Development and testing of an environmental DNA (eDNA) assay for endangered Atlantic sturgeon to assess its potential as a monitoring and management tool

• Published in: Environmental DNA (Hoboken, N.J.) N.J.), 2021-07, Vol.3 (4), p.800-814
• Main Authors: Plough, Louis V., Bunch, Aaron J., Lee, Benjamin B., Fitzgerald, Catherine L., Stence, Chuck P., Richardson, Brian
• Format: Article
• Language: English
• Subjects: Abundance; Acipenser oxyrinchus oxyrinchus; Assaying; conservation; Cytochrome; Cytochrome b; Cytochromes; decay; Deep water; Deoxyribonucleic acid; Design; DNA; Environmental testing; Fish; Fishing; Habitat utilization; Monitoring; Ponds; Population; Relative abundance; River systems; Rivers; Sampling; Shedding; Spawning; Sturgeon; telemetry; tidal river; Water analysis; Water sampling
• ISSN: 2637-4943; 2637-4943
• DOI: 10.1002/edn3.186

Significant declines in Atlantic sturgeon (Acipenser oxyrhynchus oxyrhynchus) abundances along the US east coast have spurred major research efforts and management actions over the last 50 years, yet information on spawning stock abundances and habitat use is still lacking for many river systems, including in the Chesapeake Bay, USA. Here, we developed and tested a new quantitative PCR (qPCR) assay to detect Atlantic sturgeon environmental DNA (eDNA) in water samples with the goal of providing an alternative method to monitor presence and relative abundance. We also examined Atlantic sturgeon eDNA shedding rates in laboratory experiments. A qPCR‐probe assay targeting Cytochrome B was developed and showed no amplification of other related and co‐occurring fishes. Pond trials at a density of ~0.2 g/L sturgeon produced relatively strong eDNA detections (~1,000–25,000 copies/L) in all seven water samples assayed. Water samples taken from two river systems in the Chesapeake Bay produced zero eDNA detections in the summer, while fall sampling during sturgeon spawning produced positive eDNA detections in 26% of samples, though at much lower concentrations (400–1,800 copies/L) compared with the pond (mesocosm) detections. Acoustic detections of sturgeon near river sampling sites were positively associated with eDNA detections. However, the eDNA assay failed to detect the presence of sturgeon in some samples when abundances were very low or when fish were in deep water. Finally, Atlantic sturgeon eDNA shedding rates were estimated to be on the order of estimates for other fish species, which suggests that relatively weak detections in the field are not necessarily driven by low rates of eDNA shedding. Overall, eDNA analysis represents a promising new monitoring tool for Atlantic sturgeon. Applying these methods in other rivers along the US east coast is an important next step in documenting Atlantic sturgeon distribution for management and conservation purposes. A novel qPCR‐based eDNA assay for Atlantic sturgeon was tested in two tidal rivers of the Chesapeake Bay USA, which detected sturgeon in 1/4 of water samples and eDNA detections were positively associated with proximal acoustic detections. In mesocosms, Atlantic sturgeon eDNA shedding rates were estimated to be on the order of estimates for other fish species, which suggests that weak detections in the field are not necessarily driven by a low rate of eDNA production by sturgeon. eDNA analysis of Atlantic s