PhD Position: Tracking Microbes Across Borders using Genomics to Uncover Biomass-to-Biogas Transmission Pathways

Tracking Microbes Across Borders using Genomics to Uncover Biomass-to-Biogas Transmission Pathways

Research area and project description

Biogas production supports the transition to renewable energy and a circular bioeconomy. However, the increasing use of imported animal-derived biomass creates connected biosecurity interfaces between European suppliers, international transport, Danish reception points, biogas plants and nearby livestock production. This PhD project will determine whether these pathways are microbiologically plausible and identify where hygienisation and other biosecurity barriers interrupt them.

Using a risk-informed longitudinal design, the candidate will sample linked compartments including incoming biomass vehicles, reception and unloading areas, local vehicles and machinery, plant environments, biomass before and after hygienisation, and selected onward-facing interfaces. The project will combine targeted PCR/RT-qPCR surveillance for epidemiologically relevant transboundary animal-disease agents and other animal pathogens with long-read shotgun metagenomics, culture and viability approaches, and sequencing of selected isolates. Comparative genomic analyses will assess microbial connectivity between compartments while distinguishing co-detection from evidence consistent with persistence or transfer. Findings will be integrated with biomass origin and type, transport history, season and plant/process conditions.

Controlled experiments will quantify persistence, transfer and inactivation under representative transport, storage, cleaning/disinfection and processing conditions. Where work with high-consequence agents is not feasible, appropriate surrogates, indicators or non-infectious materials will be used. The project will deliver evidence on microbial hazards, resistomes, mobile genetic elements, critical control points and effective biosecurity barriers in the Danish biogas sector.

Qualifications and specific competences

Applicants to the PhD position must hold a relevant master’s degree, or an equivalent qualification, in Genomics, Veterinary Science, Microbiology, Molecular Biology, Bioinformatics, or a closely related discipline.

Relevant experience in Molecular Microbiology, Microbial Genomics/Metagenomics, Culture-based Microbiology, Bioinformatics or Quantitative Data Analysis is an advantage; applicants are not expected to be experts in all areas.

The successful candidate should be motivated to combine field sampling, laboratory experiments and computational analysis; work carefully under appropriate biosafety and quality procedures; collaborate across institutions and with external stakeholders; and communicate effectively in written and spoken English. A driving license and willingness to travel to Danish biogas plants are advantages.

Place of employment and place of work

The place of employment is Aarhus University, and the place of work is Aarhus University, Department of Animal and Veterinary Sciences, Blichers Allé 20, 8830 Tjele, Denmark.

Contacts

Applicants seeking further information regarding the PhD position are invited to contact:

• Yaovi Mahuton Gildas Hounmanou, gil@anivet.au.dk (main supervisor)
• Anders Dalsgaard, adal@sund.ku.dk (co-supervisor)
• Karl Pedersen, karl.pedersen@anivet.au.dk (co-supervisor)

For information about application requirements and mandatory attachments, please see our application guide. If answers cannot be found there, please contact:

• admission.gradschool.tech@au.dk

How to apply

Please follow this link to submit your application.

Application deadline is 01 November 2026 at 23:59 CET.

Preferred starting date is 01 January 2027.

For technical reasons, you must upload a project description. Please copy the project description above and upload it as a PDF in the application.

Please read the full job description and apply by clicking the 'Apply' button