Benedict Borer

Research interests
My main interest is to study microbial interactions at the cell and community level using experimental and computational resources. Micrometric pore networks with controllable resource and hydration architectures mimicking soil aggregate cross-sections are used to investigate bacterial community spatial self-organisation at the pore scale. A mathematical model of the system enables further insights into experimental results and is used to guide experiments.

Bacterial community response to resource gradients
Applying chemical boundary conditions prevalent in soil-aggregates to the micrometric pore networks, community dynamics of an obligate aerobic specie and facultative anaerobic specie can be investigated. Using single-cell resolution fluorescent microscopy reveals a self-segregation of the community due to oxygen and carbon gradients, a hitherto veiled facet of soil microbiology due to the opaque nature of soil particles.

Hydration status influencing bacterial self-organisation in soil
Dynamic hydration status in soils gives rise to an ever changing environment for microbial life. A second generation of micrometric pore networks have been developed to observe the effect of hydration status - especially habitat fragemntation due to water film thickness and resulting oxygen and resource availability - on the interaction of microbes in soil aggregate cross-section analogues.

Individual based model of microbial life in soil
An object-oriented programming approach is used to model individual bacteria in soil. The model incorporates diffusive transport of substrates combined with motile bacteria represented by individual agents. The structural and chemical architectures of the micrometric pore networks can be used to mathematically mimick the prevalent conditions within the experimental setup.