What lies beneath

Scientists in Slovenia are leading the charge to understand and protect a charismatic, cave-dwelling salamander – and the subterranean habitats that supply much of the region’s drinking water.

Gregor Aljančič enters a concrete tunnel and descends into a subterranean world below the city of Kranj, in northern Slovenia. Lamps illuminate his one-minute walk down the claustrophobic passageway, which fades to pitch black as he reaches the main chamber of Tular Cave Laboratory. The 50-year-old has visited the laboratory since boyhood, when he came with his father, the lab’s founder, and he knows its occupants well. The reinforced natural cave, once a World War II air raid shelter for a factory, now serves as a safe haven for blind salamanders known as olms (Proteus anguinus). Aljančič, a cave biologist, visits every other day to ensure conditions remain comfortably dark and damp for his study subjects. 

“Continuing father’s work was at first an obligation, but then it became my passion too,” he says. “Many of these animals I’ve known since before I can remember. They’re all still alive.”

Aljančič uses night-vision goggles and the dim beam of a headlamp to search pools of water for olms slung over rocks or wedged into crevices. Direct illumination disturbs the salamanders. When light strikes, their translucent skin flashes like crescent moons and they dash for darkness, swimming in exuberant wriggles beneath the limestone ledges.

Aljančič’s father, prominent cave biologist Marko Aljančič, established the lab in 1960. He built an assemblage of concrete pools, and over time filled them with olms from cave systems in southwestern Slovenia, dedicating his life to studying their cryptic behaviour. But his amphibian charges outlived him, as he came to suspect they might. Gregor Aljančič estimates that individuals could survive to be a century old, but like many other aspects of olm biology, no one knows for sure. 

While Tular Cave Laboratory mainly serves researchers, everyday Slovenians are well aware of the olm’s existence. Slovenia is the birthplace of cave biology as a formal discipline, and it was here that olms were first encountered. Today, they are an attraction at Postojna Cave Park, one of the country’s most popular tourist destinations. Visitors can ride a train through the cave, which showcases the dramatic pillars and ornate chambers of the geological karst landscape that underlies a quarter of Slovenia. The highlight is coming face to face with the country’s iconic salamander: človeška ribica (tchlo-VESH’-khah REE’-bee-tsah). The Slovenian name  translates to “human fish,” but most observers don’t fully appreciate how much they share with an animal that lives its whole life in darkness. 

Beneath Slovenia’s bustling cities and rolling countryside, the cave systems that have shaped and sheltered olms for millions of years are changing fast. As scientists probe for insights into olms’ mysterious existence, they’re finding that human health is closely intertwined with that of the salamanders. Across the olm’s home range, people have used the subterranean environment as both a source for drinking water and a dump for waste. Now, scientists are working to illuminate ways to safeguard the “human fish” from its namesake.

Although olms seem small, reaching just 20 to 30 centimetres in length by adulthood, they are the largest of the world’s cave-dwelling animals, and fierce apex predators. Two external gills flare into scarlet tufts at the back of their flat heads, and their four tiny limbs stick out from the far ends of their elongated bodies like pushpins. Though blind, olms have remarkably heightened senses of smell and hearing. They stalk remote cave depths for fish and tiny crustaceans, lurching forward at exactly the right moment, paddle-shaped snouts agape, to gobble prey whole. Marko Aljančič described these skilled hunters as “the mysterious rulers of karst darkness”.

Olms make their home beneath the Dinaric Alps, a mountain range that starts in Italy and runs southeast through Slovenia, Croatia, Bosnia and Herzegovina, Serbia, Montenegro, and Albania. Karst unites the region underground. Its intricate topography forms when water enters surface fissures and percolates down through soluble rock, like limestone or dolomite, eroding larger conduits and chasms. Over millions of years, underground water ranging in force from small drips to large rivers carves a complex latticework of caves. 

“Underground, the karst does not follow a clear map,” says Magdalena Năpăruş-Aljančič. “It’s a network of channels that can be straight or very complex.” Born in Romania, she earned a PhD in geography with a specialty in karst, a focus that led her to Slovenia where she met and married Gregor Aljančič. Today, she’s a research fellow at Slovenia’s Karst Research Institute.

At first, Năpăruş-Aljančič was interested only in the challenging, beautiful rock formations. But Aljančič opened her eyes to the challenge and beauty of karst’s creatures. She likens her first time entering Tular Cave Laboratory to “stepping into geological times, like a living Jurassic Park, since you have the opportunity to witness animals you only see in -photos”. 

