Summary
Aarhus University invites applications for a fully funded PhD Fellowship at the Graduate School of Technical Sciences within the Department of Animal and Veterinary Sciences. This doctoral project will investigate whether imported animal-derived biomass and the transport and processing networks connected to Danish biogas plants can act as microbial transmission pathways for animal pathogens, antimicrobial resistance, and mobile genetic elements. The position is expected to start on or after 1 January 2027.
PhD Position: Tracking Microbes Across Borders using Genomics to Uncover Biomass-to-Biogas Transmission Pathways at Aarhus University
Designation
PhD Fellowship / Scholarship — Graduate School of Technical Sciences, Aarhus University (Animal and Veterinary Sciences programme)
Key Information
| Institution | Aarhus University, Department of Animal and Veterinary Sciences |
|---|---|
| Degree | PhD |
| Start Date | Preferred: 1 January 2027 (or later) |
| Application Deadline | 1 November 2026, 23:59 CET |
| Location | Blichers Allé 20, 8830 Tjele, Denmark (Aarhus University) |
| How to Apply | Online application portal (see instructions below) |
Research Area
This PhD project addresses microbial biosecurity at the interfaces created by the growing use of animal-derived biomass in European biogas production. The research combines field sampling across linked compartments (incoming biomass vehicles, reception/unloading zones, local machinery, plant environments, biomass pre- and post-hygienisation, and interfaces with livestock) with laboratory and computational studies to determine if and how microbes move through these systems.
Methodologies will include targeted PCR and RT-qPCR surveillance for transboundary animal disease agents and other pathogens, long-read shotgun metagenomics, culture-based and viability assays, sequencing of selected isolates, and comparative genomic analyses to infer connectivity, persistence, and transfer. Controlled laboratory experiments will quantify persistence, transfer, and inactivation under representative transport, storage, cleaning/disinfection and processing scenarios. Where work cannot involve high-consequence agents, appropriate surrogates, indicators or non-infectious materials will be used.
Location
Place of employment: Aarhus University. Work will be based at the Department of Animal and Veterinary Sciences, Blichers Allé 20, 8830 Tjele, Denmark. The role will involve travel to Danish biogas plants for sampling and collaboration with external stakeholders.
Eligibility / Qualification
- Master’s degree (or equivalent) in Genomics, Veterinary Science, Microbiology, Molecular Biology, Bioinformatics, or a closely related field.
- Relevant experience in one or more of the following is an advantage: molecular microbiology, microbial genomics/metagenomics, culture-based microbiology, bioinformatics, quantitative data analysis. Applicants are not expected to be expert in all areas.
- Ability and motivation to combine field sampling, laboratory experimentation and computational analysis.
- Good written and spoken English skills.
- Experience working under biosafety and quality procedures is desirable. A driving licence and willingness to travel to biogas facilities are advantages.
Scholarship Description
The fellowship supports a doctoral research project that will deliver evidence on microbial hazards associated with biomass-to-biogas systems, including resistomes and mobile genetic elements, and will identify critical control points and effective biosecurity barriers within the Danish biogas sector. The project is interdisciplinary and collaborative, involving fieldwork, laboratory assays, sequencing technologies, and comparative genomic analyses. The successful candidate will work under the supervision team at Aarhus University with co-supervisors from partner institutions.
Main supervisors and contacts:
- Yaovi Mahuton Gildas Hounmanou — main supervisor: gil@anivet.au.dk
- Anders Dalsgaard — co-supervisor: adal@sund.ku.dk
- Karl Pedersen — co-supervisor: karl.pedersen@anivet.au.dk
For questions about application requirements and mandatory attachments, consult the Graduate School application guide or contact: admission.gradschool.tech@au.dk
How to Apply
Applications must be submitted via the online application portal. For technical reasons you must upload a project description file; please copy the project description provided in the recruitment advertisement and upload it as a PDF in the application.
Submit your application here: Apply via the Research Planner portal
Full application guidance is available at the Graduate School’s application guide: https://phd.tech.au.dk/for-applicants/application-guide/
Last Date for Apply
1 November 2026 at 23:59 CET
Apply Link
Please read the full job description in the online advertisement and submit your application by the deadline. Good luck with your application!
