Introduction

In the heart of northwestern Washington state, the Nooksack River basin is home to the elusive Dolly Varden, a fish species whose population is closely monitored by environmental conservationists. Despite wielding flyrods, volunteers from Trout Unlimited are relying on a groundbreaking tool: an environmental DNA (eDNA) sampling kit. This innovative technology allows the volunteers to uncover genetic traces left in the water, enabling them to determine the presence of various fish species.

The Process of eDNA Sampling

The process begins with these dedicated volunteers collecting water samples from the stream, which they filter to capture microscopic DNA. Once the filtering is complete, they send the filter paper to a specialized laboratory, where they receive straightforward yes/no results indicating the presence of specific species.

Collaboration and Expansion

For over ten years, a collaboration between the National Genomics Center for Wildlife and Fish Conservation and Trout Unlimited has facilitated extensive basin-wide eDNA surveys. However, recent developments have injected a new level of excitement among the volunteers.

The New Biochip Technology

They are now equipped with a cutting-edge biochip that expands their research capabilities. Not only will the samples provide insights about Dolly Varden, but they will also simultaneously test for an additional ten fish species that hold ecological and cultural significance in the Pacific Northwest. These include bull trout, rainbow trout (steelhead), coastal cutthroat trout, brook trout, sockeye salmon, Chinook salmon, coho salmon, chum salmon, pink salmon, and Pacific lamprey.

Addressing Analysis Needs

Developed by the National Genomics Center, this biochip addresses a crucial need: a cost-effective and accurate method for analyzing water samples for multiple fish species at once. Traditionally, the "gold standard" for eDNA analysis has been quantitative PCR (qPCR), which is effective but can be prohibitively expensive when testing multiple species from a single water sample. Though some methods like metabarcoding exist for multi-species analysis, these typically sacrifice accuracy.

Performance of the Biochip

The newly developed biochip utilizes high-throughput quantitative PCR (HT-qPCR), delivering results closely aligned with standard qPCR methodologies. Remarkably, based on extensive side-by-side testing—a staggering 700 analyses—the biochip demonstrated a concordance rate exceeding 90% compared to traditional single-species qPCR. This level of accuracy is comparable to the variability seen in running multiple qPCR tests.

Efficiency and Cost-Effectiveness

With this advanced technology, each analysis is more efficient, requiring less sample volume, fewer chemical reagents, and substantially reduced processing time. As a result, the costs diminish to less than 40% of what conventional methods would incur for the same data outcomes.

Conclusion

The advent of this kind of biochip represents not only a significant advancement in fish detection but also a more sustainable approach to preserving aquatic biodiversity. As conservation efforts ramp up, tools like this could play a vital role in the ongoing fight against the decline of critical fish populations in our waterways.