A stream meanders through the cave lab. Overhead, stalactites have grown down from the concrete tiles, elongated mineral evidence of water’s pathways. To mark the birth of their first child last year, they flipped one of the tiles so that the growth would start anew. “We want to show our son that the stalactite is as old as he is,” says Aljančič.

Slovenians aren’t generally in such close touch with the underground, and as a result, their relationship with olms has long been marked by misconception. When villagers encountered olms in the late 17th century, after unseasonable rains flushed the salamanders into sun-splashed springs on the surface, they surmised that the pale, serpentine creatures were offspring from a fearsome dragon’s lair. In 1689, naturalist Janez Vajkard Valvasor described the olm based on these stories – fuelling Slovenia’s enduring fascination with its “baby dragons”. A formal, scientific description wouldn’t appear for another century.

Like all cave life, olms descended from surface-dwelling species. Olms and their closest living relatives, the mudpuppies or water dogs of North America, last shared a common ancestor around when the dinosaurs died off and the earliest birds began to emerge. When tectonic activity gave rise to new subterranean habitat, the olm’s ancestors eventually descended into karst. Dramatic climate shifts like the most recent ice age and aridification swept the region, wiping out many vertebrates across the present-day Dinaric Alps, but ancestors of the olm had already moved underground, serendipitously evading the worst of the weather. 

“Evolution took the same path every time an olm ancestor went underground – they lost contact, all relation to one another – but despite this isolation they all came out the same,” says Rok Kostanjšek, a molecular biologist and professor at the University of Ljubljana in Slovenia’s capital city. His team hopes to resolve whether the olm is actually seven, or perhaps nine, separate species, currently lumped into one due to morphological similarities and lack of definitive data. Each population is endemic, sometimes living entirely within a single well hole, and each one likely arose from an independent evolutionary event. This phenomenon, known as parallel evolution, happens when separate lineages evolve in the same way – mirroring one another in form – since they’re responding to similar environmental pressures.

The trying conditions of caves shaped an array of adaptations that seem like the stuff of science fiction. Special skin receptors help olms sense Earth’s magnetic field and changes in the electrical fields of other organisms. In the dark depths, vision serves little purpose, so by adulthood, the clear eyes that olms are born with have nearly disappeared beneath layers of skin, though they can still sense light. Olms have also mastered the art of doing nothing, weathering years without moving or eating, with negligible physiological consequences. In January 2020, scientists announced that a wild olm they had been monitoring remained stationary for seven years before stirring. 

Despite all that scientists have learned about the creatures’ life history through the years, mysteries still abound. No one knows where wild olms reliably live or how many there are, which makes it hard to advocate for protected areas. The International Union for Conservation of Nature (IUCN) classifies the olm only as Vulnerable, because there isn’t enough data to say definitively whether it is endangered. “These animals have been known for almost three centuries, yet we hardly know anything about natural populations,” Kostanjšek says. Traditional population monitoring techniques, like annual counts, don’t work when the animal being tracked lives beyond reach. If different olm populations indeed represent different species, as Kostanjšek and other scientists suspect, then each is far more endangered than presently supposed. 

That’s a problem, because most Slovenians confuse olms’ inaccessibility with immunity to human impact, says Năpăruş-Aljančič. “They think if something is underground it’s safe.” 

In the summer of 1983, karst researchers sampled an inconspicuous-looking spring. The spring surfaces below a limestone wall, and serves as the sole source for the Krupa River, which meanders only 2.5 kilometres through the lush Bela Krajina region of southeast Slovenia. They hoped to confirm that the spring could supply drinking water to nearby villages. Instead, they found it was laced with dangerous levels of cancer-causing polychlorinated biphenyls, or PCBs. It was just the latest example of fallout from one of the worst environmental disasters in the nation’s history. For two decades prior, a nearby capacitor factory had disposed of its PCB waste in karst sinkholes. Over time, these contaminants filtered down through soil until they hit impermeable rock – where ground-water collects and olms live – polluting the spring that feeds the Krupa River. Slovenia stopped using PCBs in 1985, but the Krupa River remains laced with the toxins.

