PhD Position on Plant-Microbiome Signalling at Utrecht University

Utrecht University

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Vacancy

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Description

This PhD position is part of the NWO funded project 'Identifying Plant Compounds and Processes that Attract and Accommodate Beneficial Microbes' (ATTACC). In ATTACC we aim to identify plant compounds and processes that attract and accommodate beneficial microbes.

The project evolves around the search for, and the characterisation of, plant components that control the root rhizosphere environment. Billions of microbes inhabit this environment and help plants to grow and stay healthy. Plants impact the rhizosphere environment by exudation of compounds that change the chemistry of the soil and provide energy for the microbes. The exact nature of these compounds, their role in attracting and accommodating microbes, and how they are regulated are mostly unknown. We believe that in order to use the plant microbiome to its full potential in sustainable agriculture, it is important to reveal and better understand the role of these compounds.

In this PhD project you will leverage a collection of transgenic Arabidopsis thaliana plants (a model plant for plant-microbe and plant-microbiome research) that express a class of transcription factors, called MYBs, that are linked to exudation. We will use automated phenotyping to characterise transgenic plants with elevated expression of these MYBs, and we will evaluate how these plants attract and accommodate beneficial microbes using diverse ‘omics techniques including microbiome profiling and transcriptomics.

Responsibilities

As a PhD candidate, you will:

• execute the ATTACC project together with a technician at the Plant-Microbe Interactions research group at Utrecht University;
• perform wet-lab experiments involving transgenic plants, microbial communities, and “dry-lab” bioinformatics analyses to profile these communities (microbiome sequencing), measure plant- and community-gene expression (transcriptomics), and in collaboration evaluate exudate metabolomics;
• collaborate with data scientists at theAI Technology for Life research groupexternal linkin the Information and Computing Science department to model and predict microbial community assembly and dynamics;
• have the opportunity to steer the project into creative new directions;
• contribute to teaching BSc and MSc students working with you on the project.

You will work under supervision of Dr Ronnie de Jonge   

Qualification

We are looking for a highly motivated and creative PhD candidate to join us in this unique project.

You are:

• intrinsically motivated and have a proactive work attitude;
• a pleasant team player who is able to collaborate within an interdisciplinary team;
• not easily put off by obstacles in your work and creative in finding solutions;
• skilled in practical lab work in the areas of plant and/or microbial biology;
• experienced with or interested in plant microbiome research;
• interested in becoming skilled in bioinformatic analysis of big ‘omics data sets;
• interested in robotised plant root and shoot phenotyping.

You possess:

• a MSc in the area of plant and/or microbe biology, plant biotechnology, or any other plant/microbe-related science field;
• experience in plant biotechnology or microbiology techniques, preferably in the context of plant microbiome research;
• an excellent command of both written and spoken English;
• good communication and organisation skills.

Experience with plant-microbiome research, and plant genotyping and phenotyping is an advantage. For the bioinformatic analysis of large ‘omics data sets, programming skills are an advantage.

If you feel that this role is the perfect match, but you do not yet meet all the qualifications, we also welcome you to apply.

We offer:

• a position for four years;
• a gross monthly salary ranging from €2,770 in the first year and increasing to €3,539 in the fourth year in the case of full-time employment (salary scale P under the Collective Labour Agreement for Dutch Universities (CAO NU);
• 8% holiday pay and 8.3% year-end bonus; 
• a pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU. 

Check the link to apply: Apply Now