Date of Award


Publication Type

Master Thesis

Degree Name



Biological Sciences

First Advisor

Daniel Heath

Second Advisor

Robert Devlin


16S Metabarcoding, Aquaculture, Bacterial Community, Environmental DNA, Quantitative Real-time PCR, Salmon Farm




Finfish aquaculture has been on a steady rise, and to match human consumption an increase of open water fish farming is inevitable; however, the impacts of rearing high densities of fish on the surrounding ecosystem remains unclear. Transgenic fish have begun to be implemented in aquaculture to improve traits such as growth rate and feeding efficiency. However, concerns about the potential ecological impact if escaped transgenic organisms are diverse and widespread. Here we characterize the eDNA “plume” from an open water Oncorhynchus tshawystcha farm, and from a transgenic Oncorhynchus kistuch rearing facility. We utilize eDNA as a biomarker of sloughed Chinook salmon DNA from the farm and test for farm effects on bacterial community changes. We found evidence of an overall seasonal effect on eDNA concentration and localized distance effects relative to the farm in the fall. Our BC analyses showed strong seasonal effects as well as evidence of a distance (from the farm) on BC diversity. Despite the well-mixed characteristics of the sampled bay our findings indicate a radial effect of the fish farm plume on the surrounding waters. We also designed a transgene-specific assay to detect transgenic Coho salmon without interference from the wild-type genome and establish the range of detection from an effluent pipe. Our transgene-specific assay detected the growth hormone construct from environmental samples to 10 m from the effluent pipe, as well as two samples 150 m away and 1300m away from the effluent pipe, detecting extremely low traces of transgene DNA copies. This spatial inconsistency in transgenic eDNA detection may be due to sloughed organic matter accumulating, rather then breaking down into a homogenous mixture in marine water. This work establishes how eDNA can be used as a valuable tool for marine surveillance, providing data on the distribution of finfish DNA from a point source and identifying ecological impacts on the surrounding aquatic environment.