Similar tales are common across southeastern Europe, where many communities use the groundwater within karst formations. In Slovenia, for example, 97% of the population relies on groundwater for -drinking. The permeability of surface soil over the karst means noxious substances like herbicides and sewage can leach down and contaminate the supply. But the complex hydrology of karst makes tracing the pathways of pollution as difficult as -tracking individual wild olms. “You can’t protect a particular surface area by saying ‘underneath this mountain ridge is an endangered population of olms’, because you cannot say where the water feeding this environment comes from,” says Kostanjšek. Water moves in different directions, without steady flow, and the farm or factory that pollutants are coming from may not be directly above olm habitat. 

Slovenia has protected olms, by prohibiting the removal of flora or fauna from caves. The country also committed to Natura 2000, a conservation network of European Union member states that works to protect rare, endangered, and endemic species and habitat types. But without knowing the distribution of olms, and how subterranean water and pollution flows across political borders, it’s difficult to prioritise what to safeguard, Kostanjšek points out. “It’s our largest problem with protecting the animal.”

Over-extraction of groundwater through such practices as intensive agricultural operations also poses problems. Land above ground may appear vibrant and green, but below, as pumps divert water to the surface and lower the water table, olms may find themselves high and dry. When fully submerged, olms breathe through their skin, absorbing oxygen directly from the water. Without it, they must rely on rudimentary lungs, circumstances under which they can last a few weeks at best, depending on the humidity in the air below ground. 

If water extraction continues to exceed replenishment over a long period of time, it can compromise the entire subterranean food chain. Because the olms are top predators, their disappearance has outsized impacts on the species with which they share the ecosystem. “They’re kind of like the T. rex of the underground,” says Năpăruş–Aljančič. “We just hope they won’t have the same fate.”

Human demands on groundwater are likely to climb, and in many regions, extraction already -surpasses the natural rate of recharge. The impacts of a changing climate on the underground environment are even more nebulous. Historic floods that used to happen only once a century are projected to occur more frequently and hit harder. Groundwater -levels can rise dramatically in extreme events, flushing olms up to surface springs where they’re susceptible to life-threatening sunburns and unfamiliar predators like birds and fish. 

Still, some injured olms displaced by flooding can survive and return home, with help. In 2008, Gregor Aljančič formalised an olm rescue program that his father started. Flyers alert nearby residents to call him if they spot an olm – dead or alive – on the surface. Aljančič retrieves the animal, treats it for visible parasites and other problems, keeps it in quarantine to monitor for pathogens such as chytrid fungus, then releases it back to a natural cave near where it surfaced. In the past 12 years, Aljančič and his team have documented about 40 stranded animals. When regional restrictions due to the coronavirus pandemic lift in Slovenia, allowing the Aljančičs to travel between municipalities again, they’ll release the -latest rescued individual back into the wild.

It may also be that olms are not as vulnerable to pollution as once feared. Back in the 1980s, when officials finally found the human residents of Bela Krajina a clean source of drinking water in the region’s other major spring, Dobličica Spring, they also discovered something new to science: a black olm, a subspecies now known as Proteus anguinus parkelj. Black olm territory is less than five square kilometres in size, meaning even the slightest spill could wipe them out. In 2011, nearly 30 years later, researchers visited a larger population near the spring and found alarmingly high concentrations of PCBs in the salamanders’ -tissues, likely magnified by their longevity and slow metabolism. Yet the olms appeared healthy and had no detectable deformities, suggesting that they may have an effective way of partially eliminating contaminants. The team called their resilience “remarkable”, though they caution that the long-term effects of PCB exposure are unknown, and plenty of other threats remain. 

“Although olms can withstand higher concentrations of chemical contaminants,” says Jennifer Lamb, an assistant professor of biology at Minnesota’s St. Cloud University who studies amphibian ecology and natural history, “the combination of that with climate change altering water use – well, then they’re no longer as resilient as we want them to be.” Given the multiple threats olms face, every new bit of information about them is vital.

Unfortunately, olms’ vulnerability and fame haven’t led to a glut of local money for research. For the Aljančičs, the olms are a full-time job funded by international grants, fuelled by passion, and supported by dedicated student volunteers. For many other Slovenian scientists, studying olms is a beloved side project. Still, they’ve made significant advances that in the long run will help guide conservation strategies.

In 2019, Kostanjšek and partners in China and Denmark finished sequencing the olm’s genome in its rawest form. Fifteen times longer than the human genome, it’s the largest animal genome yet mapped – although scientists already know larger genomes exist, like that of the mudpuppy. 

