Developing a novel and versatile approach to study populations of microbes on surfaces

Many microbial populations live on surfaces. To better understand them, we need better devices for quantitative experiments. This project aims to develop such a device. The techniques involved include modelling, microfluidics, and microscopy.

Aim: Develop, characterize, and apply a device to experimentally study populations of microbes under well-defined conditions on surfaces.

Background: Many microbial populations live on surfaces, but the ecological and evolutionary consequences of the resulting spatial structure are not well understood. This is not least due to the lack of suitable experimental techniques. Investigating colonies on standard agar plates is constrained by limited nutrient availability and the lack of options to change the environmental conditions over the course of the experiment. To enable highly quantitative experiments, spatial analogues of chemostats and microfluidic chambers are needed, which both enable continuous, and ideally infinite, growth by continuous influx of nutrients.

Project: This project aims to close this gap by developing novel techniques enabling long-term growth in two dimensions. In particular, two setups will be considered: (i) Growth of populations at an agar-air interface with supply of nutrients and control of the environment by a system of fluidic tubing below the agar surface. (ii) Growth of populations within a flat chamber made of plastic with nutrients provided and environment controlled through a membrane and a fluidic network.
The project will involve development, characterization, and application of the device. Development will be based on theoretical considerations and reaction-diffusion modelling. Once candidate devices are built, they will be characterized using populations of the well-understood bacterium E. coli, using microscopy and quantitative image analysis. In particular, experiments will entail studying the growth dynamics of colonies.
To showcase and test the device, it finally be used to study evolution of bacteria and bacteriophage over the course of many days. Possible examples are the study of the evolution of antibiotic resistance within growing colonies and the evolution of bacteriophage as they spread on lawns of bacteria. In this way, development of the technique will be coupled to its application and possibly new findings in microbial evolution and ecology.