Multitrophic Plant-Microbe Interactions

Group leader: Stéphane Hacquard

Research project:

Interplay between the plant cell wall, innate immunity, and the root microbiota.

Root cells are surrounded by an extracellular matrix — the cell wall — that not only provides a structural framework to support root growth but also act as a physical barrier that protects plants against microbial infections. Paradoxically, roots of healthy plants are colonized by a staggering diversity of microbes that evolved in different kingdoms of life. Therefore, root-colonizing microbes have evolved strategies to efficiently degrade primary cell wall components and conversely, plants have learned to recognize cell wall degradation products for innate immune activation. Here, we hypothesize 1) that difference in plant cell wall composition between plant species/genotypes is a major determinant that drives root microbiota assembly and host specificity in nature, 2) that extensive cell wall remodeling occurs during microbiota establishment and accommodation in roots, and 3) that recognition of cell wall degradation products by plant immune receptors is key to maintain host-microbe homeostasis and plant health. Therefore, we predict that plant cell components have not only evolved to restrict pathogen entry but also for accommodating beneficial microbial communities.

The project will be articulated along three major axes. First, living (but also dead) roots of Arabidopsis thaliana WT and mutants altered in cell wall composition will be kept sterile or re-colonized by a multi-kingdom synthetic community (bacteria, fungi, oomycetes) in gnotobiotic systems to identify direct links between cell wall alterations, microbial assemblages and microbiota-induced variation in plant growth phenotypes. We anticipate that specific cell wall alterations will lead to “abnormal” root microbiota assemblages that disrupt host-microbe homeostasis.

Second, we will test the extent to which the synthetic microbial community induces cell wall remodelling and immune system activation during epidermis penetration and early root colonization using epidermis-specific RNA sequencing (Translating Ribosome Affinity Purification). Genetically-encoded fluorescent markers will be also constructed to visualize gene activation in roots using real-time confocal microscopy. We also aim to visualize cell wall change during microbial colonization in roots by co-localizing primary cell wall components with enzymes of interest using antibody-based detection.
Finally, we aim at testing whether some cell wall breakdown products that are degraded by microbes in vitro and/or released during root colonization by the beneficial microbial community are immunogenic and activate the host immune responses.

A key question is whether activation of innate immunity by these DAMPs is needed for maintenance of host-microbiota homeostasis and microbiota establishment at roots. This multi-disciplinary project will involve the group of Dr. Stéphane Hacquard at MPIPZ (expertise on the root microbiota) and the group of Dr. Robertas Ursache at CRAG (expertise on primary and secondary plant cell walls).

Key publication

Potential collaborations with other research groups

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