Research enables DoD to build speed, accuracy for conducting species management activities critical to preserving military test and training lands and sustaining operations

The Department of Defense (DoD) has 27 million acres of land to manage. Harmful invasive species and federally protected species impact installations and operations on that land. Better understanding populations of invasive and rare species and how to manage them is key to operations. To help with this, the Strategic Environmental Research and Development Program (SERDP) and the Environmental Security Technology Certification Program (ESTCP) have invested in the development of a new technological partner—Environmental DNA (eDNA) sampling.

The Services use land for a variety of operationally focused uses, including testing, training, and field exercises. Maintaining that land comes with many challenges. Knowing which species’ inhabit the land, how legally to interact with them, and how to mitigate damage caused by the most invasive species’ is unavoidable and, if left unchecked, potentially inhibiting to military operations in affected areas.

“Many different subcomponents enable the DoD mission, and land management is one of them,” Kimberly Spangler, Executive Director for SERDP and ESTCP said. “In order for DoD to maintain momentum and avoid timely delays and excessive cost to mitigate or preventable concerns relating to land management, it requires specialized tools. eDNA is one such tool we provide to help ensure smooth, uninterrupted operations across a wide swath of varying regions.”

How it Works

 
Photo by Thomas Franklin
Dr Dan Isaak samples eDNA from a stream.

eDNA sampling is an emerging process that greatly accelerates the time required to identify various species populating a given area, especially in water, where invasive species can be especially harmful.

“Rare species sampling is relevant to DoD missions both for detection of new invasive species and for monitoring rare species of concern,” Taylor Wilcox, a research geneticist at the National Genomic Center for Wildlife and Fish Conservation said. “It is an ongoing challenge for managers.”

Environmental DNA sampling differs from traditional DNA sampling in that researchers collect the samples from the environment where a species has interacted with it, rather than sampling from the species directly. This creates many benefits.

“eDNA sampling is something that, with minimal training, folks who have the clearances to be in those restricted areas can do the sampling,” Wilcox said. “With eDNA sampling, we’re not actually sampling the species directly, so there’s no ‘take,’ so no harm to the actual species, and no permitting, so far less waiting.”

Researchers take DNA samples back to the lab, where they run any of a variety of analyses to determine which species are present. The process is similar to those used to detect COVID-19. In addition to the PCR tests that require lab analysis, researchers are developing rapid tests that personnel in the field can use and read on location. While these are less accurate, they provide a much quicker turnaround and require minimal training in order to use correctly.

“There are a number of ways the samples can be processed,” Kevin Hiers, SERDP and ESTCP Program Manager for Resource Conservation and Resilience, said. “In the stewardship sense, we can take more time and use tools like PCR to amplify and look for species of concern. In environmental security sense, we need rapid tests, and those tests need to be pretargeted for the invasive species. That requires the data infrastructure in which we are investing.”

That investment includes an ESTCP-funded effort Wilcox is leading to develop a 46-species biochip. This biochip enables a lab to conduct a PCR test on a single sample to screen for as many as 46 different priority invasive species at the same time.

Wilcox said that within the field of eDNA sampling, there is both exciting potential and some important remaining knowledge gaps.

“We should be able to make an inference about organism abundance because there is a known relationship between how much DNA is in the environment and how many animals are in the environment, but there are other important factors influencing DNA concentration too” he said. “That is an active area of research. Similarly, there is exciting, emerging eDNA-like tools targeting other biomolecules, like environmental RNA, which may provide more fine-scale resolution on species distributions

George Roderick, SERDP-funded principal investigator from the University of California, Berkley, provided a few more use cases for DNA sampling and eDNA applications.

There are challenges, he added, because DNA sticks around for a while, but there are many potential opportunities. Researchers are even able to pull DNA directly from the air.

“In terrestrial systems, researchers use it to wash tree bark to see which insects have crawled up,” he said. “Spider webs are another one, and we can also see gut contents so we can see what things are eating. SERDP and ESTCP funded a project on pollination in Hawaii, and we worked with that team too. They swabbed a lot of flowers to see what’s pollinating them on military installations.”

In 2021, SERDP funded Roderick’s project to “develop a biosecurity monitoring system that uses standardized field sampling and next generation DNA ‘barcoding’ of size-sorted bulk samples to speed monitoring and identification.” His work at that time also proved very valuable to all future DNA sampling work, including eDNA sampling, because it populated the DNA databases against which researchers compare samples to identify species.

