Iraq resents American drones that monitor outside the U.S. embassy in Baghdad. Iran is delighted to capture a high-tech U.S. drone. And the United States plans more drone purchases even amid slowing growth of the military budget.

As remote-control airplanes get cheaper and better, drones seem to be everywhere:

And it turns out that drones are ideal for watching wildlife: rabbits, sea lions, gulls and a range of elusive or inaccessible species.

Counting the mini-bunnies

Researchers in Idaho have used drones to track the pygmy rabbit, a hand-size mammal that eats sagebrush. The rabbit, a “species of concern” in Idaho, is already extinct in neighboring Washington State.

Pygmy rabbits are reclusive, spending much of their time inside burrows, says Jennifer Forbey, an assistant professor of biology at Boise State University. Forbey, along with Janet Rachlow at the University of Idaho, the U.S. Geological Survey, and Washington State University, is using used military drones called Ravens to explore how habitat factors like cover, forage quality and temperature affect rabbit populations.

The Ravens are small, and able to carry only one of these instruments at a time:

The drone can cover the entire two-kilometer square site in about three hours, but its gadgetry sees neither rabbits nor their burrows. Because the drone noise would scare the rabbits back into their burrows, the plane does not work when the bunnies are likely to be active.

To find the animals, Forbey says, “We have to walk for days and days, to identify where the rabbits are. We hike around, looking for fresh fecal pellets, fresh digging, fresh clipping on plants.”

But the data on forage quality, combined with tried-and true shoe-leather counting, shows that the rabbits are discriminating eaters. “They are specialized to sagebrush, but not all [sagebrush] plants are created equal, some types are more palatable, and also provide better cover for them,” Forbey says.

It’s possible that in winter drones could get a better picture of rabbit activity by looking for tracks in the snow.

To actually see rabbits from the air without frightening them, Forbey suggests a back-to-the-future approach — perhaps lighter than air craft.

“We are trying to develop some other platforms, maybe blimps, that could stay static over burrows to get infra-red video of rabbits without making noise.”

Although airborne surveys have begun, they are a help but not a panacea, says Forbey. “Not much is known about pygmy rabbits. They are cryptic. You have to spend the time walking the habitat.”

Gulls in Spain

Black-headed gulls nest in large colonies, and like many colonial birds, monitoring from the ground is difficult, and viewing from conventional aircraft can be expensive and confusing.

Pick up a battery-powered, radio-controlled model airplane, and the picture changes, says Francesc Sarda, at the Center for Forestry Technology of Catalunya, in Spain. When the drone flies over at an altitude of 30 to 40 meters, “The gulls hear it, but they don’t identify it as predator, don’t know what kind of element it is, and so they do not care about it.”

In a 2010 study,¹ Sarda equipped the plane with a still camera, pointing straight down. A video camera in the “cockpit” broadcast a live feed to a laptop on the ground, where the “pilot” operated controls.

The plane is “easy to fly, many people do it for hobby,” says Sarda, and it’s affordable — at just 1,400 Euros for the plane and the equipment. Depending on wind, the plane can stay aloft for 15 to 20 minutes, but batteries are cheap, and easily replaced before the next flight.

Water birds often nest in dense colonies, and can be difficult to study. Those that nest on cliffs can be observed from the side. On flat land, wildlife biologists may have to walk through the colony, but “If there are thousands of birds, it’s very difficult to count,” Sarda says.

Encounters with human counters can also annoy the birds, he adds. “In our case, they will fly away, even if there are chicks or eggs on the nest. You have to be very careful.”

The drone sidesteps this problem, he says. “You can do your count, and repeat your sampling” after a week or a month, to assess changes.

Laws about low-level flight are much less stringent in Spain than in the United States, Sarda says, and the system is “very cheap, compared with manned aircraft. You can use it yourself, whenever you want.”

See the sea lion

Sea lions and the fishing industry are squaring off in the Gulf of Alaska, where a rapid population decline of Stellar sea lions has been blamed on a scarcity of the fish they eat. But studying these fearsome and elusive creatures is difficult and data are sketchy, says Greg Walker, who manages the unmanned aircraft program at the University of Alaska. “The sea lion is an endangered species, and it’s affecting the fishery, but the science behind it is pretty spotty. The sea lions that have been monitored are healthy, not starving.”

Fishing restrictions are costly to the industry, and Walker observes that boats are catching more fish in the same amount of time, which suggests no scarcity of prey. “Their technology is no better than it was five years ago, and if they are catching more fish, maybe there are more fish” in the Gulf, he says.

Currently, sea lions are counted by looking at “haulouts,” rocky locations along the shore where these mammals mate and give birth, but the Aleutian Islands are hardly an ideal place to fly, Walker says. Airports can be hundreds of miles apart, and weather predictions cannot accurately say if clouds will block the view, wasting time and money.

Last June, Walker and his colleagues launched a drone from a fishing boat standing offshore. After a 12-mile flight, the drone flew over the colony, without causing obvious disturbance, and obtained video and photos clearly showing the sea lions.

Ironically, the same restrictions on fishing that were enacted to protect the sea lion have made fishing boats scarce. “We started working with a fishing cooperative; would fly off their boat while they were fishing, since they were going to be in the area anyway,” says Walker. “But closing the fishery has meant fewer fishing boats in the area,” and the lack of convenient launch pads could raise the price of drone-based monitoring.

If cost can be contained, larger surveys are possible, Walker says. “We will try to survey more of the island coastline, not just the historic haulouts. We want to know, is this a real population decline, or are they just in another part of the habitat? If you are always looking at the same street address, when someone moves down the street,” you may think they are dead, he notes. “Maybe a more consistent survey would find more of the sea lions.”

Eventually, if he can round up a bigger drone, Walker would like to use synthetic aperture radar, which can see through clouds, and could sidestep, finally, the cloud problem. But he also hopes the drones can fly at 500 feet, beneath many clouds. Flying that low is dangerous for manned aircraft, but that concern does not apply to disposable drones.

