Non-invasive Pathogen Detection
Research Assistant Ashley Sanders, USGS Researcher Dr. Claire Couch, and undergraduate student Kasey Ingram
Increasing water temperatures brought by climate change and modifications to freshwater environments have increased fish vulnerability to infection by pathogens. Pathogen detection used to monitor the health of fish is usually invasive and often requires fish to be euthanized for necropsy. Invasive sampling can be labor intensive and not ideal when working with small populations of threatened or endangered species. Our goal is to develop a non-invasive environmental-DNA (eDNA) sampling technique to accurately determine if and to what degree fish are infected.
Methods
In this study, we used steelhead trout (Oncorhynchus mykiss) and the myxosporean parasite Ceratonova shasta, a common host-parasite of concern in the Klamath basin. We exposed 3 groups of treatment fish to C. shasta and kept one group as the control. Each week, we incubated 1 fish from each group in a bucket of water and filtered a subsample of the water through filters that were then used to determine total C. shasta spore count with qPCR. Results from infected and control fish were compared while fish necropsies and fecal samples served as a point of reference for infection.
Results and Next Steps
We found that C. shasta was hardly detected before 4 weeks post-exposure, at which point fish also showed clear physical signs of infection and tested positive in necropsies. Additionally, we found that the quantity of spores between subsample replicates and tank replicates varied widely, which we think is caused by spores clumping in the incubation water. Non-invasive sampling was not effective at detecting C. shasta throughout the disease cycle, which aligns with the dispersal pattern of the pathogen. Our next experiment will add replication to infected fish at week 4 and more rigorously assess if subsampling is feasible given the non-uniform dispersal of spores in incubation water.
Chinook salmon fry infected with C. shasta from another research study at AAHL. This pathogen primarily attacks the intestinal tract and causes dramatic inflammation and eventually kills the host fish.
Kasey extracting a fecal sample from a fish
Fecal sampling to confirm pathogen loads in experimental fish
O. mykiss used in this study
Fish were incubated in 5 gallon buckets of 4 L of clean water
Kasey and Will sampling fish
Filter tower setup to filter incubation water
Fish in incubation water
Study fish before visual confirmation of infection via necropsy