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

Overview

Aarhus University in Denmark invites applications for a PhD fellowship at the Graduate School of Technical Sciences, within the Animal and Veterinary Sciences programme. The position starts on 1 January 2027 or later and is based at the Department of Animal and Veterinary Sciences in Tjele.

Biogas production supports the shift to renewable energy and a circular bioeconomy, but growing use of imported animal-derived biomass links European suppliers, international transport, Danish reception points, biogas plants and nearby livestock farms. The project will test whether disease transmission along these pathways is microbiologically plausible and identify where hygienisation and other biosecurity barriers break the chain.

What you will do

Using a risk-informed longitudinal design, the candidate will sample linked compartments such as incoming biomass vehicles, unloading areas, local machinery, plant environments and biomass before and after hygienisation. Methods combine PCR and RT-qPCR surveillance for transboundary animal-disease agents and other animal pathogens with long-read shotgun metagenomics, culture and viability approaches and sequencing of selected isolates. Comparative genomics will assess microbial connectivity between compartments. Controlled experiments will measure persistence, transfer and inactivation under realistic transport, storage, cleaning and processing conditions, using surrogates where work with high-consequence agents is not feasible. The project will deliver evidence on microbial hazards, resistomes, mobile genetic elements, critical control points and effective biosecurity barriers in the Danish biogas sector.

Requirements

Applicants must hold a relevant master's degree or equivalent in genomics, veterinary science, microbiology, molecular biology, bioinformatics or a closely related discipline. Experience in molecular microbiology, microbial genomics or metagenomics, culture-based microbiology, bioinformatics or quantitative data analysis is an advantage, and applicants are not expected to be experts in every area. The successful candidate should enjoy combining field sampling, laboratory experiments and computational analysis, work carefully under biosafety and quality procedures, collaborate across institutions, and communicate well in written and spoken English. A driving licence and willingness to travel to Danish biogas plants are advantages.

How to apply

Applications are submitted online and must include a project description uploaded as a PDF, which can be copied from the advert.

Key dates

The deadline is 1 November 2026 at 23:59 CET, and the preferred start date is 1 January 2027.