Our approach. We take a bottom-up approach in studying predator-prey interactions by combining a broad range of quantitative methods, including functional genomics, microfluidics, high-throughput microscopy, metabarcoding, metagenomics and mathematical modeling. We aim to bridge concepts in developmental microbiology and microbial ecology with the ultimate goal of understanding how microbial life cycles evolve in their natural environments.
Offense and defense mechanisms in protistan predators and bacterial prey. Most functional genomic studies on soil bacteria are performed by growing species in isolation, without including the plethora of bacterivorous protists to which these bacteria are exposed in soils. We develop genome-wide mutant libraries (CRISPR, Tn-seq, Boba-seq) in both bacterial species and protistan predators to systematically identify offense and defense mechanisms in predator and prey species, and study their effect on predator-prey interactions and evolution
Predator-prey dynamics in soil-like environments. Since microbial interactions in the soil are secluded from our sight, we cannot study predator-prey dynamics in soils directly. Instead, we are therefore developing tools to study those dynamics in synthetic soil environments. For this, we combine our expertise in microfluidics and high-throughput microscopy, where we can monitor hundreds of predator-prey communities in parallel under precisely controlled environmental conditions.
Uncovering the microbial savanna in soils. To bridge from our predator-prey model system to natural soil communities, we leverage metabarcoding and metagenomics to probe the natural diversity of bacterivorous protists and their prey in soils, isolate them and assemble synthetic soil communities in the lab. Using those communities, we study how predation affects predator-prey community dynamics, microbial adaptation and evolution.
