Short Citation:
Office for Coastal Management, 2021: Developing DNA Methods to Monitor Invasive Species and Biodiversity in Estuaries - NERRS/NSC(NERRS Science Collaborative),

Item Identification

Title: Developing DNA Methods to Monitor Invasive Species and Biodiversity in Estuaries - NERRS/NSC(NERRS Science Collaborative)
Status: Completed

This project tested the use of eDNA methods to identify fish communities, assess biodiversity, and detect invasive crabs in different types of estuaries and connected streams. Samples were collected at Apalachicola, Great Bay, He’eai, Hudson, South Slough and Wells Reserves in 2018 and 2019. The project deployed two methods to analyze DNA in water samples: metabarcoding that identifies a wide range of species, and digital droplet Polymerase Chain Reaction (ddPCR) that identifies a single target organism. The team conducted baseline community assessments for fish at five reserve sites and conducted a survey of anadromous fish in a tributary stream at the sixth reserve. The project found that fish community and biodiversity assessments are well suited to eDNA applications, while invasive crabs are much harder to detect because they

do not shed much DNA. The project developed protocols and recommendations for the collection, filtering, and extraction of eDNA samples at estuarine sites, and provided information which will support the design of sampling programs for fish communities.


Biological monitoring programs are essential foundations for effective management of estuaries and coasts, but they can be expensive to conduct and methods such as the capture of living organisms may be traumatic for some target species. Advancements in DNA methods now make it possible to identify the organisms in an area by the DNA they leave behind, but there are relatively few proven sampling protocols and example datasets from estuaries. This project established a Collaborative Learning Community of Practice around Environmental DNA (eDNA) sampling within the National Estuarine Research Reserve system and explored the potential for eDNA to support estuarine management. Scientists and staff from six reserves worked Dataset Description: eDNA data from 6 NERRs NERRS Science Collaborative collaboratively with researchers, resource agencies, and a technical advisory team to design and

implement eDNA-based monitoring protocols for specific issues and species of interest in estuarine ecosystems.

Supplemental Information:

Project Lead

Alison Watts

University of New Hampshire

(603) 862-0585

Project Type

Collaborative Research – generating science that informs decisions

==Project Partners

• Great Bay National Estuarine Research Reserve, New Hampshire

• New Hampshire Fish and Game Department

• Oregon Department of Fish and Wildlife

• South Slough National Estuarine Research Reserve, Oregon

• Wells National Estuarine Research Reserve, Maine

==About the data

The project team has made available three types data related to eDNA sequences and extractions from Wells, Great Bay, Hudson, Apalachicola, South Slough, and He’eia National Estuarine Research Reserves.

12S sequence data and summary of fish species

18S sequence data

Archived DNA extractions from water samples from 6 reserves


Theme Keywords

Thesaurus Keyword
Global Change Master Directory (GCMD) Science Keywords Earth Science > Biosphere > Ecosystems > Marine Ecosystems > Estuary
None 12S sequence data
None 18S sequence data
None climate change
None eDNA
None environmental DNA
None invasive species
None monitoring

Spatial Keywords

Thesaurus Keyword
Global Change Master Directory (GCMD) Location Keywords Continent > North America > United States Of America > Maine
Global Change Master Directory (GCMD) Location Keywords Continent > North America > United States Of America > New Hampshire
Global Change Master Directory (GCMD) Location Keywords Continent > North America > United States Of America > Oregon
None Great Bay NERR, NH
None South Slough NERR, OR
None Wells NERR, ME

Data Set Information

Data Set Scope Code: Data Set
Maintenance Frequency: None Planned
Distribution Liability:

The distributor does not assume liability.

Support Roles

Metadata Contact

CC ID: 795383
Date Effective From: 2017-10-31
Date Effective To:
Contact (Person): Cothran, Jeremy
Email Address:
View Historical Support Roles


Currentness Reference: Ground Condition

Extent Group 1

Extent Group 1 / Geographic Area 1

CC ID: 899095
W° Bound: -70.6
E° Bound: -70.535
N° Bound: 43.35
S° Bound: 43.26

Wells, ME NERR

Extent Group 1 / Geographic Area 2

CC ID: 899094
W° Bound: -70.97
E° Bound: -70.82
N° Bound: 43.18
S° Bound: 42.975

Great Bay, NH NERR

Extent Group 1 / Geographic Area 3

CC ID: 899096
W° Bound: -124.344
E° Bound: -124.265
N° Bound: 43.315
S° Bound: 43.263

South Slough, OR NERR

Extent Group 1 / Time Frame 1

CC ID: 795380
Time Frame Type: Range
Start: 2017-11-01
End: 2019-10-01

Access Information

Security Class: Unclassified
Data Access Constraints:


Data Use Constraints:

Cite this dataset when used as a source: NOAA retains the right to analyze, synthesize and publish summaries of the NERRS/NSC data. The NERRS/NSC retains the right to be fully credited for having collected and process the data. Following academic courtesy standards, the NERR site where the data were collected should be contacted and fully acknowledged in any subsequent publications in which any part of the data are used. The data enclosed within this package/transmission are only as accurate as the quality assurance and quality control procedures that are described in the associated metadata reporting statement allow. The user bears all responsibility for its subsequent use/misuse in any further analyses or comparisons. The Federal government does not assume liability to the Recipient or third persons, nor will the Federal government reimburse or indemnify the Recipient for its liability due to any losses resulting in any way from the use of this data. Requested citation format: NOAA National Estuarine Research Reserve System (NERRS) Science Collaborative(NSC).



CC ID: 795386
URL Type:
Online Resource

This site provides a project overview and links to all associated products, including data.


CC ID: 992462
URL Type:
Online Resource

All genetic sequences generated by this project have been archived and made publicly available at the National Center for Biotechnology Information.


CC ID: 992463
URL Type:
Online Resource

Processed datasets, data visualization tools, and related resources are available at the project webpage.

Catalog Details

Catalog Item ID: 54574
Metadata Record Created By: Jeremy Cothran
Metadata Record Created: 2018-11-01 11:20+0000
Metadata Record Last Modified By: Jeremy Cothran
Metadata Record Last Modified: 2020-11-11 18:20+0000
Metadata Record Published: 2020-03-11
Owner Org: OCM
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Next Review Date: 2021-03-12