Establishing and implementing eDNA as a molecular technique to assess the presence of Asian carp in large Minnesota rivers

Project manager: Peter Sorensen

Funded by: Environment and Natural Resources Trust Fund as recommended by the Legislative-Citizen Commission on Minnesota Resources

Phase I Description: Initial plans for this activity included working collaboratively with the USGS, DNR, and National Park Service  to validate findings of earlier sampling of Minnesota waters for the presence of eDNA from both Asian carp and common carp. The results of this work (which showed, among other things, that the earlier findings could not be validated) led us to suggest that the particular variant to the eDNA technique used at the time of our sampling not be adopted by DNR as a routine tool to guide Asian carp management.

The work under this activity then changed to include sampling of waters for archival and research purposes and advising DNR on developing a science-based Asian carp monitoring plan for the state. More recently, the USFWS has spearheaded coordination of the development of a statewide plan. Once the plan is finalized, this activity will likely change to include archival of samples, reanalysis if appropriate, providing scientific guidance as part of larger coordinated USFWS plan, and conducting experiments to facilitate data interpretation. For Minnesota, we are primarily concerned with failure to date to detect Bighead carp when a small population is present (i.e. false negatives). This project has been extended and amended and now includes an experiment with the St. Anthony Falls laboratory.

Project start date: 2012

Project end date: 2016

Findings:

Our last key experiment was to determine instantaneous eDNA release rates in slowly flowing water designed to mimic a river. We successfully estimated instantaneous eDNA release by bigheaded carp held into flowing water. These are the first such measurements described and are thus extremely useful to managers who previously could not ascribe significance to eDNA copy numbers in flowing river waters. Briefly, six bighead carp were put into custom-built flow-through lab tanks with a slow laminar flow rate (13 L/min), so the water turnover time was less than 20 minutes. Water temperature was then adjusted to 21°C. After fish were acclimated and feeding, the experiment started. Three 1L water samples were collected at the outlet, 30 min before feeding, and then 30 min, 3.5 hr, 6.5 hr, 9.5 hr, 12.5 hr, 15.5 hr and 25.5 hr after feeding, stored at 4°C in fridge. DNA was then extracted from the filters and extensively purified. The copy number of two molecular markers (BH-TM1 and BH-TM2) of mitochondria DNA released by bighead carp was next measured through duplex qPCR. This experiment was repeated once a week after the first run when the carp were replaced. The eDNA copy number in water samples were calculated based on the measured standard curve. The eDNA basal release rate measured by both markers was in the range of 103-104 copies/100 mL water. However, this rate increased to over 105 copies/100 mL after 30 min of feeding. It appears that feeding stimulated the eDNA releasing – an important new finding that is relevant to management.

In summary, this project demonstrated that initial 2011 measurements of eDNA in the Mississippi River were almost certainly fallacious and attributable to poor markers as new measurements conducted after that by the Sorensen lab, and later the USFWS, have been unable to confirm these measures while our studies also developed new and better techniques. The release and decay rates we have calculated for eDNA by bigheaded carp have added even greater resolution and significance to eDNA techniques and ongoing studies which can now be interpreted with much greater certainty. Our finding that eDNA release is closely correlated with feeding activity is especially germane future eDNA measurement will be much more relevant.

Updates and progress: