South and east of Brazil’s famous Amazon, the air becomes dryer and the humid rainforest gives way to emerald green patches of irrigated pasture carved from scrubby woods and native grasslands.

The real “forest” here is underground, an enormous system of branches and roots buried deep to survive fire and search for water during long dry seasons.

This is a different kind of forest, hidden in plain sight and far more threatened than the Amazon. Known as the Cerrado, it is the largest, most biologically diverse savannah region of South America, home to 5 percent of all life on the planet.

But industrial farming is fast swallowing this unique landscape. And its rapid transformation is creating a ticking carbon bomb that scientists warn could significantly affect the global carbon cycle if the current rate of destruction continues.

This enormous expanse in central Brazil was once as impenetrable as the deepest rainforest, so isolated that Portuguese settlers dubbed it Cerrado, or “closed.” Today roads connect the Cerrado’s southern boundary in the São Paulo and Mato Grosso do Sul states with its northern limits some 1,500 miles away near the Atlantic coast. Yet the Cerrado is still largely unknown, even in Brazil.

This is a vast mosaic of wide grassy plains, rivers flanked by slender palms and dense woodlands populated by a tangle of stunted-looking, thick-barked trees. It is the second largest biome in Brazil after the Amazon. The real “forest” here is underground, an enormous system of branches and roots buried deep to survive fire and search for water during long dry seasons.

Too poor for crops?

As recently as the 1950s, soil here was considered too poor to grow crops, so the region remained largely empty of development. In the 1960s, however, agronomists discovered that the Cerrado could be made remarkably productive by adding lime to reduce the soil’s acidity. That changed everything. Aided by chemical fertilizers, the dry Cerrado savannah could suddenly support large-scale commercial crops like corn, sugar cane, cotton and, most of all, soy.

Soy. That miracle legume. The crop that, more than any other, is allowing China to feed hamburger, steak and bacon to its ballooning middle class and export everything from fish to cosmetics, high-end steel water bottles to cheap plastic trinkets.

Soy alone was responsible for 10 percent of Amazon deforestation between 2001 and 2005. That prompted a global outcry, resulting in a moratorium on soy cultivation in the rainforest that helped curb deforestation. But it also helped shift more production to the Cerrado: Last year nearly two-thirds of Brazil’s soybeans were grown there.

Today, more than half the Cerrado has been cleared for crops and cattle ranching, and the region has become a global model for the development of other savannah regions in Africa and South America. Until recently, that was regarded unequivocally as positive, a productive use of otherwise “wasted” land.

Scale of development

But the scale of development has become a big concern for scientists and environmental activists, considering the region’s rich biodiversity. The Cerrado contains nearly 12,000 species of plants – more endemic species than in the Amazon – as well as more than 800 species of birds and rare and endangered animals like the giant anteater, jaguar and three-banded armadillo.

There’s another worry, too, one that until recently received scant attention. As more and more of the Cerrado gets plowed under, that underground forest is dying, releasing significant amounts of carbon, tweaking the climate in ways that increase the risk of highly destructive fires in the Amazon.

The push to maximize the economic potential of the Cerrado has overshadowed by far efforts to protect it. American, Chinese and European consumers of meat, processed foods and the multitude of other products made possible by Brazilian soy remain largely unaware that they have a role in the destruction of this ecosystem and carbon sink.

Predicting climate change

Danilo Neves and Marcelo Simon see the connection.

The two are Brazilian biologists documenting legume species across the Cerrado, trying to fill the gaps in scientific knowledge about relationships between plants and how they have evolved amid different soil and climate conditions. On a warm June day – early winter in the Southern Hemisphere – they’re in the middle of a 12-day, 1600-mile field expedition funded by the UK’s Natural Environment Research Council and coordinated by the Royal Botanic Garden in Edinburgh.

Their ultimate mission: Use plant genetics to help scientists predict how climate change and development will alter the Cerrado and its surroundings, including the Amazon, before that change becomes reality.

Simon is a research scientist at Embrapa, the Brazilian agricultural research institute that played a central role in the Cerrado’s agricultural conversion in the 1960s and 70s. Educated at Oxford, he focuses on protecting the remaining Cerrado by documenting its native plant species. He heads out to the field sporting a baseball cap and a khaki button-down field shirt emblazoned with the Embrapa logo. His English comes slowly, in a hybrid British-Brazilian accent and peppered with dry but ready humor.

“Do you know, all the important regions of Brazil – like the Amazon and Atlantic Forest – have their own national day,” he said. “But the Cerrado is so unlucky that its national day is September 11th.”

Typical Cerrado patchwork

Simon and Neves are bumping along in a Mitsubishi 4x4 pickup, about 1.5 hours’ drive from Brazil’s capital, Brasília. Neves’ hand-held GPS guides them off the highway and onto a red dirt road. Toucans occasionally fly by as they roll past eucalyptus plantations and verdant cattle pastures. They finally stop at a typical Cerrado patchwork of native grassland and low-growing forest.

