Microbial life and death in complex environments

Bacteria are arguably the simplest form of life. And yet, they perform complex functions: they travel large distances, forage for food, colonize and adapt to new terrain, communicate with each other, and reshape their surroundings.

These process often occur in complex environments such as soils & sediments and biological tissues & gels. However, lab studies typically focus on cells in idealized conditions such as in homogeneous liquid cultures or at flat interfaces. As a result, current understanding of bacterial behavior in the natural world is incomplete.

Our research addresses this gap in knowledge. We have developed new ways to study bacteria, and other microbes, in engineered environments that are more akin to natural habitats than typical lab assays. Our experiments integrate microscopy, microfluidics, soft materials science, and biophysical characterization to systematically manipulate and probe cells inside complex media of tunable structures, mechanics, and chemistries. Guided by our findings, we develop theoretical and computational models, applying ideas from biological physics, physical chemistry, and soft matter physics, to predict how microbes and other “active” systems move, grow, interact, and collectively function in complex environments. Our main thrusts and research questions include:

Physical & chemical heterogeneities

Microbial habitats are often crowded. Our work has demonstrated that confinement in a crowded space—e.g., in soil and biological gels/tissues—fundamentally alters how bacteria move beyond typical textbook descriptions [Nature Communications 2019, Soft Matter 2019, Nature Communications 2021, Biophysical J. 2021, PLoS Computational Biology 2022]. We have also shown that external polymers—e.g., mucus in the lungs, dietary fibers in the gut, and in biofilm matrices—act as crowding agents that sculpt how microbial collectives grow through osmotic interactions, forming “living gels” [PNAS 2016, eLife 2019, Science Advances 2025].

Microbial habitats are also chemically heterogeneous, with varying availabilities of nutrients and toxins that the cells sense, respond to, and reshape in turn. Our work has demonstrated that microbial collectives behave like cohesive “active” fluids that process local chemical information to autonomously and robustly spread large distances, adapt shape to resist perturbations, and regulate growth in spatially-organized communities [Biophysical J. 2021, eLife 2022, Physical Review Letters 2022, PNAS 2022, eLife 2022, Physical Review Letters 2023, Physical Review X 2025].

Building on these advances, we continue to investigate: How do physicochemical heterogeneities (e.g., crowding, biochemical signals) alter the motion and growth of single cells and multicellular collectives? What mathematical principles describe these alterations? And how can we use these insights to control bacterial behavior?

Collective behaviors

In many natural settings, microbes self-organize into intricately structured communities, with distinct cell types coexisting by occupying distinct spatial domains. We have developed a way to 3D-print and visualize microbial communities of defined structures and compositions inside transparent hydrogel matrices [JoVE 2024]. We are now using this technology to investigate: How do cell-cell and cell-environment interactions impact the spatial organization of such communities? How does the spatial organization of a community impact its functioning — e.g., growth, stability, resilience to stressors, and ability to perform chemical transformations — in turn? And how can we harness these insights to design microbial communities that are optimized for a given function?

This research program is helping to uncover and harness the organizing biophysical principles of microbes, and other forms of active matter, more generally—helping to bridge the gap between idealized lab studies in uniform environments and complex microbial processes in real-world settings. Ultimately, our goal is to develop quantitative guidelines for the control of microbial behavior in biotechnology, environmental remediation, sustainable agriculture, and therapeutic interventions.

In addition to reading our papers, you can find out more about some of this research in two video lectures on bacterial motility and proliferation.