Emergent benefits of bacterial collectives under predation by soil-derived protists

• Applicant: Dr. Jordi van Gestel
• Subject Area: Microbial Ecology and Applied Microbiology ; General Genetics and Functional Genome Biology
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 568896107

Bacteria express a wide diversity of collective phenotypes, such as fruiting bodies, biofilms, pellicles, and filaments. To understand how collectives are organized, they are often studied in isolation under optimal laboratory conditions, while their benefits are often thought to emerge from interactions with other microbes in their environment. In the soil, for instance, bacterial collectives can provide resistance to protistan predation – one of the primary causes of bacterial cell death. To map out their emergent benefits, we should therefore ideally study collectives in their natural community, where we can observe how collectives interact with other community members. Here, we propose to use a custom-designed ‘soil-on-a-chip’ microfluidic platform to study the emergent benefits of bacterial collectives in exposure to soil-derived protists. Building on our preliminary data, we will focus on B. subtilis collectives, which express several properties that affect predation resistance. With the goal of studying different collective properties, we start by systematically comparing the collectives expressed by B. subtilis wild-type and mutant strains. For this, we will knock-out different genes underlying collectivity, affecting biofilm formation, filamentation, stress responses, secondary metabolite production, and sporulation. Each mutant will be cultured in our microfluidic device, which mimics a soil-like porous space and therefore allows for the emergence of small micro-scale collectives. Using long-term spinning-disk confocal microscopy, we will quantify how collectives emerge and decay over time and study their spatiotemporal organization. Altogether, this will result in the largest systematic comparison of micro-scale collectives performed to date. After studying collectives in isolation, we will barcode mutants to perform pooled competition experiments in the presence of soil-derived protists. The pooled mutants and a soil suspension will be loaded from opposite ends of a microfluid device, where B. subtilis functions as ‘bait’ to attract protists from the soil. We will explore how these soil protists interact with B. subtilis collectives through a combination of fluorescent time-lapse microscopy and barcode sequencing, allowing us to link the relative fitness of B. subtilis strains, their collective properties and their resistance to diverse protistan predators. Our multi-modal dataset will thus map out the functional benefits of collectivity in the context of predator-prey ecology. By bridging the gap between the controlled laboratory environment where bacterial collectives are often studied and the intricate reality of community ecology, we hope that our soil-on-a-chip experiments will spark future research that investigates the implications of bacterial collectivity for an even broader range of ecological interactions, with the ultimate goal of obtaining a comprehensive view on the impact of collectivity on natural soil communities.

• DFG Programme: Priority Programmes
• Subproject of: SPP 2389: Emergent Functions of Bacterial Multicellularity