Soil-on-a-Chip - Deciphering dynamics of root colonization in microfluidic habitats

Plant roots establish symbiotic interactions with soil microbes, enhancing nutrient uptake, pathogen resistance, and resilience to stress. To unravel the regulatory mechanisms behind these relationships, we study the interactions between Arabidopsis thaliana roots and Bacillus species, known for their growth-promoting and immunomodulatory effects.

We focus on the role of cell type differentiation in Bacillus subtilis during root colonization, hypothesizing that these traits support adaptive strategies under plant immune pressure, similarily to their pivotal role in biofilm formation and mainentance. By combining transcriptional reporter strains of B. subtilis, ROS-sensitive dyes, and immunity markers in A. thaliana, we visualize the spatiotemporal dynamics of colonization, assessing immune interference, ROS production, and bacterial cell state.

Adapted microfluidic RootChips allow dynamic, highly resolved and minimally invasive observations of the root microenvironments, enabling controlled studies of signaling processes. Additionally, structured microdevices simulating soil architecture let us dissect each phase of B. subtilis colonization and track the activation and modulation of plant immunity. This approach highlights the interference of plant defense and cell type differentiation in structuring root colonization by Bacillus subtilis.