The riverscape on a chip: An efficient method to assess western North American fish distribution

Natural resource managers need to know where wildlife species of concern occur, but determining this for riverine fishes can be tricky. It is difficult to see fish underwater, so historically managers have had to either catch the fish through electrofishing or trapping or go in after them with snorkel gear. Increasingly, natural resource managers are complementing these historical sampling methods with environmental DNA (eDNA) sampling - the inference of species presence from genetic traces in the water. This allows anyone, including citizen scientists, to rapidly gather species information from sampling of the water alone. 

Photo Credit

Alex Weinmann

Two salmon swim upstream

Environmental DNA sampling is a powerful tool, but most laboratory analysis options have trade-offs. Targeted approaches, such as single-taxon quantitative PCR (single-taxon qPCR), can detect rare species from a tiny amount of DNA, but they only tell you about one species at a time. Non-targeted approaches, such as metabarcoding, can detect dozens or even hundreds of species with a single analysis, but they are also more likely to miss rare species. To allow managers to cost-effectively gather information on a suite of ecologically and culturally important species, scientists at the National Genomics Center for Wildlife and Fish Conservation took a third way: high throughput qPCR (HT-qPCR). This method uses a “biochip” printed with an array of species-specific test reagents and dozens of samples to provide nearly 1,000 species occurrence inferences in a single analysis. 

Scientists conducted extensive validation of this new biochip by benchmarking against single-taxon qPCR to ensure that it is ready for use. Based on both laboratory tests of analytical sensitivity limits and nearly 700 side-by-side comparisons with single-taxon qPCR on environmental samples, the team found that data from the biochip is just as reliable as single-taxon qPCR but is less than 40 percent of the cost. This was further demonstrated by collaborating with Trout Unlimited volunteers to use the chip to inventory fish distributions (brook trout, bull trout, rainbow trout, coastal cutthroat trout, sockeye salmon, Chinook salmon, coho salmon, chum salmon, pink salmon, and Pacific lamprey) across the Nooksack River – a basin covering over 700 square miles. The combination of the sampling approach and the new biochip demonstrate the feasibility of conducting standardized, cost-effective, whole-basin assessments of fish presence and give natural resource managers the up-to-date information on species distributions that they need. No trapping or wetsuits required. 

Our Nation’s forests and grasslands provide some of the most important habitats for a wide range of wildlife and aquatic species. These animals provide extraordinary benefits — ecological, recreational, economic, and cultural — to nature and humans. Existing and emerging threats, such as habitat loss and fragmentation, changing weather patterns, and invasive species, affect our ability to support wildlife and fish populations, making our goal to maintain healthy forests even more important.