Resurrecting A Forest

ORIGINAL: NatGeo

by Carl Zimmer

Loggers in a chestnut forest. Courtesy Forest History Society

For the cover story in the April 2013 issue of National Geographic, I explore an idea that sounds like pure science fiction: bringing extinct species back to life. What was once the purely the domain of Crichton and Spielberg is becoming a new field of research. Thanks to spectacular advances in cloning, reproductive technology, and DNA sequencing, scientists can now seriously explore the possibility of reviving some species from extinction. If not dinosaurs, then perhaps mammoths or passenger pigeons.

“De-extinction,” as its advocates sometimes call it, is part of a bigger trend these days in the world of conservation. Over the past five decades, conservation has usually taken the form of removing threats so that endangered species can recover–ban pollutants, protect habitats, stop hunting, and the like. Conservationists saved the brown pelican, for example, by protecting it from DDT and similar chemicals and by preserving the coastal wetlands where it lives. What they did not do, however, was tinker with brown pelican DNA to make the birds better able to survive. Indeed, the brown pelican gene pool–the product of millions of years of evolution before humans turned up–was ultimately what the scientists were trying to protect from oblivion.

Meanwhile, over those same five decades, molecular biologists have become adept at probing and manipulating genes. Sequencing genomes went from a dream to just another day’s work at the lab. In the 1970s, scientists began inserting genes from one species into another, and they can now build simple genetic circuits.

Conservation biologists have taken up many of these tools. They learned how to sequence DNA, for example, so that they could map populations of endangered species and track the flow of genes between them. They’ve used advanced reproductive technology to raise their success rate with captive breeding programs. The San Diego Zoo has frozen stem cells and tissues from thousands of species of animals to investigate for new ways to conserve them in the wild.

But conservation biologists have also seen some risks to biotechnology. If a synthetic organism could establish itself in the wild, for example, it could become an invasive species, putting native species at risk. (It’s important to point out that there’s no evidence that such an invasion has happened yet.) If we think of biodiversity as the world’s storehouse of genetic variation, then biotechnology has the potential to drive it down. Genetically engineered plants or animals might interbreed with wild relatives and spread their modified genes into the environment, reducing genetic variation in the wild.

Despite the potential risks, a number of conservation biologists are gingerly considering making even greater uses of biotechnology in order to protect biodiversity. Next month, for example, the Wildlife Conservation Society is hosting a meeting called “How Will Synthetic Biology and Conservation Shape the Future of Nature?”

Here’s a passage from the meeting’s framing statement:

“Critics have focused on the threats posed by novel life forms released into the environment, but little attention is paid to potential opportunities–to reconstruct extinct species or create customized ecological communities designed to produce ecosystem services. They may change the public perception of what is “natural” and certainly challenge the notion of evolution as a process beyond human construction.”

One of the few surviving American chestnuts,
located in Maine.
Photo courtesy of William Powell

To me, there’s no better example of the ambiguous future of conservation biology than the story of the American chestnut.

When Europeans arrived in North America, they found forests filled with American chestnut trees. These mighty plants, which could grow to be 100 feet tall, were the most abundant trees in the forests, making up 25 percent of the standing timber of the eastern United States. In the summer, the peaks of Appalachian mountains appeared to be capped with snow, thanks to the explosion of white chestnut flowers. Chestnut trees anchored the ecosystems of eastern American forests, providing food and shelter to bears, Carolina parakeets, and a vast number of other species. They were also a mainstay of loggers, who could fill an entire train car with boards cut from a single tree.

In 1904, a scientist observed that a chestnut tree at the Bronx Zoo was dying. It turned out to be infected with a fungus that came to be known as chestnut blight. No one is quite sure how it got to the United States, but all the evidence we have indicates it hitch-hiked its way in the 1870s on chestnut trees imported from Japan.

Chestnut blight, while harmless to Asian trees, proved devastating to the American ones. The fungi released a toxic substance called oxalic acid that killed off the tissue, allowing them to feed on it. An infected tree developed cankers on its trunk, and once they spread around the full circumference of a tree, it could no longer carry water and nutrients from its roots to its branches.

