The Next Big Thing Is Really Really Small

10 ways the microbial universe could change how we go about saving species, habitats—and even the planet.

By Richard Conniff

When the Deepwater Horizon oil rig exploded in 2010, spilling 4.9 million barrels of petroleum into the Gulf of Mexico, the television cameras focused mostly on mopping-up efforts by human responders. But beneath the surface, away from the bright lights, the hard work of cleaning up the mess was being handled mainly by nontelegenic microbes.

A group of little-known proteobacteria called Oceanospirillales, which normally occur in low numbers, suddenly proliferated. At one point, they represented 90 percent of the microbial species in and around the plume, according to research by the Lawrence Berkeley National Laboratory. These microbes did not merely gang up on the spill but also switched on genes specifically geared to digesting hydrocarbons. And when they had broken down the original pollutants into different chemical forms, other kinds of bacteria took their place in an ecological succession.

Seeing that hidden cleanup for the first time made the microbiological world suddenly seem capable of astonishing things. In the past, scientists could identify and begin to understand only the small fraction of microbes that would grow in a Petri dish; they thought of bacteria, fungi, and viruses mainly in terms of the diseases they could cause. But over the past ten years, genetic sequencing technology has made it practical to identify every single microbial species in its own environment and begin to understand how it functions there. And that has revealed not only that microbes are present everywhere, but that they influence everything—often to our considerable benefit.

Much of the recent excitement has focused on the human microbiome—with the idea that manipulating the microbes living in and around our own bodies will radically alter the practice of human medicine. But every plant and animal species has its own microbiome, too, and researchers are beginning to explore this microbial universe. Listening to them talk about this work, it’s easy to get the impression that microbes could dramatically change how we go about saving species, habitats, and perhaps Earth itself.

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1. Wildlife Probiotics
2. Working on the Right Mussels
3. Eats Dry-Cleaning Fluid for Breakfast
4. Nine Billion Served
5. A Crop for All Seasons
6. Disarming the Enemy
7. Post-Antibiotic World
8. Brewing a Better Biofuel
9. Turning Electricity into Fuel
10. Gluttons for Greenhouse Gases

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1. Wildlife Probiotics

A few years ago, herpetologist Reid Harris of James Madison University was puzzling over the strange way in which some female salamanders weave in and out among the eggs in their nests. It turned out that the mama was inoculating the eggs with antifungal bacteria from her skin—and that this probiotic treatment protected them from a common egg fungus.

It made Reid and a colleague, Vance Vredenburg of San Francisco State University, contemplate using microbes to fight chytrid fungus, an epidemic killer of amphibians worldwide. When this deadly blight strikes, fungal spores enter the animal’s skin, block normal respiration, and cause listlessness and lingering death. Over the past few decades, the fungus has contributed to the extinction of an estimated 100 amphibian species, with many more to come—possibly including California’s endangered mountain yellow-legged frogs.

Following Reid’s example, Vredenburg found that yellow-legged frogs also carry an antifungal bacteria species on their skin—but not always enough of it to defeat the chytrid fungus. He began to brew up the bacteria in his lab, producing buckets of purple liquid. Then he briefly dipped lab-reared yellow-legged frogs into this probiotic bath and, a few days later, exposed them to the chytrid fungus. In the group that received the probiotic treatment, all of the frogs survived. In the untreated control group, 80 percent died.

smooth cells The Next Big Thing Is Really Really SmallThe right microbes could also be the key to keeping some species alive and breeding in captivity. For instance, tamarins and marmosets in zoos are prone to callitrichid wasting syndrome, characterized by diarrhea, loss of hair, and paralysis of the hind limbs—ending in death. Researchers have generally suspected that the choice of food is the problem. But maybe what these monkeys really lack are the microbes necessary to digest it, the authors of a recent editorial in the journal Conservation Biology suggest. The idea of managing the microbiomes of animals still seems strange and unlikely to zoos. But that’s how physicians felt about the human microbiome a few years ago. New discoveries about how microbes shape animal health will take hold in the care of captive animals, much as they have in the treatment of human illness.

Microbiome research is simultaneously frustrating and tantalizing: microbial communities are astonishingly diverse and can vary dramatically from place to place—or species to species. This means that getting microbial conservation methods to work will require patience and a high degree of precision. The tantalizing part is that sequencing technology is now cheap enough to make that kind of precision practical.

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2. Working on the Right Mussels

zebra mussels The Next Big Thing Is Really Really SmallNorth America is a mother lode of freshwater mussels, with almost 300 native species. Their looks are dull, but their behaviors aren’t. In one species, for instance, the female puts out a fleshy mantle that does a convincing imitation of a minnow. But when a real fish comes to investigate, the mussel blasts larvae into its gills, turning the fish into a mussel incubator.

