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.”

Among all animals, amphibians are in the worst shape; fully 30 percent are classified as threatened or endangered. Amphibians – including frogs, toads and salamanders — are under attack by a deadly fungus. They are losing habitat to farms and cities, and collected as food or pets. Amphibians are suffering from chemical pollution and the warming climate.

The present is harsh enough, but the future seems worse.

This week, Nature publishes the first global attempt to forecast the impact of three big threats to amphibians by 2080 – a year chosen to be one century after the study’s baseline data.

By comparing areas with plenty of amphibian species with projections of climate change, land use change and the chytridiomycosis fungus, the researchers forecast a grim future for these cold-blooded, four-legged vertebrates. “The bad news is that more than two-thirds of all high-richness regions will probably be affected, to a high intensity, by one of these three threats,” said lead author Christian Hof, who did the work as a Ph.D. student and post-doctoral fellow at the University of Copenhagen.

The geographic study of data on 5,527 amphibian species found little overlap between the cool, moist areas afflicted by fungal serial killer chytridiomycosis, and the places likely to suffer the worst effects of changes in climate and land use.

And the losers win!

In forecasting the future of amphibians, the study coined two technical terms: “losers” — species that are expected to suffer due to disease or changes in climate or land use, and the less numerous “winners,” which are expected to prosper by 2080.

The projection hinged on whether an expected change would make a habitat more or less suitable to the species, says Hof, who’s now at the Biodiversity and Climate Research Center in Frankfurt, Germany. “We ran a number of climate-change models and based on them, calculated a change in climate suitability for each region across the globe.”

Based on these changes in suitability due to climate, land use and disease, Hof adds, “We calculated the number of species that would probably decline due to a decline in habitat suitability. We classify the species as a loser in a particular region, but that does not mean it will decline across its whole range.”

Overall, the researchers found an increasingly dire future for amphibians. For example, 54 percent of frogs are likely to be “climate losers” in the average grid cell of their model. And heavy impacts are projected for about two-thirds of the regions with the highest species richness in frogs and salamanders.

In fact, the future could be even worse, since the study ignored a number of potentially damaging factors, including chemical pollution from cities, factories and agriculture.

Photo: Robert Fletcher, Ohlone Preserve Conservation Bank

Tougher times might await this prowling California tiger salamander, an endangered California native.

Going down!

It’s frustrating but understandable that the study could not predict rates of decline among amphibians. “For many species, we are not sure about the actual distribution, many have tiny ranges and we don’t know where they occur, so we can’t relate historic changes to, say, climate change. We were very careful not to predict extinctions, based on these uncertainties.”

Data are scarce in the study of amphibians, agrees Anna Pidgeon, an assistant professor of forest and wildlife ecology at University of Wisconsin-Madison. “It’s frustrating, amphibians are out at night, often in remote areas, they are small and many are cryptic, so it’s a huge challenge” to understand their populations and ecologies. “We work with the best data we have all the time … and try to make inferences from what we know about close relatives.”

Pidgeon, an expert on habitat needs of vertebrates, says predicting 70 years into the future is always dicey, but that the study’s analysis of multiple threats and global scope are major accomplishments. “They did a lot of things to make sure they were using consensus data, and that makes it a pretty solid approach.”

Although the study looked at overlapping threats, it did not actually look at interactions between those threats, Hof says. “What needs to be done, and we could not do that with our model, is to look at, for example, how climate change would affect susceptibility to the fungus. How would habitat fragmentation affect susceptibility to climate change?”

Although the study does not suggest practical changes that could sustain amphibians in the short run, “The general conclusion is that it’s very important, when thinking about the future for amphibians, to consider different threats together,” says Hof. “Just looking at one threat will not give us the whole picture.”

– David J. Tenenbaum

In a world studded with intractable conflicts, none seems more nettlesome than he one between Israelis and Palestinians. In this and many other conflicts, people are often trained to believe the worst about the other side, who are variously stereotyped as immoral occupiers or immoral terrorists.

These conflicts, as history has shown, are not ideal for peacemaking based on compromise, and yet the conflicts in Northern Ireland and South Africa have come to peaceful resolutions.

But during the conflict, even mentioning the opposing side can backfire, says Eran Halperin, a professor of political psychology at the Interdisciplinary Center in Herzliya Israel. “When you try to tell an Israeli something positive about a Palestinian, or vice versa, the immediate reaction is defensive. In many cases, they are not willing to hear positive information about the other side.”

A sideways approach, however, may be more effective at changing attitudes and creating a willingness to compromise. In a study just published in Science¹, Halperin and co-authors demonstrated that simply reading a few sentences about the successful resolutions of historic conflicts elsewhere made Israelis and Palestinians more amenable to compromise.

“There are positive pieces of information that the parties could absorb, that could lead to a change in positions,” says Halperin, “but people in almost every group involved in a conflict are not willing to hear it. But if you try to go more indirectly … to talk in a general way, you hope they will apply these beliefs to the other group, and this is what our results show.”

Testing tolerance

In a series of experiments, Halperin and colleagues asked Palestinians and Jewish and Arab Israelis to read a few paragraphs in a supposed “reading comprehension” test. Then, as part of a supposedly different study, the same people were asked about their attitudes toward the opposing side.

The tested paragraphs that contained a more positive interpretation of history strongly affected willingness to compromise to resolve conflicts.

Instead of confronting the subjects by stressing that the other side could change its views, Halperin says, the test paragraphs “say that people in other conflicts went through meaningful change in their positions and behavior, and we expect people to understand by themselves that this can happen here.”