“There are circumstance where you don’t know what you’re looking for and that‘s the case with a lot of terrestrial arthropods (insects, spiders and relatives) out there. Many are undescribed,” Roderick said. “We don’t always know what invasive species we should be looking for.”

Historically, a researcher would need to sort through samples manually to identify them and if one was not identified, the researcher would need to find an expert to send the sample to, which was time-consuming. Through his work, what Roderick calls DNA metabarcoding, this is all greatly streamlined.

“Now, we can get the DNA from the sample and sample it non-destructively, which preserves the specimens,” he said. “We sequence all of them and hopefully match them to a database. DNA tools have been an amazing shortcut for sampling all kinds of communities, but especially arthropods, where we don’t have the taxonomic expertise.”

Invasive Species in the Indo-Pacific

DoD has an Invasive Species Management Program, with the goals of preventing and controlling invasive species on military installations, and restoring native plants. Invasive species can directly limit military training activities and degrade realistic conditions for training and testing operations. Additionally, biosecurity measures required to control invasive species can slow or hinder strategic mobility, and controlling invasive species requires additional resources that pull from primary mission activities.

Roderick has done much of his research in the Indo-Pacific region, based primarily in Hawaii, conducting research on the various military lands across the Islands.

More than a decade ago, groups started tracking ecosystems across the planet to establish baseline DNA data and assembled it into a database. This, and others similar to it, are what researchers compare DNA samples against in order to identify species.

“The problem we have,” Roderick said, “is, unlike the aquatic systems in the continental U.S. where they pretty much know all the species and the invasive ones, we don’t. In Hawaii, the worst problem

is that a lot of the arthropod species are not in existing databases. So, if a student discovers a new insect, we add it to the database.”

Roderick estimated around 30% of the invasive species introduced in Hawaii are not yet part of these databases. He and his team are working to catalog these species and add them to the databases.

“We’ve tried to use existing, already identified specimens,” he said, “whether from museums or collections researchers already have, and add those to the databases. We’re also sequencing a lot of native species. At Schofield Barracks Army Base on Oahu, Hawaii, we found eight undescribed species on one, small valley and all those will show up in the barcoding approaches, but they aren’t in these databases yet. Military installations have a lot of properties that most people can’t access. These areas are incredible for biodiversity, but threatened by invasive species.”

DNA sampling continues to evolve while the database continue to grow. In the meantime, Roderick said, while these DNA databases continue to develop, unidentified samples can still prove valuable to the DoD.

“If we have a piece of DNA, we can usually tell if it’s invasive or not,” Roderick said. “The native things look really different genetically from invasive species. So, we can still make progress on monitoring invasive species while we’re waiting to get all of these into the database. We can at least tell the managers whether or not we have detected an invasive species, whether we know the species’ name or not.”

SERDP and ESTCP and DNA Sampling

“Around 2010 is the first time we received an eDNA proposal,” Hiers said. “At that time, we questioned the feasibility of eDNA. We considered it high risk, yet high reward. I think John Hall was the first to recognize at our program level, how important being able to identify species without confirming an animal would be [Dr. John Hall previously managed the Resource Conservation program area under SERDP and ESTCP]. Since that time, there has been a significant advancement in biotech. eDNA has become, at least in the research world, one of the real standards for sampling—everything from ancient bio found in sediment to really hard to sample endangered species, or exceptionally disruptive invasive species, and SERDP has been one of the leading funding agencies.”

Hiers said SERDP has funded projects ranging from marine mammals and muscles to pollinators. He added working with researchers, such as Wilcox and Roderick, has provided standards and a new suite of tools to help scale up the effort.

“Within SERDP and ESTCP, we’re not approaching this independently of our natural resource managers,” Hiers said. “Our implementation colleagues, installation managers, and partners program are all helping to advance and take these tools the last mile to deployment. We are working very closely with installations and colleagues within the Office of the Secretary of Defense

to get these right and move as quickly as possible, so when we’re ready to scale, we don’t have any implementation barriers, and we have managers that are already understanding and testing the tools. We aren’t doing research in a vacuum, but it’s been fostered across DoD installations.”

Roderick took it a step further, pointing specifically to the annual SERDP and ESTCP-hosted DoD Energy and Environment Innovation Symposium, held in Washington D.C.

“We’ve developed a great group of collaborators,” Roderick said. “We have a great symposium that links the terrestrial and aquatic systems researchers. Our cohort is able to leverage real-time developments. We have some great collaborations now across these proposals, and they’re all funded by SERDP and ESTCP.”