Neves, a post-doctoral researcher at the University of Leeds with a trim beard, scans a field, searching for the best place to recover soil samples. His curly hair is pulled into a half ponytail, the long sleeves of his gray jersey pushed up to his elbows. With a Zen-like indifference to the heat and ticks, he maneuvers through a barbed wire fence and into the field of tall grasses, their razor-sharp edges grabbing at his dirt-smudged jeans. Neves kneels and uses a trowel to scoop the dirt into a clear plastic bag.

On the other side of the road grow gnarled, twisted trees with peculiar rough bark several inches thick. The bark looks a bit like alligator skin, yet it’s light and soft, like cork. It is an example of how trees here have adapted to protect themselves against fire and a prolonged dry season, two important characteristics of the Cerrado.

The other remarkable adaptation of many Cerrado plants is the sheer volume of biomass that exists underground. Because of the long dry seasons and fires that routinely sweep across the savannah, some have developed deep subterranean trunks and root systems. In some cases 70 percent of the plants are underground, reaching depths of up to 30 feet. For that reason, the Cerrado is sometimes called “the upside-down forest.”

Vulnerable to human activity

But the very adaptation that helps the Cerrado thrive despite fire and dry conditions makes it vulnerable to human activity: because people don’t see this part of the forest, they fail to recognize the value of protecting it.

“With land transformation, people think the Cerrado would lose less carbon stock compared to Amazon, since the Amazon has those massive forests,” says Neves. “But a huge amount of carbon stock in the Cerrado comes from those underground structures.”

Simon clips a few branches from a tree with rows of slim, finger-like leaves and carries them to the back of the 4x4. He carefully folds them in sheets of newspaper and presses them between stacked squares of cardboard. Tonight, he and Neves will dry all the day’s samples in a portable oven. In less than two weeks, they will fill the back of the Mitsubishi with these small but important pieces of the Cerrado’s evolutionary history.

For the next several days, the pair continue north on the Belém-Brasília highway, a two-lane road in central Brazil. Fifty years ago, this was the only artery connecting the new capital of Brasília with Belém, a port city near the Atlantic coast more than a thousand miles to the north that serves as a gateway to shipping on the Amazon River. The construction of the highway through large wilderness areas in Goiás, Tocantins and Pará states helped make possible the agricultural transformation of the region.

The change is dramatic. Unlike the cattle pastures, woods and grasslands of the previous day’s journey, the drive north through Tocantins state passes through endless crops of sunflowers, soy, sugar cane, corn, sorghum. Thick smoke rises from burns as farmers clear new cropland. The practice promotes invasive grasses that dramatically amplify the effects of naturally-occurring fires during the long dry season.

Dusty towns

Small, dusty agricultural towns dot the route, with storefronts offering tractor dealers, livestock suppliers and heavy machinery mechanics. The scientists stop for the night in Formoso do Araguaia, breaking for dinner at one of a handful of casual restaurants with red plastic tables clustered on the sidewalk. Most are occupied by farmers who have gathered on this warm evening over meals of beans, rice and local trout washed down with cold Antarctica, a popular Brazilian beer.

Listening to the banter, Simon observes that the farmers’ accents suggest they hail from southern Brazil, likely part of a wave of migrants seeking cheap land and generous government incentives in the 1960s aimed at transforming the Cerrado into an agricultural heartland. It worked. During the next 30 years, the Cerrado saw an agricultural revolution. Until farmers started adding fertilizer, soybeans had never successfully been grown in the tropics. Today, thanks to technology, soy farmers here can sometimes even exceed the yield of growers in temperate climates like the U.S. Midwest.

The transformation was well timed.

As plows ripped across the Cerrado, global demand for soy was skyrocketing.

Appetite for meat

Worldwide, soy production has grown nearly ten-fold in the last half a century, according to recent report by the World Wildlife Fund. That’s been driven largely by the planet’s growing appetite for meat: Eighty percent of soy is now used for animal feed. Today, Brazil is the world’s second leading soy exporter, after the United States. And that gap is closing fast.

Two-thirds of the demand for Brazilian soy comes from China and the European Union. But a wide variety of products imported and consumed in the United States – everything from meat and dairy products to cosmetics, soaps and chocolate – depend on Brazilian soy.

Several of the leading multinational commodity traders that drive soy production in Brazil are headquartered in the U.S., including Monsanto, Cargill, Archer Daniels Midland and Bunge.

But Chinese companies wield increasing influence over the future of the Cerrado. China is now Brazil’s most important trading partner. In spite of a 2010 crackdown on foreign land ownership in Brazil, China continues looking for ways to expand its control of agricultural lands in the Cerrado through production agreements, land leases and investments, primarily to grow soy. Soybeans are China’s largest agricultural import, mostly to feed the country’s growing demand for meat: Today, Chinese consume just under two servings of meat per day on average, twice as much as in 1990. By 2020, meat consumption is expected to increase another 12 percent, according to U.S. Department of Agriculture projections.

Large footprint

That activity leaves a large footprint. Conversion of Cerrado to grassland pumped more than 275 million tons of carbon dioxide into the atmosphere each year between 2002 and 2008, according to a recent analysis by Brazil’s Ministry of Science, Technology and Innovation. That’s more than half the annual CO2 emissions of the United Kingdom, the world’s 10th largest emitter – and more than the annual emissions of the Brazilian Amazon. Nothing suggests that pattern will change any time soon.