The study opens a crack in the despair aroused by prolonged conflicts, says Halperin. “We have now the first indication of what kind of message we should convey to people, to make them more open to the other side. And we already have preliminary data showing that the exact same pattern occurs in other long-term intractable conflicts around the world.”

Still to come, he acknowledges, is “the biggest challenge, using a larger scale intervention to make these changes.” Using the education system and mass media, he proposes a “simple message: Groups change, and behavior that is violent and immoral is a result of a specific situation, leaders and economics. They are not the result of a long-term culture with a fixed character.”

The intervention was focused on hope, Halperin says. “One of the biggest barriers to peace is because people don’t have hope, they don’t believe that the other group can change. If you don’t believe the other side can change its attitude, and as a result its behavior, there is no reason to offer a gesture or compromise, to take a risk in negotiation, and then you can’t make any progress in any intergroup conflict.”

– 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.

As deadly American drones work the skies over Afghanistan and Pakistan, we got to wondering how similar remote-control approaches are contributing to science. In science, as in war, leaving the staff behind can slash costs and allow sustained exploration of no-go zones.

Part of the story is propulsion: New science vehicles can travel long distances through the ocean and atmosphere with minimum energy. Brains-on-board also matter: Computers enable these super-sensors to make decisions and work long stretches with little or no back-seat driving.

The result is a lot of science per gallon.

Although the vehicles we’ll look at have scientific purposes, they get major financial and technical support from the Department of Defense, proving that military and peaceful pursuits are inextricably linked in extreme environments.

If you dig the deep ocean, WHOI — the Woods Hole Oceanographic Institution on Cape Cod — is a good place to be. The renowned saltwater scientific outfit has a new, deep-water explorer that works without a lifeline.

Meet Sentry, which can take photos and make chemical and geophysical measurements down to 4,500 meters depth, and has worked two high-profile environmental issues: global warming through methane release, and BP’s Deepwater disaster.

Sentry has been used to look for “cold seeps,” regions of the seafloor that release large amounts of methane, says Chris German, WHOI’s chief scientist for deep submergence. “Cold seeps are like the overlooked younger sisters of hydrothermal vents,” the “black smokers” that release superheated fluids and anchor unique ecosystems at the sea floor, usually in mid-ocean.

Cold seeps are located closer to the continents, and “are not as spectacular thermally or geologically, but they do have some of the same chemistry,” says German, “and a lot of the same kinds of animals, even the exact same species.” Cold seeps may explain the distribution of deep-sea organisms around the ocean, he adds. “We want to understand … whether animals are using these locations as stepping stones.”

Most cold seeps were found by accident, but German thought Sentry could detect subtle chemical clues, and last October, he got to test that idea at an underwater landslide off the coast of Norway. The landslide had released pressure on a material called methane hydrate, and a large amount of methane was bubbling from the seafloor mud, creating a “mud volcano.”

Methane is a much more powerful greenhouse gas than carbon dioxide, and given the staggering amount of methane held in methane hydrates, such releases could create a nightmare feedback: warming releases methane, which traps more heat, causing more warming that releases more methane.

Getting engulfed

By prowling around the known cold seep near Norway, German confirmed the detection hypothesis.

Then, the day after Sentry returned to Woods Hole, a real-world opportunity appeared for the new technique.

Biologist Charles Fisher at Penn State was about to embark on a mission into the aftermath of BP’s blowout in the Gulf of Mexico, and he wanted help locating a coral patch to compare to another he’d already located 1,200 meters deep, 11 kilometers southwest of the blowout.

That coral was coated with a brown goop that looked suspiciously like crude oil. Could Sentry locate, for long-term comparison purposes, a similar coral outside the oil plume?

Fisher was part of a National Science Foundation-sponsored “rapid response” cruise to the Gulf, but German was still unpacking. “We’d have two weeks to turn around and get going, and I went to our guys Monday morning and asked, ‘Can you do this?’”

The maintenance crew figured out who would miss what weekend, and they agreed to do it, German says.

Cold seeps and deepwater coral in the Gulf of Mexico are linked, German explains, because the coral live on bare rock, which is often carbonate, and carbonate rock forms at cold seeps when methane is oxidized into carbon dioxide. “So beneath every healthy deep coral, is an active or historic cold seep.”

Suddenly, a theoretically interesting search technique became relevant to the biggest American oil spill in a century.

“Flying” with a map

Based on oil-industry data about the sea bottom, Sentry visited one location southeast of the Macondo well and found no coral. But at the second location, German says, “We hit pay dirt. We flew backward and forward, and found an active cold seep and evidence for tube worms, mussels and coral.”

Ocean-floor research seldom moves so fast, German says, and within hours, he was one of three people to visit the spot in Alvin. “In 36 hours, we went from nothing other than a hunch, to having a topographic map and photos,” German says. “We dove to the sea floor, and there was no mysterious driving around in the dark. Within 15 minutes, we drove to the site because we had a perfect map of where to go.”

In fact, German was holding a fresh, glossy photo of the target, taken less than two days previously.

Sub-terra cognita? Not!

And so is the ocean bottom, as people often say, still less familiar than the far side of the moon? German insists that it still is, despite years of research and an increasingly capable flotilla of deep-sea ships. “In December, in the Gulf, I could see at least 10 to 20 oil rigs… but I’m pretty sure, driving across that seafloor a couple of hours offshore from the United States, that nobody ever laid eyes on it before.”

