The Wildlife Microbiome: A New Way of Understanding Species

Here’s my latest piece for Yale Environment 360:

A few years ago, as he was puzzling over the egg-tending behavior of a common forest salamander, herpetologist Reid Harris began to wonder if he might be looking at a novel solution to one of the most devastating global pandemics of our time. No one knew it at the time, but the four-toed salamander was about to become a pioneer species in the incipient field of microbial conservation biology, a dramatically different way of understanding and protecting wildlife.

The salamander Harris was studying lives in the leaf litter around forest pools from Michigan to Florida. Not all females in the species tend their nests, but the ones that do have an oddball way of weaving in and out among the eggs.

In 2008, Harris and other researchers at James Madison University in Virginia demonstrated that this weaving behavior serves to inoculate the eggs with antifungal bacteria from the female’s skin — and that the ones receiving this form of probiotic maternal care have a much higher rate of survival against infection by a common egg fungus.

At a herpetological conference three years earlier, Harris had suggested that it might be possible to identify anti-fungal bacteria species occurring naturally on the skin of other amphibian species and “bio-augment” them as a probiotic protection. And he thought it might work not just against the egg fungus, but also against the chytrid fungus that is causing massive declines in amphibian species worldwide. That fungus has rapidly spread around the world over the past two decades and now affects more than 500 amphibian species in 52 countries. Spores from the chytrid fungus, Batrachochytrium dendrobatidis (or Bd), invade the skin of amphibians and block normal respiration, leading to electrolyte imbalance, brain swelling, and death.

The chytrid fungus has already pushed at least two species over the edge into extinction (the golden toad in the Costa Rican cloud forest, and the gastric brooding frog in Australia). Though scientists are cautious about saying such things categorically, the pandemic may have caused

Coal: The Biodiversity Fuel

Paradise for a strange new world.

Before we get started, a warning. What you’re about to read is going to sound at first like something cooked up by the same folks who gave us the oxymoronic (and otherwise moronic) advertising slogan “Clean Coal.” It will sound like a fantasy story even a Fox News anchor would not dare announce: “Coal—The Biodiversity Fuel.”

In a paper being published in the journal Biological Conservation, researchers in the Czech Republic, who have been studying bees and wasps, report that some of that country’s endangered species, including four insects that had been presumed regionally extinct, have turned up instead thriving in the fly ash heaps at coal-fired power plants.

Fly ash, as the paper helpfully explains, is what’s left over after a power plant burns coal, and it’s composed of “glass-like particles of mineral residua which are carried out of the boiler in the flow of exhaust gases,” plus bottom ash, boiler slag, and “flue gas desulphurization materials.” To be clear, the “fly” in “fly ash” is not a reference to insects; rather, it has to do with the fact that the substance is so light and fine that it flies up during combustion.

The study found 227 species of bees and wasps, including 35 that were endangered or critically endangered, living at two power plant sites. Some of these insects are important pollinators, and others may be valuable as predators and parasitoids for controlling agricultural pests.

To  read the rest of this story click here.

Grandma’s Pregnancy Test and the Extinction of Species

An African clawed frog, the species that introduced the chytrid fungus to the world. (Photo: H. Krisp/Wikimedia Commons)

Ever since The Hot Zone became a non-fiction bestseller 20 years ago, people have been fretting about the likelihood that an emerging pathogen could cause a global pandemic, killing tens of millions of humans. But they seldom pause to consider that it is already happening in the animal world—or that the pandemic that’s now decimating frogs and other amphibians provides a perfect model for how it could also happen to us.

The pathogen this time is the chytrid fungus, which has raced around the world over the past two decades, and now afflicts more than 500 amphibian species in 52 countries. When spores of this fungus penetrate a victim’s skin, a slough of dead cells builds up on the surface, blocking respiration. The electrolytes go out of balance. The brain swells. The frog sits with its legs skewed out oddly to the sides. Death soon follows, often for an entire community of amphibians around a pond or wetland. The chorus of peepers goes silent.