Having proved the concept of drone-powered surveillance of the sea lions, Walker and associates are planning to begin a three-week campaign in March.

Stop us from droning on!

Drones have a broad range of advantages compared to other ways of studying the environment. We’ve already mentioned how they can get access to awkward locations without bugging the animals.

Flying low and slow, drones can also identify and measure invasive weeds or many other types of ecological dislocation.

H. Franklin Percival, program leader for unmanned airplane research at the University of Florida, says safety is a critical motivation for using drones. “Low-level manned aircraft is the leading cause of workplace mortality for wildlife biologists. Wildlife biologists do this kind of thing all the time, studying salmon nesting, alligators in Florida, seals in Alaska, there’s a lot of low-level stuff.”

In 2010, a pilot and two biologists died in a helicopter crash while studying salmon nesting on the Selway River in Idaho. “That drives the interest [in drones] now,” says Percival. Before nesting, salmon fan away sand and gravel on the river bottom, “and we can see these from the air.”

FAA blues

In the United States, a major limitation on scientific use of drones comes from the Federal Aviation Administration, which is, rightly, worried about collisions between piloted planes and drones. Currently, the FAA requires that the pilot or a spotter be a licensed pilot, and limits a drone’s range and altitude to avoid danger. Those restrictions raise both the cost and bureaucratic rigmarole, and ecologists and the unmanned airplane industry are hoping for a change.

On Feb. 6, the Senate sent legislation to the President requiring FAA action on the issue within three years, USA Today reports.

If the concern is safety, new, more relaxed standards seem most appropriate to drones that fly short distances at low altitude.

If the FAA redrafts regulations to maintain safety while allowing more civilian use of drones, Forbey of Boise State expects ecologists to be lining up for unmanned aircraft. “This integration of technology with ecology and conservation is really exciting. I think what these planes provide is a spatial level that you can’t get from satellite, and can’t get from being on the ground. Both in terms of the area they can cover, and the type of data they offer, they fill a gap.”

Let a thousand drones bloom

Robot planes and the associated technology of cameras, communications and GPS-based recording of location are moving ahead even as the FAA promulgates regulations. At the University of Florida, Percival, who has directed the development of five generations of a robot plane called Nova, says drones should be designed according to the scientific goal. “What are the data required? Can it deliver that kind of data, and can you do the appropriate statistics to give reliable information? The airplane should be built around your question.”

As drones with ever more sophisticated sensors return a growing quantity of data, Percival favors automating data-processing to spit out reliable data that can be manipulated statistically. “To estimate the number of nesting birds in a pelican colony, we want to differentiate the components in the imagery with a computer as opposed to some guy’s eyeballs.”

Photos show a lot, but they do not automatically reflect reality, Percival says. “Just because we can see well does not mean the numbers are as precise, as accurate, as we’d like.”

Robots are great at what they do — if the job is dull and predictable. Throw in the unexpected, and robots can do the unpredictable.

The task of programming a robot’s brain for the real world can be gnarly, says Josh Bongard, an assistant professor in the University of Vermont College of Engineering and Mathematical Sciences. “It turns out that building a robot, and programming it to do something interesting is a very non-intuitive process, and it’s a difficult one for humans to do well.”

The real world, he says, “is quite messy.”

Robots, in the jargon, need “adaptive behavior” to accommodate changing circumstances, says Bongard. When programming a free-roaming robot, “We are not likely to factor in a lighting change or people moving in and out of the field of view.”

It’s not clear how animals or people make adaptations, Bongard says, “and so it’s difficult to program a robot to do them.”

Robots: Are they alive?

Bongard, like a number of roboticists, is turning to biology for answers. But he does not want to emulate living structures. Instead, he wants to use evolution to craft robot control.

The process is akin to the “artificial selection” that helped lay the foundation for the science of evolution. Darwin, after all, wrote about how animal breeders had changed their livestock by repeatedly breeding the best animals and eating the rest.

In January, 2011, Bongard reported that he had taught four-legged, digital robots to stand and run toward a light source, by grading their control software on its ability to meet those goals.

Adaptive behavior was necessary, he says, because the light source could appear anywhere, or even take evasive action, “so the robot can’t just move its legs blindly every time.”

The robots had five seconds to do or die, and their first movements were grotesque because the control software initially moved their body parts at random. After every attempt, the control programs were graded by their ability to walk, stay upright and approach the light.

It’s brutal. More than 100 million failed programs went to the virtual graveyard in the name of science, Bongard says. The programs that showed some promise were retained, randomly varied and re-tested.

The same process is found in nature, where successful genes that face random mutation are re-tested by tomorrow’s environment.

Like the average biological mutation, the mutated robot software usually failed. But over a year of supercomputer time — equivalent to 1,000 years on a desktop computer — the winning programs evolved the ability to walk toward the light.

Weird winners

Considering the amount of trial and error, that was a satisfying but not necessarily surprising result. But here’s something to chew on. Bongard found that robots “born” with four legs had a handicap. During repeated simulations, the robots that started as snakes and developed legs during the five-second experiment were much quicker to learn the task.

You might guess — we would have — that the quick learning would have occurred in robots with full-time four-leg drive, given their longer experience with legged locomotion, but Bongard says the leg-free starters benefited by chunking the challenge: a) learn to approach the light, and b) learn to walk.

These robots “could evolve the ability to go from point A to point B while they still look like a snake, they don’t have to worry about balance, because they are already on the ground,” Bongard says. “Once evolution has figured out how to move toward the light, the ability to move on four legs could evolve.”

Meanwhile, the four-legged counterparts may still be flipping, flopping and floundering (Note to self: sell soul as political hit-man if science-writing gig crash-burns?) “The robots that had to stand upright would fall over, and it took evolution a long time to master balance,” Bongard says.

The approach — take the winners and vary them for a retest — resembles directed chemical evolution, which aims to create a better antibiotic by modifying and retesting molecules that show some ability to kill bacteria. “It’s basically the same idea,” says Bongard, “but instead of a candidate drug, we have virtual robots, and instead of selecting for … resistance to disease, they are selected for the ability to get to the light.”

