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

Citation

Plough, Louis (2021), Data from: Development and testing of an environmental DNA (eDNA) assay for endangered Atlantic sturgeon to assess its potential as a monitoring and management tool, Dryad, Dataset, https://doi.org/10.5061/dryad.q83bk3jgs

Abstract

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.

Methods

Water samples were collected from two rivers in the Chesapeake Bay (Nanticoke River, Pamunkey River), pond mesocosms, and indoor mesocosms (both with Atlantic sturgeon), and processed to detect Atlantic sturgeon eDNA using a quantitative PCR (qPCR) assay. 

Usage Notes

The ATSDecay_Feb2021_R_Final.csv dataset contains eDNA abundance data over time from two replicate mesocosms (tanks ATT1 and ATT2, with 2 replicate water samples, A and B, at each time point) from the shedding rate experiment. The  ATS_Env_Detections_Final.fasta file contains the trimmed Sanger sequences produced via the re-amplification and sequencing of all positive eDNA detections of Atlantic sturgeon in ponds and environmental (river) samples. 

Note that previous versions of these files (datasets) contained errors so only the latest versions (February 2021) are accurate. 

Funding

Maryland Department of Natural Resources, Award: KOOB7400109

Virginia Department of Wildlife Resources

Deerbrook Charitable Trust, Award: DCT‐19‐34A

NOAA Species Recovery Grants to States (Section 6 Program), Award: A19NMF4720101

Deerbrook Charitable Trust, Award: DCT‐19‐34A

NOAA Species Recovery Grants to States (Section 6 Program), Award: A19NMF4720101