About This Project

Urban development is changing coastal waterways, altering salinity and pollution in ways that affect marine life. I study bioluminescent bacteria living inside cardinalfish in Australia and found that bacteria from polluted areas carry far more mobile DNA elements, which copy themselves across the genome and disrupt normal bacterial functions. I hypothesize that environmental stress drives this, and I will test it by sequencing bacterial communities across a salinity/pollution gradient.

Ask the Scientists

What is the context of this research?

Urban development is altering coastal waterways, exposing marine bacteria to novel salinity fluctuations and environmental pollutants. One response that bacteria have to combat this stress is the proliferation of mobile DNA elements, which can allow rapid adaptation to changing environments but also disrupt normal gene function.

I study the bioluminescent symbiosis between cardinalfish and their bacterial partner Photobacterium mandapamensis, which lives in the fish's light organ and produces light used to evade predators. When I sequenced these bacteria from Sydney Harbour, I found a dramatic proliferation of mobile elements in bacteria from more polluted sites. Prior work shows that these elements can be activated by stress, but whether this occurs in coastal marine ecosystems is unknown. I hypothesize that environmental stress triggers this proliferation, and that mobile element density scales with environmental stressors.

What is the significance of this project?

Insertion sequences (IS) are a major engine of rapid bacterial evolution, as they can help spread useful traits but also disrupt important functions. This project will reveal whether salinity and pollution levels in coastal waters can directly trigger IS activity, giving biologists, conservationists, and lawmakers a new lens for understanding how urbanization affects bacterial communities. It would also raise an important practical question: if what we put into coastal waters is triggering large-scale genomic changes in bacteria, we may need to rethink how we assess the biological impact of urban runoff and pollution. By connecting genomics, microbial ecology, and environmental change across a salinity and pollution gradient, this project generates data directly relevant to bacterial adaptation in an era of increasing coastal urbanization and climate-driven salinity shifts.

What are the goals of the project?

This project aims to determine whether environmental stressors in coastal areas increase the number of insertion sequences in marine bacteria. My Australian collaborators will collect water samples at 4 sites along the Sydney Harbour estuary transect, spanning a salinity and pollution gradient from approximately 0 ppt (freshwater/urban runoff) to 35 ppt (open marine). After receiving the samples, I will perform long-read metagenomics to test whether IS density in bacterial communities correlates with salinity or pollution levels. All samples will be multiplexed and sequenced in a single Oxford Nanopore MinION run, expected to generate approximately 10–12 Gb of data total. Long-read sequencing is essential because IS elements are repetitive and short-read technology cannot reliably resolve them. If a signal emerges, this will form the foundation for experimental evolution work testing what stressors directly cause IS expansion in the lab.