Robots resemble rodents?

As a final exam for the digital robots, Bongard tested their balance with a blast of air. Although the leg-less robots “had evolved into legged robots that looked exactly like the other species, they were better able to run around under simulated windy conditions,” Bongard reports.

Bongard is first to acknowledge that he is “stealing from biology to help us build better robots,” but says, “the more interesting question is what this tells us about biological evolution. This recent work suggests that robots that change their bodies gain an adaptive advantage … and you see the same radical changes in body plan in nature: in insects, reptiles and in humans as they develop from infant to adult.”

Astronomers have just discovered two Earth-size, rocky planets around a nearby star. Though the planets are way too broilsome for life, they suggest that steady improvements in telescope technology has made the discovery of habitable planets just a matter of time.

But as astrobiologists continue to search for life in space, geo-biologists (ok, we coined that) continue to find bizarre life in strange places on Earth: in the dark ocean depths, between grains of sand, and at roasty-toasty temperatures once considered deadly.

Hot, humid, and totally alive!

Fifty years ago, nobody believed organisms could survive near the boiling point of water. When Thomas Brock started probing the hot springs in Yellowstone in the 1960s, he was not looking to overthrow a ground rule of biology. Instead, the University of Wisconsin-Madison professor, then at Indiana University, sought to study bacteria in a simplified, real-world environment.

At the time, and even today, precious little was known about how bacteria live their lives — unless they cause disease.

As Brock sampled his way up a hot stream, he approached its source in a hot spring, and the water temperature rose steadily.

At the time, biologists thought life would not tolerate temperatures near 80° C. But Brock kept finding bacteria, so he kept looking. Eventually, he found some that could live and reproduce near the temperature of boiling water — 100° C.

The prize of his collection was a bacterium he named Thermus aquaticus (for its hot-water habitat) and placed in a public repository for study by other scientists.

Over the years, T. aquaticus proved interesting indeed. For one thing, it was the first of more than 50 species of thermophilic bacteria known to tolerate or require temperatures near water’s boiling point.

For another, it was the first of the Archaea (ancient ones), primitive microorganisms that scientists now regard as a separate and highly primitive kingdom of life.

Deep roots indeed

Because thermophiles are Archaeans, and prefer the steamy conditions typical of early Earth, many scientists think they may tell us about the origin of life itself.

To any basic scientist, those contributions would be enough. But because their enzymes work in high temperatures, where chemical reactions are faster, the thermophiles have proven to be extraordinarily useful.

Today, enzymes derived from thermophiles are used to convert millions of pounds of corn (maize) into sugar to sweeten soft drinks.

But more important, at least to scientists who don’t guzzle fizzy pop at the lab bench, T. aquaticus supplied TAQ polymerase, the essential enzyme for polymerase chain reaction, AKA PCR.

PCR is an artificial technique that does what living critters do every day — replicate DNA. But PCR is the rocket ship of replication, since it allows you to multiply a piece of DNA a billion times in a few hours. That produces enough DNA to analyze to your heart’s content — for genetic engineering, biotechnology and forensic purposes.

PCR depends on TAQ polymerase.

Aware that PCR and soda pop are both billion-dollar industries, corporations and scientists around the world have frantically searched for other thermophiles that may have equally useful enzymes. They’re looking in odd places — not just hot springs and volcanoes, but also deep-sea vents, hot petroleum-bearing rock, the outflow of geothermal power plants, and smoldering piles of garbage.

Prowling for glow-in-the-dark squid

Call me Bob.

Short for bobtail squid. (Did I mention that I’m a 3-4 centimeter cephalopod, formally Euprymna Scolopes?)

Anyway, I hang out in shallow waters around Hawaii. Save your crocodile tears — somebody’s got to live in the sunny, tropical ocean. Anyway, here’s my problem: Even though I have 10 tentacles, I don’t have spines, poisons, or any other decent defense.

So I spend my days burrowed in sand at the ocean bottom, trying to keep out of mischief. Still, a fellow’s got to eat, don’tcha know, so I cruise at night, looking to grab a bite.

Here’s the snag: All sorts of nocturnal predators seem to have this thing about calamari sushi.

Light before flashlights

A long time ago, my ancestors evolved a nifty defense against their big teeth: stealth. Even their tiny squid brains figured out that predators could see them from below, as tasty dark blobs against the bright ocean surface.

Since this was before flashlights, my relatives had to improvise. So they press-ganged billions of luminescent bacteria into making light for them. The idea was to make us just as bright as the ocean surface — and hence invisible.

At least, this is how my great-aunt Tentacla tells it. To tell the truth, I think it had more to do with the evolutionary advantage of being hard to see.

Anyway, my ancestors fed the bacteria, and gave them a home in two specialized light-emitting organs. These “photophores” have a reflective membrane to shine all their light down, toward the hungry predators. They use a diaphragm to control brightness, and even have a lens to spread the light.

The photophore reminds me of a backwards eye — one that makes light rather than detects it.

My folks even figured out how to switch the bacteria “on” when needed.

In return, the bacteria got room and board, in the biological deal they call “symbiosis” or “mutualism.” Sometimes I think people could learn from this cooperative spirit….

But that’s enough thinking for today. My squid brain is squashed.

As I burrow into the sand for another daytime nap, permit me to introduce somebody who considers me almost as fascinating as I do.

Seriously speaking…

Margaret McFall-Ngai, a biologist at University of Wisconsin-Madison, says the bobtail squid may pretend it’s cooperating in a symbiosis with those light-making bacteria, but the reality is more ominous.

She says there’s evidence that this may be slavery, not symbiosis, since the squid, “inhibits the growth of the bacteria to enhance their luminescence.” The bacteria, Vibrio fischeri, could make a better living drifting in the ocean, or in the gut of another marine animal, McFall-Ngai observes.

