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

Aarhus University; Denmark; On-site; DKK 192,000 - 267,000; Full time

Benefits offered by this job

Travel opportunities

Job summary

Aarhus University invites applications for a PhD fellowship in the Animal and Veterinary Sciences programme. The project will investigate biomass-to-biogas transmission pathways using genomics and metagenomics, with field sampling, lab work and computational analysis.

The successful candidate will join a multidisciplinary team, publish results, and collaborate with Danish biogas facilities. A master’s degree in a relevant field and English communication skills are required.

Qualifications

• Must hold a relevant master’s degree or equivalent in Genomics, Veterinary Science, Microbiology, Molecular Biology, Bioinformatics or related field.
• Experience in Molecular Microbiology, Microbial Genomics/Metagenomics, Culture-based Microbiology, Bioinformatics or Quantitative Data Analysis is an advantage.

Responsibilities

• Combine field sampling, laboratory experiments and computational analysis.
• Perform surveillance and sequencing to study microbiological pathways in biomass-to-biogas systems.
• Collaborate across institutions and communicate results in English.

Skills

English communication

Education

Master's degree in Genomics

Master's degree in related discipline

Tools

PCR/RT-qPCR

Long-read sequencing

Job description

Applicants are invited for a PhD Fellowship/Scholarship at Graduate School of Technical Sciences, Aarhus University, Denmark, within the Animal and Veterinary Sciences programme. The position is available from 01 January 2027 or later.

Title

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, [e-mail] (main supervisor)
• Anders Dalsgaard, [e-mail] (co-supervisor)
• Karl Pedersen, [e-mail] (co-supervisor)

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

Preferred starting date is 01 January 2027.