Joe Valle, a congressman representing the Federal District, where Brasília is located, is an organic farmer growing vegetables and raising dairy cows on 345 acres of what 50 years ago was Cerrado woodland. Valle, whose business has become a model for organic farming in Brazil, is planting seeds of social and environmental change: He’s a fervent advocate for Cerrado conservation and more government support for small producers, sustainable farming practices and the harvesting of native Cerrado plants like the cashew, baru nut and palm fruits.

“We have many different laws and kinds of institutions that try to defend the Cerrado biome, but it’s in dispute, a daily dispute, with agribusiness and economic powers. The only way for us is the conscience of the people. Without that, the economic powers will prevail,” Valle said.

Valle, a forest engineer by training, is a strong critic of recent changes to Brazil’s Forest Code, a landmark set of laws that are credited with slowing destruction of the Amazon. A recent paper published in the journal Science affirms his concern. The authors warn that, by granting amnesty for some illegal deforestation that took place before 2008 and relaxing standards for conservation and restoration, the amended, watered-down version of the Forest Code could lead to additional deforestation in the Cerrado over an area nearly the size of California.

At September’s climate summit in New York, 27 parties signed on to an accord limiting deforestation, including the United States, the Philippines and Indonesia, as well as multinational companies like Cargill and Unilever. Brazil was absent.

Other iconic landscapes

This is a story written before on other iconic landscapes, from California and the U.S. Great Plains to Chile’s Central Valley, cautionary tales of what can happen when humanity’s demands push nature toward an ominous tipping point.

Other developing countries eager to establish a productive agricultural base are adopting the Cerrado model. Embrapa, the Brazilian agricultural research agency credited with transforming the Cerrado, is lending its expertise to a number of countries looking to apply efficient, high-yield approaches to agriculture in Africa and South America, including Paraguay, Argentina, Colombia, Ghana, Sudan and Mozambique.

Mozambique in particular has embraced the Cerrado model. A long-term partnership with Brazil and Japan will transform millions of acres of the country’s northern savannah into high-yield soy and other crops, mainly for export. The project, called ProSavana, is expected to attract billions of dollars in regional infrastructure projects. But critics question whether ProSavana will significantly improve food security for poor Mozambicans, given that the project has thrown the doors open to multinationals primarily aiming to export commodities to Europe and Asia.

With global population projected to grow by 2.6 billion people in the next 35 years, it’s inevitable that more land will be needed for agriculture, and increasing productivity will be essential. Proponents of the Cerrado model point out that intensive farming means more food can be grown on less land, slowing deforestation. But many questions remain about whether it will achieve the goal of feeding a hungry world, or simply enable ever-increasing consumption in China and developed Western countries.

Cerrado’s image problem

Marcelo Simon, the biologist, laments that his beloved Cerrado hasn’t attracted more attention.

He recounts how he once drove through the Cerrado with a friend from Rio de Janeiro. Glancing out the window at a pristine landscape, the friend assumed the scrubby trees, grass and brush must be the remnant of a once lush forest. “He looked at the Cerrado and said, ‘Oh, this is so sad – all the forest here is gone and look what is left, all this secondary vegetation.” Simon says with a rueful smile.

This is the core of the Cerrado’s image problem: A wooded grassland is just not what people think of when they imagine a carbon sink or priority conservation area. They think rainforest. International concern about the rainforest forced Brazil to focus on the Amazon, but there’s no such impetus for protecting the Cerrado.

“Nobody in the rest of the world knows about the Cerrado, and if they do know about it, they say ‘thank God it’s not the Amazon,’ says Donald Sawyer, founder of the Institute of Society, People and Nature, an independent non-governmental organization based in Brasília that works on conservation and sustainable development projects in the Cerrado. “And that’s what the soybean planters say: ‘We’re not clearing the Amazon.’”

In the lead-up to the United Nations climate change negotiations in Copenhagen in 2009, Sawyer pushed for the Cerrado to be incorporated, along with the Amazon, into Brazil’s plan to reduce greenhouse gas emissions. At the conference, Brazil won international goodwill with a deal to reduce emissions from Amazon deforestation by 80 percent.

The reduction target for the Cerrado? 40 percent.

Hot on the trail

Back in Tocantins, Danilo Neves and Marcelo Simon are hot on the trail of another elusive legume. Simon gingerly climbs up a slender tree perched atop an embankment along a wetland in order to confirm that they’ve found the species they were looking for. He grins; it is. He clips some leaves and tosses them down to Neves to add to the collection bag.

It’s one more genetic clue about how this varied landscape – here an arid tangle of tick-infested grasses and gnarled trees with crackling green leaves, there a lush oasis of riverside palms and leafy vines – evolved.

This matters, says Neves. If climate change, as some studies predict, leads to a hotter, dryer Amazon and a dying back of rainforest species, some deep-rooted, drought-tolerant Cerrado plants may be best-suited to fill in.

But they have to find them first. And then, somehow, the world has to protect them.