Article

Hands Off! Assessing Aquatic Ecosystems with eDNA

October 02, 2023

Species Detection Made Easy With eDNA

Imagine a real-world tool that can detect the presence of a living being by filtering water it recently was exposed to. Sure, you might see a similar cutting-edge method on a late-night investigation show on TV, where a person in a tailored lab coat stares at a vial of liquid in a dimly lit laboratory. Interestingly, half of that primetime TV depiction is actually true — the incorrect component is a dimly lit lab (no genetic labs are ever that dark).

Researchers have developed a methodology to identify individuals of a species by filtering their shed environmental DNA, or eDNA. Essentially, as you move through the earth, you slough off bits of DNA that can be amplified and analyzed. So, the next time you go swimming in a pool, you can only imagine the slurry of eDNA floating around you. Nonetheless, the potential applications for this tool are incredible.

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So how does eDNA work? A sample of DNA can be collected in water, soil, sediment or from a surface swab. The DNA is then extracted, purified and amplified for analyses. Analyses are completed through a quantitative polymerase chain reaction, or qPCR, by which a known signature for mitochondrial DNA, or mtDNA, is sought after and identified. Analyses can be used to look for a single species or more broadly identify which communities of species are found within each sample.

Factors affecting the persistence and transport of eDNA in a waterbody, like degradation and transport, can be addressed and evaluated by study design, such as more frequent sampling on temporal or spatial scales, as needed. Different species groups may shed eDNA at different rates. Fish and macroinvertebrates shed relatively large amounts of eDNA to the water column. Submerged aquatic vegetation typically sheds eDNA in detectable amounts during senescence in late summer and fall, indicating a need for seasonal-based sampling if aquatic macrophytes are of interest. The goals of the project and species of interest dictate the study design.

There are numerous advantages to using eDNA for species presence detection. Finding rare species can be very difficult. Using methods to visually hunt and identify cryptic or otherwise well-hidden individuals that are few in number can take countless hours. More aggressive sample approaches to capture and catalog species distribution are less palatable for populations with distressed population status. Also, detecting the presence of an invasive or undesired species as well as pathogens can be critical for natural environments or even commercial applications, such as rearing ponds for planting in public lakes. In addition, eDNA may be used to assess harmful algal blooms in public waters. Using eDNA allows for a rapid sample collection effort and detection without ever handling or observing the individual. Therefore, the approach is less impactive and time-saving.

The database of mitochondrial DNA signatures for species identification is large and growing. However, if you encounter a species that has not been analyzed, a reference sample of DNA is required to develop a species profile. Archival catalogs of both common and rare species are readily available, and even aged DNA can be analyzed to develop a profile in the matter of weeks.

The method just seems too good to be true, so it must be cost prohibitive, right? Surprisingly, no. Lab analyses for species identification for small- to moderate-sized projects often cost tens of thousands of dollars after the effort for field collection. In the end, the sample collection, analyses and results can be completed in weeks for a relatively low fee, making eDNA a true paradigm shift in how we conduct fieldwork, locate species presence and map population distribution.

While the idea of eDNA may seem new or untested, the actual method has been around for over a decade and has undergone a wealth of examination. In recent years, eDNA has become an acceptable approach for scientific investigation in regulatory processes, such as a Federal Energy Regulatory Commission relicensing of a hydropower facility. HDR has implemented eDNA investigations on multiple different FERC projects with successful outcomes and results that passed regulatory scrutiny.

South Sutter Water District – Bear River, Northern California

The South Sutter Water District recently needed to complete the regulatory process to relicense its hydropower operations as part of the Camp Far West Project and receive approval for another 30 to 50 years of license of operation by FERC. During investigation to understand the aquatic resources in the Bear River, a request was made to document the status (presence or absence) of rainbow trout, Chinook salmon, green sturgeon, and white sturgeon. All of these species can be difficult to monitor, and regulatory protections are provided for steelhead and green sturgeon, limiting more aggressive sampling approaches. Sturgeon in particular are a very difficult species to identify due to their preference for deep water and ability to rapidly avoid detection.

Our field biologists mobilized to collect 50 samples in spatial intervals along the entire length of the river. Staff adapted a customized backpack-mounted peristaltic pump system to actively filter water across a specialized filter. As water was filtered, genetic material was left behind. The filter samples were handled using best practices commonly applied for water quality sampling. The filters were kept cool in an ice chest that was readily provided to a local genetic lab for testing and reporting of results.

Overall, our field team was able to conduct the river sampling in a little over one week with only two staff. The crew rigorously sampled the entire river, which would have otherwise been a much longer and more labor-intensive effort using past standard practices. The results of the study confirmed the presence of salmonids and also provided insight into the absence of sturgeon during the survey (both green and white). Regulatory representatives suggested a likelihood that sturgeon were present, but the data reflected otherwise. Data provided direct support for focusing mitigative actions by the district to only address known species in the basin and limited the requirement for extra effort that was not necessary.

California Department of Water Resources – Piru Creek, California

The California Department of Water Resources operates the South State Water Project, which includes a number of large facilities and complex interconnections for generation of power and distribution of water. Similar to the Camp Far West Project, CDWR was required to complete a FERC relicensing process to allow for future operation of its hydro facilities. During the environmental investigation into aquatic resources, it was determined that a survey was needed to document the presence and distribution of Santa Ana Sucker, arroyo chub and rainbow trout. Given the small number of sucker and chub potentially present, a non-invasive approach using eDNA was selected.

During technical study development, it was realized there was not a DNA barcode or genetic species voucher for the Santa Ana sucker or arroyo chub. By working with local resource agencies, we obtained a preserved DNA sample for each species. The sample was then processed by a genetic lab to allow for identification from eDNA samples. Uniquely, the study provided the first usage and development of genetic species identification using eDNA for both species.

Following development of species markers, our field biologists collected filtered water samples for eDNA. The area of survey interest was the Pyramid Reach of Piru Creek (tributary to the Santa Clara River), downstream of Pyramid Dam, with 60 samples and duplicates. Sites were spaced every 500 meters over 18.5 miles. Sampling was conducted twice in the spring of 2018. By employing a custom frame-mounted pump, the team was able to effectively mobilize into remote areas to conduct the sampling successfully.

Navigating Piru Creek

The results of the study documented the presence of all target species and mapped their distribution. Interestingly, the study also found that hybridization was occurring between the Santa Ana sucker and the Owens sucker. The hybridization indicated that the Santa Ana sucker population was not a distinct genetic unit and helped to revise management needs for the future of project-required activity.

Conclusion

Recent project successes during highly scrutinized regulatory processes have tested the efficacy of the technique and found the results to be sound. Further, the cost efficiency, reduced field effort and minimal permitting requirements all build upon the many benefits of the application. Our field team specializes in obtaining and interpreting eDNA studies and has partnered with prestigious labs to ensure the best overall project. We are excited about the future of using eDNA in a number of varied and diverse applications.