A recent survey of marine biodiversity shows a chain of ignorance stretching across the Pacific, located near regions of extremely high biodiversity near the Philippines and Australia, German says. “In many of those locations, they’re 300 miles square, there have been fewer than 50 biological measurements in the history of the ocean. This is a chain across the South Pacific ocean, the single biggest contiguous ecosystem on the planet, and it has not been studied.”

And that’s the rule, not the exception, German says. “Close to one-half of the planet is at least 3,000 meters deep, and it’s much further away [and deeper] than the Gulf. From satellite altimetry we have an idea where the bumps are on the seabed, but we don’t know what’s going on; we have a vanishingly small idea.”

Deep water may be the sexiest place in oceanography, but long-term studies are also difficult and expensive in shallow waters, especially if they are remote, icy, stormy, or all three. Propellers, the standard way of moving through water, require a lot of energy and quickly drain batteries on artificial fish.

Gliding — think of soaring like a hawk as opposed to flapping like a sparrow — is a much more conservative approach.

And gliding is the MO of Seaglider, a project built by the University of Washington with money from the Office of Naval Research and the National Science Foundation. Using battery power, the glider alters its buoyancy, causing it to rise or fall through the water. By altering its center of gravity and adjusting its fins, the metal fish moves horizontally with minimal amounts of electric current.

How minimal? In 2009, a Seaglider traveled a record 3,050 miles through the North Pacific during a 9-month journey, without the caress of a human hand or an electric transfusion.

Costing “only” about $100,000 apiece, about 60 gliders are working around the globe, says Craig Lee, a principal oceanographer at UW’s Applied Physics Laboratory, recording basics like temperature, salinity, dissolved oxygen and optical characteristics of its surroundings.

In 2008, south of Iceland, gliders and floats studied carbon uptake by phytoplankton — floating plants that bloom in spring and play a major role in the global carbon cycle. The goal was to follow “parcels” of water during the entire bloom — which ends after some weeks when plankton are eaten or sink in the water. Both processes can remove carbon dioxide from the atmosphere for long-term storage, and therefore have implications for global warming.

“We were trying to learn what drives the carbon flow,” says Lee. “Nobody had done this before: the Seagliders and the buoys had the persistence, the ability to be there for the entire duration of the bloom. You would have to schedule a ship one year ahead, and … if you got there on time, it would be too expensive to keep the ship out there for the whole bloom.”

If ice is nice, under ice is nicer!

In 2009, a Seaglider spent 51 days in Davis Strait, the frigid water separating Greenland and Baffin Island, traveling more than 450 miles under the ice. The Strait is a chief source of melt-water from the frozen Arctic Ocean.

Climatologists worry that a rush of cold, fresh water through the Strait could alter the warm Gulf Stream and freeze Northern Europe.

Getting measurements from Davis Strait is expensive and dangerous, especially considering how much of it is under ice. But the Seaglider did just fine, says Lee. “This was very exciting, that ability to stay out there for a long time, and the ability to get to places that otherwise would be difficult. In winter in the North Atlantic, nobody wants to be there…”

The fish navigated under the ice using five anchored sonar beacons that created an undersea version of GPS, Lee says. Ten times, using its software, the glider found holes in the ice, poked its nose through them, and phoned home via satellite telephone. “It tries to sense ice by looking at the temperature of the water,” says Lee. “It emits a ping and tries determine whether ice is overhead, and it has a climate map that tells it, for a given position at a given time, is ice likely to be overhead? Using all that information, it decides whether to surface.”

During those famous North Atlantic storms, “It just keeps working, it does just fine, continues to navigate, continues to report. We’ve been in 40-foot seas, with 60- to 80-knot winds, and everybody’s happy, although it takes a little longer to get a phone call through.”

The glider carries a quarter for the phone call, but no Dramamine…

A fruit of the military’s desire to see everything from a safe vantage, Global Hawk is a secretive, high-flying, pilot-free jet that can fly at 60,000 feet for 30 hours, non-stop.

For its occasional forays into peaceful work, Global Hawk carries a large cargo of scientific instruments that can monitor light, pollution, ozone, water vapor, weather, clouds, incoming and outgoing radiation, even particles smaller than 1 millionth of a meter across.

The Hawk, which flew scientific missions from NASA’s Dryden Flight Research Center in California in April, 2010, can also be used for earth observation, such as tracking algal blooms in the ocean, vegetation on land, and various resource issues.

Hawk has tracked pollution from Asia above the North Pacific as it moves toward North America and looked at large-scale atmospheric circulation, which influences weather and the distribution of radiation-blocking high-altitude ozone.

We could not get through to a source at the National Oceanic and Atmospheric Administration, which plays a role in Hawk’s science, but we grabbed a press release issued after Hawk’s first environmental flight.

According to Paul Newman, an atmospheric scientist from NASA, “The Global Hawk is a revolutionary aircraft for science because of its enormous range and endurance. No other science platform provides this much range and time to sample rapidly evolving atmospheric phenomena. This mission is our first opportunity to demonstrate the unique capabilities of this plane, while gathering atmospheric data in a region that is poorly sampled.”

In their quest for data on the deep, scientists have gotten a trickle of info from sensors attached to deep-diving marine mammals. In November, 2009, the Scripps Institution of Oceanography launched SOLO TREC (Sounding Oceanographic Lagrangrian Observer Thermal RECharging vehicles; glad you asked?), a bobber that can sink 500 meters into the ocean, then return to the surface to report via satellite to scientists who may prefer sipping lattes at a Java Joint to crowding the rail on a topsy-turvy research ship.

