National Oceanic and
Atmospheric Administration
United States Department of Commerce

Metagenomic Responses of Commercially Important Fisheries and their Food Chains across Coastal Pacific and Alaskan Waters - Enhancing the Blue Economy

Metagenomic Responses of Commercially Important Fisheries and their Food Chains across Coastal Pacific and Alaskan Waters - Enhancing the Blue Economy

The global ocean is rapidly undergoing changes in temperature, hypoxia, and acidity, whose effects are especially acute in the colder waters of Northeast Pacific coastal and Alaskan ecosystems that house some of the most important US fisheries and marine mammals. These conditions are driving ecosystem shifts for growing the "blue economy", including fishery stocks, catches, and aquaculture. Observed and expected changes are altered food availability, geographic distribution, growth rates, reproduction, disease, and mortality for commercially important fish and shellfish species. Community changes in species compositions, diversity, and numerical representation, in response to physical, chemical, and biological factors, however, are currently poorly documented and understood, and conventional sampling is limited by ship availability, personnel, time, money, and seasonal constraints. Increased understanding of these effects will help us to predict responses and enhance growth of the blue economy, thereby contributing to the NOAA OAR and OER missions to explore, conserve, and manage our ocean's natural resources.

We are developing and applying cutting edge metagenomics and bioinformatics to determine the dynamic responses of entire marine biological communities, focusing on commercial fisheries, to ongoing physical and chemical oceanographic changes in the Northeast Pacific and Alaskan waters. Metagenomics harnesses the power of targeted high-throughput sequencing (HTS) multi-locus metabarcoding assays to rapidly and simultaneously sequence billions of environmental (e)DNA and eRNA fragments in plankton samples or shed into water by living organisms (in mucus, waste products, etc.). This approach generates diagnostic sequence data to (1) identify entire communities to species or nearest possible taxon level, (2) estimate relative biomass representation, and (3) determine population and stock structure of key commercially important fish, crab, and shellfish species. Results are projected to provide greater efficiency in time and cost, and often taxonomic accuracy, than traditional surveys. Ongoing partnering research expeditions will collect plankton and water (eDNA) samples, and associated physical and chemical oceanographic data (temperature, pH, dissolved oxygen). Metagenomic results will be compared with traditional sampling for ground-truthing, and with physical and chemical data to understand responses. Findings will aid understanding and prediction of the effects of environmental change on fisheries and aquaculture, enabling management and industry to grow the blue economy.