Many marine fish and crab species spend their critical early development stages of life in shallow, coastal waters. Scientists at the Alaska Fisheries Science Center’s Auke Bay Laboratories conducted a pilot study using environmental DNA (eDNA) techniques in 2020. They identified more than 40 species in nine sites around Juneau, Alaska.
Every marine organism sheds small amounts of tissue and waste into the water. This material potentially contains eDNA from the source organism. Genetic analysis of the eDNA can help us to identify species and detect the diversity of species. It can also possibly determine the abundance of each species that have been present in the water sample even days after the organism has left the area. Environmental DNA can complement traditional surveys that are able to identify the age or size of a species.
The major objective of this study was to demonstrate that eDNA metabarcoding represents a feasible and cost-effective alternative to traditional sampling for collecting species diversity data and identifying Essential Fish Habitat (EFH). While eDNA has been used to assess biodiversity in many environments, it is important to verify the technique and compare it to data collected from traditional surveys to ensure that results are robust. This is especially important in dynamic environments such as those found in Alaska, where variables such as large tidal swings and severe weather can influence eDNA transport and detection.
“There are so many ways eDNA research can help us do our jobs better,” said Wes Larson, program manager, Genetics Laboratory. “We are able to detect a fish after it has left an area. It is also a less invasive means for sampling habitats that enables us to detect cryptic fish. Cryptic fish are fish that may not typically be sampled in traditional survey gear or may be a rare or low-density organism that surveys miss. Additionally, eDNA can help us detect important pelagic fish like cod and pollock that may be offshore and could avoid smaller nets. ”
2020 Survey Plan
Scientists chose their sampling locations based on the historical species presence as determined from the Nearshore Fish Atlas of Alaska. Sites included different habitat types based on the fish atlas classification (i.e., kelp, sand-gravel, eelgrass, and bedrock). The researchers collected water samples from shore by wading a few feet into the water. At each location, nine 1-liter samples were taken, and the water was vacuum-filtered through nitrocellulose membranes and preserved in alcohol.
Extracting eDNA from Collected Water Samples
To assess species diversity, scientists used an approach called eDNA metabarcoding. This is a cutting-edge method that allows for identification of numerous species from a single water sample.
In the laboratory, DNA was first extracted from the filters. Second, it was amplified with fish-specific primers to help identify specific fish genetic material in a given sample. Next, it was sequenced using an instrument called an Illumina MiSeq platform. Sequencing DNA means determining the order of the four chemical building blocks—called "bases"—that make up the DNA molecule. For example, in the human genome there are about 3 billion base pairs that spell out the instructions for making and maintaining a human being. This information is used to determine the species present in the water sample. Sequence data were then analyzed to create a species presence/absence matrix for each site.
Pat Barry, a postdoctoral fellow working with NOAA and the University of Alaska‐Fairbanks, developed a software program to help with this analysis (an R package). The package pulls taxonomic information from databases and facilitates the process of combining similar species into species groups to facilitate analysis. This is an extremely onerous step in the eDNA workflow and the package will help to streamline the process while also providing more reproducible results.
Scientists then analyzed these results to investigate variation in species composition across habitats and tidal stages.
Importance of Research for Identifying Essential Fish Habitat and More
Resource managers at NOAA Fisheries Alaska Regional Office and the North Pacific Fishery Management Council along with the U.S. Army Corps of Engineers are interested in this project. They see potential for helping identify important coastal habitats for fish and crabs. This information will inform sustainable coastal development and resource management decisions.
"We are excited about the possibility of using eDNA as a cost effective way to learn which fish and crab species are present in specific locations throughout Alaska," said Gretchen Harrington, NOAA Fisheries Alaska Region Habitat Conservation Division. "With this information, we can better identify, and promote the protection of, essential fish habitat and managed species."
Resource managers would be able to use eDNA to get site-specific species presence/absence data for EFH consultations with the Army Corps of Engineers and other federal agencies. Results may also be used to augment existing predictive habitat models used to map EFH by providing known presence/absence locations in rarely sampled regions.
Using eDNA metabarcoding techniques may also help with the development of predictive models for a suite of species and their habitat associations with coral, sponges, and other benthic organisms. This is important for protecting these vulnerable species and determining the least sensitive areas for human activities to occur.
“Genomic tools and eDNA studies will allow us to investigate the distribution, phenology, and abundance of managed species. We also hope to learn more about stock structure of commercially important species and investigate how these species are adapting to climate change,” said Larson.
Larson sees this work as an important complement to their long-term genetic studies. These studies include estimating stock compositions of salmon caught as bycatch in federal fisheries and understanding stock-specific impacts.