Antimicrobial Resistance Dynamics in Freshwater Microbiomes

Antimicrobial resistance (AMR) is one of the most significant emerging threats to global public health. Freshwater environments play an important role in the evolution and dissemination of antibiotic resistance genes, yet the environmental processes that drive resistance activation and gene transfer remain poorly understood.

This PhD project will investigate how environmental stress, particularly changes in redox conditions and oxidative stress, influences the activation and dissemination of antibiotic resistance genes in freshwater microbial communities.

The project will combine environmental microbiology, experimental microcosm systems, and multi-omics analysis, including:

• Metagenomics and metatranscriptomics
• Strain tracking
• Hi-C sequencing to identify host plasmid associations
• Computational modelling of resistance gene dynamics

Freshwater samples will be collected from multiple sites across New Zealand with different levels of anthropogenic pollution. Controlled microcosm experiments will track the activation and transfer of resistance genes through time. Genomic and transcriptomic data will be used to identify environmental drivers of resistance emergence.

The student will be supervised by Dr Olin Silander (Liggins Institute) but the project is collaborative across faculties and also includes Prof Naresh Singhal (Engineering) and Prof Simon Swift (FMHS).

MSc in microbiology, genomics, bioinformatics, environmental science, or a related field.

Tuesday 31 March 2026