A numerical model of Vibrio fischeri growth and intraspecific competition

E. scolopes is a species of small squids living off the coast of Hawaii. Early in its life cycle, it forms a life-long symbiosis with V. fischeri bacteria. The squids need the bioluminescent bacteria for counter-illumination, a form of camouflage that help the squid blend in with the moonlit ocean surface at night. Scientist also find that the bacteria is crucial in squid’s development – without the bacterial infection, squids do not develop mature light organs [1].

When E. scolopes hatches, it does not have any bacteria in its light organ (the dark blob), either does it have a fully matured light organ.
Soon it recruits V. fischeri from the environment. Once partnered, the light organ stops allowing more microbes in. The bacterial infection starts a complex process of developmental changes in the squid that leads to a mature light organ.
Regulating the bioluminescence form the microbes, the squid can blend in with the ambient light in the shallow water when it hunts, hiding both from preys and predators.

This simple symbiosis serves as a model system for studying host-microbe interactions. To study this system, there are many angles we can take. This project focuses on the bacterium, and in particular, when it is grown on a petri dish.

Some strains of V. fischeri have the ability to kill other bacteria using the Type VI secretion system (T6SS). Individuals with T6SS can assemble a molecular “syringe,” then use it to inject toxins into neighboring cells. The toxins can cause cell death, unless the cell is immune to it. Cells from the killing strain are typically immune to their own toxins. We typically call killers strains T6SS+ or lethal strains, and the non-killer strains T6SS- or nonlethal strains.

The lethal strains are sometimes present in the squid light organ. The light organ has 6 chambers, called crypts. In experiments, it has not been observed that lethal strains coexist with any other strain in the same crypt. But it is also not the case that lethal strains take over the entire light organ [2].

On a petri dish, when two nonlethal strains are grown together, they are well-mixed. Microcolonies are form around the initial seed bacterium (or an initial cluster of bacteria), but the sizes are small. However, when two lethal strains are grown together, the microcolonies become larger, the two strains are more separated [2].

Chris and I developed a multi-agent model for cell growth, division, and death in 2D. Though we use our model for V. fischeri, the model can be generalize to look at many other phenomena.

In our model, we simulate mechanical interactions and T6SS killing between cells. We also solve the diffusion equation for resource field, which the bacteria feed on (acting as sinks, in the math lingo).

I will be presenting at American Physical Society March meeting (2019) on the progress in this project. I’m cautiously optimistic to say that we see good agreements between simulation and experimental data, but more experiments (both numerical and physical) are underway!

Mutually lethal strains in a range expansion simulation, starting out in a small circular inoculation with 1:1 population ratio.

[1] McFall-Ngai, M.(2014), Annu. Rev. Microbiol. 68, 177-94.

[2] Speare, L, et al.(2018), PNAS 115, E528-E537.

Biofilm Multi-agent models Research interests

Y Luna Lin View All →

I’m a grad student studying Applied Mathematics at SEAS, Harvard University. My interest lies in using mathematical models and computation to explore problems and phenomena in the natural world. Together with my Ph.D. advisor, Prof. Chris Rycroft and my collaborators, we explore topics such as numerical methods for fluid-solid interaction problems, simulations of diffusion-limited dissolutions, modeling bacteria growth and pattern formation in biofilm.

When I’m not doing math or coding, I enjoy being outdoors and playing music with Tobi.