Millions of years ago, a cluster of coral reefs stood firm here as the water receded, leaving them surrounded by the marshy, mangrove-studded Mekong Delta.

Today, these reefs have been carved by the wind and rain into spiky limestone cliffs known as karsts that stand stark against the Cambodian landscape, even as the lowland rainforest around them has been denuded by centuries of intensive rice cultivation and logging.

The karsts are full of nooks and crannies that have nurtured highly specialised plants and animals found nowhere else. They are also important to humans, studded with small altars and temples that are thought to be homes to neak ta, landscape spirits in the local animist pantheon.

Soon, they will be gone.

A small group of scientists are now racing to document rare plant life in these limestone karsts before local companies quarry them to dust and grind them up for production of the cement that is fuelling this country’s building boom.

Most of the wood in mainland Southeast Asia has already been logged to support the region’s rapid economic growth and its relentless appetite for luxury hardwood. (Nearly all the forest cover in neighbouring Thailand is gone and Cambodia is now experiencing the fastest acceleration of forest loss in the world, despite a putative ban on logging.)

Cement and concrete are also in high demand, so the karsts are next in line.

“They are the last refuges of what made it to the Mekong Delta, natural harbours for a specialised kind of vegetation that has very little timber value, sanctuaries of rare species,” said J Andrew McDonald, a botany professor at the University of Texas Rio Grande Valley, who is spearheading the plant-collection project with support from the International Union for Conservation of Nature.

The limestone habitats can act as “arks” of biodiversity that replenish surrounding areas after ecological damage. But they are so complex that, once destroyed, they can never themselves be recreated.

They have scant access to water for six months of the year, creating a harsh, alkaline environment that has led to the evolution of desertlike flora in the middle of a hot, wet country. McDonald calls them “Dr Seuss-type plants”, ones that look and behave like cactuses and succulent desert flora, but are related to the local tropical foliage.

There are fat, succulent grapevines, fig trees with thick, waxy leaves, and false cactuses as spiky and segmented as those that grow in the American desert, but actually members of the poinsettia family that evolved independently. Perhaps most unusual are the large, phallic flowers known as Amorphophallus, which look like a cross between an orchid and a Muppet’s nose.

The toughest and most determined plants nestle themselves into the fissures and cracks atop the karsts, or cling to the razor-sharp outcroppings exposed to the wind and sun. More delicate tropical flowers feathery orchids and little white touch-me-nots – make homes in the grottoes within, sucking up the water that drips through the limestone. At the bottom, the karsts are like Swiss cheese, full of water-carved pockets that open up into large underground lakes where rare bats feed and mushrooms grow.

Over four days in January, armed with rice sacks and pruning shears, McDonald and several colleagues and students pored over two linked karsts, Phnom Kampong Trach and Phnom Domrei, climbing atop their jagged surfaces and passing all the way through them in a network of caves.

McDonald, 62, is a plain-spoken Texan with a mystical streak who spends his spare time working on a 1,000-page manuscript on the religious iconography of the lotus. He can clamber up and down the slippery, precipitous karsts like one of the mountain goats that live here (another anomaly in flat Cambodia).

“Fruits! Flowers! Fruits! Flowers! Eyes on the prize!” he chanted, trying to urge the group to collect specimens. Among the group was a pair of technophilic Vietnamese botanists lugging huge cameras who kept falling behind to take close-up shots of the foliage.

At first glance, McDonald was excited by a novel-looking parasitic Balanaflora with droopy, bulbous male flowers (“they latch onto this tree and have sex there”) and a huge, feathery white blossom at the edge of a grotto. It was an unusual variant of dogbane, a nocturnal plant with a dangling structure that dusts the underside of a visiting moth or bat with pollen.

“I’ve never seen an Apocynaceae with an irregular flower like that!” he exclaimed, before gingerly tossing the specimens, one by one, across a huge fissure to the safe hands of a waiting colleague.

Ultimately, over the course of two botanical excursions, the group found more than 130 species of vascular plants native to this patch of limestone, a comparatively rich assortment, including some thought to be new to science: an Amorphophallus and another related flower, a new type of jasmine, and a member of the coffee family.

Along with discovering these rare species, the scientists wanted to document the karsts’ biodiversity and the ways in which different parts of the habitat work together before it is gone. Ultimately, they hope to persuade the government to make these two karsts a protected area and declare them off-limits to future cement quarrying.

The team was accompanied by a representative of the Ministry of Environment who was to report back to his superiors on the merits of the protection proposal. The ministry is bereft of plant experts, so they sent Neang Thy, the country’s leading herpetologist, instead.

