The plant microbiome is rapidly becoming one of the most transformative fields in sustainable agriculture. A new fully funded PhD project at the Université d’Angers offers an exciting opportunity to explore one of its least studied components: seed-associated yeasts. This doctoral research focuses on understanding how yeasts colonize seeds, how they are transmitted to seedlings, and how they influence plant health. By combining microbial ecology, genomics, and bioinformatics, this project aims to unlock new strategies for plant microbiota engineering.

This PhD on seed-associated yeasts represents a frontier in plant microbiome research. By combining ecology, genomics, and applied plant science, the project contributes directly to the development of sustainable and resilient agricultural systems. For candidates passionate about microbial ecology, plant health, and bioinformatics, this opportunity at the University of Angers offers both scientific depth and real-world impact.

Host Institution and Research Unit

The PhD will be conducted within:

• Institut de Recherche en Horticulture et Semences (IRHS – UMR 1345)

IRHS is a joint research unit affiliated with:

• Institut national de recherche pour l’agriculture, l’alimentation et l’environnement (INRAE)

The doctoral program is part of the:

• École doctorale Végétal, Animal, Aliment, Mer, Environnement (VAAME)

The successful candidate will join the FungiSem and EmerSys research teams in a dynamic, interdisciplinary scientific environment.

Thesis Title

Ecology and Transmission of Seed-Associated Yeasts
Acronym: Eco-Yeast

Start Date: October 1, 2026
End Date: September 30, 2029
Funding: Public doctoral contract (in acquisition phase)
Employer: INRAE

Why Study Seed-Associated Yeasts?

Seeds are not just carriers of plant genetic information. They also transport complex microbial communities that form the first inoculum of the emerging seedling. These microorganisms influence:

• Germination success
• Disease resistance
• Plant growth
• Crop productivity

While bacteria such as Bacillus and fungi like Trichoderma have been widely studied in biocontrol, yeasts remain largely overlooked in agriculture. Yet, recent studies have demonstrated that yeasts are consistent members of the core seed microbiota.

Their systematic presence in seed lots makes them promising candidates for plant health innovation and sustainable crop establishment.

Research Objectives

The PhD is structured around three main scientific questions:

1. What Is the Diversity of Seed-Associated Yeasts?

Using data mining approaches and metabarcoding datasets, the doctoral researcher will analyze more than 10,000 samples from 50 plant species. These samples include multiple ecological compartments:

• Soil
• Water
• Air
• Pollinators
• Flowers
• Leaves
• Roots
• Seeds

This large-scale ecological mapping will help describe yeast distribution patterns and colonization pathways.

2. How Are Yeasts Transmitted Across Plant Generations?

The project investigates vertical and horizontal transmission routes:

• From mother plant to seed
• From seed to seedling

Through controlled in planta inoculation experiments, selected yeast strains will be tested for:

• Colonization ability
• Effects on parental plants
• Impacts on seedling development
• Potential protective roles against stress or pathogens

Understanding these processes is essential for microbiome-based crop management strategies.

3. Which Genetic Determinants Enable Seed Colonization?

The third component of the thesis focuses on genomics and phenotyping. Selected isolates with contrasting behaviors will be analyzed to identify:

• Survival traits on seeds
• Stress tolerance mechanisms
• Transmission efficiency factors
• Genomic markers linked to colonization ability

By combining genome sequencing with phenotypic assays, the research aims to uncover the molecular foundations of yeast adaptation to the seed habitat.

Scientific and Agricultural Impact

Plant microbiota engineering is now considered a major lever for reducing synthetic fertilizer and pesticide use. As agriculture shifts toward agroecological systems, beneficial microorganisms will play an increasingly strategic role.

This project addresses a major knowledge gap: the role of yeasts in plant microbiomes.

Potential applications include:

• Biological seed treatments
• Enhanced crop establishment
• Sustainable disease management
• Reduced chemical inputs
• Climate-resilient agriculture

Because yeasts are already widely used in medical and industrial biotechnology, expanding their use into agriculture could open significant commercial and environmental opportunities.

Research Environment and Infrastructure

The IRHS hosts approximately 260 researchers and technical staff across 14 research teams. The unit benefits from advanced platforms within SFR QuaSav, including:

• High-throughput sequencing tools
• Imaging platforms
• Phenotyping facilities
• Microbial culture collections

The PhD candidate will also leverage datasets, strains, and resources generated through ongoing projects such as INHERSEED and SUCSEED.

This supportive environment provides access to cutting-edge research infrastructure and interdisciplinary collaboration.

Candidate Profile

The ideal applicant should have:

• A Master’s degree in microbiology, plant biology, ecology, or related fields
• Strong skills in bioinformatics and genome analysis
• Experience in microbiology and molecular biology
• Ability to work under sterile laboratory conditions
• Fluency in English (French is a plus)
• Motivation to contribute innovative ideas to the project

Candidates with experience in sequencing data analysis and microbial ecology will be particularly competitive.

Career Opportunities After This PhD

Graduates with expertise in plant microbiome research and microbial genomics can pursue careers in:

• Academic research
• Agricultural biotechnology companies
• Seed industry innovation
• Biocontrol product development
• Environmental microbiology
• International research institutions

As global agriculture transitions toward sustainable intensification, expertise in microbiome engineering is becoming highly valuable.

How to apply

APPLY NOW Deadline is 13/05/2026

Frequently Asked Questions (FAQ)

Is this PhD fully funded?

Yes, the project is supported through a public doctoral contract under INRAE, with funding currently in acquisition and associated project support already secured.

Where is the research conducted?

The research takes place at IRHS in Angers, France, within a leading plant science research environment.

Do I need bioinformatics experience?

Yes. The project involves large-scale metabarcoding data mining and genome analysis, so strong computational skills are required.

Will the research involve laboratory experiments?

Absolutely. The PhD combines computational analyses with in planta inoculation experiments and microbial phenotyping.

Is knowledge of French mandatory?

Fluency in English is required. French is beneficial but not mandatory, as the research environment is international.

What makes this project unique?

Unlike most plant microbiome research that focuses on bacteria, this thesis explores yeasts — a largely untapped but potentially transformative group of microorganisms for agriculture.