By Jonathan Veit
Photography by Ashley Jones

Researchers at Clemson are on the forefront of a national effort to understand why bats across North America are dying in tragic numbers and to divine how this massive die-off is shifting the structure of bat communities and altering fragile ecosystems.

As she stands before the gaping, dripping entrance of Stumphouse Mountain Tunnel zipping into her Tyvek coveralls, graduate research assistant Pallavi Sirajuddin says, “Word of caution: Last week there was a copperhead just off the path in chamber B of the tunnel. If it is there again today, I will point it out to you.”

It is a clear late-fall day in the mountains north of Walhalla, South Carolina, just 20 miles from Clemson. Sirajuddin and a cohort of Clemson University researchers are here to set up a complex tangle of coaxial cable, aerial antennas, super-sensitive listening devices and data loggers, along with battery packs to power it all, along the 1,600-foot tunnel.

A few weeks from now, when the weather grows colder and tricolored bats turn Stumphouse Mountain Tunnel into their winter home, Sirajuddin and an assistant will begin applying tiny radio transmitters to the backs of the small creatures.

By recording body temperature and arousal patterns, these radio transmitters will help the researchers understand how decreased physiological activity during hibernation — known as torpor — makes the tricolored bats more susceptible to white-nose syndrome, the deadly fungal disease that is wiping out populations of bats across North America. The researchers will then compare data collected from the Stumphouse bats to data they collect from a healthy tricolored bat community that is hibernating in a cave with similar temperatures in Mississippi.

A total of nine bat species, including two endangered species and one threatened species, have been confirmed with white-nose syndrome in North America. The tricolored bat is not currently on the federal threatened and endangered species list, but reviews are being done to determine whether it should be listed, primarily due to mortality from white-nose syndrome. Among other benefits they provide, bats control insect populations, which is important to forestry, agricultural and even human health.

Clemson’s location in the Southern Appalachians within short distance of hibernation spaces such as Stumphouse Mountain Tunnel gives these researchers unique opportunities to make discoveries that might one day thwart or impede the scourge of white-nose syndrome.


The Blue Ridge Railroad began tunneling into Stumphouse Mountain in 1852 in an effort to build a railroad through the mountains to Knoxville, Tennessee, but construction was disrupted by North-South hostilities and momentum for the railroad ebbed. In 1940, a Clemson A&M dairy science professor recognized the tunnel might be perfect for curing blue cheese. Clemson bought the tunnel in 1951 and used it as the ideal place to cure cheese until 1956.

On this fall day, we walk across the pea gravel floor of the public part of Stumphouse Mountain Tunnel with the exaggerated sound of our footfalls echoing off graffitied granite walls.

“We’re going all the way to the back of the tunnel,” Sirajuddin says. “Then we’ll set up the equipment as we work back toward the entrance. We can talk, but it’s best to whisper so we don’t disturb any bats we find.”

The bats we find will be few and far between on this day. It isn’t cold enough yet for them to begin hibernating in the tunnel, and white-nose has already taken a devastating toll on the Stumphouse bats. Their numbers have plummeted from 321 individuals in 2014 to just 37 in 2017.

Sirajuddin’s mentor, Susan Loeb, follows closely behind. Loeb is a renowned Southeastern bat researcher, Clemson adjunct professor and research ecologist for the U.S. Forest Service Southern Research Station. She co-leads a robust multipronged bat research group with David Jachowski, assistant professor of wildlife ecology in Clemson’s Department of Forestry and Environmental Conservation.

The light from the tunnel entrance is still reaching us when we arrive at a gate of iron bars, secured by a heavy chain and padlock. The gate is locked because of instances of falling rock in the tunnel.  Sirajuddin wears the key on a lanyard around her neck and snakes her wrists through the narrow bars to open the lock.

The numbers of Stumphouse bats have plummeted from 321 individuals in 2014 to just 37 in 2017.

She opens the gate, and we step through. We are at the midway point of the tunnel, and a 16-by-20-foot airshaft punched into the mountain above us extends upward 200 feet to the surface. The upper rim of the airshaft is ringed by mountain laurel and rhododendron. We are now standing in ankle-deep water and a snarl of decaying boughs fallen through the airshaft over the years. The water is the collected drip of rainfall through the airshaft and condensation formed on the tunnel ceiling and walls.

Sirajuddin closes and locks the gate behind us, and we turn on our headlamps and stumble our way through the fallen branches and slick rocks to a pathway bordered by railroad ties.

Sirajuddin is out front. “Copperhead to the right,” she stage-whispers.

A few more steps and the shafts of light from our headlamps find the snake on the path, its head slightly raised and looking mildly perturbed.