Let’s call this Solo, and let’s agree that it’s a strange vessel. Solo can adjust its buoyancy, but lacks propellers and cannot drive laterally, so its location is at the mercy of the currents.

Solo records basic ocean conditions, but the real accomplishment is proving that its power system needs no recharging and could, theoretically, operate more or less forever – or at least until it breaks or barnacles or plants foul the fish up and slow it down.

Solo had already completed 300 dives by March, 2010, and although it sounds like a perpetual motion machine, it actually sucks its energy from the ocean as it rises toward the surface:

According to Yi Chao of the Jet Propulsion Lab, a Solo principal investigator, “This technology to harvest energy from the ocean will have huge implications for how we can measure and monitor the ocean and its influence on climate.”

Funded by NASA and the U.S. Navy, Solo’s technology is also obviously useful for monitoring animals and the movement of ships and submarines.

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

With fanfare that even snared some attention outside scientific circles, the 10-year Census of Marine Life came to a conclusion Oct. 1. The headlines and self-congratulation were deserved: our “ocean planet” is predominantly covered with salt water, and the Census had strength in numbers: 2,700 scientists from more than 80 nations spent $650 million exploring life in salt water. Working in 25 groups, the scientists sifted and collated old data and performed new studies on 540 field expeditions.

The Census also crafted the ground-breaking Ocean Biogeographic Information System. This public database contains 30 million records on more than 100,000 marine species, derived from new studies and about 800 existing databases that were harmonized for easy digital access (or so we’re told; we confess we’ve not looked up our favorite lobster in the database).

Kiwa hirsuta, Ifremer, A. Fifis, 2006

South of Easter Island in the Pacific, Census explorers discovered the yeti crab, which became the first member of a new biological family, Kiwida (Kiwa was the mythological Polynesian goddess of shellfish). The yeti crab supposedly resembles the abominable snowman, the “yeti.”

The effort was monumental, but necessary, considering that roughly 71 percent of our planet is covered by ocean. For reasons of remoteness, expense, logistics and physics, ocean science is difficult and expensive, and as a result, we know a lot less about life in the oceans than on land.

And even on land, scientists cannot agree on the total number of multicellular species, let alone count the bacteria and other one-celled critters.

The effort to explore salty sections of the planet that began in 2000 has already boosted the number of known marine species from 230,000 to 250,000. About 5,000 more candidate species await analysis in jars and freezers around the world.

What is the big picture?

Educated guesstimates suggest that the oceans may hold 1 million multicellular species – four times the number that’s been cataloged. In total, since 2000, an average of 1650 new marine species have been named each year — proof that the age of biological discovery continues. That number includes about 150 species of fish.

Courtesy Patricia Miloslavich

Half of fish biodiversity in the Caribbean is located near venerable marine science stations (circled). “Very few samples come from the huge, deep-sea basin in the middle,” says Census scientist Patricia Miloslavich. “If you go to places where you have never been, you will find new species.”

Our view of marine biodiversity suffers from sampling bias – we find more species near scientific stations, and that is one error Census projects are trying to correct, says Patricia Miloslavich of Simon Bolivar University in Venezuela. Miloslavich, a co-senior scientist for the census and head of its Caribbean project, says biodiversity data for the Caribbean, “did not show the location of biodiversity so much as the location of marine scientific institutions. There are little hot spots around … the places where most research been carried out in the last 50 to 80 years.”

Because South America extends so far north and south, and fronts two major oceans, it posed a good test for the notion that biodiversity would peak in the tropics and taper off toward the poles. Miloslavich says Census data from South America refuted that conventional wisdom.

Near South America, at 40° to 50° south latitude, biodiversity is much higher in the Pacific than the Atlantic, probably due to the many biological niches in Chile’s convoluted coastline. Scientists traditionally expect to find more biodiversity in the tropics.

In the tropics, the expected high biodiversity did appear in the Pacific and the Atlantic, Miloslavich says. But the Pacific also showed a biodiversity hotspot between 40° to 50° south latitude. “The Chilean fjords are a very irregular coast, with a lot of biodiversity,” Miloslavich says, “but at the same latitude on the Atlantic side, off Argentina, biodiversity was low.”

No way can we summarize this huge effort to catalog and measure ocean life. Instead, we’ll encourage you to browse for yourself while we focus on new data about:

Canada’s coldest realm

The Census of Marine Life studied Canada’s Atlantic, Pacific and Arctic coasts, which by themselves account for 16 percent of the globe’s coasts, says Philippe Archambault, first author of the report on Canada’s “three oceans”.

The Census attempted to negate sampling bias, which had suggested that the Atlantic was more diverse than the enormous Arctic coast, which stretches more than 160,000 kilometers.

Colossendeis colossea, Mylène Bourque, Benthic Ecology Laboratory, Institut des sciences de la mer, Rimouski, Quebec.

This large sea spider, from the Canadian Arctic, feeds on corals and other organisms by sucking their contents through his enormous mouth, or proboscis, located at lower right. Although the sea spider has a small body, its vital organs, including gonads, are housed in its elegant legs.

On the Arctic coast, biodiversity counts covering just 53 square meters (“the size of three Canadian kitchens!” Archambault says) revealed 1,200 species (mainly animals longer than 1 millimeter). In comparison, studies of 170 square meters of the shorter Atlantic coast showed 1,300 species. We offered the conventional wisdom, that the Arctic is biologically boring. “This was not the case when we put out a similar sampling effort,” Archambault says.

