Hole-y c*@p! How bat excrement is sculpting Borneo’s hidden caves

Deep in the heart of the Borneo rainforest lies one of the South East Asia’s most important natural sites: the Gunung Mulu National Park, Sarawak. Despite being home to one of the most diverse tropical rainforests on the planet, arguably the world heritage area’s most astonishing feature lies underground.

The caves of the Gunung Mulu National Park

Under the limestone ridge of Gunung Api lies the extensive Clearwater cave system. At over 260 km in length, and with passages often exceeding 30 m in diameter, it is believed to be the world’s largest cave system by volume, and a haven for local wildlife.

The nearby Deer Cave is home to an estimated three million wrinkle-lipped bats who fly out of the cave each evening to feed, creating a stunning visual display. Cave swiftlets fly many kilometres into the Clearwater cave system to make their nests (they also happen to be prized as a local delicacy and used to make bird’s nest soup). Lying in wait to try and catch them as they fly past are cave racer snakes, whilst an astonishing array of cockroaches, millipedes, crabs, crickets and spiders are sustained by the piles of guano (bat poo) that line the cave floor. (This ecosystem featured in a memorable episode of the BBC’s Planet Earth series.)

However recent research within this incredible cave system led to a surprising discovery about the formation of the caves.

History of the caves

Caves are fantastic repositories of geological and archaeological data, preserving information that would otherwise be lost to surface erosion and degradation. They and the deposits they contain hold clues to past landscape change, allowing us to reconstruct how the Earth’s surface has changed over millennia.

The caves were first explored as part of a Royal Geographical Society expedition in 1978. Working in collaboration with the Sarawak Forestry Corporation and the national park, the Mulu Caves Project has been exploring, surveying and undertaking research in the caves ever since. This includes caving expeditions led by Andrew Eavis, a veteran of the 1978 expedition.

Dating of stalagmites and cave sediments indicates the Mulu caves are up to 3 million years old. Analysis of cave stalagmites has yielded a climate record spanning hundreds of thousands of years, whilst volcanic ash provides evidence of a massive volcanic eruption in the Philippines 189,000 years ago. More recent archaeological finds also provide evidence of human activity and burials in some of the caves.

Unusual dissolution

One of the unusual aspects of the Mulu caves is the way the cave passages have been sculpted.  Most caves in the region are formed by the dissolution (dissolving or break down) of limestone by acidic water, primarily from rivers flowing through the cave. The action of flowing water on the limestone rock creates small asymmetrical scoops etched into the passage walls, called scallops. These are preserved on the passage walls even after the formative river has abandoned the passage, as the water finds new, lower routes through the rock. The scallops are of interest to scientists as they can be used to deduce past water flow, providing a record of how water flowed through the caves over time.

In the Clearwater cave system, typical scallops are present in the lower levels of the cave system, close to the present river. However, in the older, higher levels of the cave system, which have long since been abandoned by the river, they are strangely noticeable by their absence, having been dissolved away and replaced by unusual corroded and pitted rock architecture.

The passage walls are frequently eroded into small dissolution pots and coated with a weathered crust: analysis has shown these are composed of calcium phosphate minerals, which is highly unusual in caves. Corroded stalagmites are common, dissolved away like rotten teeth to reveal their internal growth rings. These features suggest some form of atmospheric dissolution of the passage walls and stalagmites has taken place in the time since the passage was abandoned by the underground river.

Comparison with other caves suggests these features are generally restricted to tropical cave systems. One of the key aims of recent Mulu expeditions has been to understand how these features form and why. A team of researchers led by BGS geologist Dr Andrew Farrant, cave microbiologist Prof Hazel Barton (University of Alabama), her PhD student J Max Koether and BGS isotope geochemist Dr Andi Smith set out to investigate what may be happening.

Caving and exploration

Undertaking cave research can be hard work. Sampling trips into a cave system over 250 km long takes time, and in some cases involved making camp underground. It is hard, sweaty, sometimes muddy work, occasionally requiring ropes to climb up pitches or descend vertical drops. But the rewards are enormous: the caves are spectacular, with stunning formations, huge chambers and amazing biota.

The Clearwater streamway is probably one of the finest cave passages in the world. Not only is there the prospect of new scientific discoveries, but also the chance to explore new cave passages where no human has ever trodden. On one trip, the team crawled through a flat-out squeeze to emerge into an undiscovered chamber over 200 m long, 70 m wide and 50 m high (big enough to hold two Airbus A380 jets) and adorned with 20 m-high stalagmites.

Research

Complex ecosystems are a distinctive feature of tropical caves, driven by the daily input of guano from bats and swiftlets. Bats create large piles of pungent excrement beneath their roosts, whilst the swiftlets’ guano is dispersed more widely, sometimes kilometres into the caves. The teams’ initial hypothesis was that the guano was somehow implicated in creating the unusual dissolution forms and smooth walls seen in the caves. Initial analysis of the guano piles in the caves indicated that they are strongly acidic, and comparable to stomach acid or lemon juice, with a pH as low as 1.9. This could account for dissolution beneath the guano pile, but not the pervasive dissolution features seen throughout the caves.

Further work on the microbiology of the guano showed that microbial breakdown of urea (bats) and uric acid (birds) generates significant quantities of ammonia and carbon dioxide which are released into the cave air. Measurable plumes of ammonia can be detected in some caves; could this be responsible for the unusual features?

Attention turned to the weathered ‘paste’ seen on many passage walls. This turned out to be teeming with microbial life, in some places containing a higher microbial cell count than cultured yogurt. Analysis of condensation water droplets on the cave walls revealed extraordinarily high levels of nitrate (up to 7000 mg/l; for comparison, the UK drinking water standard is 150 mg/l), whilst drips feeding the stalagmites had little or no nitrate.

These observations suggest that ammonia released into the cave air by the microbial decay of bat and bird guano adsorbs onto water droplets on the passage walls and stalagmites. Here, microbes use the ammonia as a food source, producing nitrate, nitric oxide, nitrogen dioxide and nitric acid as a byproduct. This acid dissolves the passage walls and stalagmites, removing the original dissolutional scallops and replacing them with a suite of biogenic dissolution features. It is estimated that, in some places, several metres of dissolution has occurred in just a few tens of thousands of years: a very short time period, geologically speaking. Further work is ongoing to learn more about the microbial processes that occur within the guano and on the cave walls. The discovery of this novel mechanism of cave development has significant implications, such as how we interpret past environments from caves, the preservation of cave art, and the impact of this acidic environment on ropes and other caving equipment.

The great thing about the Mulu Caves Project expeditions is they have enabled us not just to explore new caves, but to do some amazing science too. One thing is clear from our work in the caves; the surface and underground environments are inextricably linked. There is much we still have to discover and one wonders what other secrets are waiting to be discovered beneath Gunung Api…

Publication

Our research has been recently published in the journal Geomorphology.

Farrant, A R, Koether, J M, Barton, H A, Lauritzen, S E, Pennos, C, Smith, A C, White, J, McLeod, A, and Eavis, A J. 2025. Pervasive speleogenetic modification of cave passages by nitrification of biogenic ammonia. Geomorphology, Vol. 483, 109822. DOI: https://doi.org/10.1016/j.geomorph.2025.109822

Thanks                 

Thanks go to Andrew Eavis and members of the Mulu Caves Project, the Sarawak Forestry Corporation and the Gunung Mulu National Park management and staff, without whom this work would not have been possible. Part of the research was funded by a NEIF steering committee grant to Andi Smith.

About the author

Dr Andrew Farrant

Geologist and karst geomorphologist

BGS Keyworth

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