“This is just a first step,” says Kostanjšek. The olm genome currently exists as seven terabytes of data on an external hard drive at the University of Ljubljana. A specialised computer is required to read it, so Kostanjšek and his co-leader are working to partner with experts and labs across the world to help interpret the sequence. Decoding the olm’s “superpowers” of slower metabolism, limb regeneration, and negligible signs of aging could offer novel prospects in regenerative medicine for people. But first and foremost, the scientists hope the genome will offer deeper insight into the animals’ life history – and how to help them survive climate change and human incursions.

Others have also made significant progress on understanding olms in their spare time. Lila -Bizjak Mali, a developmental biologist and professor at the University of Ljubljana (and Kostanjšek’s lab colleague), squeezes her olm research in around a full-time teaching schedule. “When you study olms, you should be patient, and you should have a passion,” she says. As one of the world’s foremost experts in olm reproductive biology, she hopes the genome will help with captive breeding efforts – an important insurance policy for a species that rarely reproduces and whose hidden world faces so many threats. 

Reliable captive breeding is currently a -guessing game. Unless an individual is in a visible stage of reproduction, it’s challenging to determine sex by physical features alone, and female olms lay eggs only every 12.5 years, on average. More challenging still is that male and female sex chromosomes look the same, unlike the typical XX/XY sex classification. The genome could help researchers identify sex–determining genes – and their corresponding molecular signatures in the blood – in order to sort out which is male and who is female. “This is a lifetime project,” says Bizjak Mali. “I’m not sure if I’ll retire… before it’s possible to establish reproduction in our lab.”

Still, insights about optimal tank conditions from work there have already contributed to a significant captive breeding success at Postojna Cave Park. In 2016, a female olm captured imaginations around the world when the park lab broadcast footage of her laying a clutch of 64 eggs, suspended underwater like glimmering, hope-filled galaxies. Twenty-one of those eggs hatched, a remarkable achievement. In the wild, scientists estimate that only two of the hundreds of eggs a female lays over her lifetime will successfully hatch. 

Despite uncertain prospects for wild olms, Gregor Aljančič hopes that they can inspire regional unity that will lead to better safeguards for the subterranean world that both people and salamanders depend on. Many of the countries where the olm lives were once part of Yugoslavia. The country broke up, but peace was never fully restored and ethnic conflicts have ravaged the region in recent decades. 

The Aljančičs must take extra precautions when doing fieldwork in Bosnia and Herzegovina, where the landscape is still laden with landmines. But co–operation is alive in the region’s scientific community, Aljančič says. “Although we may not speak the same language, the olm is a positive idea for countries within the Dinaric Karst that are concerned with karst management.” 

Five years ago, Tular Cave Laboratory organised a recurring international meeting called SOS Proteus to bring together researchers working on groundwater pollution and salamander conservation. Its 90 participants came from across the Dinaric Alps as well as the United States, the United Kingdom, and China. Last spring, the meeting revealed a new logo: a black olm and a white olm framing a drop of drinking water. 

“People pump water, bring it into their homes, and then this absurd circle is completed through the glass of drinking water – so putting the olm beside this is very interesting,” says Aljančič, emphasising how important it is to visually remind residents why protecting olm habitat is in their best interest.

 Grassroots momentum is building for Slovenia’s symbolic salamander. Postojna Cave Park includes conservation messaging in its tours, and the Aljančičs lecture in communities and schools to build local pride for the olm. They expect their son will someday learn the fierce research spirit that has driven two generations of his family. “We hope the olm lasts until he’s old enough to understand it,” says Năpăruş–Aljančič. “Especially the black olm.”

Olms have always found a way to wait things out, enduring huge changes as they patiently navigate the depths. But time may no longer be on their side – or ours. “There’s this tension in science to reap from nature … we always want to benefit,” says Aljančič. “However, we have to ask ourselves what we can do the other way around, because that’s what will save us.”

In 2017, Slovenian president Borut Pahor joined the Aljančičs and their students to release a rehabilitated olm back into its cave habitat. They carefully lowered a water-filled tray, suspended from the corners by string, to the pulsing stream below. Each corner had to stay level, to avoid spilling the salamander into a potentially damaging fall. Looking at photos from the event now, the strings seem to represent the bond that ties the fate of Slovenians to that of the olm. One wrong tug could jeopardise it all. But with careful balance, the olm makes a clean getaway.  

This in an edited version of a story that ran in –bioGraphic, an online magazine about nature and sustainability powered by the California Academy of Sciences.