Life’s basic building blocks used in search for threatened species

U.S. Army Corps of Engineers
Published Oct. 14, 2022
Updated: Oct. 14, 2022
A woman in a hat and water wading gear stands in a lake collecting water samples. The water is full of green leaves and surrounded by vegetation.

Dr. Jinelle Sperry, a wildlife biologist with the U.S. Army Engineer Research and Development Center’s Construction Engineering and Research Laboratory, collects a water sample at Camp Ripley in Minnesota. Sperry’s team uses water samples, as well as those samples taken of soil and air, around military training lands and those around USACE civil works projects, to search for any threatened or endangered species. (U.S. Army Engineer Research and Development Center photo)

The Department of Defense maintains 30 million acres of critical military installations and training land. The U.S. Army Corps of Engineers oversees 12 million acres of public lands and water and oversees much of our nation’s vital infrastructure components.

And while the missions overseeing this acreage and facilities differ, the need to serve as responsible conservators and ensure those assets continue to serve our nation’s needs remains the same. And both face the need to be keenly aware of how training and civil works projects may impact threatened or endangered species that may call those areas home.

In fact, according to the U.S. Army Environmental Requirements and Technology Assessments, threatened and endangered species are the number one environmental impact to military training operations.

For this reason, military installation managers need to better understand what species live in training areas and which species travel through them.

Dr. Jinelle Sperry, a wildlife biologist with the U.S. Army Engineer Research and Development Center (ERDC), is among the leaders in researching, locating and accessing threatened and endangered species, and has deployed new technology that is making the search for these species easier and faster.

“Monitoring and surveying for endangered species can be a real challenge for installation managers. We are trying to find ways to do this cheaper, faster, better,” Sperry said. “One way is this emerging technology that uses molecular tools to survey for endangered or invasive species. Instead of sampling for animals directly by trapping them or looking for them with binoculars, we can instead sample for the DNA they slough off in the environment.”

Using environmental DNA – or eDNA – scientists can sample sections of training grounds to determine what species live in the area. This molecular sampling does not do away with the need to trap or otherwise physically capture a particular species but is a starting point for better assessments.

“We have found that eDNA can be between two to 70 times more cost efficient than traditional sampling,” she said. “You can collect from water. You can collect from soil. You can even collect from the air. Yes, you can know what species are present just by collecting air and looking for DNA.”

Even though military planners are good at adapting training regimens to account for threatened and endangered species, being able to identify those species and locations faster allows for better decision making and protection of those species.

“The presence of endangered species can influence training. It can be expensive to manage the species, but more importantly, whole areas of an installation can be off limits to training due to the presence of these species,” Sperry said. “It can be large swaths of land that are off limits, or it can be where an endangered species will just pass through an area, such as a landing strip that has to be shut down due to the presence of an endangered species.”

The development and use of eDNA has grown rapidly in recent years after first appearing nearly two decades ago.

“The Department of Defense (DOD) actually has been at the forefront of all the eDNA work,” Sperry said, adding the DOD’s research arms, the Strategic Environmental Research and Development Program and the Environmental Security Technology Certification Program, invested heavily in the technology’s development. “The DOD has been really proactive, adopting the use of eDNA across a lot of its installations.”

The use of eDNA within the USACE civil works program has started to grow, even beyond its use in managing DOD lands.

The technology has been used in the Chicago District to track and monitor the spread of invasive carp, which threatens the vast and valuable fishing industry within the Great Lakes area. 

In addition to results from the use of eDNA that allowed for faster and more detailed sampling efforts, it has allowed teams to sample far more land.

Fish slough their DNA into the environment from mucus, feces and urine. DNA degrades in the environment, but this process is not instantaneous, and DNA can be held in suspension and transported, where it may be discovered within collected water samples.

“The DOD and USACE are managing huge areas, millions of acres, and it is really difficult to effectively sample across those large swaths of land using traditional tools,” Sperry said. “We use eDNA as a first pass. We can go out and collect sites – 30, 60 sites – in a couple of days with eDNA and look at where these species may occur.

“So, you use it as a first pass to see where the species are, and then you can really dive into more extensive surveying.”

And to process billions of DNA sequences, Sperry said her team leverages global databases and DNA repositories and a partnership with the University of Illinois’ high-performance computing capability.

Even though eDNA has proved to be a valuable tool, there are still some limitations to the information it can provide, Sperry said, leaving more traditional sampling efforts with questions to answer.

“With eDNA, you’re not going to know how many of those animals are there, you’re not going to know how they’re doing, you’re not going to know if they have diseases. There are questions you cannot answer with eDNA, but I would say we are moving closer to being able to answer a lot more of those questions,” she said.

Ongoing monitoring on several installations using eDNA metabarcoding is also offering a better understanding of change within animal communities.

“You can collect water and know all the species present in that water. So, you’re not just looking for one particular species. You can actually use eDNA to look for all of the species that are present,” Sperry said. “It’s extremely difficult using traditional methods to be able to quantify entire communities, but I can collect water and tell you about an entire community in a couple of weeks.”

Sperry said the use of eDNA can also play a vital role in USACE’s research and development efforts to mitigate the impacts of a changing and warming climate.

“I really feel this technology can help give us a better understanding of how those species, those communities, are functioning and then understand and predict how those communities may change or be vulnerable to potential impacts,” she said.

DNA is often called the building blocks of life. For Sperry’s team, and USACE overall, the use of eDNA is quickly becoming the building block for future advancements and discoveries.