To achieve the goals of the project, we have built a microscopy setup that enabled us to analyze the dynamics of the reaction of Arabidopsis roots to stimuli in an unprecedented high spatio-temporal resolution. This setup consists of a spinning disk fluorescence microscope with a vertical stage – where the roots can grow downwards, combined with a microfluidic chip platform – where we can perform various treatments without disturbing the growing Arabidopsis roots. In addition, we have established novel approaches to quantitatively analyze the behavior of roots using advanced image analysis methods. We have published the description of the microscopy setup as a part of a scientific publication (Serre et al., 2021, Nature Plants 7: 1229), and we have described the image analysis program called ACORBA in another publication (Serre et al., 2022, Quantitative Plant Biology 3, e9).
To visualize the dynamics of cellular process in real time, we optimized the usage of genetically-encoded fluorescent sensors that monitor cellular physiology, such as hormone levels, ion concentrations and pH of cellular compartments. This toolbox enabled us to analyze the earliest events by which Arabidopsis roots response to the phytohormone auxin. We introduced a novel tool to quantify the potassium levels in the cytoplasm (Wu et al., 2022, PLoS biology 20, e3001772). We have further visualized and quantified the ability of roots to acidify the rhizosphere and we have identified the pathway that controls the longitudinal zonation of acidification in the Arabidopsis root tip (Serre et al., 2023, eLife 12, e85193).
Further, we have focused on revealing the signaling pathway that underlies the ultra-rapid responses of Arabidopsis roots to the phytohormone auxin. We have established that one of the auxin receptors called AFB1 triggers rapid membrane depolarization in root cells, and that this response is required for an efficient response of root to the change in gravity direction (Serre et al., 2021, Nature Plants 7: 1229). In a follow-up publication, we have discovered that the AFB1 receptor functions in a fundamentally different manner from the auxin receptors described so far. The AFB1 receptor perceives auxin in the cytoplasm of root cells and triggers changes in transmembrane ion fluxes, characterized by rapid changes in cytoplasmic calcium concentrations (Dubey et al., 2023, Molecular Plant 16, 1120).
In another line of research, we aimed to dissect the genetic network that underlies the growth decisions that condition the ability of the root to navigate in the heterogenous environments of the soil. To achieve this, we have established a specific system to speed up and slow down root elongation using a genetical trick to modulate the auxin gene transcription pathway. We harnessed this system to identify genes responsible for steering the cell expansion dynamics in the root elongation zone of Arabidopsis thaliana (Kubalova et al., 2024, New Phytologist 241, 2448).
Finally, we contributed to a major study that demonstrated that an ultra-rapid auxin response pathway is deeply conserved over the plant kingdom (Kuhn et al., 2024, Cell 187, 130). This finding underscores the importance of studying the dynamics of auxin responses. In addition to peer-reviewed scientific publications, the results were presented at numerous international conferences and invited seminars at scientific institutions. The results were also communicated towards the general public using press releases and interviews for media in Czechia.
