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 pollution/salinity 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 genetic elements (MGEs), which can lead to rapid adaptation to changing environments but can also disrupt normal gene function. I became interested in mobile genetic elements in early 2025 when I sequenced bioluminescent bacterial DNA from siphonfish I collected from Sydney Harbor. Though I originally wanted to identify bacterial species, I instead found a dramatic proliferation of mobile elements in bacteria isolated from highly polluted areas. Prior work shows that stress can activate mobile elements, but it is unknown whether this occurs in coastal marine ecosystems. I hypothesize that environmental stressors in coastal water can trigger mobile element proliferation in marine bacteria.

What is the significance of this project?

Mobile genetic elements (MGEs) are a major engine of rapid bacterial evolution, as they can spread useful traits but also disrupt important functions. This project will reveal whether salinity and pollution levels in coastal waters can directly trigger MGE activity, giving biologists, conservationists, and lawmakers a new lens for understanding how urbanization affects bacterial communities. This matters because if what we put into coastal waters triggers 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 pollution and salinity 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?

To test whether mobile genetic element (MGE) density increases with environmental stress, I will travel to Sydney, Australia in March 2027 and collect triplicate water samples from four Harbour sites spanning a gradient from urban runoff to open marine. I’ll measure pollution levels (e.g., heavy metals), salinity, and temperature, filter the water, extract DNA, and sequence it with Nanopore long-read metagenomics, which is needed to resolve repetitive MGEs that short-read sequencing cannot. I’ll quantify MGEs per megabase and test whether density correlates with each water parameter, with sequencing and analysis finished by July 2027. Funds cover flights, lodging, meals, sampling supplies, extraction kits, and Nanopore flow cells and library prep. If a signal emerges, it will motivate future lab experiments to test which stressors drive MGE expansion. I’ll publish the results and share the data openly.