For this particular team of scientists, research goes beyond microscopes, shiny laboratory equipment and pristine white lab coats. Here, it takes the brute strength of pack mules, the technological skill of computer networkers and the soul of an explorer to be on the forefront of a national effort to understand why bats across North America are dying in tragic numbers and to divine how this massive die-off is shifting the structure of bat communities and altering fragile ecosystems.


The fungus, Pseudogymnoascus destrucans, causes white-nose syndrome, the disease that is destroying North America’s bats at a horrifying rate. Bats with white-nose syndrome experience sleeplessness and disorientation that disrupts their physical and mental health. Pseudogymnoascus destrucans, spread by microscopic spores carried by the bats’ fur, causes the bats to rouse more frequently from hibernation.

“This increased waking from torpor is using up their fat stores during a time of year when there are not a lot of insects for them to eat,” Sirajuddin says.

Eventually, the bats starve to death. The fungus can also produce lesions on the delicate skin of the wings, disrupting flight and causing dehydration.

White-nose syndrome is believed to have been brought to North America from Europe. The first cases were found in bats in 2006 near Albany, New York. Since then, the disease has marched rapidly across 31 states and five Canadian provinces. The disease has killed six million to eight million bats across North America.

It only affects bats that hibernate in cold caves and similar structures, such as mines and tunnels, called hibernacula. White-nose typically kills 70 to 90 percent of bats in an infected hibernaculum. Cases of 100 percent mortality have been found.

White-nose syndrome was first found in South Carolina in 2013 near Table Rock State Park and in the historic Stumphouse Mountain Tunnel in 2014. Until 2016, the disease had only affected bats in the eastern U.S., but in March of that year, a group of hikers near Seattle found a dying bat. The U.S. Geological Survey Wildlife Health Center confirmed that white-nose had spread into the western U.S.

Unfortunately for the tricolored bats and fortunately for the Clemson researchers, Pseudogymnoascus destrucans thrives best in 50-58 degrees Fahrenheit, the temperature range of many caves in South Carolina and the Southeast — and exactly that of the tunnel being explored in the fall of 2017.

So as coincidence would have it, the humidity level and temperature that was once ideal for curing Clemson Blue Cheese is also perfect for growing bat-killing fungus.

Susan Loeb makes adjustments to monitoring equipment in Stumphouse Mountain Tunnel.

Researchers setting up equipment


The value of bats to the North American agriculture industry is roughly $53 billion per year, according to the U.S. Geological Survey. The estimates include the reduced costs of pesticide applications that would otherwise be needed to suppress the insects consumed by bats. Some bat species can eat the equivalent of more than 70 percent of their body mass in insects per night. In an hour, a single little brown bat can eat up to 1,000 insects such as mosquitoes that can carry dangerous diseases, including the West Nile virus.

Bats are also pollinators. Long-nosed bats, which inhabit the dry portions of the North American tropics from El Salvador to northern Mexico, are the primary pollinators of the agave plant, from which tequila is derived. Through pollination, the bats promote the genetic diversity and vitality of wild agave. So, without bats, there might be no tequila.

In addition to the important role bats play in insect and pest control, pollination and seed dispersal, soil fertility, and nutrient distribution, they are also important prey for higher-level predators, such as owls, hawks, raccoons and snakes.

As a researcher, Loeb has been studying bat ecology since 1999. In partnership with scientists from the National Park Service, U.S. Fish and Wildlife Service, U.S. Geological Survey and Canadian Wildlife Service, she created the North American Bat Monitoring Program (NABat).
NABat’s mission is to identify priority bat species for conservation and measure the success of conservation efforts. In 2015, NABat published A Plan for the North American Bat Population that prescribes four approaches wildlife ecologists and land managers can use to gather data to assess changes in bat distributions and abundances: winter hibernaculum counts, maternity colony counts, mobile acoustic surveys along road transects and acoustic surveys at stationary points.

“The disease [white-nose syndrome] has progressed faster than I thought it would,” Loeb says. “It’s only going to get worse and continue to spread until a treatment or cure is found. But we’re continuing to work here on campus and with our partners to understand the spread of this deadly disease and to minimize its impacts.”

Currently 40 states and all 10 Canadian provinces participate in the NABat survey and data collection system.

Last year, Loeb and Jachowski performed a survey of bats at 11 sites in the Sumter and Chattahoochee national forests. They also deployed acoustic technology to record bat calls in an effort to document species variety, as they are doing in Stumphouse Mountain Tunnel. They then compared their findings to data collected at the Sumter and Chattahoochee sites in 2006, the year the deadly disease arrived in the U.S. The survey results were disheartening.

“Bats affected by white-nose syndrome have vanished from some of the survey sites,” Loeb says. “It can take years to rebuild bat colonies, if they can even rebuild at all. Bats don’t reproduce quickly. Most species only have one pup per year, and many of those die.”