“I can’t think of another disease on the planet more significant than this amphibian disease,” says Peter Daszak, president of EcoHealth Alliance, a New York-based group focused on the role of the wildlife trade in the introduction of dangerous pathogens. “No disease of humans has ever wiped us out.” But he estimates that the chytrid fungus pandemic has already caused the extinction of more than 100 species, including the golden toad in the cloud forests of Costa Rica, the gastric brooding frog in Queensland, Australia, and 20 or 30 species of brilliantly colored Harlequin frogs in Central and South America. “And it’s still causing extinctions.”

A paper being published today in the science journal PLOS ONE adds new evidence to the story of how innocent and even seemingly humane missteps unleashed this killer on the amphibian world. Maybe it’s best to start with our own families: For anyone born from the 1920s up until the late 1970s, the way our mothers generally got the happy news of our impending arrival was by way of the African clawed frog, an East African species in the genus Xenopus.  … click here to read the rest of the story.

Jurassic Park and the Fear of Feathers

Anchiornis huxleyi in full feather (Illustration: Michael DiGiorgio)

The much-delayed Jurassic Park 4 sequel was delayed again early this week, and it’s tempting to imagine that animal science might be the reason. (Okay, tempting and really, really stupid, but indulge me for a bit.) This lucrative movie franchise dates back 20 years now, to 1993, which is like saying it started somewhere in the Cenozoic as far as our understanding of dinosaurs goes.

When the original Jurassic Park was still in its first theatrical run, paleontologists were already digging up what has since become a gaudy parade of fossils demonstrating that dinosaurs were in fact frequently tricked out with feathers, feather-like filaments, and even a three-inch-thick coating of “dino fuzz.”

Universal Pictures grudgingly acknowledged this new science when it released Jurassic Park III in 2001. Like an anxious parent in the Punk Rock era, it allowed Velociraptor to flaunt a miserable little mohawk of about a dozen filaments sprouting out of the top of its head. 

But otherwise the franchise has conformed to the stereotype of dinosaurs as scaly, naked red-eyed monsters. And for an obvious reason: A Tyrannosaurus rex that looked like Big Bird might not have audiences wetting their pants in the balcony, or opening their wallets at the box office. So back in March, Colin Trevorrow, tapped as the latest director in the series, tweeted:  “No feathers. #JP4”

But maybe now he’s gone back for a re-think.

A Hollywood velociraptor

Here’s where the fossil evidence currently stands, as outlined by Julia Clarke, a University of Texas paleontologist who is also the author of an article “Feathers Before Flight,” appearing today, May 9, in the journal Science: Paleontologists have been thinking about the connection between dinosaurs and living birds since the discovery of the fossil bird Archaeopteryx back in 1861, and especially since 1970, when John Ostrom at Yale University pointed out the many similarities between bird skeletons and those of the Theropoda dinosaurs, including T. rex and Velociraptor.

The current revolution began in the mid-1990s, when  … to read the full article click here.

The Body Eclectic on C-SPAN’s Washington Journal

http://www.c-spanvideo.org/program/Microb

On “Washington Journal” this morning, Greta Brawner interviewed me about my microbiome story in the May issue of Smithsonian.  You can see the show here.  Look carefully and see me not smile for 42 minutes!

Shape Shifter

 

(Photo: Cally Harper)

Tongues can do delightful and astonishing things. I am thinking of the way a frog fires its sticky tongue halfway across the universe to snag a passing insect (see below). Or how an alligator snapping turtle wriggles its tongue like a worm as a dinner invitation to fish. And now the Pallas’s long-tongued bat (Glossophaga sorcina) joins this elite club of astonishing animal tongue artists.

These bats, found from Argentina to northern Mexico, and sometimes into Arizona and New Mexico, have the fastest metabolism ever recorded in a mammal, says a 2007 study in the journal Nature. They burn half their body fat each day, and have to make up for it at night by consuming as much as 150 percent of their body weight in nectar from flowers. And of course, they have to do it on the wing. According to a study published today in the Proceedings of the National Academy of Science, the secret to its success is a remarkable ability to change the shape of its tongue into a hemodynamic—or blood-swollen—“nectar mop.”

