Study reveals role of 3D environments in influencing bacterial survival and growth

A study from the National Centre for Biological Sciences (NCBS) has uncovered how 3D environments influence bacterial growth and survival. By using 3D models to mimic natural settings such as mucus and soil, researchers found that the shape of bacteria plays a crucial role in their ability to thrive in complex environments.

According to researchers, for over 300 years, scientists have studied bacteria primarily using liquid cultures or flat 2D plates in laboratory settings. While this approach has been convenient and essential for biological research, it does not accurately represent the natural 3D environments bacteria encounter in soil, mucus, or plant and animal tissues. Consequently, bacterial growth in these complex settings with diverse material properties remains largely unexplored

“From decades of past research using simple liquid or flat plates, we have learnt that mutations, chemical signals, and behavioural patterns all affect bacterial physiology. But bacteria inhabit a wide range of environments—from the soil beneath our feet to the mucus lining our guts. So, we wondered: How would such physical differences in their environment impact their survival?” explains Sreepadmanabh M, the study’s lead author.

To replicate mucus-like mechanical environments in the lab, researchers used carbomer—a common thickening agent in creams and gels. This enabled them to create a 3D model that mimics the viscosity, stiffness, and porosity of mucus while remaining optically transparent to allow high-resolution visualisation of bacterial cells and colonies

Using computational simulations and microscopy, the team discovered that rod-shaped bacteria thrive much better than spherical bacteria in highly confined spaces, as they can elongate and disperse their progeny more effectively during growth. In contrast, spherical bacteria form tightly clustered colonies where those in the center struggle to access air and nutrients, resulting in slower, less efficient growth. To investigate whether rod-shaped bacteria possess special genes that provide unique survival advantages, the researchers transformed them into spherical shapes without impacting their health or growth rate. They found that, under high confinement, these spherical bacteria were unable to match the growth performance of their rod-shaped counterparts.

“These findings completely change the way we think about how microbial populations survive and adapt across diverse ecological settings. We show that there exists a rich class of regulation through the mechanical environment that decides the fate of microbial communities. Our work opens the door for future questions, such as how evolutionary fitness can all be modulated by the physical constraints imposed by an organism’s surroundings,” states Dr Tapomoy Bhattacharjee, the principal investigator of the study.