial cells, the availability of resources, and the distribution of chemical signals for communication. Yet, due to the multi-scale structure of these complex systems, it is hard to assess how different biotic and abiotic properties work together to control the accumulation of bacterial biomass. Here, we explore how flow-mediated interactions allow the gut commensal Escherichia coli to colonize a porous structure that is composed of heterogenous dead-end pores (DEPs) and connecting percolating channels, i.e. transmitting pores (TPs), mimicking the structured surface of mammalian guts. We find that in presence of flow, gradients of the quorum sensing (QS) signaling molecule autoinducer-2 (AI-2) promote E. coli chemotactic accumulation in the DEPs. In this crowded environment, the combination of growth and cell-to-cell collision favors the development of suspended bacterial aggregates. This results in hot-spots of resource consumption, which, upon resource limitation, triggers the mechanical evasion of biomass from nutrients and oxygen depleted DEPs. Our findings demonstrate that microscale medium structure and complex flow coupled with bacterial quorum sensing and chemotaxis control the heterogenous accumulation of bacterial biomass in a spatially structured environment, such as villi and crypts in the gut or in tortuous pores within soil and filters.

Genetic mixing and demixing on expanding spherical frontiers

Genetic fluctuation during range expansion is a key process driving evolution. When a bacterial population is expanding on a 2D surface, random fluctuations in the growth of the pioneers at the front line cause a strong demixing of genotypes. Even when there is no selective advantage, sectors of low genetic diversity are formed. Experimental studies of range expansions in surface-attached colonies of fluorescently labelled micro-organisms have contributed significantly to our understanding of fundamental evolutionary dynamics. However, experimental studies on genetic fluctuations in 3D range expansions have been sparse, despite their importance for tumour or biofilm development. We encapsulated populations of two fluorescent Escherichia coli strains in inoculation droplets (volumes [Formula: see text] nl). The confined ensemble of cells grew when embedded in a hydrogel-with nutrients-and developed 3D colonies with well-defined, sector-like regions. Using confocal laser scanning microscopy, we imaged the development of 3D colonies and the emergence of sectors. We characterized how cell concentration in the inoculation droplet controls sectors, growth rate, and the transition from branched colonies to quasi-spherical colonies. We further analysed how sectors on the surface change over time. We complement these experimental results with a modified 3D Eden growth model. The model in 3D spherical growth predicts a phase, where sectors are merging, followed by a steady increase (constant rate), and the experimentally analysed sectors were consistent with this prediction. Therefore, our results demonstrate qualitative differences between radial (2D) and spherical (3D) range expansions and their importance in gene fixation processes.

The biophysical basis of bacterial colony growth

Bacteria often attach to surfaces and grow densely-packed communities called biofilms. As biofilms grow, they expand across the surface, increasing their surface area and access to nutrients. Thus, the overall growth rate of a biofilm is directly dependent on its "range expansion" rate. One factor that limits the range expansion rate is vertical growth; at the biofilm edge there is a direct trade-off between horizontal and vertical growth-the more a biofilm grows up, the less it can grow out. Thus, the balance of horizontal and vertical growth impacts the range expansion rate and, crucially, the overall biofilm growth rate. However, the biophysical connection between horizontal and vertical growth remains poorly understood, due in large part to difficulty in resolving biofilm shape with sufficient spatial and temporal resolution from small length scales to macroscopic sizes. Here, we experimentally show that the horizontal expansion rate of bacterial colonies is controlled by the contact angle at the biofilm edge. Using white light interferometry, we measure the three-dimensional surface morphology of growing colonies, and find that small colonies are surprisingly well-described as spherical caps. At later times, nutrient diffusion and uptake prevent the tall colony center from growing exponentially. However, the colony edge always has a region short enough to grow exponentially; the size and shape of this region, characterized by its contact angle, along with cellular doubling time, determines the range expansion rate. We found that the geometry of the exponentially growing biofilm edge is well-described as a spherical-cap-napkin-ring, i.e., a spherical cap with a cylindrical hole in its center (where the biofilm is too tall to grow exponentially). We derive an exact expression for the spherical-cap-napkin-ring-based range expansion rate; further, to first order, the expansion rate only depends on the colony contact angle, the thickness of the exponentially growing region, and the cellular doubling time. We experimentally validate both of these expressions. In line with our theoretical predictions, we find that biofilms with long cellular doubling times and small contact angles do in fact grow faster than biofilms with short cellular doubling times and large contact angles. Accordingly, sensitivity analysis shows that biofilm growth rates are more sensitive to their contact angles than to their cellular growth rates. Thus, to understand the fitness of a growing biofilm, one must account for its shape, not just its cellular doubling time.