A stand of blight-infected chestnuts in New York, 1915. Courtesy of William Powell

Over the course of about eighty years, the chestnut blight spread across almost the entire range of the American chestnut, from Maine to Missippi. It conquered nine million acres and infected three billion trees. A few lone trees still survive unharmed here and there, but no one under the age of sixty has ever seen the forests of the eastern United States as they once were.

In the pantheon of extinction, American chestnuts are poised awkwardly at the door. Chestnut blight doesn’t kill the trees outright; as it spreads down to the roots, it encounters other microbes that outcompete it. As a result, infected trees become stumps. Sometimes they send up a new shoot, but once it reaches a few feet in height, the fungus attacks it again, and the shoot dies back.

“It’s basically functionally dead,” William Powell of SUNY College of Environmental Science and Forestry in Syracuse, New York, told me. “They sprout up, they get the blight again, and they are killed down to the ground. You know the story of Sisyphus? The guy who rolled the rock up the hill and it just kept rolling back down? Well, that’s kind of like what’s happening with the chestnut.”

It’s been a century since American foresters started trying to save the tree. They sprayed the trees with fungicial chemicals, to no avail. They infected the blight with fungus-invading viruses, but resistant strains continued to kill trees. They tried burning down chestnut trees to create a fungal firebreak, only to discover that the blight could silently infect oak trees, too.

They did what conservationists have always done–try to remove the threat–but nothing worked.

In the 1980s, a group of scientists embarked on a different approach, one that is now showing signs of success. If they couldn’t stop the blight, they would help the trees defend themselves.

The reason that chestnut blight was able to come to America in the first place was that Asian chestnuts can fight the fungus. They have genes that allow them to hold the cankers in check and scar them over. The trees can continue to grow and produce pollen and seeds. American chestnuts, evolving thousands of miles across the Pacific, never got the opportunity to evolve defenses against the blight. So the American Chestnut Foundation, a non-profit established to save the tree, decided to start breeding the two trees together, to see if they could provide the American chestnuts with Asian defenses.

When the foundation’s scientists interbred the American and Asian trees, the plants mixed together their genes in different combinations in their hybrid seeds. The scientists grew the seeds into saplings, and after a few years, it became clear that some of the hybird chestnuts had inherited some of the Asian defense genes. The cankers grew more slowly on them than on their American ancestors.

But the trees were no longer recognizable as American chestnuts, since half of their DNA came from Asian chestnuts. Asian chestnuts are small, orchard-like trees, and so the hybrids were far smaller than their towering American ancestors. These hybrids were not the solution to the chestnut blight, in other words. Their defenses were still weak, and they would not survive in American forests in the shadow of oaks and other big trees.

So the scientists kept breeding the trees. They used another tried-and-true method, known as backcrossing. They bred the American-Asian hybrids with American chestnuts, producing trees with only a quarter of their DNA coming from Asian chestnuts. Again, some of the new trees could resist the blight, while the others couldn’t. That was because the quarter of their DNA from the Asian trees contained the genes essential for fighting the disease. At the same time, the trees more closely resembled American chestnuts, because they inherited more of their DNA.

From this generation, the scientists picked the best-defended trees and back-crossed them again. They also mated hybrids with one another, shuffling the genes into new combinations, and selectively breeding the chestnuts that were both more resistant and bigger. They’ve now got thousands of trees that are 15 parts American and one part Asian growing on their experimental farm in Virginia.

A diagram of backcrossing experiments. American Chestnut Foundation

That one-sixteenth of Asian chestnut DNA may not sound like a lot, but it is. “There are thousands of genes in there,” says Powell. For all we know, some of those genes may impair the success of chestnuts in American forests. “It’s better to be precise about the genes you put in,” Powell argues. Working with the American Chestnut Foundation, he and his colleagues have developed a surgical approach to breeding resistant chestnut trees.

In 1990, Powell and some colleagues started investigating how to move single genes into American chestnuts. It took years to get the project off the ground. You can’t insert genes into a tree simply by sticking a needle into a trunk. Genes can only be inserted into individual cells. So Powell and his colleagues had to figure out how to rear chestnuts in their lab.