The concept of bacterial enslavement broadens our perspective on the many possible relationships in the living world.

Most people, if they think about bacteria at all, conjure up disease and decay, but people would be dead without bacteria, since the little critters play essential roles in producing vitamins and preventing disease.

Since the bacteria in our guts vastly outnumber the cells in our bodies, it helps that they’re helpful!

Nevertheless, and for understandable reasons, bacteriologists have traditionally focused on disease-causing organisms, and, for simplicity, on one species at a time. But that skews our view of how bacteria actually live, says McFall-Ngai.

Three cheers for complexity!

Complexity and subtlety may be the hallmarks of these interactions, and the complexity begins by recognizing that V. fischeri is closely related to V. cholerae, which causes the human intestinal disease, cholera.

Cholera is caused by a V. cholera toxin similar to a toxin produced by the light-emitting bacterium. But far from harming the poor little bobtail, that toxin signals it to secrete food for V. fischeri, so the toxin is really a chemical “dinner bell.”

And this raises the intriguing notion that a cholera bug secretes toxins not to kill its host but to discuss its menu. If so, our whole notion of pathogenesis may need rewriting, McFall-Ngai suggests. “Maybe when we’ve been studying cholera pathogenesis we’ve been studying an aspect of a normal conversation that’s gone wrong.”

Indeed, the traditional bacteriological view of bacteria as pathogens to be studied in pure culture may be “like trying to understand the complexity of all the cultures that lived in Paris by studying the activity of the Nazi occupiers,” McFall-Ngai suggests. “You are studying groups that don’t belong there, and have disrupted the normal activities.”

Want more on how the flashlight squid bullies its bacterial brethren?

Between the grains

(1996 story, only photos have been updated)

To zoologist Robert Higgins, small is beautiful. His infatuation with small creatures — “meiofauna” — dates to a student job in a biology lab that paid 35 cents an hour. Instead of quitting for more lucrative work, Higgins was intrigued.

He’d heard about tiny, amazingly diverse creatures, and put grains of sand and muck through a fine mesh, and used a microscope to find hundreds of organisms.

Forty-four years later, Higgins has retired from the Smithsonian Institution, but he’s still goggling at meiofauna — a complex group of animals found in most Earthly environments.

Indeed, a handful of wet sand could contain more biological diversity than a whole rain forest, Higgins says.

In the course of peering through countless microscopes, Higgins has discovered hundreds of species. With Danish biologist Reinhardt Kristensen, he found an entire phylum, called Loricifera.

Phyla are the broadest categories of organisms, based on structure, and according to the International Association of Meiobenthologists, “The majority of recognized phyla have meiofaunal representatives. Currently, 20 phyla considered to be meiofaunal from the 34 recognized phyla of the Kingdom Animalia. Out of these 20 phyla, five are exclusively meiofaunal in size.”

Photo: Giulio Melone, department of biology, Milan University.

A bdelloid (a type of meiofauna) shrinks when it undergoes anhydrobiosis. The dormant, dehydrated bdelloid has greater resistance to environmental stress but is ready to spring back to the active form in conducive conditions.

Meiofauna living between grains of sand have made some fancy adaptations to their harsh environment. Some have hooks on their feet, used to grab the sand. Others have hooked mouthparts, also useful for locomotion.

Beyond freeze-dried

To survive a difficult environment, meiofauna called tartigrades have evolved an amazing adaptation called “anhydrobiosis.” In this form of suspended animation, the animals replace water in their cell membranes with sugar, protecting the membrane from destruction through radiation and freezing. Microorganisms die when their cell membrane ruptures.

During anhydrobiosis, organisms are rather like plant seeds or bacterial spores, Higgins explains. “They can dry up for 100 years, and be rewetted, and come right back to active metabolism.”

Fun is fun. But what is the practical importance of studying stuff that can hardly be seen, doesn’t seem to cause disease, and is — at least to some — utterly ugly?

In other word, who cares about microscopic beach crud?

Meet the beach-cleaning crew

Anybody who likes to hang on the sand should be interested, Higgins says. “This is the system that helps keep our beaches clean.” Plankton, bacteria, all sorts of dead material is continually washing ashore, and a lot of people love to sit on beaches.

There’s a public-health angle here. Hookworms occur on beaches where dogs defecate, but meiofauna may consume hookworms, along with other nematodes. “So if we upset that, we could upset beach cleanliness,” Higgins says.

Higgins notes that meiofauna comprise a basic part of the food web, and disturbing them could have unforeseen consequences for the entire system.

Still, it’s hard to escape the notion that most of the motivation here is the pure scientific urge to discover, to classify, to understand. Meiofauna, Higgins notes, were seen under the microscope Anton van Leeuwenhoek invented in 1683.

The key to finding these things, Higgins indicates, in patience, technology, curiosity — and institutional support. “If you stare through a microscope for hour after hour, you have a chance of finding these things, but if you need to get out a certain number of papers each year, you have to take shortcuts and you won’t find as much.”

Fantastic freak show

Wondrous weevils sport super screw!

In animal appendages, some joints resemble hinges. Others, like your hip, are unmistakably akin to the ball-and-socket joint, another mechanical mainstay.

Now, scientists have found a biological screw in a type of beetle called a weevil. Obliquely described as having “rotational movement combined with a single-axis translation,” the new screw-and-nut assembly was first seen in a weevil from New Guinea, says entomologist Alexander Riedel.

The discovery of the first biological screw-and-nut assembly emerged from an exploration of the weevil’s characteristic defense mechanism, says Riedel, an entomologist and curator who specializes in weevil classification at the State Museum of Natural History in Karlsruhe, Germany.

Two things weevils have in common are small size – the Trigonopterus oblongus under study was about 4 millimeters long – and legs that fold under the body. “We wanted to look at their particular defense mechanism,” says Riedel, “to know how it works.”

Using a microscopic counterpart to CT scanning, German researchers snapped electron micrographs of the weevil’s trochanter (“screw”) and (ROLLOVER) coxa (“nut”).”

