Postdoctoral Researcher in Molecular Ecology

Postdoctoral Researcher in Molecular Ecology

Uppsala University - Department of Ecology and Genetics

Uppsala, Sweden

Project description

We are hiring a postdoctoral researcher for 2.5 years to the project “Invertebrates as vectors of antimicrobial resistance genes in urban landscapes”. The overall aim is to provide insights into the role of invertebrates (Chironomidae: non-biting midges) in the spread and dynamics of antimicrobial resistance (AMR) from wastewater treatment plants. We will use a unique combination of field surveys and laboratory experiments. Fieldwork will document the spatial patterns of AMR in urban environments, while controlled laboratory experiments will help elucidate the mechanisms and processes of AMR transmission within landscapes and across food webs. The majority of the work will involve metagenomic analyses and laboratory experiments on chironomids.

Duties

Duties include assembly and binning of metagenome-assembled genomes (MAGs) from shotgun metagenomic data, perform taxonomic assignment and identify plasmids and antimicrobial resistance genes. The analyses consist of applying multivariate statistical methods. In addition, the postdoctoral researcher will design and conduct controlled laboratory experiments on chironomids and other aquatic insects to study the transfer of AMR across individuals, generations, and species. This part of the work involves rearing of aquatic invertebrates collected from the field, maintaining factorial experimental setups, and analyzing AMR transmission in these invertebrates using agar plate assays.

Qualifications required

Ph.D. degree or a foreign degree equivalent to a doctoral degree in microbiology, molecular biology, bioinformatics, environmental genomics, or a related field. The degree needs to be obtained by the time of the decision of employment. Those who have obtained a PhD degree three years prior to the application deadline are primarily considered for the employment. The starting point of the three-year frame period is the application deadline. Due to special circumstances, the degree may have been obtained earlier. The three-year period can be extended due to circumstances such as sick leave, parental leave, duties in labor unions, etc.

We are looking for a highly motivated, independent, and proficient researcher to drive the project forward. The ideal candidate is a collaborative team player with a strong interest in microbial transmission in animals (horizontally and vertically). They should have experience in one or several of the abovementioned tasks, and demonstrated proficiency in academic English writing and publishing in peer-reviewed journals.

Qualifications desired

The candidate should ideally have experience in the analysis of metagenomic shotgun data. Familiarity with metagenome-assembled genome (MAG) reconstruction and antimicrobial resistance (AMR) gene identification is highly desirable. Strong skills in scripting languages (e.g., Python, R, or Bash) and experience working in Unix/Linux environments are advantageous. Experience in laboratory culturing of aquatic invertebrates and in conducting controlled life-cycle and/or factorial laboratory experiments will be considered an asset. Experience with agar plate assays is also desirable.