“The vegetation you see here, you may not see anywhere else,” he said. “If it is destroyed, that is a problem.”

Cambodia has almost no botanists and the study of plants in the country came to a standstill from 1970 to 1992 during an extended period of war and unrest punctuated by the trauma of the Khmer Rouge takeover from 1975 to 1979.

The country’s main herbarium is a single room at the Royal University of Phnom Penh. It houses about 12,000 specimens, many of which have not been inventoried and are simply piling up on shelves. They are meant to be kept cool and dry by two air-conditioners, but one air-conditioner is broken and there is no money to fix it.

“You talk about a herbarium in another country and it should be very big, but this is just one room,” said Ith Saveng, who runs the university’s Center for Biodiversity Conservation. “We hope to expand to another room within the next two years.”

Rare plants found in karsts have to be shipped to Vietnam so better-trained scientists can do the precise work of matching species to species.

In Kampot, the scientists were led through some of the more treacherous cave networks by Ken Sam An, a 61-year-old native of a village just below the Phnom Kampong Trach karst. He knows more about these caves than just about anyone else.

As a teenager, he watched as the Viet Cong hid in the caves, resulting in retaliatory bombing campaigns by the United States that drove the population to flee. Soon, ultra-Communist rebels swept into the area and he was conscripted into a Khmer Rouge youth unit.

Whatever scientific research apparatus still existed was totally dismantled by the victorious Khmer Rouge government, which declared higher education anathema and sent city-dwellers back to the land to work as rice farmers and dam builders. Although Sam An possesses vast botanical knowledge, he has not attended school since the sixth grade.

After the fall of the Khmer Rouge in 1979, Sam An spent years working for a limestone quarrying company. But now he serves on a local committee that tries to preserve the karsts, urging local residents to stop stripping them and chopping off rocks to sell.

“I tell them, ‘If you break the mountain, it’s not good for the environment, and if you work in tourism you can come and sell things to the tourists instead of breaking rocks.’”

A far bigger risk is large-scale limestone quarrying by companies producing cement. Kampot (K) Cement, a joint venture between the well-connected local company Khaou Chuly Group and the Thai cement manufacturer Siam Cement, has claim to large karsts in the area. The site is churning out 1 million tonnes of cement a year.

Another local company, Chip Mong, formed a partnership with a different Thai firm and started building a $262 million factory in the area last year, with the goal of producing 1.5 million tonnes a year. This is still not enough to slake Cambodia’s growing thirst for cement, expected to reach 5 million tonnes this year.

The cement firms have also spawned a mini-land boom in Kampot, where prices have risen thirtyfold in the last decade, according to locals. In interviews, the inhabitants complained that rocks being blasted off the mountains were falling on their homes and angering the local neak ta, who had to be propitiated with offerings of roast pigs.

Tony Whitten, the international regional director for Fauna and Flora International’s Asia-Pacific division said he had tried for years, fruitlessly, to determine whether environmental impact assessments had been carried out before cement companies were given permission to dynamite the karsts.

The Ministry of Mines and Energy, which is responsible for granting and regulating concessions for limestone quarrying, declined to comment.

Even when environmental assessments are conducted, they often focus on large mammals, overlooking plants and small species that are highly endemic to certain caves. The slimy, squishy invertebrates and strange plants that live in karsts can be a hard sell to donors, who prefer what are known as “charismatic megafauna” cute, easy-to-anthropomorphise animals like elephants, tigers and dolphins that appeal to the public.

“It takes a botanist to appreciate the charisma of a plant,” McDonald said.

The karsts his group wants to protect have the advantage of already being a minor tourist attraction, with a Buddhist pagoda sprawling out at their feet, small shrines nestled into the caves and a set of stone steps leading down to an underground pond where monks bathe.

“They are linked together – people come to pray at the pagoda and then they always go to the cave,” Sam An said. It is also common for him and his neighbours to make offerings to the spirits believed to inhabit the karsts, going to different caves on different holy days. Each one is believed to be the domain of a different neak ta.

Sam An can rattle off their names as if they are members of his extended family: “There’s the Red Neck spirit, the Eight Heads spirit, the spirit of the 100 Rice Fields, the spirit of the Monk Who Lives in the Jungle, the White Elephant spirit, the Dragon’s Mouth spirit, the Magic Boy spirit, the Reincarnated Grandmother spirit and the Magic Mushroom spirit.”

Altogether, the caves are thought by locals to be chambers in the stomach of a dragon that beached here when an ancient sea receded thousands of years ago – a tale not entirely different from the stories told by geologists and botanists.

“This is what we lose when they take out a mountain,” McDonald said.

The New York Times