Image © Science/AAAS

It’s all in the scan, man!

Given the small size, the scientists relied on a kind of micro CT scan driven by X-rays from a synchrotron, “We realized there is a very nice screw joint,” Riedel says, “We’ve had this information for some time, but while talking with a herpetologist colleague, we realized there is no other case in the whole animal kingdom, in all of biology, with a similar screw joint.”

The nut-and-screw are located at one of three major joints in the beetle’s leg; when the leg is retracted, the screw tightens in the nut, which remains stationary, Riedel says. Overall, the screw and nut would be able to turn 345 ° although the leg itself does not move that much.

A (good) turn of the screw!

“The weevils, or snout beetles, have been known from ancient times,” says Riedel. “There are grain weevils and lots of other species, including the boll weevil [a cotton pest]. Many other species are not pests … and so are of no particular interest to humans, which is why nobody knows much about them.”

Why does every weevil species that that Riedel examined have such a mechanism? Weevils, which spend a lot of time climbing on vegetation, apparently evolved from beetles that usually walk on a flat surface or underneath bark, Riedel says. “If a weevil is sitting on the edge of a leaf and wants to walk on a small twig, it’s essential that it can grip under its body, and this motion goes very nicely with this screw joint. A ground [walking] beetle would have great difficulty walking in similar conditions.”

The screw joint now joins the hinge, ball-and-socket and saddle joint as fundamental technologies invented by evolution, Riedel says. Historians of technology have long wondered about the origin of the incredibly useful screw, and it turns out that screws and nuts were in their flour bins all along – but only visible to those who happened to have a handy synchrotron!

– David J. Tenenbaum

For controlling agricultural insects, bats are worth at least $3 billion a year to U.S. agriculture, according to a 2011 study from Boston University. “People often ask why we should care about bats,” said study co-author Paul Cryan, a research scientist with the U.S. Geological Survey in Fort Collins, Colo. “This analysis suggests that bats are saving us big bucks by gobbling up insects that eat or damage our crops. It is obviously beneficial that insectivorous bats are patrolling the skies at night above our fields and forests—these bats deserve help.”

As conservation officials scramble to respond to white nose, they are enacting quarantines to prevent people – cavers, bat-lovers and scientists alike – from transporting the fungus between caves. Last year, for example, the National Wildlife Refuge System halted public access to all caves and mines on its refuges, and set protocols to prevent scientists from spreading the infection.

In May, 2011, the Fish and Wildlife Service rolled out a national plan for confronting and controlling white nose syndrome.

But bats can do plenty of transportation on their own. Even non-migratory bats may fly 200 miles between their hibernation site and their summer range, says David Blehert, a microbiologist at the U.S. Geological Survey National Wildlife Health Center in Madison, Wis., and a leader of white nose studies. “They can move large distances, across state lines, so there is potential for significant disease spread based on bat-to-bat interactions.”

What is the white nose syndrome situation now? Why is it so deadly? What bright ideas are afoot to preserve insect-eating bats, and what is the likely end game?

Why deadly?

In the short time since white nose syndrome appeared in 2006, scientists have pinpointed a fungus called G. destructans as the killer. But how does G. destructans do its work? One clue comes from the fact that it only kills during hibernation, when bats live in mines and caves at a rather chilly 7°C. “The fungus only grows in the cold, and when insectivorous bats hibernate in a temperate region, they drop their core body temperature to the ambient level,” says Blehert.

(The fungus is not likely to attack fruit-eating bats, says Blehert, because they do not have long periods of “torpor,” the slow-metabolism hibernation state that is conducive to the white-nose fungus.)

A low body temperature allows the bats to survive winter without eating, but it could also curtail the immune system, Blehert says. “Studies of bat immunology are in their infancy, but based on what is known about the physiology of other hibernating mammals, especially the 13-lined ground squirrel it’s likely that the immune system becomes suppressed, and that leaves them particularly vulnerable” to the fungus.

How does the fungus kill? It apparently does not enter systemic circulation, as internal organs are not damaged. All mammals awaken from hibernation occasionally, but Craig Willis of the University of Manitoba has speculated that infected bats have more waking hours, causing them to run out of energy during a period when they neither eat nor drink.

Blehert and his colleagues favor a second explanation: dehydration. Despite the “white nose” name, Blehert says, the most significant infection occurs on the wings. “The wings of a bat have eight times as much skin as the trunk; it’s a massive, very delicate and exposed membrane” with a single layer of epidermis surrounding a thin layer of connective tissue and some muscles and glands. “The fungus selectively invades the wing skin, and destroys everything in its path,” Blehert says.

Beyond their role in flight, bat wings are also needed to regulate temperature, fluids and electrolytes. “The wings may be the Achilles heel that exposes them to such significant infection,” Blehert says.

Indeed, an emerging disease that is devastating amphibians, the chytrid fungus, also affects the skin, and is thought to kill by causing an electrolyte imbalance. “The amphibian’s skin is very important for the balance of water and electrolytes, which has been the basis for our hypothesis about why white nose syndrome is so deadly. There was a paper¹ in 2009 that demonstrated that a superficial chytrid infection causes an ion imbalance in frogs, causing a disruption of the potassium gradient that causes the heart to stop. A superficial fungal infection causes a cardiac arrest! This is a very different concept than getting athlete’s foot and having an itchy foot.”

Stopping the wave of death

As dead bats pile up in caves, what can be done to stop the spread of G. destructans? The first step, trying to slow dispersal, is already under way in affected states, with restrictions on cave entry, and new protocols for disinfecting equipment and people who have a legitimate reason to visit hibernation spots.

The fungus does respond to common anti-fungal agents, according to a 2011 study, which found, unexpectedly, that the meds worked at the low cave temperatures that the fungus prefers. “The challenge is, how could you use pharmaceuticals to manage a disease in free-ranging wildlife?” says Blehert. “They don’t go to the doctor, and they inhabit environments that are likely contaminated with fungus. Say you could treat bats and cure them of the infection. If you can’t remediate their hibernation sites, they will become reinfected when they re-enter the cave.”