Unfortunately, many native mussels are now being overwhelmed and suffocated by invasive zebra and quagga mussels. Researchers have been testing scores of microbes in search of a way to kill the invaders and save the homegrown species. The common North American soil bacterium Pseudomonas fluorescens didn’t sound like a contender at first. It’s a beneficial microbe used in agriculture to protect the roots of some plants against fungi and nematodes. One strain even helps turn milk into yogurt. But when researchers tried strain CL145A, it killed the invasive mussels without harming anything else.

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3. Eats Dry-Cleaning Fluid for Breakfast

It sometimes seems as if the entire world is irreversibly contaminated with industrial chemicals. Groundwater, for instance, is widely tainted with the industrial solvent trichloroethylene (TCE) and the dry-cleaning fluid tetrachloroethylene (PCE). Microbes may be our best hope for cleaning up the mess. When researchers first discovered in the 1990s that chlorine-hungry bacterial species in the Dehalococcoides genus could break TCE and PCE down into harmless ethane—the same gas used to ripen fruit—it sounded too good to be true. In the first test case, researchers injected a beer-keg’s worth of bacterial culture into the heavily contaminated groundwater beneath Kelly Air Force Base in Texas. Monitoring of wells showed the progress of the bacteria as they quickly spread through the polluted area—and after just 115 days, the PCE problem there was fixed. Dehalococcoides treatment, combined with a little molasses or lactose as a feedstock, is now a standard commercial cleanup technology. Other researchers are also working on bacterial methods to clean up mercury and other heavy metals, mining wastes, and 500 million gallons of North American groundwater contaminated with uranium.

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 4. Nine Billion Served

spiny bacteria The Next Big Thing Is Really Really SmallThe great challenge in agriculture is to double the amount of food being produced without plowing under what’s left of the natural world. The twentieth-century Green Revolution did it with massive doses of commercially manufactured fertilizer. Now we need to ramp up food production again—but without the environmental costs. Conventional fertilizer-manufacturing processes release large amounts of carbon dioxide from fossil-fuel combustion. Even worse, only a fraction of the nitrogen fertilizer actually gets into the crop. The rest ends up in ocean dead zones such as the one at the mouth of the Mississippi River—or in the atmosphere in the form of nitrous oxide, a far more potent greenhouse gas than carbon dioxide.

But researchers have recently discovered an unexpected diversity of soil microbes capable of breaking down nitrous oxide into nitrogen. They’re also figuring out how farmers can use these bugs at precise temperatures or moisture levels, or at certain stages in the life cycle of a plant, in order to get more nitrogen fertilizer into crops—and less into the environment. “Precision agriculture” is the term for that kind of farming, and microbes will play a major role in making it happen.

For instance, one reason it’s so hard to feed families in the tropics is that the clay soils there trap phosphate. A farmer may need to dump 100 units of imported fertilizer onto the land just to get 10 units into his crops. A lot of farmers go without costly chemicals, or they clear more forest to grow the food needed. But researchers at the University of Lausanne and the National University of Colombia are now working with a mass-produced root fungus that efficiently delivers phosphate to cassava, a staple food for much of the developing world. In the first season of field testing, this fungus cut phosphate use in half while boosting yields by 20 percent.

Microbes in the roots of plants are also nature’s way of getting nitrogen into plants, thus enabling peanuts, soybeans, and other legumes to extract (or “fix”) it out of thin air at a rate of hundreds of pounds of nitrogen per acre. Researchers have developed nitrogen-fixing bacterial strains that can increase yields for some crops by 50 percent. The hitch is that hardly anyone invests in getting those improved strains to farmers in the developing world, says Ken Giller of N2Africa. Given access to nitrogen-fixing bacterial strains that already exist, he says, subsistence farmers would have far less need to cut down forests to make new fields.

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5. A Crop for All Seasons

A few years ago at a hot spring in Yellowstone National Park, scientists were astonished to discover panic grass flourishing at 158 degrees Fahrenheit. The secret to this extreme tolerance wasn’t just about the plant itself. It also required interaction between a root fungus and a virus. That discovery led researchers to seek out root microbes from plants in various extreme environments, from dunes to alpine slopes.

Why bother? The weather is rapidly becoming more extreme and less predictable, complicating life for farmers everywhere. Scientists have responded with crops that are genetically engineered for a trait such as drought tolerance. But the Yellowstone discovery suggested a more flexible approach, one that doesn’t require farmers to predict the future and buy the right seeds at the start of the season. Instead, they’ll be able to treat a crop with a cocktail of different extreme-climate microbes so that the most beneficial microbes will proliferate, even as growing conditions shift.

