Integrated Study of Tripartite Interactions Between Plant–Bacillus– Xanthomonas: Towards Sustainable Biocontrol Solutions Under Environmental Stress

Background:

Understanding stress adaptation mechanisms in plant–microorganism systems is essential for improving crop resilience and promoting sustainable agriculture. Calcium signaling plays a key role not only in plant responses to stress but also in bacterial processes such as biofilm formation, which are crucial for the establishment of microbial communities, host colonization, and plant–microbe interactions.

This project investigates the links between calcium signaling, bacterial motility, and biofilm formation in both beneficial (e.g., Bacillus) and pathogenic (e.g., Xanthomonas) microorganisms, with the aim of better understanding the mechanisms underlying tripartite communication. The goal is to determine how these interaction dynamics are modulated by environmental stress.

Stress-induced calcium signaling is well documented in plants for its central role in adaptation mechanisms. In bacteria, calcium also influences cellular processes such as biofilm formation and motility. In Arabidopsis, root-to-shoot calcium signals appear to be modulated by interactions with soil bacteria, while in bacteria, calcium signaling regulates community behaviors, motility, and plant colonization efficiency. However, the role of calcium as a signaling molecule in plant–microbe interactions remain poorly understood at the molecular level.

In this project, we aim to uncover bacterial enzymatic activities that may be modulated by the plant, and vice versa, thus revealing deep mechanisms of cross-kingdom communication. A better understanding of the limits of stress adaptation in plant–microbe systems could lead to the identification of new key effectors and the discovery of previously unexplored molecular mechanisms.

Our approach relies on advanced technologies: genetically encoded fluorescent biosensors, omics tools, and microfluidic devices to analyze plant–microbe interactions under stress conditions and define their adaptive limitations. We use next-generation biosensors to visualize calcium signaling dynamics with high spatiotemporal resolution in plant–microorganism systems exposed to pathogenic attacks and environmental stress.

This project contributes to efforts to reduce the use of chemical phytosanitary products, particularly in the context of climate change, by supporting the development of more sustainable biocontrol strategies.

References :

1. Dong, Qiuyan, et al. "Ca2+ signaling in plant responses to abiotic stresses." Journal of integrative plant biology 64.2 (2022): 287-300.

2. Kolodkin-Gal, Ilana, Matthew R. Parsek, and Marianna A. Patrauchan. "The roles of calcium signaling and calcium deposition in microbial multicellularity." Trends in Microbiology 31.12

(2023): 1225-1237.

3. Zhang, Yachun, et al. "Real-time calcium imaging in living plants." Trends in Plant Science 28.11 (2023): 1326-1327.

4. He, Fuxin, et al. "Simultaneous editing of three homoeologues of TaCIPK14 confers broadspectrum resistance to stripe rust in wheat." Plant Biotechnology Journal 21.2 (2023): 354- 368.

Objectives:

1. Understand inter- and intra-organism signaling dynamics among Bacillus, Xanthomonas, and host plants (Arabidopsis as the model).

2. Analyze the influence of environmental factors (e.g., temperature, drought stress) on these interactions.

3. Develop biocontrol strategies using PGPRs to reduce infections caused by Xanthomonas.

4. Identify key molecular targets and signaling pathways that could enhance plant resistance.

5. Investigate plant–microbe interaction mechanisms, focusing on the transition from motile to sessile (biofilm-forming) states driven by environmental conditions such as root exudates, salt stress, and mechanical constraints.

6. Explore the role of calcium in both plant and bacterial systems using ratiometric fluorescent biosensors to track real-time Ca2⁺ signaling with high resolution.

7. Characterize the genetic regulation of bacterial motility and biofilm formation using reporter fusions and transcriptomic analysis (RNA-seq), especially under environmental stress.

8. Utilize microfluidic platforms and confocal/LSFM microscopy to image calcium oscillations and biofilm development in real time.

9. Investigate how plant immune responses and environmental stress affect microbial colonization and biofilm stability.

Scientific Program & Methodology:

• Use of genetically encoded fluorescent biosensors in Bacillus and Xanthomonas to monitor calcium, ROS, and nutrient signaling during interactions with plants.

• Real-time imaging via confocal and light-sheet microscopy (LSFM) combined with microfluidic platforms to simulate natural environments under controlled conditions.

• Transcriptomic analyses (RNA-seq, digital PCR) to profile gene expression responses of the three partners under varying stress conditions.

• Genome editing (CRISPRi/Cas9) in Bacillus and Xanthomonas strains to study the roles of key genes in colonization, virulence, and bioprotective effects.

• Functional plant assays to validate the beneficial or pathogenic outcomes of interactions.

Doctoral School:

E2M2 – Ecology, Evolution, Microbiology and Modelling

https://e2m2.universite-lyon.fr

L’Université de Lyon est une Communauté d’universités et établissements (ComUE) qui rassemble 10 membres et 25 associés, et qui porte la coordination territoriale du site académique Lyon-Saint-Étienne: https://www.universite-lyon.fr

Recommended Education: Master’s degree (or equivalent, e.g., engineering school) in Plant Biology, Microbiology, Molecular Biology, Microbial Ecology, Plant Physiology, or a related field. Preferred Experience: Experience in molecular biology techniques, microbiology, plant– microbe interactions, or bioimaging methods. Familiarity with omics approaches (e.g., transcriptomics), fluorescence microscopy, and genome editing (e.g., CRISPR) is an advantage. Personal Qualities: Autonomy, teamwork, rigor, strong interpersonal and writing skills. Experience in supervising student interns is a plus.