The authors of the anti-fungal study did raise the possibility of using meds to decontaminate caves, but this process is not being done, Blehert says. “Going into a cave with a general fungicide would be like dropping a nuclear bomb on a city. Caves are full of bacteria, fungi, invertebrates and vertebrates that may only exist in that unique ecosystem, and getting rid of such an important group of organisms [fungi] could risk significant unintended consequences.”

Willis has proposed using little heaters, since bats seem to fare better in warmer regions of caves, perhaps because that sustains immune function. Small heaters are being tested as bat refuges in some New York State caves, says Lisa Warnecke, a post-doctoral fellow at Manitoba.

Lessons from Europe

G. destructans is an “emerging exotic disease,” and to investigate such diseases, scientists always want to know how the pathogen interacts with hosts in its land of origin, which seems to be Europe:

In 2009, the fungus was found in a greater mouse-eared bat in France²;

ENLARGE

Photo: Gabrielle Graeter, NCWRC

Is this bat unhappy about the tufts of fungus on its muzzle — or the researcher’s big hands?

During the winter of 2009-2010, infected bats were found in 76 of 98 sites in the Czech Republic; and

A 2010 study³ in Europe found a white nose pathogen in 21 of 23 suspected bats that was “100% identical” to the U.S. pathogen.

Although the fungus been found in at least five bat species in Europe, die-offs have not been seen there, suggesting that something is different about how the pathogen, host and environment interact. Pathogens and hosts co-evolve through time in a complex dance:

The pathogen may become milder, improving its own survival (and that of its host);

hosts may evolve immune resistance; and

hosts can change their behavior to reduce exposure to the disease.

In the lab in Manitoba, Willis and Warnecke are studying how long little brown bats are awake during hibernation, whether the fungus is a necessary and sufficient cause of death, and if the North American or European strains of fungus have different effects on the bats. “If both isolates show the same severity for North American bats, that may mean that bats in Europe have co-evolved with the fungus and are resistant to it,” says Warnecke. “On the other hand, if the European isolate does not cause trouble for North American bats, then the fungus in North America is a mutant that has gotten really aggressive.”

Other factors could explain the lack of disease in Europe, says Blehert. “European bats are larger, which may provide them with more of a buffer against a physical insult like a fungal infection.” The little brown bat, the preeminent victim of white nose, weighs about 6 grams – about the weight of two pennies, Blehert says.

European bats also tend to hibernate in small groups. “They don’t have those 100,000-plus hibernacula like we see in the United States. With fewer animals, the disease transmission dynamic is likely to be reduced, with less amplification of the fungus, and lower rates of bat-to-bat transmission.”

In the long run, Blehert says, American bats may evolve some resistance. “In general, the population decline in caves and mines comes to about 78 percent, but the bats have not disappeared. We would expect something that gets into population to cause high mortality and a steep drop-off in population. Then, with fewer animals around, disease transmission could moderate.”

Although the regional extinction of the brown bat has been predicted to occur 16 years from now, “our bats may ultimately develop population dynamics more like Europe, with fewer animals and moderated disease transmission and progression,” Blehert says.

Evolution, in other words, could select for animals that, for behavioral or immune reasons, are less susceptible to white-nose.

But letting the situation play out without trying to help the bats, Blehert says, amounts to a high-stakes gamble with one of the wonders of the night sky.

Trust Charles Darwin to be his own severest critic. Having expounded a revolutionary evolutionary theory of natural selection, he realized that the past gives birth to the present. Darwin knew about fossils, including the famous, three-section trilobites, that dated to the Cambrian period, now known to have begun about 540 million years ago.

Never one to duck logic, Darwin wrote:

Indeed, according to J. William Schopf, professor and director of the Center for the Study of Evolution and the Origin of Life at UCLA, what came before was totally mysterious when Darwin wrote “Origin of Species” in the 1850s. “Darwin knew about the Cambrian era, and the big extinctions after that were known, but he knew nothing about the earlier fossil record. This was the case for about 100 years.”

And then, starting in 1953, University of Wisconsin-Madison geologist Stanley Tyler noticed ring-like structures in rocks in Minnesota and Ontario’s Gunflint formation.

The rock — a fine-grained quartz relative called chert — was 1.9 billion years old – almost four times as old as the earliest Cambrian fossils.

Tyler, collaborating with Elso Barghorn at Harvard, recognized the circular structures as stromatolites, mushroom-shaped rocks formed by layers of microorganisms called cyanobacteria. In 1965, the two reported that stromatolites were the oldest fossils ever seen.¹

I can see you now!

Why did it take so long for Precambrian life to be recognized? “They had assumed that it would be like younger life, there would be coral, snails and trilobites,” said Schopf, an expert on the oldest life. “The basic problem was that a wrong assumption had been made. Life in the Precambrian turned out to be substantively different in organization and size.”

By exploring the interior of rocks using an increasing array of scientific techniques, Schopf and a growing group of colleagues have found life as early as 3.5 billion years ago.

Not bad for a planet with an estimated age of 4.7 billion years.

Double-not-bad, considering the exceeding scarcity of truly ancient rocks, hidden through the constant tectonic churning of the crust. The oldest rocks yet located are 3.8 billion years old, but any fossils they contain have been distorted by severe heat and pressure.

Still, Schopf said, four lines of evidence show the ancient roots of life on our planet: microfossils, molecular biomarkers, proportions of carbon isotopes and stromatolites. Stromatolites are layered rock formed by layers of microorganisms called cyanobacteria (formerly blue-green algae), which produce oxygen in sunlight.

While some of the fossilized microorganisms found in ancient rock apparently have gone extinct, the cyanobacteria closely resemble living organisms, Schopf told an audience at the University of Wisconsin-Madison on April 26. “Cyanobacteria do the same sort of photosynthesis as a blade of grass today. These are the guys that invented this process, probably 3-plus billion years ago.”