Motility mediates satellite formation in confined biofilms

Bacteria have spectacular survival capabilities and can spread in many, vastly different environments. For instance, when pathogenic bacteria infect a host, they expand by proliferation and squeezing through narrow pores and elastic matrices. However, the exact role of surface structures-important for biofilm formation and motility-and matrix density in colony expansion and morphogenesis is still largely unknown. Using confocal laser-scanning microscopy, we show how satellite colonies emerge around Escherichia coli colonies embedded in semi-dense hydrogel in controlled in vitro assays. Using knock-out mutants, we tested how extra-cellular structures, (e.g., exo-polysaccharides, flagella, and fimbria) control this morphology. Moreover, we identify the extra-cellular matrix' density, where this morphology is possible. When paralleled with mathematical modelling, our results suggest that satellite formation allows bacterial communities to spread faster. We anticipate that this strategy is important to speed up expansion in various environments, while retaining the close interactions and protection provided by the community.

Instabilities in a growing system of active particles: scalar and vectorial systems

The physics of micron-scale biological colonies usually benefits from different out-of-equilibrium sources. In bacterial colonies and cellular tissues, the growth process is among the important active sources that determine the dynamics. In this article, we study the generic dynamical instabilities associated with the growth phenomena that may arise in both scalar and vectorial systems. In vectorial systems, where the rotational degrees of particles play a role, a phenomenological growth-mediated torque can affect the rotational dynamics of individual particles. We show that such a growth-mediated torque can result in active traveling waves in the bulk of a growing system. In addition to the bulk properties, we analyze the instabilities in the shape of growing interfaces in both scalar and vectorial systems.

Interfacial morphodynamics of proliferating microbial communities

In microbial communities, various cell types often coexist by occupying distinct spatial domains. What determines the shape of the interface between such domains-which in turn influences the interactions between cells and overall community function? Here, we address this question by developing a continuum model of a 2D spatially-structured microbial community with two distinct cell types. We find that, depending on the balance of the different cell proliferation rates and substrate friction coefficients, the interface between domains is either stable and smooth, or unstable and develops finger-like protrusions. We establish quantitative principles describing when these different interfacial behaviors arise, and find good agreement both with the results of previous experimental reports as well as new experiments performed here. Our work thus helps to provide a biophysical basis for understanding the interfacial morphodynamics of proliferating microbial communities, as well as a broader range of proliferating active systems.

A novel model for biofilm initiation in porous media flow

Bacteria often form biofilms in porous environments where an external flow is present, such as soil or filtration systems. To understand the initial stages of biofilm formation, one needs to study the interactions between cells, the fluid and the confining geometries. Here, we present an agent based numerical model for bacteria that takes into account the planktonic stage of motile cells as well as surface attachment and biofilm growth in a lattice Boltzmann fluid. In the planktonic stage we show the importance of the interplay between complex flow and cell motility when determining positions of surface attachment. In the growth stage we show the applicability of our model by investigating how external flow and biofilm stiffness determine qualitative colony morphologies as well as quantitative measurements of, e.g., permeability.

Pattern formation by bacteria-phage interactions

The interactions between bacteria and phages-viruses that infect bacteria-play critical roles in agriculture, ecology, and medicine; however, how these interactions influence the spatial organization of both bacteria and phages remain largely unexplored. Here, we address this gap in knowledge by developing a theoretical model of motile, proliferating bacteria that aggregate via motility-induced phase separation (MIPS) and encounter phage that infect and lyse the cells. We find that the non-reciprocal predator-prey interactions between phage and bacteria strongly alter spatial organization, in some cases giving rise to a rich array of finite-scale stationary and dynamic patterns in which bacteria and phage coexist. We establish principles describing the onset and characteristics of these diverse behaviors, thereby helping to provide a biophysical basis for understanding pattern formation in bacteria-phage systems, as well as in a broader range of active and living systems with similar predator-prey or other non-reciprocal interactions.

Gene expression dynamics in input-responsive engineered living materials programmed for bioproduction

Engineered living materials (ELMs) fabricated by encapsulating microbes in hydrogels have great potential as bioreactors for sustained bioproduction. While long-term metabolic activity has been demonstrated in these systems, the capacity and dynamics of gene expression over time is not well understood. Thus, we investigate the long-term gene expression dynamics in microbial ELMs constructed using different microbes and hydrogel matrices. Through direct gene expression measurements of engineered E. coli in F127-bisurethane methacrylate (F127-BUM) hydrogels, we show that inducible, input-responsive genetic programs in ELMs can be activated multiple times and maintained for multiple weeks. Interestingly, the encapsulated bacteria sustain inducible gene expression almost 10 times longer than free-floating, planktonic cells. These ELMs exhibit dynamic responsiveness to repeated induction cycles, with up to 97% of the initial gene expression capacity retained following a subsequent induction event. We demonstrate multi-week bioproduction cycling by implementing inducible CRISPR transcriptional activation (CRISPRa) programs that regulate the expression of enzymes in a pteridine biosynthesis pathway. ELMs fabricated from engineered S. cerevisiae in bovine serum albumin (BSA) - polyethylene glycol diacrylate (PEGDA) hydrogels were programmed to express two different proteins, each under the control of a different chemical inducer. We observed scheduled bioproduction switching between betaxanthin pigment molecules and proteinase A in S. cerevisiae ELMs over the course of 27 days under continuous cultivation. Overall, these results suggest that the capacity for long-term genetic expression may be a general property of microbial ELMs. This work establishes approaches for implementing dynamic, input-responsive genetic programs to tailor ELM functions for a wide range of advanced applications.