The planetary warming that is melting the Arctic ice is already affecting sea life, Archambault adds. In areas that were normally covered with ice for most of the year, the summer melt allows a brief pulse of sunlight that energizes plants, starting a simple food chain in which animals graze the plants and drop to the sea floor, to be eaten by predators. But when the water remains ice-free for more time, Archambault says, small crustaceans called copepods in the water eat the grazers before they can reach the sea floor. “So you now have copepod feces going to the sea floor, and you don’t have the same animals living down below.”

Photo: Casey Debenham, University of Alaska Fairbanks

These subarctic sunflowers live in the shallow waters of Prince William Sound, Alaska; part of an Arctic that now seems unexpectedly rich in biodiversity.

The studies organized by the Census are documenting today’s conditions in the Arctic, so we can understand what happens as the climate changes. “The Arctic is almost the last pristine area on the planet,” Archambault says. “When the ice melts, there will be more shipping, more potential for oil spills, and yet we don’t have baseline information” to help track the anticipated changes. (This video shows biological exploration in the Arctic.)

The Canadian studies highlighted how biology is hobbled by a shortage of taxonomists — experts who can distinguish one species from another. “We are losing taxonomic expertise in Canada, and everywhere,” says Archambault. “We have much more technology for counting species, but this can only help us know how many species are there, it won’t tell us what they are doing.” He notes that the Census of Marine Life had to send 25 samples of polychaete worms, a common sea-bed resident, to Mexico for analysis, and one turned out to be an unknown species. “We cannot do this identification in Canada anymore,” says Archambault. “Taxonomy is not sexy enough!”

A lot of biology is at stake in the frozen realm, Archambault says, yet we don’t even know what’s living there. “Each time we send in equipment, in the Arctic, in the Pacific or the Atlantic, there is a big chance of finding something new.”

Tracking fish

Migrations always fascinate biologists, whether it’s the monarch butterfly winging thousands of miles between central Mexico and the American Midwest, or the Arctic tern, flying a round-trip of about 9,000 miles from the South Atlantic to Norway.

Whales migrate, turtles migrate, and so do fish like the salmon. Because tracking migrations, especially for smaller critters, is difficult, one Census project has laid strings of underwater microphones across rivers, straits and the continental shelf along British Columbia.

The strings can be used to track fish or other animals that carry tiny noisemakers.

On the continental shelf, receivers spaced 800 meters apart can detect 90 percent of the fish swimming past, says Jim Bolger, executive director of POST, the Pacific Ocean Shelf Tracking project. Because the network can identify individual animals, remote-control migration tracking becomes possible once the noisemakers are in place.

Scientists who use the network “are not only looking at where they go and how fast they traveling, but are identifying bottlenecks for survival, where fish fail to show up,” says Bolger, who also directs the Vancouver Aquarium. Such information can abet management measures designed to make life easier for many types of marine creatures.

2004 photo, POST

Acoustic units prepare for a swim in the Strait of Georgia, British Columbia, to prove that these arrays of microphones can track animals bearing distinctive noisemakers.

Salmon in the Northwest have been a focus of concern for many years — as their spawning rivers are dammed, fewer are returning to the ocean to mature. Fish tagging can be used to track salmon, if you can find the fish later on, but POST works much quicker, Bolger says. “We don’t have to wait four or five years to see how they survive; we can measure survival almost in real time.”

Bolger says salmon swim complex routes. A POST study of four salmon species in British Columbia found major variations in swimming speed and route.

A second study of young salmon in British Columbia linked survival to the timing of migration: young salmon that hit the ocean when plankton were blooming had 150 percent to 300 percent better survival.

This type of data could help conservation groups and hatcheries trying to restore salmon, but . “There is no one-size-fits-all strategy,” Bolger says. “Even within the same species, on the same river, we have tremendous complexity in how they swim and where they go. Some go north, others to the south. This could be a survival strategy; they don’t send all their progeny in one direction.”

Photo: POST

The new noisemakers are so small they can even be placed inside young salmon, before they start their migration down rivers and into the ocean.

Information from the acoustic array can also be melded with data on genetics and physiology, Bolger says. “We can see whether fish with high levels of stress hormone behave differently than those with low levels. Scientists can examine the blood chemistry and genetics when the tag is implanted,” and then correlate the data with their subsequent movement.

The magic of microbes

Perhaps the biggest single question about ocean life concerns microbes — bacteria, their primitive relatives called Archaea, and other single-celled organisms such as protists and ameba. Species are difficult to define in bacteria and Archaea, which is why scientists use “taxa” instead, but the numbers are daunting: the oceans could contain tens of millions of taxa, and the exploration has just begun.

“Small” does not mean insignificant: the approximately 10²⁹ microbes in the sea weigh one trillion (1,000,000,000,000) tons, and comprise an estimated 90 percent of life in the ocean, by weight. Not only are microbes critical to the food chain, but they also engineer many of the basic chemical reactions that move fundamental elements like carbon and nitrogen through the oceans.

Global Seafloor Biomass

Photo: Chih-Lin Wei and Gilbert T. Rowe

By measuring carbon, scientists estimated biomass, including creatures from bacteria to plants and the biggest animals, at the seafloor. Generally, the tropics seafloor is low in biomass compared to temperate and polar regions.

Scientists long ago gave up trying to distinguish microbes by growing them in culture, and now count them with genetic techniques nick-named “molecular bar-coding.” These methods evaluate similarities and difference in a specific section of the genes, then use the data to build an evolutionary tree. Bar-coding applies to all life, and is widely used to assess evolutionary relationships in higher organisms as well as bacteria.