As a Clemson University wildlife biology graduate student, Ben Neece led the first South Carolina statewide bat survey as part of the NABat project. The project was funded by the South Carolina Department of Natural Resources.

The goal of the study was to check the efficacy of the NABat survey for South Carolina bat populations, understand the factors affecting detection success and assess environmental factors influencing populations.

Neece used both mobile and stationary surveys to collect bat echolocation sounds from 38 survey cells across South Carolina. The survey sites were chosen for an array of factors, including habitat variety, maximum bat species diversity and low clutter that would interfere with recording.

The value of bats to the North American agriculture industry is roughly $53 billion per year, according to the U.S. Geological Survey.

It was a big job, and Neece relied on assistance from government agencies such as the South Carolina Department of Natural Resources, USDA Forest Service, Department of Energy and South Carolina Forestry Commission. The survey also received help from South Carolina Master Naturalists, who have undergone training through the Clemson University Master Naturalist Program and the Edisto Island Open Land Trust.

After using computer software and noise filtering technology to cull insect sounds and other ambient noise, Neece was able to classify the species of 42,672 bat calls from the 38 survey sites and detected some bat species far outside their known distribution area.

“Many bat calls are similar,” Neece says. “But there are subtle differences by species. Since the bat calls are at frequencies humans can’t hear, computer software helps us identify them visually. The ones that are too similar for the computer software to distinguish, I categorized myself.”

South Carolina is home to 14 bat species, including the big brown bat (Eptesicus fuscus), Mexican free-tailed bat (Tadarida brasiliensis), tricolored bat (Perimyotis subflavus), eastern red bat (Lasiurus borealis), eastern small-footed bat (Myotis leibii), evening bat (Nycticeius humeralis), hoary bat (Lasiurus cinereus), little brown bat (Myotis lucifugus), northern long-eared bat (Myotis septentrionalis), northern yellow bat (Lasiurus intermedius), Rafinesque’s big-eared bat (Corynorhinus rafinesquii), Seminole bat (Lasiurus seminolus), silver-haired bat (Lasionycteris noctivagans) and Southeastern bat (Myotis austroriparius).

South Carolina is home to 14 bat species.

The survey found that the federally listed threatened northern long-eared bat, previously found only in the Blue Ridge region of northwestern South Carolina, was detected and caught at two locations along the South Carolina coast.
While the discovery of these northern long-eared bats far from their known range cannot necessarily be connected to the ravages of white-nose syndrome, Jachowski and graduate student Katie Teets are working to understand how the ruinous disease is affecting the structure of remaining bat communities.

From 2003 to 2011, Jachowski and colleagues at Virginia Tech led a study of bats in upstate New York that was published in the journal Diversity and Distributions. The study spanned the time immediately prior to and following the first appearance of white-nose syndrome in the region. The researchers found that before the disease outbreak the species of bat known as the little brown bat was five to 53 times more active than all other bat species. Little brown bats were also consistently detected during evening hours.

Following the arrival of white-nose syndrome in 2006, little brown bats and other cave-roosting bat species have been decimated. Results from the New York study suggest that the direct die-off of little brown bats is causing behavior changes in other bat species not directly impacted by white-nose syndrome. The unaffected bat species are filling the spatial void left in the less-occupied night skies. The ecological implications of this shift are unknown.

“There’s evidence that the presence of high numbers of certain bat species can suppress other bat species through competition, but we don’t know a lot about the effect of bat species decline on the overall structure of bat communities,” Jachowski says. “Essentially, we are seeing a reshuffling of where and when remnant bat communities are using the landscape. It appears that areas formerly dominated by little brown bats are being made available to other, historically imperiled bat species.”

Jachowski believes this “reshuffling” could have major implications for how biologists and land managers try to identify areas to protect and conserve remaining vulnerable populations.


In a project funded by a grant from the U.S. Department of Interior, Katie Teets, a graduate student in Jachowski’s lab, has been using acoustic devices to monitor bat populations at sites in South Carolina and Georgia, while researchers from Virginia collected data from sites in New England and the Mid-Atlantic states.

Teets and her Virginia colleagues surveyed the same sites that were sampled during and prior to the arrival of white-nose syndrome to evaluate whether bat communities have changed since the previous survey.

“We want to understand what habitats need to be conserved and the effect white-nose syndrome is having on individual bat species populations and their habitat use, so it’s very important to understand how population numbers and community structure are being affected by white-nose syndrome and other stressors,” Teets says.

In winter 2016-2017, the Clemson researchers conducted a pilot study of tricolored bats roosting under bridges in the upper Coastal Plain of South Carolina. The preliminary data suggests the tricolored bats hibernating in roosts rather than caves and mines have skin temperature within the optimal range for growing and spreading white-nose syndrome, but that these bats might not stay in torpor long enough for the disease to progress.