As testimony to nature’s predilection for retaining stuff that works, other fossil microorganisms resemble modern counterparts that require oxygen, cannot tolerate oxygen, or use it when convenient. “We’ve found 12 to 15 major families of cyanobacteria, the same ones that are important today, the same ones that are seen throughout the geological record,” Schopf says.

Tyler did not live to see the publication of his 1965 article, but it revolutionized paleontology, and has been cited by scientists at least six times since 2010.

“Stanley Tyler was a hero for this world,” says Schopf. “As [microbiologist Louis] Pasteur said, chance favors a prepared mind. Here was an economic geologist [concerned with finding minerals and mines] … and yet he saw these scrubbly things, and thought, ‘I bet they are fossils,’ even though they were almost two billion years old. This is the guy who made the discovery.”

– David J. Tenenbaum

When Deepwater Horizon blew up and melted down in April, the wound it tore in the Earth’s crust released a gusher of crude oil, estimated at 4.2 million barrels, into the Gulf of Mexico.

The massive microbial munching of methane during the BP spill may be the only good news from the Deepwater Horizon disaster.

The blowout also released about 160,000 tons of methane. If you counted molecules in BP’s blowout, methane (CH₄), the simple hydrocarbon that fuels stoves, furnaces and electric generators, was the single most abundant one.

But a report published in today’s Science shows that BP’s methane was totally devoured by microbes in the Gulf of Mexico, leaving less than .01 percent of the methane to enter the atmosphere. “We measured the sea-to-air flux of methane and found it was completely negligible,” says first author John Kessler, an assistant professor of oceanography at Texas A&M University.

Within four months of the April 20, 2010, blowout, a population explosion among methane-eating bacteria native to the Gulf decomposed virtually all of the methane, mainly in deep water, says Kessler.

Study author John Kessler extracts a water sample from a device that detects changes in water conductivity and temperature with depth.
NOAA Pisces.

The study offered three lines of evidence that bacteria were “eating” the released methane:

• Methane levels in the Gulf fell up to 10,000 times between June and October.
• Methane-munching microorganisms became extremely abundant downstream of the blowout. “Over the summer, the methane degraders were higher than we have ever seen at any other place in the world,” says Kessler.
• Dissolved oxygen in the water dropped as methane and oxygen reacted to form carbon dioxide and water, Kessler says. “Once we summed up all the lost oxygen in the area of the methane plume, we saw that it could only be explained by a complete [microbial] consumption of this methane.”

Although oxygen depletion is already a concern in the Gulf’s “Dead Zone,” the average loss was only 3 percent, Kessler says.

In a previous study, ethane and propane, two other natural gases that BP also released, decomposed even faster than methane, and were no higher than background levels by early fall. In both studies, Kessler collaborated with David Valentine of the University of California at Santa Barbara.

Cool news for your atmosphere

In the short term, spilled methane is less environmentally dangerous than crude oil, but it can pose a global warming problem in the long term, since a molecule of methane stores much more heat than a molecule of carbon dioxide.
Methane seeps are frequently found at ocean floors, where methane from decomposition enters the ocean. And unfathomable quantities of frozen methane are stored beneath the seabed.

So inquiring minds want to know: If and when this methane enters the ocean, could it reach the atmosphere and accelerate global warming?

Pisces, a research ship of the National Oceanic and Atmospheric Administration, was a floating laboratory to study Deepwater Horizon's aftershocks.
Photo: John D. Kessler/TAMU

The giant Deepwater spill contained too little methane to affect atmospheric levels, says Kessler, “but it does simulate a very energetic release from a seep or a methane hydrate, and so we were interested in using it as an analog for understanding how a massive submarine release of methane might behave.”

Although the microbes-eat-methane story provides a rare bright spot in BP’s ecological disaster, it’s not clear what would happen in shallow water, and in places lacking natural methane and a ready supply of methane eaters.

“The Gulf of Mexico has many natural methane seeps,” says Kessler, “that probably account for why Gulf waters are populated with these microorganisms, which are ready to degrade methane once there is a massive restocking of their ‘buffet.’ How this may play out at another place, without the natural seeps, I’m not sure.”

Within four months, bacteria had spawned enough offspring to devour essentially all of the added methane in the Gulf. “But if the bacteria are at lower abundance, would this take five months or two years? We don’t know.”

– David J. Tenenbaum

Even people who can’t distinguish the periodic table from a dining table know arsenic is poisonous, although few realize why. Arsenic is chemically akin to phosphorus, one of life’s essential elements. But it’s not identical, and when arsenic substitutes for phosphorus, it produce a toxic compound instead of a protein or chunk of DNA.

So we weren’t the only ones to be surprised by a study in today’s Science that identifies a bacterium that thrives on arsenic, at least in the lab, and incorporates this normally-poisonous element into proteins, fats and DNA.

Image: Wikipedia

A more typical reaction to arsenic comes from the elderly poisoning victims in the macabre comedy “Arsenic and Old Lace.” In that play and movie, two dotty spinsters spiked elderberry wine with arsenic, strychnine and cyanide for a freelance euthanasia project.

The new study is the first to show that it is possible to substitute for one of the elite elements (carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur) that were thought to be found in all life, says Ariel Anbar, a professor of earth and space exploration at Arizona State University. “No one has previously shown that arsenic can be substituted, and I am not aware that anyone has found a substitution for any of the six essential elements. And that’s why this is a big deal.”

Arsenic: It’s what’s for dinner

Felisa Wolfe-Simon, a former post-doctoral fellow with Anbar, gathered sediment and water from salty, alkaline, arsenic-rich Mono Lake in California and placed them in cultures intended to replicate Mono Lake water.

Images courtesy of Science/AAAS

These bacteria, viewed under an electron microscope, metabolized arsenic as if it were phosphorus. Mouseover to see the same strain of bacteria growing with phosphorus but without arsenic.

“Over time we made serial dilutions, one in 10, one in 10,” always including a strain of lake microbes, says Wolfe-Simon.