Ten years ago, scientists using molecular bar-coding concluded that a single liter of ocean water might contain 3,000 types of microbe, says Mitch Sogin, of the Marine Biological Laboratory in Woods Hole, Massachusetts, and a leader of the International Census of Marine Microbes, “But what blew the doors off that estimate was a very deep molecular sampling effort in 2005 … which revealed that the number is at least an order of magnitude higher.”

Today, it’s estimated that a liter of seawater may have 30,000 to 40,000 types of microbes, Sogin says, “so if we take all 1,200 samples [from the microbial wing of the ocean census], we very conservatively estimate that they contain one-half million kinds of microbes.”

There are reasons to suspect that the actual number may be much higher, Sogin says, but even using this definition, “Every time we look at a new sample, we identify new taxa, and yet we have only sampled 1,200 liters, which is 1 in 10 ¹⁸ parts of the total ocean.”

when bacteria make rock

Loihi Seamount, courtesy Katrina Edwards

An iron-processing bacteria (bean-shaped object) forming iron-oxide needles.

Unfortunately, molecular bar-coding does not show what newfound microbes are eating, or how they affect their surroundings. At Loihi Seamount, a submarine volcano near Hawaii, marine census scientists have explored microbial iron-mongers. Katrina Edwards, a professor of marine and environmental biology at the University of Southern California, says, “At Loihi, we could dig our heels in to study a particular class of microbes that we think are pretty ubiquitous at the seafloor.”

These bacteria “play a very large role in iron oxidation and the deposition of enormous quantities of iron oxide,” which eventually becomes rock, Edwards says. “If we can understand how these rocks are formed in the modern world, and can understand the physiology, genome and ecology of the bacteria, we can interpret” old rocks found in other locations.

Microbes: Why so many?

Linda Amaral-Zettler, a microbial ecologist and program manager for the International Census of Marine Microbes, has a question: “Why are there so many different kinds of microbes living in this environment, that at first blush, seems uniform?”

One answer comes from the billions of years of every that have produced so many life patterns and genetics. But another answer, she says, may be “that there are a lot more niches or places to live than we have appreciated. Somehow these organisms are sensing these micro-habitats and are able to survive despite the competition.”

Photo: Enric Sala

Coral reefs serve as the perfect haven for co-habitation between microbes and sharks!

Microbes can be extremely specialized, and scientists have found that the most common microbes living on one species of sponge are not among the most common on another sponge, says Amaral-Zettler, who works at the Marine Biological Laboratory in Massachusetts. “Animals, plants and other multicellular organisms are likely to be havens for microbes, and we have barely sampled them. Essentially any surface that is out in the ocean can be colonized.”

Even trash?

Apparently. “All the signs say that even garbage is something the microbes are taking advantage of; likely they are degrading it and using it for an energy source,” says Amaral-Zettler, who is starting to examine microbes on plastic in the sea in collaboration with the Sea Education Association.

Here’s another question: Why are most of the microbial taxa discovered by the Census so rare? Having a few dominant species and plenty of rare ones is often characteristic “of an environment that is impacted in some way” Amaral-Zettler says, “but it seems to be a repeating pattern in the sea; we see it everywhere we look. We are struggling to understand the ecological consequences of having so many rare microbial species.”

Photo: Karen Gowlett-Holmes

Plant or animal? The leafy seadragon confuses predators by mimicking drifting seaweed.

This business of the “rare biosphere” fascinates Sogin, a specialist in microbial evolution, who suggests that the many rare species:

Should we worry?

If there is an uncountable diversity of microbes in the sea, should we ignore the conventional cavil about biodiversity — that too many species will go extinct? Why worry if the sea has more microbes than we can count?

Not so fast, says Sogin, who warns that we are changing the sea in ways that could harm microbes and boomerang back to harm us.

It’s not just that all multicellular organisms evolved from single-celled creatures, Sogin says. Life can survive happily without people, but life relies on microbes. “During 80 percent of the history of life, microbes transformed the planet into something that was habitable by multicellular organisms. They created an environment we can live in. This process continues, because so many microbes in the ocean carry out processes that are essential to our survival.”

People, after all, are dumping garbage, sewage and fertilizer into the ocean, warming it with greenhouse gases, and as the ocean absorbs our carbon dioxide, it becomes more acidic.

Since we don’t understand how the ocean works, we cannot predict the consequences of a major change in the environment.

However, Sogin says, “We know from lab work in microbiology that tremendous shifts can occur in population structures and lead to an imbalance and then a further change in environmental conditions. What will happen with continued ocean acidification or a dramatic shift in seawater temperature? We are going to have a disruption of the microbial community. Is that good or bad? We don’t know.”

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

The “recall” of 550 million eggs (many of them already eaten) reminds us of the benefits of taking control of your food. We figure the recall will fuel an uptick in interest in backyard hens, which are now legal in some cities.

But avoiding salmonella (which can infect backyard chickens as well as commercial hens) is just one reason to favor urban agriculture. In the past few years, we’ve heard that it can:

• Reduce “food miles”: Food from the backyard or an empty lot across town will carry less of a diesel scent than veggies trucked in from California or Texas. Thus growing food locally may reduce the global warming impact of agriculture.
• Promote reality: Too many city people probably think food is made in a supermarket.
• Teach kids about work, the environment and cooperation.
• Get city people outside and liberate them from computer screens, phones and TVs.
• Grow fresher veggies, which should persuade more people to eat their vegetables, perhaps stemming obesity.
• Promote neighborhood solidarity by creating a gathering place.
• Earn money by selling at farm stands and farmer’s markets.

