Life & death in a tight spot: how bacteria grow and confront their foes in crowded 3D environments

Synopsis

Bacteria inhabit nearly every ecosystem, with critical implications for biogeochemistry, agriculture, and health. Many bacterial habitats are complex 3D environments, e.g., soils, hosts, and bodies of water, where they form spatially structured multicellular communities. This spatial organization is pivotal for community growth, cross-feeding, and diversity, and for withstanding challenges such as competing species, toxins, and bacteriophages—viruses that infect and kill bacteria. However, laboratory studies of well-mixed cultures and surface-attached colonies miss key spatial arrangements, ecological interactions, and defensive strategies that emerge in such environments. As a result, such functions of 3D bacterial colonies remain largely unknown, despite their prevalence in nature.

In this talk, I will first discuss how bacterial colonies acquire their shape in complex 3D environments. By integrating experiments with biophysical modeling, I will show how colonies growing in 3D transparent granular environments develop distinct architectures—driven by differential access to nutrients—that fundamentally differ from their flat-culture counterparts and are generic across species and environmental conditions. I then turn to phage–bacteria interactions in 3D and ask how anti-phage defense systems operate in such 3D-structured populations. To address this question, I will focus on abortive infection systems, where programmed cell death of infected cells prevents rapid phage infection by creating firewalls of suicidal cells in 3D. Finally, I will discuss multi-species communities. Combining experiments and modeling, we uncover quantitative principles that determine when interfaces between distinct cell populations remain smooth or develop fingerlike protrusions, with implications for cell-cell communication and community function.

These findings reveal how spatial structure governs bacterial collective dynamics and function—from growth and anti-phage defenses to interspecies interfaces—and provide a framework for studying microbial interactions in realistic 3D environments that bridges simplified laboratory settings and natural ecosystems.