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6. Disarming the Enemy

mosquito The Next Big Thing Is Really Really SmallIn 2010, mosquito-borne malaria made 210 million people sick. Of these, about 660,000 died, most of them small children in sub-Saharan Africa and South Asia. Dengue fever, another disease spread by mosquitoes, is almost as devastating. It afflicts up to 100 million people each year and now threatens to advance into the U.S. Standing in the path of both diseases is a Michigan State University microbiologist named Zhiyong Xi and a bacterium named Wolbachia. Wolbachia is present in about 28 percent of all mosquito species—but not the ones that transmit dengue or malaria. But Xi has figured out how to establish a heritable Wolbachia population in these species and has demonstrated that it prevents these mosquitoes from transmitting dengue fever or malaria.

For anyone who has been driven mad by mosquitoes, the old approach of killing as many as possible had obvious emotional appeal. But it was often environmentally disastrous, most notoriously with the broadcast application of the pesticide DDT. Xi believes the strategy of merely disarming mosquitoes could be safer while also giving public health officials a new tool to use in tandem with existing methods. Insecticide-treated bed netting, for instance, might still be the best protection from some night-biting mosquitoes. But Wolbachia could become the weapon of choice to neutralize the more challenging day-biters.

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7. Post-Antibiotic World

turkey The Next Big Thing Is Really Really SmallReckless use of antibiotics over the past 60 years has produced an epidemic of resistance. Our most important line of defense against infectious disease is rapidly crumbling. In the post-antibiotic era, the director-general of the World Health Organization recently warned, “Strep throat or a child’s scratched knee could once again kill.”

Massive overuse of antibiotics in livestock has been a particular target of criticism. But it could also be the easiest part of the problem to fix. New technology makes it possible, for the first time, to understand the microbes involved at every stage in an animal’s life. That could give livestock producers a way to simply tweak “good” bacteria instead of routinely feeding their animals antibiotics to kill off “bad” bacteria.

It’s not just about pork, chicken, and cattle farming. Commercial fish farming has also faced sharp criticism for its reliance on antibiotics that can escape into surrounding environments. But in an experiment at the Norwegian University of Science and Technology, researchers tried a new approach. Instead of treating the water in hatchery tanks with antibiotics to prevent infections, the researchers instead colonized the tank water with a diverse community of beneficial bacteria to keep out opportunistic pathogens. This strategy of “competitive exclusion” lowered the death rate and produced young fish that were healthier and more robust. It also translated into reduced need for antibiotics or other treatments later in life, when the fish move out to pens in the open ocean.

Cargill, the American meat-packing company, recently tested a similar approach. Using competitive exclusion with healthy bacteria, its researchers reduced the amount of salmonella present in factory-reared turkeys by 90 percent. The only thing delaying implementation of these probiotic methods is the food industry’s unlimited access to antibiotics—and the persistent myth that the only good bacteria are dead ones.

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8. Brewing a Better Biofuel

Our efforts at shifting from fossil fuels to biofuels have been largely a bust so far. Using corn as a feedstock takes food off the table or drives up its price—with little or no reduction in carbon dioxide emissions. It would make more sense to turn farm wastes such as corncobs and stalks into biofuel. So far, though, it’s been too difficult to break down tough, woody fibers into simple sugars. But tweaking the relationships within teams of microbes may provide a way forward. University of Michigan researchers recently teamed the fungus Trichoderma reesei, which breaks down corn stalks and other tough plant wastes into sugars, with a strain of the bacterium Escherichia coli that had been genetically engineered to convert the sugars into isobutanol. Isobutanol produces about 82 percent as much energy as gasoline, a big jump up from the 67 percent produced by ethanol—and the process still leaves the edible part of the plant on the dinner table.

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9. Turning Electricity into Fuel

The big problem with solar and wind technologies is that they generate power only intermittently. That means they require batteries or compressed air methods to store power during peak production and make it available when production drops. But microorganisms that have evolved in some of the most extreme environments on Earth promise to handle this task more efficiently. In a pilot study at the Vienna University of  Technology, researchers have demonstrated that they can use the surplus electricity from renewable energy sources to split water into hydrogen and oxygen. Then they feed the hydrogen to microorganisms, which convert it almost instantly into natural gas. That fuel is easily stored and can fire conventional generators when the solar and wind generators are idle.

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10. Gluttons for Greenhouse Gases

The nightmare climate scenario is that melting permafrost in the Arctic will unleash massive quantities of methane, a greenhouse gas potent enough to spin the planet into catastrophic and irreversible warming. But researchers have also identified microbes called methanotrophs that proliferate as the permafrost thaws. They consume methane and keep it from entering the atmosphere. So far, scientists haven’t characterized most of these species, much less figured out how they work.

“But if we know what kinds of microorganisms are the first responders,” says Janet Jansson, a microbial ecologist at Lawrence Berkeley National Laboratory, “we can learn how to help them. Do they need nutrients? Are there ways we can tweak the environment to get them to grow and do the things we want them to do?”

The bottom line: In the Arctic and elsewhere, Earth’s fate may rest with obscure species we have, until now, tended to dismiss or even despise. And in the end, our long history of waging war on microbes may turn out to have been a misguided attack on our own best hope of salvation.

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