There are limits: City eggs and veggies will never replace the majority of our commercial supply. In January, Minnesota is not going to supply much lettuce compared, say, to California or Florida. Heavy metals found in many city soils can contaminate veggies, and finding enough sunny land is a constant hassle.

We figure people have been growing food in the city since the dawn of agriculture, and the modern rendition of urban ag can involve vegetables or animals. It can take place at home, on rented land, or on rural plots owned or rented by city people. The farms can be aimed at subsistence, the market, or both.

Serving

The Troy Community Garden in Madison, Wis., embodies many of these purposes. It has five acres devoted to an urban farm with a community supported agriculture operation, a five-acre community garden with 20-foot square plots, and a kids garden that hosts about 1,000 kids annually, says Christie Ralston, associate director of Community GroundWorks, the non-profit that runs the garden.

Interns at the five-acre farm at Troy Community Garden work on the harvest. The Why Files

The farm began in 2001 and is Madison’s oldest urban farm. Still, it’s a toddler compared to Fairview Gardens in Santa Barbara, Calif., which began as a community garden in 1895.

Troy also took part in a test project related to obesity. For three hours a day, five days a week, ten overweight high-schoolers have been learning to grow, prepare and eat vegetables as part of the UW-Madison’s GardenFit program. By increasing exercise and promoting vegetable consumption, the goal is to avoid a big summer jump in weight, a trend seen in overweight children. “We’re not necessarily trying to cause a lot of weight loss over the summer,” says Sarah Jacquart, a nutritional sciences graduate student, who runs the program. “We’re trying to prevent that rapid three- or six-pound weight gain that others have seen.”

This Asian squash, planted by Hmong gardeners, may have no English name. The Why Files

City gardens face unique challenges, such as obtaining approval for a new farm greenhouse, and serving immigrants who speak little or no English. Ralston says all-garden meetings are translated into Hmong, Lao and Spanish.

‘r chickens us?

Skeptics may doubt that urban agriculture will survive the dimming of its “new ‘n trendy” aura, and they are right that “farms” on vacant lots and railroad corridors will not put California’s fruit and vegetable farmers out of business.

So is urban agriculture today’s fad or a fact of the future? The Why Files shopped the aisles for a solid published assessment of the trend in the United States, but we wound up with an empty cart. “Since there’s no strict definition, it’s hard to say” how fast urban agriculture is growing, says Alfonso Morales, an assistant professor of urban and regional planning at the University of Wisconsin-Madison, and an expert on urban markets. “I am confident it is growing; there is all sorts of anecdotal evidence. The number of professional organizations around the different facets — urban poultry, urban gardening, urban beekeeping…”

But many of these organizations are less concerned with agriculture than with raising food for personal consumption. Sure, raising chickens in the city is legal in some places, but most people doing it are less interested in egg production than in having “a neat experience for the kids,” says Ron Kean, a poultry expert with the University of Wisconsin who advises backyard poultrophiles.

The “locavore” movement — which esteems local food for many of the reasons mentioned above — seems have boosted the number of small flocks raised on the fringes of the city, Kean notes, but most live in rural areas and sell directly to city people, and thus are not truly urban agriculture.

Dearth of data

Community gardens, which usually rent plots to people in the neighborhood, are a large part of urban agriculture, but urban mini-farms can also be run by a single operator who grows food for sale.

There are many explanations for the dearth of data on urban ag:

• Definitions: much of the new-found interest in urban agriculture concerns “local food,” but that is often grown in the countryside — even if the farmers live in the city.
• Size: Urban farms are small and their output is diverse and hard to measure.
• Age: Many urban farms are young, and any record of success would be short.
• Motivation: Urban farms often aim beyond food to social and psychological benefits, which are not captured by the yield and profit measures used to evaluate farms.

The “simple” task of approximating the number of “urban agriculturists” is difficult indeed. The United Nations Development Program produced a widely cited estimate that 800 million people practice urban agriculture, and 200 million grow for profit. Urban agriculture, the group said, produced the equivalent of 150 million full-time jobs.
But a 2010 publication¹ called these high numbers unreliable, since they emerged from a 1996 “thumbnail sketch” based on the authors experience. The 2010 survey saw wide variation in city-farming participation: from 11 percent of households in Indonesia to almost 70 percent in Vietnam and Nicaragua. More than 30 percent of city households in 11 of the 15 nations surveyed had a significant farm inside or outside the city.

In four nations, at least one urban household in three kept livestock.

Although the study also found that city farmers were eating better than non-farmers, farming may not explain that benefit, since in many cities farmers tend to be less poor than non-farmers.

The energy picture

Pamela Martin, an assistant professor geophysical science at the University of Chicago, agrees that data are short on the urban-ag phenomenon in the United States, largely because researchers are just now focusing on the topic. Local food has the potential to reduce the energy needed to grow and transport food – but does it actually do so?

According to the U.S. Department of Agriculture, agriculture produces about one percent of U.S. greenhouse gases, but food processing, distribution and marketing also are major users of fossil fuels.

The energy cost of urban agriculture varies with the farm location, the individual crop, and the methods used for growing, irrigating and transporting them. But do local vegetables save energy? No, said a recent New York Times commentary, which claimed that “The statistics brandished by local-food advocates to support such doctrinaire assertions are always selective, usually misleading and often bogus.”

Not so, says Martin. “One fact that was based on our research in Chicago was flat-out wrong, a pound of [local] lettuce does not embody the same number of calories” as a pound of lettuce that was shipped 2, 000 miles. At a city farm, “a piece of produce is grown, perhaps stored in a cooler overnight, then taken to market and it heads home. The whole supply chain is more direct than for conventional produce.”

