Kelp forest, Catalina Island, 2019. Photo by Zack Gold.
Pacific Red Octopus, WA, 2024. Photo by Zack Gold.
Watts, A.W., Z. Gold (PMEL), N.V. Patin, N.G. Adams (NWFSC), J.D. Baker, F. El Baidouri, E. Grey, A.E. Holmes (CI: Northern Gulf Institute, MSU/AOML), K. Jacobson (NWFSC), S. Jungbluth, T. Kajita, A. Kiledal, M.A. Lemay, E. Montes (AOML), F.E. Muller-Karger, J.T. Miller, M.B. Ogburn, K.J. Pitz, K. Silliman (CI: Northern Gulf Institute, MSU/AOML), A. Thompson (SWFSC), and L.R. Thompson (CI: Northern Gulf Institute, MSU/AOML) (2026): Guidance and best practices for species identification using eDNA metabarcoding - When do you call a cod a cod? Metabarcoding and Metagenomics, 10, e174450. https://doi.org/10.3897/mbmg.10.174450
Imagine being able to identify every fish, mammal, invertebrate, and microbe in a patch of the ocean just by sampling a single cup of water. Environmental DNA (eDNA) metabarcoding is a process that allows scientists to detect the genetic fingerprint left behind by marine organisms. While eDNA has become a valuable tool for monitoring ecosystem health, it has faced a major hurdle: how do we ensure that we accurately identify species from our eDNA sequences?
A new study co-authored by NOAA scientists at the Pacific Marine Environmental Laboratory (PMEL), Atlantic Oceanographic and Meteorological Laboratory (AOML), Northwest Fisheries Science Center (NWFSC), and Southwest Fisheries Science Center (SWFSC) provides a comprehensive set of best practices to solve this puzzle, making eDNA data ready for ocean conservation and fisheries management.
The process of assigning a taxonomic name to a DNA sequence is rather complex. Scientists treat DNA like a library system. Primers act as bookmarks, which allow researchers to flip past billions of lines of genetic code to find a specific barcode that helps identify a species. They then have to compare their results to a master catalog, an online repository of known species, to confirm the ID. Different labs use varying methods and primers in different habitats, making it hard to know what the best method is for a researcher’s question. The methods used by one lab may result in a specific species of Pacific cod, whereas a slightly different approach could lead to a genus-level cod identification, a problem the study’s authors call the "When do you call a cod a cod?" challenge.
In this new study, published in Metabarcoding and Metagenomics, the team synthesized years of research to create a best practices framework for putting names to DNA sequences. This review provides the rigor needed for accurate, reproducible results; it ensures that when the data points to a specific fish, scientists can say with certainty, "Yes, this really is that species of cod." This level of accuracy is essential for NOAA’s mission to monitor invasive species, track the health of commercial fish stocks, and understand how climate change is shifting where marine animals live.
By leading the charge on these national standards, NOAA is helping transition eDNA from an experimental tool into a routine part of how we observe the ocean. These guidelines allow data collected by different ships and agencies across the country to be combined into a trusted, accurate, and clear picture of ocean health, providing a more efficient and cost-effective way to protect our nation’s marine resources.