When lead author Cally Harper, a doctoral candidate in biomechanics at Brown University in Rhode Island, began her study, specialists already knew that bats of this species have an unusual fringe of hair-like structures around the tip of the tongue.  They assumed these were useful for collecting nectar—but passively, like raking icing off a cake using your fingernails. Biologists also knew that these bats have enlarged blood vessels in their tongues. But they didn’t know what to make of them. Harper had a hunch that the two features might be connected, especially since …  Read the full article here.

Attack of the Killer Shrimp

Come closer, see how pretty I am. (Photo: Michael Bok)

This is my latest post for TakePart:

One day early this year, on the Connecticut beach where I have walked most days for the past 15 years, I came across an animal I’d never seen before, washed up in the seaweed. At first, a neighbor and I thought it might be an immature lobster. It was about eight inches long, with a greenish-gray segmented carapace, and goggle eyes mounted on stalks. But in place of a lobster’s formidable claws, it seemed to have only a couple of feathery antennae.

So: Lobster-like, but lame.

Lord, were we ever wrong. It was in fact one of the most violent creatures on Earth, “enchantingly violent,” in the words of a biologist who studies them, violent enough to bring to mind the old “Jaws” soundtrack (DUNT-dunt, DUNT-dunt) and the teaser line: “You’ll never go in the water again!”

It was a mantis shrimp, so named because many people think they look like a cross between a preying mantis and a shrimp, though they are actually members of their own crustacean order, the Stomatopoda. There are about 400 species of mantis shrimp and they inhabit coastlines worldwide, leading mostly solitary lives, typically burrowing in mud and silt on the sea floor, or hiding out in rocky formations.

But let’s get to the violence.  Click hear to read the rest of the story.

How to Destroy a Mainland Madagascar

This is a review I wrote for the Wall Street Journal:

Gold Rush in the Jungle

By Dan Drollette Jr.
(Crown, 310 pages, $25)

If you delight, as I do, in strange, colorful animals, and like to see a lot of them at the same time, the usual strategy is to visit islands, where isolation has a way of breeding eccentricity. But over the past few decades, Vietnam has revealed itself, improbably, as a sort of mainland Madagascar. It is a mother lode of newly described species, many of them upland refugees in a region cut off from mainland Asia during the ice age.

Recent discoveries there include a tube-nosed bat named M. beelzebub for its devilish good looks, a walking catfish, a striped rabbit, and, just this year, a flying frog and a turquoise-headed crocodile lizard. The saola, a large forest-dwelling antelope first described in 1992, is so odd that it required the invention of a new genus, Pseudoryx. Since no one has been able to keep a saola alive in captivity, the species remains an enigma—and an enigma that is probably en route to extinction: Vietnam resembles Madagascar not just in the diversity of its wildlife but in its catastrophic rush to destroy it.

You might think that outsiders had already taken care of that. During what is known there as “the American War,” U.S. forces doused Vietnam with about 20 million gallons of herbicides and defoliants, destroying 7,700 square miles of forest. Earlier, in the French colonial era, a single big-game hunter in the Annamite Mountains gunned down 600 deer, 50 tigers and panthers, and 40 elephants (about as many as now survive in the entire nation).

But the era of mass extinctions has really taken off as Vietnam has developed into an economic powerhouse, with average annual GDP growth of 6.3% over the past dozen years. The rising middle class has so far developed an appetite for the natural world only in the most literal sense: The craving for exotic meats and traditional medicines often leads to what naturalists call “empty forest syndrome.” In 1992, for instance, Vietnam designated Cát Tiên National Park, north of Ho Chi Minh City, as a reserve for mainland Asia’s last population of Javan rhinos. But the government never provided adequate protection, particularly during a world-wide rhino-poaching crisis said to be largely driven by Vietnam itself. At Cát Tiên in 2010, poachers butchered the nation’s last surviving rhino for the imaginary medicinal value of its horn.

In “Gold Rush in the Jungle,” science writer Dan Drollette Jr. attempts to tell this story of discovery amid pell-mell destruction. He focuses primarily on the work of Tilo Nadler, an East German immigrant whose Endangered Primate Rescue Center south of Hanoi has become a final refuge for many species, including some rescued from Vietnam’s rampant illegal traffic in wildlife and some new species discovered by Mr. Nadler’s team.