Wolfe-Simon, who is now at the NASA Astrobiology Institute and U.S. Geological Survey, says the dilutions removed “essentially all” of the phosphorus. In some samples, she jacked up the arsenic roughly 2,000 times above the concentration in Mono Lake, which gets its arsenic from rocks and is already about 20,000 times above the Environmental Protection Agency standard for arsenic in drinking water.

“This is a huge amount of arsenic,” Wolfe-Simon says. “It’s surprising that they could grow, even with phosphorus, in that condition.”

Although the bacteria died in the absence of phosphorus and arsenic, they survived if only arsenic was available. “The arsenic seems to be substituting for phosphorus,” says Wolfe-Simon. “We have identified arsenic in cellular structures that are consistent with where we would expect to see phosphorus.”

Photo: ©2010 Henry Bortman

Mono Lake, California, is salty, alkaline conditions, and toxic to many organisms. The lake is ideal for the study of extremophiles, microbes that live under bizarre temperature or chemistry.

Stepping out of line

This elemental swaperoo could operate more broadly, since the elements in each column of the periodic table have chemical similarities. If one neighbor of phosphorus can sustain life without phosphorus, could the elements below carbon, nitrogen or oxygen do the same?

Photo: ©2010 Henry Bortman

“This is not just about arsenic or Mono Lake,” says Wolfe-Simon. Life on Earth and the rest of the universe will be limited if it always requires six elements, but “If microbes can use arsenic as they can use phosphorus, that opens the door. What else can life do that is not yet known?”

In searching for life in the universe, NASA has focused on liquid water, another prerequisite for known life, but Anbar asserts that a search for the chemistry of life should stay broad. “Felisa’s results say we should think harder about which elements we should follow. We don’t want to be too influenced by the particular example of life on Earth. We want to push the boundaries.”

Call it “Arsenic in a new place.” Roll cameras!

From French bread to non-fossil fuel?

Yeast can ferment corn starch into ethanol to be added to gasoline, but that diverts millions of tons of food from hungry people. Researchers are trying to ferment many other plant carbohydrates, especially cellulose, the tough chain-like molecule that stiffens the cell wall so plants can stand by themselves.

Unfortunately, the yeasts used to make ethanol have no taste for cellulose.

In this week’s Science, Jamie Cate, in the department of molecular and cell biology at the University of California at Berkeley, reports a transfer of two genes from a fungus to ethanol-making yeast. Although the fungus was discovered on French bread in the 1840s, the result was not exactly a fine Burgundy, or even a gallon of cheap jug wine, but it was a proof of principle that a single organism could, almost single-yeastedly, convert cellulose into ethanol.

Mon dieu!

The advance may hasten the day when waste wood, crop residues and fast-growing crops such as switchgrass can replace edible crops like corn and sugar cane in producing fuel.

Raise a glass to success!

“It’s a proof of principle using lab strains,” says Cate.

The genetic transfer enabled a single strain of yeast to convert cellulose in plant cell walls into ethanol. After commercial enzymes busted the cellulose into short chains of glucose units, the yeast:

The short chains of glucose that the Neurospora crassa fungus extracts from cellulose do not normally enter the yeast cell, but the transporters ensure that they will enter the transformed yeast, enabling the yeast to make ethanol from normally indigestible compounds.

Taking lessons from fungi

The research began with a basic question. A large portion of plant biomass is cellulose, and “microorganisms in the wild live on plants; they obviously have figured out how to degrade plants as food,” says Cate. “Plants have been figuring out ways to prevent microbes from doing this, so there’s this ongoing battle, and we knew some fungi would be very good at decomposing cellulose.”

Cate focused on N. crassa, a well-studied fungus that lives in burned-over areas, but also has a taste for a stale baguette. The research team moved two genes from the fungus into Saccharomyces cerevisiae, a yeast widely used to ferment sugar into ethanol.

One gene forms structures in the yeast’s cell wall that draw short chains of glucose into the cell. The second gene makes beta-glucosidase, an enzyme that the fungus (and now the yeast) use inside the cell to snip the short chains of glucose into individual glucose molecules, where the yeast converts them into ethanol.

Raise a glass to success!

Although the short chains of glucose that the fungus extracts from cellulose is not digestible to normal yeast, the transformed yeast used these short chains to produce an abundance of ethanol. “It’s a proof of principle using lab strains,” says Cate. “We in the Energy Bioscience Institute [a collaboration of UC-Berkeley, the University of Illinois, Lawrence Berkeley Laboratory and BP] have colleagues who are helping us look at some really robust, industrial yeasts to see how the transporters work in those systems.”

Cate says transporters are key. “Any cell is a fortress, with a membrane or a cell wall that keeps things out to protect its innards. To get a small molecule in or out, there has to be a way, and these are the transporters, which live in the cell membrane, with parts on the outside and parts on the inside.”

The study was “a pretty slick example of how genomic technology can rapidly get you to the gene you care about,” says Steven Slater, associate director of the Great Lakes Bioenergy Research Center. “They used a combination of published literature on genes that are differentially expressed when several fungi are exposed to cellulose, and were able to rapidly go from there down to something that looks like transporter.”

Training a workhorse

The key, Slater says, is that “they took a workhorse organism that is primarily used for the production of ethanol and gave it a new genetic tool that could be used to get things other than glucose inside the cell; that’s important for producing ethanol from cellulosic biomass.”

Indeed, Cate says, many organisms have ways to transport fragments of cellulose: “You can find these all over in nature, including in the black truffle, a fungal delicacy that grows symbiotically on oak trees.”

Cate expects further progress. “We in the Energy Bioscience Institute [a collaboration of UC-Berkeley, the University of Illinois, Lawrence Berkeley Laboratory and BP] are testing some really robust, industrial yeasts.”

This process may not be limited to ethanol, Cate says. “It’s modular, and it may benefit research groups that have been working on yeast to make all sorts of interesting biofuels: alcohols, or things like diesel or jet fuel.”

David J. Tenenbaum