Charting new waters with microfluidics technology
A high-throughput lab in the fish basket of the US is shining a light on the world’s largest sockeye salmon run
Bristol Bay, AK, a place referred to as the “fish basket” of the US, is the most productive salmon ecosystem in North America. In 2023 alone, 54.5 million wild salmon migrated there. The area’s river systems support the largest sockeye salmon run in the world, which produces about 46% of the global wild sockeye harvest, and also see smaller runs of chinook, coho, chum and pink salmon.
Salmon are not just the lifeblood of the local ecosystem: They also represent a cultural keystone for the region’s indigenous peoples, who have been acting as stewards of the land for millennia. These communities have long relied on salmon for food and commerce, but the species also contributes to social and spiritual well-being.
However, pressures such as climate change, population growth and a global increased demand in food, ocean carrying capacity, fishing pressure and emerging infectious and parasitic diseases all threaten the health of salmon and other wild fish stocks. Therefore, preserving this resource is both environmentally and culturally imperative.
Using high-throughput tools to take a deeper look into salmon DNA can shed light on how factors such as water temperatures and hypoxia, marine parasites and viral pathogens affect fish health. DNA genotyping also allows researchers to pinpoint genetic markers that help track salmon migration patterns with unparalleled accuracy. Scientists can understand more about the habitats fish rely on and how those habitats affect their growth; how a fish’s genetics influence its migration timing; and how to track dwindling stocks to protect them from overharvesting.
The Port Moller Test Fishery (PMTF), part of the Bristol Bay Science and Research Institute (BBSRI), leads sample collections every year in an effort to assess the timing, composition and abundance of sockeye salmon returning to commercial fishing districts in Bristol Bay. Since 1967, the PMTF has used drift gillnets set at test fishing stations ranging from 30 to 150 nautical miles offshore from Port Moller, AK, to predict the run strength of sockeye salmon. “The Port Moller Test Fishery is a seven-day preview of what is to show up in the actual commercial fishing districts,” says Jordan Head, Executive Director at the BBSRI.
Samples are collected from fish at the end of each drift gillnet set, preserved and, until recently, were offloaded in Port Moller and shipped to the Alaska Department of Fish and Game (ADF&G) Gene Conservation Laboratory (GCL) in Anchorage for genetic analysis. The shipping process was long, complicated and unwieldy: The samples had to be flown from Port Moller to King Salmon to Anchorage, and ADF&G staff had to be on call 24/7 to be available for when the plane landed.
“Sometimes getting the samples off the boat and into Anchorage took longer than us actually running the data through our lab,” says Heather Hoyt, who works in Laboratory Archives & Sampling Logistics at the ADF&G GCL.
The team needed a faster, more flexible option: They wanted to install an instrument on the boat to create a portable on-vessel genotyping lab. Assessing variables such as cost, space needs, skills needed, sensitivity to movement, method accuracy and data compatibility with their current methods, they decided Standard BioTools™ microfluidics technology was the best option for them.
“This technology is efficient at high-throughput SNP genotyping, provides an easy workflow by using microfluidic technology, and supports both TaqMan™ and SNP Type™ assays,” the ensuing report says.
Standard BioTools high-throughput genomics delivers comprehensive, scalable sample profiling with minimal operator contribution and improved productivity. The on-vessel genetics lab is used to help the PMTF truly understand what’s happening in fisheries, determining things such as:
- How or when to divert tenders and resources to districts seeing higher numbers of fish
- If fisheries are meeting proper escapement goals (the number of fish that escape past commercial fisheries and into the spawning streams)
- The ideal number of spawners to ensure that fisheries are sustainably managed, maximizing benefit to Alaskans while preserving fish for the future
“As such, GCL personnel are extremely familiar with the process, and we place more confidence in our assessment of the suitability of this method to meet the needs of at-sea processing tissue samples.”
And it’s happening in a fraction of the time. “Now, with the onboard genetics, it takes a day or two at the most to get … information,” says Tim Sands, Nushagak/Togiak Area Management Biologist at ADF&G. This means the team can dedicate more of their time and energy to monitoring and protecting salmon populations.
The PMTF onboard genetics lab isn’t just about preserving fish. It’s a beacon of hope for maintaining the traditional ways of life for the indigenous peoples of the region and a step on an exciting journey of innovation and tradition. Supporting initiatives like DNA genotyping in fisheries not only helps optimize fishing efforts, it also means becoming part of a global movement to ensure that the world’s natural resources are sustainably and responsibly managed.