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When freshwater mussel surveys are needed, eDNA can show the way

November 22, 2022

By Cody Fleece and Nathaniel Marshall

Infrastructure projects often require freshwater mussel surveys. Environment DNA is an effective and safe way to conduct those surveys.

Sheepnose. Rabbitsfoot. Purple wartyback. With colorful names like those, native freshwater mussels are among North America’s most fascinating aquatic animals.

You may never see a freshwater mussel—they live partially buried on the bottom of rivers and lakes—yet they play a vital role in filtering and cleaning water. In a river distance of just two football fields, a healthy bed of freshwater mussels can filter more than half million gallons of water daily, according to the U.S. Fish and Wildlife Service. They also have complex life cycles, relying on fish hosts to carry and distribute their tiny parasitic offspring.

Mussels are sensitive to pollution and habitat disturbance, and their populations have declined across North America. Roughly 70% of North American species are of conservation concern. Federal and state laws protect mussels, and more than 90 species are federally listed as threatened or endangered. 

When freshwater mussel surveys are necessary, eDNA sampling can be an effective alternative to traditional mussel surveys using diving equipment.

Project developers—whether power, transportation, infrastructure, or something else—working in rivers and lakes may be required by regulators to take major steps to protect mussels.

Those steps can start with mussel surveys to determine if a project will disturb mussel beds. After that, regulators may require project developers to collect and move mussels out of harm’s way.

For all those reasons, projects that may disturb mussels require unique expertise and extensive planning to relocate and protect them. The first step in this rescue process depends on efficient and effective methods for finding and identifying them.

eDNA: a new way to survey mussels

Our team has wildlife experts experienced in mussel regulations, identification, and relocation. We have worked on client projects to relocate thousands of live mussels, including threatened and endangered species.

Our experts typically use snorkeling or scuba gear for underwater surveys. Recently we have used a new and effective assessment method: environmental DNA (eDNA).

Federal and state laws protect mussels, and more than 90 species are federally listed as threatened or endangered.

All aquatic animals leave behind traces of their DNA in their environment from feces, urine, mucus, and skin cells. eDNA involves collecting water samples and testing for signatures of this genetic material.

Like DNA analysis in criminal forensics, we can use eDNA to confirm the presence of animals without directly seeing or disturbing them or their habitat. eDNA is a powerful tool to determine the presence of species at low densities or species difficult to see and find.

We recently showed the effectiveness of eDNA as a survey method for mussels as part of a mussel assessment during a dam removal project on Ohio’s Walholding River.

Six Mile Dam removal

Prior to the Six Mile Dam removal on the Walholding River, the U.S. Fish and Wildlife Service hired our team to test the presence (or absence) of mussel species in the river using eDNA. We knew that the river was home to one of the most abundant and diverse mussel populations in Ohio, including some federally listed species.

Our goal was to test the effectiveness of eDNA to detect species and compare those results with rescue and relocation surveys scheduled to occur after the dam was removed and the reservoir drained.

We collected 66 eDNA water samples from 22 sites spanning about a mile of the river. The eDNA testing successfully detected 22 of the 24 mussel species present in the river. The two species that eDNA failed to detect were only collected as single individuals out of more than12,000 total mussels found. Other species known to occur in low densities (less than 5 total individuals) were detected with eDNA, an impressive feat. 

This stretch of Ohio’s Walholding River was sampled for the presence of freshwater mussels using eDNA methods. The project proved that eDNA can successfully show the presence of multiple species of mussels.

Additionally, one species, the pink heelsplitter, was detected by eDNA but not by traditional methods. 

Importantly, the eDNA found two federally protected species—rabbitsfoot and sheepnose—in the project area.

The project on the Walholding River demonstrated that eDNA can successfully detect the presence of multiple species of mussels. With only a fraction of the search effort, eDNA can find protected species and even those that elude traditional survey methods. You can learn more about this work by reviewing our recent publication in Freshwater Biology

Bridges, levees, and power projects

Where could eDNA mussel surveys prove useful for projects?

The answer: any infrastructure project where mussels may be present. The list of water dependent projects is long and includes bridges, dam repair and removals, bank stabilization projects, hydroelectric power licensing studies, water intake projects, floodway construction and levee repair, and projects involving utility lines, pipelines, and buried cable repair. Projects involving recreation areas are also on the list, including marina improvements and dock installation.

Whether it is new construction, repair, or removal, any project that impacts mussel beds is an opportunity to use eDNA testing.

State and federal natural resources agencies often need to update the classification of rivers to evaluate where mussel populations are present. They often want to know:

  • Are certain endangered species still present?
  • Have their populations increased or declined in certain river reaches?

eDNA can help answer those questions.

Whether it is a survey for an infrastructure project or updating a certain species status, eDNA is an effective means of testing for mussel presence. eDNA sampling is a quick and effective survey method to provide a mussel inventory list within a project site. This is especially useful in the initial stages of a project to support planning for follow-up physical surveys and to determine project impacts.

Freshwater mussels, like these sheepnose mussels, are protected by state and federal regulators, and many species are listed as threatened or endangered.

Meeting your deadlines and in a safe way

Project schedules are sometimes constrained by the need to complete mussel work. For example, some states have specific timeframes for when surveys may be conducted, such as May through September. Those tight time windows can put developers in a tough spot.

Stormy weather, lightning, and flooding can postpone or cancel a traditional mussel survey.

Scuba diving or snorkel are two traditional methods of surveying mussels, and they come with some challenges and risks. Compared to diving or snorkeling, eDNA mussel surveys are safer and do not always have the same time restrictions for sampling water or conducting lab analysis.

eDNA is an effective and easy tool for sampling a wide variety species. Our team has used eDNA to find endangered Jefferson salamanders in breeding pool waters and Atlantic salmon living in small creeks. The list of applications for eDNA to survey aquatic and terrestrial creatures grows every year.

Major infrastructure projects are ramping up across North America. Many of them will involve in-water disturbance of mussel beds. eDNA is an effective tool to find these often-elusive aquatic animals and to keep projects on deadline and safe.

  • Cody Fleece

    As national technical lead for freshwater ecosystems, Cody is an aquatic ecologist, restoration specialist, and consultant with a reputation for executing well-designed study plans and delivering scientifically defensible work products.

    Contact Cody
  • Nathaniel Marshall

    Focused on the development and implementation of environmental DNA (eDNA), Nathaniel has worked on freshwater mussel conservation and the early detection of invasive species.

    Contact Nathaniel
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