Using a concept called “embedded-energy,” which counts how much energy is used, for example, in irrigation, tractors and fertilizer, Martin compared energy usage in conventional agriculture with local food and urban farming, based on reports from students who recorded what Chicago farmers grew and did.

To avoid polluted soil, many urban gardens import clean soil. Looks like Chicago's buildings are not stealing the sun from this garden! Courtesy: Linda N.

In first-year data from Chicago farms, local lettuce was much more energy-efficient than California lettuce, which is grown, irrigated, washed in California, and then shipped 2,000 miles, Martin says. “In terms of the environment, farms that grow lettuce in Chicago make a lot of sense. Energy and related greenhouse gases were lower than values for conventional produce, based on previous work that we did, on other studies, and on USDA [U.S. Department of Agriculture] data.”

Urban agriculture: modern melting plot?

Many advocates point out that urban farms are about growing neighborhoods as much as growing food, and this benefit has gained importance now that so many people are migrating. In the United States, urban farmers include a disproportionate number of immigrants, especially on the coasts, says Gail Feenstra, of the sustainable agriculture program at the University of California at Davis. “A lot of immigrant folks maybe don’t have enough money to purchase a whole farm, but are able to have a small plot of land, on the urban edge or in the city, where they can grow food, and they have a lot of expertise.”

Most urban immigrant farmers in California are Asian, Feenstra says, or in some neighborhoods, Hispanic. Joining a peaceful, productive enterprise can have social benefits, she adds. At a San Diego garden she recently visited, “Asian, Hispanic and African farmers grow food for sale or family use. This garden brings together these disparate ethnic groups, who have learned to cooperate; the amount of produce growing on that property is totally amazing. One gentleman exceeded a thousand pounds from his [20- by 30-foot] plot. Everything was packed really close, he did multiple cuttings, he knew what he was doing.”

Gardens can foster assimilation and health, says Feenstra. “These men were sitting around, watching TV, bored; it was not a good situation. Then, some of them started organizing: ‘We know how to grow food, we can do that for our families, can start eating more healthily.’ Now their kids are asking for vegetables, coming to the garden, hanging out with friends. The garden has made a huge difference in the neighborhood.”

A social mission

Social benefits are on the mind of David Iaquinta, a professor of sociology and demography at Nebraska Wesleyan University, who has studied urban gardening and agriculture in Germany, the Philippines and elsewhere. “Gardens allow immigrants to practice the new language, to learn about culture,” he says. “Gardeners like to talk to each other, to learn about different vegetables and different ways to grow them.”

In the United States and Europe, Iaquinta says, gardens are a “tremendous access point for subsistence, marketing, and exchange of ideas.” Many community gardens include a common area, sometimes with a playground, that makes a good site for informal language lessons. “Many of the gardeners come from cultures where women don’t attend much school, but that can happen in the garden.”

Urban gardens require a regulatory structure, which can become a means of teaching principles of democracy at the small scale, Iaquinta says.

Gardens also need land and access to water, which can be difficult to find in the city. “We need to see urban agriculture as a sector that needs to be planned for,” says Iaquinta. “Poor people are going to raise food rather than starve, and planners in urban areas need to add urban agriculture to their hand basket of tools to solve problem that do not appear to be food problems: the integration of people, dissemination and acquisition of democratic institution-building skills, poverty alleviation, childhood nutrition.”

"Allotment gardens" started in Germany more than a century ago, and have become a prototype of multi-purpose urban gardens that function rather like the American lawn, complete with the flowers and vegetables. Zurich, Switzerland, Roland zh

Making it work

Urban farms and community gardens need non-governmental support, says Feenstra. “Community buy-in is the basic requirement. If you come in from outside and try to impose something on the community, if a non-profit organization says ‘Start this,’ but the community has not bought in, it won’t last.”

Having outside advocates also helps, Feenstra adds, especially if the gardeners are recent immigrants. “They come here, have nothing, nobody respects them, understands them. Working with people who understand their culture and what skills they bring” can be essential to building an urban farm.

The ideal outside advocate is open-minded and “asset-oriented,” who can match skills to needs and turn obstacles into opportunities, Feenstra says.

A relationship with the surrounding community can even help neutralize development pressures. Feenstra points to Fairview Gardens, near Santa Barbara, which “was really pressured to sell out to development, and they decided to grow their relationship with the neighborhood, and started community-supported agriculture and a farm stand. They talked with neighbors, who helped them buy an easement on the land, because they were getting fresh vegetables from the farm.”

Training ground?

One of the major supposed benefits of participation in urban farms and gardens is the opportunity to learn business. Does this work? “I don’t know of any good assessment of that,” says Alfonso Morales of Wisconsin, who worked in, and now studies, city markets. “I predict, I am confident, that it will be a normal distribution. For a small fraction, it will be a life-changing experience, they will go on to become important business people. For most, it will be interesting experience, they will burden their children with stories about the city farm. And for some number, it will be a terrible experience that they would not wish on their worst enemy. But how much entrepreneurship will come about, we just don’t know.”

“I used to milk a cow,” says Morales, “and people said, ‘Go to college, you don’t want to be here all your life.’ Now all that experience I basically fled is important. It’s an interesting thing about urban agriculture, there is no single dominant entrée, nor any dominant outcome. People can weave their own tapestry from their activities. If a kid works at a laser tag shop, it’s a wage labor job. For people who garden, it’s an entrée into so many different parts of life.”