Having started in 1993 with a few acres and a budget of just $20,000 a year, Mr. Nadler now maintains about 15 species in captivity, mainly highly endangered monkeys. To critics who argue for protecting whole habitats rather than plucking out a few charismatic species for captive breeding, Mr. Nadler replies: “The biggest problem in Vietnam is that

Her Last Chance at a Baby (Body Eclectic–Part 1)

(Illustration: Stephanie Dalton Cowan)

This is a piece I wrote for the May issue of Smithsonian Magazine, about life on the human body.

Of all the cases Barbara Warner has faced as a pediatrician specializing in newborns, the one that sticks hardest in her mind involved a couple who had been trying for years to have children. Finally, in 1997, the woman was pregnant. She was in her mid-40s. “This was her last chance,” says Warner. Then, too soon, she gave birth to twins. The first child died at two weeks of respiratory failure, at the time the most common killer of preterm babies.

A week later—it happened to be Thanksgiving Day—Warner folded down the blanket on the surviving twin, and even now she draws in her breath at the memory. The baby’s belly was reddened, shining and so swollen “you could have bounced a nickel off it.”

It was necrotizing enterocolitis, or NEC, little known outside neonatal intensive care units, but dreaded there as a sudden, fast-moving bacterial inflammation of the gut. On the operating table, a surgeon opened the baby boy’s abdomen and immediately closed it again. The intestinal tract from stomach to rectum was already dead. Warner, in tears, returned the child to die in the arms of his shattered parents.

“It’s 15 years later, and there’s nothing new,” Warner says bleakly as she moves among her tiny patients, each one covered in tubes and bathed in soft violet light, in a clear plastic incubator. NEC is still one of the leading killers of preterm babies. But that may soon change, thanks to a startling new way of looking at who we are and how we live.

Over the past few years, advances in genetic technology have opened a window into the amazingly populous and powerful world of microbial life in and around the human body—the normal community of bacteria, fungi and viruses that makes up what scientists call the microbiome. It’s Big Science, involving vast international research partnerships, leading edge DNA sequencing technology and datasets on a scale to make supercomputers cringe. It also promises the biggest turnaround in medical thinking in 150 years, replacing the

Foodie Gift Giving: A Stool Sample? (Body Eclectic Part 3)

How Our Microbes Keep Us HealthyThe public has also embraced the microbiome, beginning a few years ago when researchers at Washington University noticed a curious fact about obesity: Fat mice have more of a bacterial group called Firmicutes in their guts and thin mice have more Bacteroidetes. Feed the mice the same diet, and the ones with more Firmicutes extract more calories and lay on more fat. When the same differences showed up in humans, it seemed to explain the common complaint of many overweight people that they get fat just smelling food their skinny friends gorge on with impunity.

Such studies have stirred up remarkable enthusiasm in a subject matter most people would once have dismissed as yucky, gross or worse. It’s as if people suddenly loved Gulliver’s Travels for the passage where Jonathan Swift depicts a scientifically inclined student trying to return human excrement to the foods from which it originated.

This past winter, two rival efforts invited microbiome enthusiasts to submit their own fecal, oral, genital or skin samples for microbial analysis, and each raised more than $300,000 from crowd-funded donations typically under $100 apiece. The first effort, managed by Rob Knight’s Colorado lab and called American Gut, emphasized participation by top scientists in the field. Prevention magazine ranked the project’s $99 “map of your very own gut bacteria ecosystem” among its top 10 foodie gifts for the holidays. (For romantics, the $189 “Microbes for Two” package included analysis of a stool sample for both you and your partner. Or your dog.)

Microbiome excitement has spread to venture capitalists, who have so far invested in at least four start-ups with the aim of developing new microbiome-focused drugs and diagnostic tools. At Second Genome outside of San Francisco (motto: “The most important genome in your body may not be your own”), chief executive Peter DiLaura has nearly $10 million in seed money and a plan to get to clinical testing within three years for drugs targeted at common conditions like ulcerative colitis, where the micro­biome probably plays a causative role.

That timetable may seem optimistic, especially given that research on the first genome—that is, the human genome—has barely begun to produce the abundance of new therapies originally predicted. But at least in theory it ought to be easier to manipulate individual microbes. According to researchers in the field, several major drug companies working on diabetes and obesity now have