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Using DNA Methods to Monitor Invasive Species and Biodiversity in Estuarine Systems

Water and sediment carry traces of DNA from fishes and invertebrates that inhabit rivers, streams, and estuaries. By analyzing water and sediments for DNA, we can discover what species are present. This method can complement or augment traditional monitoring techniques.

Project Summary

Scientists at the Wells, Great Bay, and South Slough reserves will work with the University of New Hampshire to design and implement a pilot environmental DNA (eDNA) monitoring program at several National Estuarine Research Reserve sites. The focus will be on estuarine species of concern, especially invasive invertebrates (various crabs). Partners will develop eDNA sample collection and analysis protocols, training materials, and recommendations for the appropriate use of eDNA in estuarine monitoring. Sampling will occur alongside traditional monitoring programs to allow direct comparison and verification between methods.

Download eDNA Fact Sheet (NERRS Science Collaborative)

Project Period

November 2017 to October 2019

Resource Management Questions

Will advanced eDNA methods provide reliable information on biodiversity and the presence of target invasive species within a research reserve at geographic scales that are relevant to managers?

Will incorporating eDNA methods into monitoring programs provide an early warning system for invasive species at low cost?


  1. eDNA sample collection and analysis protocols
  2. Training materials and recommendations for appropriate use of eDNA methods
  3. Collaborative Learning Community of Practice


Laura C. Crane, Jason S. Goldstein, Devin W. Thomas, Kayla S. Rexroth, Alison W. Watts. 2021. Effects of life stage on eDNA detection of the invasive European green crab (Carcinus maenas) in estuarine systems. Ecological Indicators 124:107412. Read Online | Download PDF

Crabs, and likely other benthic crustaceans, shed relatively low concentrations of DNA during most life stages. This highlights the importance of considering life stage and sampling methodology when applying eDNA techniques.

Principal Investigators

Project Lead: Alison Watts, Ph.D., Assistant Research Professor University of New Hampshire
Project Scientist: Jason Goldstein, Ph.D., Wells Reserve
Project Scientist: Bree Yednock, Ph.D., South Slough Reserve
Technical Lead/Project Scientist (genomics): W. Kelley Thomas, University of New Hampshire
Collaborative Lead: Steve Miller, Coastal Training Coordinator, Great Bay Reserve
Project Scientist and NERRS Advisor: Paul E. Stacey, Great Bay Reserve


  • Wells Reserve
  • University of New Hampshire
  • Great Bay Reserve
  • South Slough Reserve


NERRS Science Collaborative — $496,887 to University of New Hampshire

The National Estuarine Research Reserve System’s Science Collaborative supports collaborative research that addresses coastal management problems important to the reserves. The Science Collaborative is managed by the University of Michigan’s Water Center through a cooperative agreement with the National Oceanic and Atmospheric Administration (NOAA). Funding for the research reserves and this program comes from NOAA. Learn more at or

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