New Technology for Old Problems

Developing DNA Methods to Monitor Invasive Species and Biodiversity in Estuaries


Photo - South Slough Reserve at high tide.

SSNERR View_HighTide.jpg

eDNA in Estuaries

Biological monitoring programs are essential to effective management of estuaries and coasts, but they can be expensive to conduct and traumatic to the target species. Advancements in DNA methods now make it possible to identify the organisms in an area by the DNA they leave behind. Environmental DNA (eDNA) comes from feces, gametes, scales, and cells that an organism sheds, and is easily collected from water and sediment samples. The eDNA from these samples allows us to identify dozens of species without having to capture live animals or plants. We are working collaboratively with resource managers in Oregon, Maine, and New Hampshire to pilot and refine DNA-based monitoring protocols that can be applied to specific issues and species of interest in estuarine ecosystems.

eDNA was recently featured in National Geographic magazine as one of the most exciting recent developments in Marine Science.

This work is sponsored in part by the National Estuarine Research Reserve System Science Collaborative, which supports collaborative research that addresses coastal management problems important to the reserves. The Science Collaborative is funded by the National Oceanic and Atmospheric Administration and managed by the University of Michigan Water Center (NAI4NOS4190145).

Our Approach

Our pilot eDNA program is a collaboration between the University of New Hampshire and six National Estuarine Research Reserve sites nationwide. Scientists and staff from these reserves are working with University researchers and a technical advisory team to develop eDNA sample collection and analysis protocols. The project is sponsored by a grant from the NERRS Science Collaborative.

Resource managers & key stakeholders helped identify a list of estuarine species to target using eDNA methods, and the pilot eDNA sampling has been conducted in coordination with existing monitoring programs including larval fish tows, purse seining, and crab trapping, to allow direct comparison and verification between methods. Our goal is to assess the value of eDNA monitoring at research reserve sites and provide end users with key training to support informed decisions regarding the implementation and use of eDNA monitoring in estuarine systems.


About eDNA

eDNA (environmental DNA) refers to the genetic material found in an environmental sample (water or sediment). This material may come from microorganisms such as algae and bacteria or fragments of tissue from larger organisms such as feces, gametes, scales, and cellular material. eDNA analysis can identify what species are in a system through the byproducts they leave in their environment, without having to capture and identify living organisms.

The project utilizes two types of eDNA methods. Single species Polymerase Chain Reaction (PCR) (below, left) assays are a rapid, low cost method of identifying a single species in a sample, such as a particular invasive or rare species of interest. Metabarcoding (below, right) identifies multiple species, but is more complex to analyze.

Single-species PCR

Single-species PCR



Why eDNA in estuaries?

Estuaries are unique and delicate environments. As a transitional ecosystem, they host not only true estuarine species but also freshwater and marine visitors who may come to the estuary to spawn or feed. Shifting tidal zones, variable salinity, sediment disturbance, and other features of estuary systems mean that they have long required a unique approach compared to freshwater and oceanic systems. eDNA methods are no different – we must develop tools that are appropriate for the environments where they will be applied.

Through genomics we can develop improved methods to track the biodiversity of estuaries and detect the presence of invasive species who may upset the fragile balance of these ecosystems. We aim to provide tools that will aid the researchers and resource managers who study and protect these precious systems.