EMBARQ Master Project: Horizontal Gene Transfer and Plasmid Dynamics in Agricultural Microbiomes
Microbial bioinoculants, including biopesticides and biofertilizers, have the potential to provide more sustainable alternatives to conventional chemical agents in agriculture. However, their safe and sustainable use requires a better understanding of how living microorganisms behave after introduction into the environment. Unlike chemical products, they can reproduce, interact with indigenous soil microbial communities, and potentially exchange genetic material through horizontal gene transfer (HGT).
Plasmid-mediated gene transfer may contribute to the spread of antibiotic resistance, virulence, or other potentially undesirable traits. Understanding the mobility of these genetic elements and their microbial hosts is therefore an important aspect of microbial risk assessment.
This Master's project is linked to WP3 of EMBARQ, which focuses on plasmid mobility, plasmid-host relationships, and the potential for horizontal gene transfer in agricultural environments.
Possible research topics include:
- Characterize the plasmid-encoded gene pool in soil systems
- Investigate plasmid transfer dynamics
- Investigate whether the plant select for plasmids in the rhizosphere
About EMBARQ
EMBARQ is a multidisciplinary research project funded by the Novo Nordisk Foundation. It develops knowledge, methods, and tools to improve the environmental risk assessment of microbial bioinoculants. The project brings together expertise in microbiology, ecology, metagenomics, bioinformatics, and risk assessment to better understand the potential impacts of introduced microorganisms on microbial communities and the environment.
The overall aim is to support more science- and evidence-based assessment of microbial products for researchers, industry, and regulatory authorities.
More information: embarq.dk
Techniques
Depending on the specific project, techniques may include:
- Classic culturing and microbiology techniques
- Tracking bacteria and plasmids with reporter genes
- PCR, qPCR and fluorescence-activated cell sorting (FACS)
- DNA extraction and metagenomic sequencing
- Bioinformatic and network analysis
The project can be primarily experimental, bioinformatic, or a combination of both, depending on the student's interests and activities.
Keywords
Microbiome, soil microbiome, rhizosphere, plasmids, mobile genetic elements, horizontal gene transfer, antibiotic resistance, virulence genes, metagenomics, bioinoculants, biopesticides, biofertilizers, microbial risk assessment, sustainable agriculture
Host institution/supervisor
Institution: Department of Biology, University of Copenhagen
Supervisor: Professor Søren J. Sørensen
Contact: sjs@bio.ku.dk
The project will be hosted at the University of Copenhagen, with opportunities for collaboration across the EMBARQ consortium, including Aarhus University, Statens Serum Institut, and Aalborg University.