Searching Desert Springs for Rare Species With Environmental DNA

Wildhorse Tinaja, Saguaro National Park. NPS photo.

DNA without the animal

Biologists have long looked for ways to study wildlife that are less invasive for the animals and less work for people. Hair snares and remote cameras do this for some mammals, but it's much harder to take a scale from a fish or set up a camera underwater. Gene sequencing now makes it possible to learn which species use a place without capturing any part of an animal — not even its image.

At nine parks of the Park Service's Sonoran Desert Network, the springs-monitoring crew now adds environmental DNA (eDNA) sampling to its usual work:

Chiricahua National Monument · Coronado National Memorial · Fort Bowie National Historic Site · Gila Cliff Dwellings National Monument · Montezuma Castle National Monument · Organ Pipe Cactus National Monument · Saguaro National Park · Tonto National Monument · Tuzigoot National Monument

How a sample is taken

• A vacuum or peristaltic pump pulls 250 mL of springwater per sample through a 0.45-micron filter, using methods developed partly by intern Josh Richards.
• The filter is removed and folded with "clean room" techniques — while sitting beside the spring — using single-use filter sets, fresh gloves and sanitized forceps for every sample.
• It goes into a 2-mL vial of 100% molecular ethanol, is stored in a freezer, and is sent to a lab at Washington State University.
• The filter holds fragments of DNA from any animal that recently used the spring — fish, mammals, birds, reptiles, insects, anything that is or was alive. The lab compares them with known assays for the genomes being sought.

The eDNA process, from sampling to sequencing. NPS figure.

What they're looking for

Every animal needs water, which makes springs and tinajas ideal places to look. So far, 231 samples have been collected. Besides the regular monitoring sites, crews are sampling Quitobaquito Pond (Organ Pipe Cactus), Tavasci Marsh (Tuzigoot) and Montezuma Well (Montezuma Castle). Sampling will be repeated in the fall to improve the odds of detection, because DNA is more diluted when there's more water in the system — in spring, for example.

At Gila Cliff Dwellings, a special set of analyses will look for species that were common in the early 1970s but not found in the 1990s inventories: the Chiricahua leopard frog, three toads common in the region, and the narrowheaded garter snake. Are they still there, but too rare for traditional field surveys to catch? eDNA may tell.

Why it matters

• Animals at last: when the network chose its vital signs, animal monitoring was highly rated, but sampling animals is harder and costlier than sampling things that don't move. Cameras and eDNA now make it possible by adapting existing protocols, without more sampling effort.
• Future-proofing: some samples will be preserved, so they can be tested for other species later.
• Better choices: the results may change which springs are monitored — a spring with an important find could become a higher priority — help managers choose springs to conserve, and add to what's known about which species are most common where.

Practicalities

The Inventories program of the Inventory & Monitoring office in Fort Collins bought most of the equipment, funded the agreement with Washington State University, at $140 a sample, and supported Tucson Audubon field staff to help collect data. The same collection equipment is widely used in COVID testing, so supply-chain problems have made it harder to get, and shipping ethanol, a hazardous material, takes specific and complicated procedures.

Other Inventory & Monitoring networks are running eDNA inventories too, but the Sonoran Desert Network's results will be among the first. All seven targets already have assays, which makes results faster and easier to get. The Chihuahuan Desert Network will repeat the work at its springs, also looking for bullfrogs, chytrid and ranavirus but otherwise targeting slightly different species; developing assays for some may require live capture.

Sources

Based on "eDNA Inventories to Reveal Species Use of Sonoran Desert Network Springs," Sonoran Desert Network, National Park Service; a work of the United States government in the public domain. A photograph of a frog by a non-federal photographer is not reproduced, and a river the source names at Gila Cliff Dwellings is left out, as it appears to be an error.