Based on the preliminary findings, Loeb and Jachowski received funding from the U.S. Fish and Wildlife Service to further study the roosting bats, using similar technology to the Stumphouse study. The goal is to track the roosting bats throughout the winter to understand their alternate roosting sites and determine their torpor patterns, foraging habits and white-nose syndrome vulnerability.

The data will also be used by the U.S. Forest Service and other land management agencies and transportation departments to inform the management of areas where tricolored bats use roosts rather than hibernacula.

If the data shows that the roosting tricolored bats are less susceptible to white-nose syndrome, then the roosts may be able to serve as refuge for the species and warrant special conservation strategies.

It may even be possible to build roosts specifically designed to serve as winter sanctuaries for the species.

Pallavi Sirajuddin prepares to attach a radio transmitter to a bat.


On the December day that Sirajuddin and her assistant Kayla Goodman make their weekly trek into the darkness of Stumphouse Mountain Tunnel, the condensation from the airshaft drips down upon them. They are carrying fresh battery packs to power the scientific equipment strung out along the length of the tunnel. They will carry the old packs back to the lab to be recharged for future use.

Wearing their Tyvek coveralls and rubber boots, they negotiate the ankle-deep water and tangle of decaying debris and walk along the path to the depths of the tunnel. Sirajuddin stops and points to a bat high up the wall. It is fuzzy, the size and color of a wine cork, and faintly iridescent in the light of our headlamps. And it is by itself.

Photos in nature magazines show caves filled with bats clinging to ceilings and walls shoulder-to-shoulder, guano mounded on the floor beneath them. This is not the case in Stumphouse Mountain Tunnel where the sparseness of the bats that remain make them look alone and vulnerable.

Sirajuddin and her assistant put down their backpacks, battery packs and laptops, and set up a makeshift workstation. They put on surgical gloves, and Sirajuddin stands on her toes stretching to the bat but it is just beyond her reach.

Ideally, she wants to select specimens at equal intervals along the length of the tunnel, but the reduced numbers of Stumphouse bats makes this difficult.

She walks deeper into the tunnel and returns moments later carrying a small white cloth string bag, its contents making it pulse and writhe. Then she opens the bag to give me a glimpse of the tiny tricolored bat that is squirming and squeaking in her gentle grasp.

Pallavi Sirajuddin preparing bat to attach transmitter.

Sirajuddin sits on the tunnel floor and begins her work, Goodman kneeling at her side with a pencil and clipboard. Sirajuddin keeps the bat in the bag while she weighs it. Then with the fine motor dexterity of a surgeon, she stretches the bat’s wings to check for the lesions that can be a sign of white-nose syndrome. The skin of the bat’s wings is translucent as tissue-paper.

The first time Sirajuddin handled and radio tagged a bat was 2014 when she was working for the University of Tennessee, Knoxville. The first bat she handled was a red bat, and she was under someone else’s supervision.

“I remember feeling extremely anxious because he was so much smaller than I expected,” Sirajuddin says. “It was a long summer of handling bats and taking them out of nets, but by the end of the summer, I felt comfortable and confident.”

She is happy to find that this tricolored bat is lesion free. Next, she parts the fur near the bat’s abdomen to check its sex. It’s male.

Now it’s time to attach the radio transmitter and tag. She reaches in her bag for a small pair of scissors and trims the fur from the bat’s back down to the skin. This will allow the transmitter to collect data on the bat’s physiological patterns during torpor. She puts the fuzz she clipped from the bat into a plastic tube. It will be sent to a lab for testing that will help determine if the bat is local or has migrated from far away to this winter home.

Sirajuddin dabs surgical glue on the radio transmitter and affixes the transmitter to the bat’s back, the antenna as long and thin as a cat’s whisker. In the weeks that follow, the transmitter will send data about torpor temperature and duration to the data logger. After a time, the glue will dissolve and the transmitter will fall harmlessly away.

It is now time to secure a metal band with an identification number to the bat’s wing. The band is the size and weight of a grain of rice. The band number has already been written on the form. She stretches the bat’s wing and uses a small pair of plyers to attach the band, loosely enough that it can slide along the length of the bat’s forearm but firmly enough that it will still be there next year if this squealing, impudent little Perimyotis subflavus is able to avoid the ravages of the disease that is wiping out his brethren.

Normally Sirajuddin would finish by placing the bat against the cave wall where it would instinctively cling, but this specimen is too impatient for formalities, so she raises her arm and opens her hand.

The small bat flies into the darkness, and Sirajuddin continues on with research to ensure its future.

Jonathan Veit is communications director for Clemson PSA and the College of Agriculture, Forestry and Life Sciences.

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