Objective: This project aims to investigate how soil-modified microbiota—through inoculation with soil and synthetic microbial communities—affects Arabidopsis thaliana ecotypes (wild-type Col-0 and potentially knockout lines targeting glucosinolate and strigolactone pathways). The focus will be on exploring the following impacts:

1. The influence of the rhizosphere metabolome on the activity of Phelipanche ramosa (branched broomrape).
2. The metabolite composition of the rhizosphere.
3. The taxonomic and functional profile of the soil microbiota.

The results will create a roadmap for controlling broomrape infestation in vitro, with potential field applications in the future.

Parasitic seeds of the branched broomrape (P. ramosa) which parasitizes Brassicaceae plants, including rapeseed or the model plant A. thaliana, are able to perceive germination stimulants exuded by the host plant at very low levels in order to initiate their germination and their biological cycle. The most important signaling pathway in the Brassicaceae rhizosphere is the glucosinolate pathway, where glucosinolates can be hydrolyzed by myrosinase enzymes of plant or microbial origin into isothiocyanates which are the main germination stimulants. These isothiocyanates also have a biocidal effect which induces a strong selection of the microbiota in the rhizosphere.

The recruited student will be supported by ANR Plant2Mi project which aims to demonstrate i/ the role of the soil microbiota in altering the metabolic profiles of glucosinolates and isothiocyanates and conversely ii/ the role of the host plant, via the exudation of glucosinolates and its related isothiocyanate compounds, in structuring microbial communities having particular activities and functions.

The student will work at US2B, Rhizoplante lab and will use their facilities and will be supervised by Ahmed Choukri, Phd student, and Lucie Poulin, ass. prof.

Tasks:
1. Soil Inoculation and plant cultivation: Inoculate inert substrates with microbial strains or soil macerates, and cultivate A. thaliana ecotypes using a miniaturized system that supports continuous medium recycling. Exudates and soil microbiomes will be monitored throughout.

2. Exudate analysis:
◦ P. ramosa germination effects:
– Quantitative: track P. ramosa germination over time, comparing conditions with controls.
– Qualitative: when P. ramosa germination is detected, use bio-guided analysis (RP-HPLC, solid-phase extraction) to identify active metabolites.
◦ Parasitic attachment and aggressiveness: Use established protocols to assess P. ramosa’s attachment and aggressiveness toward A. thaliana in mini-rhizotrons.
◦ Metabolomic analysis: Quantify glucosinolates and isothiocyanates using LC-MS/MS (outsourced to P2M2, Rennes) and analysis (upon data availability).

3. Rhizosphere metabarcoding:
◦ Perform rhizosphere DNA extraction at week 3 (when the plant is well-grown), amplify 16S & ITS1 gene markers for Illumina sequencing (outsourced), and analyze the microbial diversity using in-house bioinformatics tools (upon data availability).

Activities:

• Pasteurian microbiology: microbial strain inoculation, basic microbiology techniques
• Metabolomics/Biochemistry: RP-HPLC, solid-phase extraction
• Plant assays, cultivation and sampling
• Molecular biology/bioinformatics: dna extraction, metabarcoding analysis using dada2/phyloseq

• Wet Lab skills: familiar with DNA extraction, analytic standard preparations.
• Bioinformatics / biostatistics skills as assets: R, python, shell…
• Knowledge in plant molecular biology, microbiology and/or biochemistry