Stage M2 Angers 2026: Plant microbiota transmission between generations across 60 crop species, from mother plant to seedlings

The team EmerSys (IRHS Angers – INRAE) will be recruiting a Master 2 intern in 2026 (January-June 2026, dates are flexible)

Context and research objectives.
Plant and their microbial partners are considered an indivisible unit: the holobiont. A key feature of the holobiont theory is the inheritability of microbial symbionts and their potential role on seeds and seedlings development. Still, the relationships between the maternal holobiont, the seeds characteristics and the resulting progeny (i.e., phenotype and microbiota) have not been established at a large phylogenetic scale. Studying seed-mediated maternal effects is crucial as they could strongly affect plant species fitness and crop yield in an agricultural context.
Leveraging the expertise on crop species and seed microbiota at the EmerSys team of the IRHS, the project aims to shed new light on:
1) Seed microbiota diversity and transmission to seedlings across 60+ crop species
2) The drivers of seed microbiota assembly and transmission.
3) Relations between seedling phenotypes and mother plant fitness (e.g., germination rate, progeny growth, etc…)
These questions have both fundamental and applied implications as the agro-industry is looking for microbial-based solution to reduce pesticide usage.
During this internship, you will perform greenhouse experiments to perform germination assays of numerous crop species. The growth and traits of the plants will be monitored using high-throughput phenotyping based on digital imaging (PHENOBEAN experimental setup of PHENOTIC platform) and manual measures. The characterization of plant microbiota will be done using amplicon sequencing on fungal (ITS1) and bacterial (gyrB) gene markers on the Illumina MiSeq platform hosted in the lab (ANAN platform), followed by bioinformatic pipelines. You will then use R to test the existence of seed microbial transmission and relations between microbiota and phenotypes in seedlings.

Degree, Skills and technics: Master 1 in Ecology or Microbiology
We expect the applicants to have at least two of these skills (Community ecology of plants or microorganisms, Bioinformatics, Microbiology, Plant phenotyping) and to not be repelled by data analysis and large datasets.
Team: This internship will be performed at the IRHS of Angers. The co-supervision of the student will be done by two researchers (Tristan Boureau and Marie Simonin) and a PostDoc (Tristan Lafont Rapnouil). This internship will be conducted in the frame of the ANR JCJC INHERSEED project led by Marie Simonin.

Application before Sept 15th: Send a CV, motivation letter and Master 1 results to marie.simonin@inrae.fr

Address:
Centre INRAE Pays de la Loire
Institut de Recherche en Horticulture et Semences (IRHS Angers), Equipe EmerSys
Adresse : 42 rue Georges Morel – BP 60057
49071 Beaucouzé cedex