PhD Fellowship in Microbial Ecology Full-time

PhD Project On Biological Nitrification Inhibition And Plant-Microbe Interactions In Wheat

The Section of Microbial Ecology and Biotechnology, anchored in the Microbial Interactions Group, invites applicants for a 3-year PhD fellowship. The project is funded by the Novo Nordisk Foundation as part of the CropSustaiN program and will be conducted in close collaboration with the Plant Defence Genetics Group at the Section for Plant and Soil.

Expected start date is 1 July 2026.

The project aims to elucidate the microbial mechanisms underlying biological nitrification inhibition (BNI) in wheat, focusing on ammonia-oxidizing bacteria (AOB) and archaea (AOA) and their interactions with root-exuded benzoxazinoids and other BNI compounds. The project will also enhance and develop microbial methods for BNI phenotyping and link microbial responses to plant growth conditions, fertilization regimes, and rhizosphere ecology.

The specific objectives are:

1. Characterize AOA and AOB responses to BNI compounds produced by wheat, using controlled growth chamber experiments, microcosm studies, and in vitro assays.
2. Develop and optimize microbial BNI screening methods, including whole-cell bioreporter assays and bioreporters based on Nitrosomonas europaea and Nitrosospira multiformis.
3. Investigate effects of plant growth stages and fertilization treatments on BNI expression and microbial activity in the rhizosphere.
4. Collect and analyze rhizosphere and soil samples to assess microbial community composition and functional gene abundance.
5. Link microbial responses to wheat genotypes, including lines with and without Leymus racemosus (Lr) chromosome translocation fragments, and identify potential microbial indicators of BNI capacity.
6. Integrate molecular and microbial ecology approaches to provide a mechanistic understanding of BNI and support the development of microbial-informed breeding strategies.

Main tasks of the appointed applicant:

• Cultivate and phenotype AOB and AOA in relation to BNI compounds from wheat.
• Develop, implement, and optimize microbial BNI assays.
• Conduct controlled growth chamber experiments to study BNI expression across wheat genotypes, growth stages, and fertilization conditions.
• Analyze microbial community structure and functional genes using amplicon sequencing, qPCR, and metagenomics, and link findings to plant growth.
• Collaborate with national and international partners in the CropSustaiN project.

Qualifications:

• MSc in Biotechnology, Biology, Environmental Sciences, or equivalent.
• Minimum 1 year of hands-on experience in research.
• Experience in working with ammonia-oxidizing organisms (AOB or AOA) is essential.
• Experience with plant-microbe interactions or rhizosphere microbiology is advantageous.
• Ability to work independently and across multiple disciplines.
• Fluent in English (oral and written).

Research environment:

The Microbial Interactions Group studies microbial community assembly, microbial functions, and plant-microbe interactions in sustainable agriculture. The group provides:

• Modern laboratories, controlled growth chambers, sequencing facilities, and bioreporter platforms.
• Collaboration with the Plant Defence Genetics Group for integrative plant-microbe research.

Principal supervisor: Associate Professor Mette Haubjerg Nicolaisen, meni@plen.ku.dk, +45 3533 2649.

Terms of employment in the regular programme:

The candidate will be enrolled in a three-year full-time study within the framework of the regular PhD programme (5+3 scheme).

To be eligible for the PhD programme, you must have completed a degree programme, equivalent to a Danish master's degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project. For information of eligibility of completed programmes, see General assessments for specific countries.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

The terms of employment and salary are in accordance with the agreement between the Ministry of Finance and the Danish Confederation of Professional Associations on Academics in the State (AC). The position is covered by the Protocol on Job Structure.

Responsibilities and tasks in the PhD programme:

• Carry through an independent research project under supervision.
• Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE.
• Participate in active research environments, including a stay at another research institution, preferably abroad.
• Teaching and knowledge dissemination activities, including participation in international microbiology conferences.
• Write scientific papers aimed at high-impact journals.
• Write and defend a PhD thesis based on your project.

Application and Assessment Procedure:

Your application, including all attachments, must be in English and submitted electronically by clicking APPLY NOW below.

Please include:

1. Motivated letter of application (max. one page)
2. Curriculum vitae including information about your education, experience, language skills, and other skills relevant to the position
3. Original diplomas for Bachelor of Science or Master of Science and a transcript of records in the original language, including an authorized English translation if issued in a language other than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
4. Publication list (if any published papers)

Application deadline:

The deadline for applications is 31 March 2026, 23:59 GMT +1.

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process:

After the deadline, some applicants will be selected for academic assessment by an unbiased expert assessor. You will be notified whether you will be passed for assessment. The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills, and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/.

Questions:

For specific information about the PhD fellowship, please contact the principal supervisor. General information about PhD study at the Faculty of SCIENCE is available at the PhD School's website: https://www.science.ku.dk/phd/.

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.