Spatial constraints subvert microbial arms race
Authors: Copeland Raymond , Yunker Peter J. 
Published: June 2023

Biofilms, surface attached communities of microbes, grow in a wide variety of environments. Often, the size of these microbial community is constrained by their physical surroundings. However, little is known about how size constraints of a colony impact the outcome of microbial competitions. Here, we use individual-based models to simulate contact killing between two bacterial strains with different killing rates in a wide range of community sizes. We found that community size has a substantial impact on outcomes; in fact, in some competitions the identity of the most fit strain differs in large and small environments. Specifically, when at a numerical disadvantage, the strain with the slow killing rate is more successful in smaller environments than in large environments. The improved performance in small spaces comes from finite size effects; stochastic fluctuations in the initial relative abundance of each strain in small environments lead to dramatically different outcomes. However, when the slow killing strain has a numerical advantage, it performs better in large spaces than in small spaces, where stochastic fluctuations now aid the fast killing strain in small communities.

Finally, we experimentally validate these results by confining contact killing strains ofVibrio choleraein transmission electron microscopy grids. The outcomes of these experiments are consistent with our simulations. When rare, the slow killing strain does better in small environments; when common, the slow killing strain does better in large environments. Together, this work demonstrates that finite size effects can substantially modify antagonistic competitions, suggesting that colony size may, at least in part, subvert the microbial arms race.

Author summary

Biofilms are often crowded with many bacteria in direct contact. As a result, the competition for space and resources often turns deadly. Bacteria have evolved many mechanisms with which to kill each other; this bacterial warfare is often studied in large communities on agar plates or in flow cells [1]. However, in nature these colonies are often smaller, due to spatial constraints or shear forces. It is unclear how bacterial warfare proceeds in small systems.

We performed individual based model simulations of bacterial warfare comprising two strains, each capable of killing the other on direct contact. We found that the community size played a substantial role in determining the outcome. When at a numerical disadvantage, the slow killing strain survived at much higher rates in small communities. In fact, there were many conditions in which the slow killing strain survives in small spaces but is completely eliminated in large ones. Conversely, when the slow killing strain is more common, it performs better in large spaces. Together, these observations demonstrate that finite size effects aid the strain that is at a disadvantage, and in some conditions, can even flip which strain increases its abundance.

Finally, we experimentally tested the results of these simulations. Two mutual killing strains ofV. choleraewere grown unconfined on agar plates (i.e., in large spaces) or confined within square holes with sides 7.5μmlong (i.e., in small spaces). In these experiments we found that the slow killing strain survived at significantly higher rates in confinement, validating simulation results.