Proliferating active matter

The fascinating patterns of collective motion created by autonomously driven particles have fuelled active-matter research for over two decades. So far, theoretical active-matter research has often focused on systems with a fixed number of particles. This constraint imposes strict limitations on what behaviours can and cannot emerge. However, a hallmark of life is the breaking of local cell number conservation by replication and death. Birth and death processes must be taken into account, for example, to predict the growth and evolution of a microbial biofilm, the expansion of a tumour, or the development from a fertilized egg into an embryo and beyond. In this Perspective, we argue that unique features emerge in these systems because proliferation represents a distinct form of activity: not only do the proliferating entities consume and dissipate energy, they also inject biomass and degrees of freedom capable of further self-proliferation, leading to myriad dynamic scenarios. Despite this complexity, a growing number of studies document common collective phenomena in various proliferating soft-matter systems. This generality leads us to propose proliferation as another direction of active-matter physics, worthy of a dedicated search for new dynamical universality classes. Conceptual challenges abound, from identifying control parameters and understanding large fluctuations and nonlinear feedback mechanisms to exploring the dynamics and limits of information flow in self-replicating systems. We believe that, by extending the rich conceptual framework developed for conventional active matter to proliferating active matter, researchers can have a profound impact on quantitative biology and reveal fascinating emergent physics along the way.

Vertical growth dynamics of biofilms

During the biofilm life cycle, bacteria attach to a surface and then reproduce, forming crowded, growing communities. Many theoretical models of biofilm growth dynamics have been proposed; however, difficulties in accurately measuring biofilm height across relevant time and length scales have prevented testing these models, or their biophysical underpinnings, empirically. Using white light interferometry, we measure the heights of microbial colonies with nanometer precision from inoculation to their final equilibrium height, producing a detailed empirical characterization of vertical growth dynamics. We propose a heuristic model for vertical growth dynamics based on basic biophysical processes inside a biofilm: diffusion and consumption of nutrients and growth and decay of the colony. This model captures the vertical growth dynamics from short to long time scales (10 min to 14 d) of diverse microorganisms, including bacteria and fungi.

Morphology and Size of Bacterial Colonies Control Anoxic Microenvironment Formation in Porous Media

Bacterial metabolisms using electron acceptors other than oxygen (e.g., methanogenesis and fermentation) largely contribute to element cycling and natural contaminant attenuation/mobilization, even in well-oxygenated porous environments, such as shallow aquifers. This paradox is commonly explained by the occurrence of small-scale anoxic microenvironments generated by the coupling of bacterial respiration and dissolved oxygen (O₂) transport by pore water. Such microenvironments allow facultative anaerobic bacteria to proliferate in oxic environments. Microenvironment dynamics are still poorly understood due to the challenge of directly observing biomass and O₂ distributions at the microscale within an opaque sediment matrix. To overcome these limitations, we integrated a microfluidic device with transparent O₂ planar optical sensors to measure the temporal behavior of dissolved O₂ concentrations and biomass distributions with time-lapse videomicroscopy. Our results reveal that bacterial colony morphology, which is highly variable in flowing porous systems, controls the formation of anoxic microenvironments. We rationalize our observations through a colony-scale Damköhler number comparing dissolved O₂ diffusion and a bacterial O₂ uptake rate. Our Damköhler number enables us to predict the pore space fraction occupied by anoxic microenvironments in our system for a given bacterial organization.

Stress anisotropy in confined populations of growing rods

A central feature of living matter is its ability to grow and multiply. The mechanical activity associated with growth produces both macroscopic flows shaped by confinement, and striking self-organization phenomena, such as orientational order and alignment, which are particularly prominent in populations of rod-shaped bacteria due to their nematic properties. However, how active stresses, passive mechanical interactions and flow-induced effects interact to give rise to the observed global alignment patterns remains elusive. Here, we study in silico colonies of growing rod-shaped particles of different aspect ratios confined in channel-like geometries. A spatially resolved analysis of the stress tensor reveals a strong relationship between near-perfect alignment and an inversion of stress anisotropy for particles with large length-to-width ratios. We show that, in quantitative agreement with an asymptotic theory, strong alignment can lead to a decoupling of active and passive stresses parallel and perpendicular to the direction of growth, respectively. We demonstrate the robustness of these effects in a geometry that provides less restrictive confinement and introduces natural perturbations in alignment. Our results illustrate the complexity arising from the inherent coupling between nematic order and active stresses in growing active matter, which is modulated by geometric and configurational constraints due to confinement.