Periodic Reporting for period 1 - MINIMA (Microbial navigation strategies in ecologically relevant porous media)
Reporting period: 2023-08-01 to 2025-07-31
Microorganisms may be too small to see, but they are everywhere around us—and inside us. In fact, the number of bacteria living in our body is roughly the same as the number of human cells we have. These tiny companions keep us healthy by aiding digestion, defending against harmful germs, and even shaping how we feel. Just as importantly, microorganisms sustain the environment by recycling nutrients, enriching soil, and purifying air and water. They make life possible on both our bodies and our planet.
Most microorganisms live in tiny porous spaces, much like we live in houses or shelters. These pores give them protection from predators and help keep their surroundings stable and comfortable. At the same time, living in such tight spaces also brings challenges: limited room to grow, slower access to nutrients, restricted movement, and even physical pressure from the surrounding walls. Yet microorganisms find ways not just to survive, but also to spread and flourish in these confined spaces. The clever strategies they use remain a source of fascination and inspiration for scientists.
But many of these strategies are still a mystery. How do such small organisms overcome the physical limits of the environments they inhabit? What rules guide their movements and choices when the landscape becomes complex? Our project, MINIMA (“Microbial navigation strategies in ecologically relevant porous media”), takes on these questions. We want to know: How do the sizes of pores, compared to the size of the microbes themselves, affect their ability to move efficiently? What do microorganiams do—both in their behavior and in their biology—when they face difficulties such as tight spaces or rough surfaces? And can the very structure of these porous spaces decide whether microbes keep swimming freely or settle down to form communities? Beyond curiosity, this project also has real-world impact: it can help us better understand how soil helps regulate carbon in nature, how underground spaces might be used for clean energy storage, and even inspire new biomedical microrobots that navigate the human body.
Most microorganisms live in tiny porous spaces, much like we live in houses or shelters. These pores give them protection from predators and help keep their surroundings stable and comfortable. At the same time, living in such tight spaces also brings challenges: limited room to grow, slower access to nutrients, restricted movement, and even physical pressure from the surrounding walls. Yet microorganisms find ways not just to survive, but also to spread and flourish in these confined spaces. The clever strategies they use remain a source of fascination and inspiration for scientists.
But many of these strategies are still a mystery. How do such small organisms overcome the physical limits of the environments they inhabit? What rules guide their movements and choices when the landscape becomes complex? Our project, MINIMA (“Microbial navigation strategies in ecologically relevant porous media”), takes on these questions. We want to know: How do the sizes of pores, compared to the size of the microbes themselves, affect their ability to move efficiently? What do microorganiams do—both in their behavior and in their biology—when they face difficulties such as tight spaces or rough surfaces? And can the very structure of these porous spaces decide whether microbes keep swimming freely or settle down to form communities? Beyond curiosity, this project also has real-world impact: it can help us better understand how soil helps regulate carbon in nature, how underground spaces might be used for clean energy storage, and even inspire new biomedical microrobots that navigate the human body.
In this project, we looked closely at what happens when bacteria grow under physical confinement. We grew colonies in controlled spaces where the walls pressed against them, and carefully measured how their growth and shape changed over time. We found that confinement acts like a stress factor: the bacteria initially slowed down and even shrank in size, before gradually adjusting and resuming growth. By tracking these changes, we discovered that colonies use different strategies at different stages to cope with the pressure, showing both short-term responses and longer-term adjustments. These findings provide one of the first clear pictures of how bacteria manage life in confined habitats. They also highlight the broader importance of physical forces in shaping microbial communities, with potential applications in understanding infections, improving industrial bioprocesses, and designing new biophysical models of microbial growth. Besides, we have written a review article, “Microbes in porous environments: from active interactions to emergent feedback”, highlighting how microbial traits enable them to migrate efficiently, colonize new niches, and cope with environmental stresses. The article has drawn significant attention from researchers in microbial ecology and soil science.
Our results advance the state of the art by showing how physical confinement reshapes bacterial colony growth and adaptation, linking single-cell physiology to collective colony dynamics. These insights open new possibilities for understanding infections in confined tissues, improving industrial bioprocesses, and designing biophysical models of microbial growth. To broaden the impact, we have also begun exploring applications through ongoing collaborations on antimicrobial and anti-adhesion surfaces. Using patterned materials supplied by collaborators, we carried out preliminary tests with our experimental setups, demonstrating the potential to connect confinement studies with strategies for controlling bacterial colonization on engineered surfaces.