Some plants can survive as cells in a lab forever. But chestnuts are not one of those plants. Powell and his colleagues found that they had to combine pollen and ovules to produce embryos. With just the right concentration of hormones, the embryos bud off more embryos, which bud off embryos in turn. The scientists can then pick off individual embryonic cells, insert genes into the, and then grow the cells into full-blown chestnut trees.

After figuring all of this out, the scientists began to search for genes to insert into the chestnut cells. At the time, no one had mapped Chinese chestnut genes, so Powell and his colleagues turned to better studied plants. Plant scientists had figured out how wheat fights fungi, making enzymes that chop up the oxyalic acid into harmless byproducts. Powell and his colleagues inserted the wheat gene for the enzyme into chestnut cells and then grew the cells into trees.

At first the enzyme wasn’t much help, so the scientists fine-tuned the genes so that the chestnuts made more of it. The more oxalic acid they made, the better they fought the chestnut blight. The scientists eventually produced trees that could limit the cankers and heal them over.

William Powell inspects American chestnuts with blight-inhibting enzymes. Photo: Syracuse University

Last spring, the New York Botanic Gardens planted a few of the chestnuts for public display. (You can see the video of the ceremony here.) You can go to the gardens now and can see for yourself that the trees are growing and thriving, despite being exposed to chestnut blight spores wafting by. “We want to do everything transparently,” says Powell. “We don’t want people to think we’re hiding anything here.”

It may be five years or longer before these trees start growing in the wild. Powell and his colleagues need to spend a couple more years collecting data before submitting an application to the U.S. Department of Agriculture, and then the Environmental Protection Agency has to sign off on the project. Even the Food and Drug Administration will have to get in on the act, because the trees will produce nuts that people might eat.

But the trees growing in the Bronx are not the final version Powell hopes to see reviving America’s forests. It’s now finally possible for him and his colleagues to explore the Chinese chestnut tree genome, and so they’ve started  hunting for blight resistance genes. One gene for chopping up oxalic acid won’t be enough to provide full resistance, Powell suspects. He’s pretty sure that Chinese chestnut trees have evolved a number of genes that together render the blight harmless.

Adding in extra genes is essential, Powell believes, because the chestnut blight is not a fixed target. It is evolving, and it will probably be easy for it to evolve its way around just one line of defense. Each tree will need to be equipped for many attacks from evolved pathogens over the course of its lifetime, which can be as long as a century. Powell suspects a few genes will provide a durable defense, but he can’t say for sure which genes those are. So far, he and his colleagues have identified a list of candidate genes in Chinese chestnuts. “We’ve narrowed it down to about 900 now,” Powell told me with a laugh.

If, a century from now, Powell’s chestnuts tower once again over the eastern United States, how will we think of those forests? Will we think of them as nature restored to its former glory, ecosystems thriving once more? Or will we think of them as unnatural, the product of human tinkering? Or both? Given the past century of struggle to save the chestnut, the choice here is not natural versus unnatural. It’s chestnuts versus no chestnuts. “It’s not going to fix itself,” says Powell.

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(Update, 3/12: I got a good question on Twitter when I pointed readers to this post:

There are indeed companies developing patented genetically modified trees. This article in the Guardian in November describes a company that has produced a eucalyptus tree that can grow faster and produce more wood, which could be raised in plantations. Environmental groups like the Sierra Club have criticized  this research because of the potential environmental damage it might lead to and called for a moratorium.

Powell and his colleagues have not patented their chestnut trees, however, nor do they have any plans to do so. As I wrote above, they’re searching for additional genes for resistance, and they’ve avoided patented ones as much as possible. Once they have figured out which genes they need to use, they will do a complete patent search. If the genes do turn out to be patented, they’ll ask the patent holders for a license for free use. “I view this as a not-for-profit endeavor,” says Powell.)

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Powell and I will both be among the speakers at TEDxDeExtinction, taking place at the National Geographic Society in Washington DC this Friday. You can buy tickets to the all-day event here, or watch it livestreamed for free here. My story for National Geographic will be available online on Friday as well. For more information, visit National Geographic’s DeExtinction Hub.