Microbes can be used to break down and detoxify substances. They also can be encouraged to make them.

L-R: Roger Koide, Bing Xu, and Erin Wakefield survey the dense mat of pine roots that exists on the forest floor. These roots are colonized by dozens of species of ectomycorrhizal fungi, each of which may help the pines by performing a different function for the plant. Some may be good at absorbing water, others may be particularly good at absorbing nitrogen, and still others may be better at absorbing phosphorus.

Encouraging microbial activities in soils is nothing new. Farmers have been taking advantage of the association between legumes and Rhizobium bacteria to increase nitrogen fertility in soils for years. By trading favors, the two organisms—plant and bacterium—help each other thrive. The bacteria synthesize ammonia from atmospheric nitrogen and supply it to the plant. In turn, the plant converts sunlight and carbon dioxide to carbohydrate and shares it with the bacteria.

Few people, however, know about another important partnership between plants and microorganisms: the mycorrhizas.

“The association between plants and mycorrhizal fungi is much more common than the legume-rhizobium symbiosis, and—overall—probably more important in nature,” says ecologist Roger Koide.

“Eighty percent of the world’s plants, including important crop and timber species, wouldn’t thrive without mycorrhizal fungi,” says postdoctoral researcher Ian Dickie. “Mycorrhizas are so common in nature that they’re the rule, not the exception.”

Mushroom hunters know that to find certain kinds of mushrooms, you look near certain trees. Look beneath the Douglas fir for white truffles; the oaks for chanterelles. “About half of the mushrooms in the forest come from mycorrhizal fungi growing symbiotically with trees,” Dickie says.

The plant and fungus are connected underground, which allows the fungus to provide the plant with water and nutrients. The fungus—whose body is an intricate net of filaments—covers the surface of feeder roots and grows out into the soil for distances up to several meters.

Besides increasing the plant’s surface area for absorbing nutrients, the fungus can slip into spaces too fine for root hairs to enter, and can extract nutrients that plants usually can’t use, like the protein from dead organisms. In return, the fungus receives a constant pipeline of sweets from photosynthesis.

Studying mycorrhizal communities is tricky. First, try telling one fungus from another when it’s not attached to a mushroom. Fungi basically all look alike: pale, microscopic threads winding through the soil and leaf litter.

Second, try counting them. When you’re dealing with a thread-like organism that might cover several square meters of territory, how do you know what’s connected to what? “Until now, all of the surveys of mycorrhizal fungi have been done on plant roots,” Koide explains. “But one root may support 300 to 8,000 times its length in fungi—and the abundance of fungi on the root doesn’t necessarily correspond to the abundance of fungi out in the soil.”

Koide and Dickie worked through a molecular method to track mycorrhizal fungi in the soil. They extract all of the DNA from soil samples, amplify the DNA from the fungi using primers with fluorescent markers, chop up the DNA with restriction enzymes, then analyze the DNA fingerprint, which is based on the lengths of terminal DNA fragments.

“We use a DNA sequencer to size the fragments,” Koide says. “The scanner only sees the fluorescent terminal pieces of DNA—and their lengths are diagnostic. We can identify the fungi with incredible accuracy. It’s a beautiful technique.”

There are thousands of different mycorrhizal fungi waiting to be identified. “We’d like to know which trees they infect, how fast they grow, which nutrients they absorb, whether they can transfer water to the plant, and so on,” Koide says. “These are all very important questions, because—in large measure—a tree’s capacity to take up water and nutrients from the soil is determined by the capacity of the fungi that infect it.”

First, Koide is identifying the mycorrhizae in a very simple system—a red pine plantation, rather than a natural forest. This limits the number of variables in the study. “The plantation has one species of tree, all the same age,” Koide says. “Even so, we’ve collected mushrooms from about two dozen species, and there are probably about 50 species living there. We want to know how such a simple ecosystem supports such fungal diversity.”

This kind of basic research on microbial ecology is essential. In fact, it might be helpful to think of plants and mycorrhizal fungi as one large organism when considering the effects of pollutants and other problems.

Ylva Besmer, a graduate student in Koide’s lab, is applying what they learn about mycorrhizal communities in temperate climates to subsistence farming systems in the semi-arid topics, in hope of improving crop yields.

In Zimbabwe, people are facing food shortages. The soils are poor and highly weathered, and the government no longer subsidizes fertilizer. The staple crop, corn, requires a lot of nitrogen, so yields are very, very low. One potential solution is the legume-rhizobium symbiosis, which increases nitrogen fertility, but there’s a hitch: legumes don’t grow or fix nitrogen well when they’re phosphorus-deficient.

“Trying to solve the nitrogen problem with legumes creates a new problem with phosphorus fertility,” Koide says. “But legumes are highly mycorrhizal, and Ylva is investigating the potential of using mycorrhizal fungi to solve the problem.”

In preliminary greenhouse tests, Besmer was able to stimulate nitrogen-fixation in the legumes by adding either phosphorus or mycorrhizal fungi to pots of soil from Zimbabwe. She got similar results in fields when she applied phosphorus. Now she’s preparing mycorrhizal inoculum using “trap cultures” to apply to the fields.

“We grow a host plant in pots of soil in the greenhouse for three months, which allows the fungi to multiply,” she explains. “Then we take the contents from the pot—soil, spores, fungal threads, colonized root pieces, and all—and do inoculation experiments with soils from the field.”

If inoculating the fields helps to increase nitrogen-fixation, Besmer will study ways to promote the activity of the native fungi in the field. For instance, she’ll look for ways to minimize the time that the fungi are left in the soil without a plant host. She’ll also vary tillage intensity and timing, since tillage can break up and kill the fungi.

By optimizing the natural interactions between three vastly different organisms—plant, fungus, and bacteria—the subsistence farmers may be able to improve their crop yields.

These are just a few of the projects college researchers are conducting in the underground. So the next time you take a walk across the dark, quiet forest floor, remember: it’s a jungle down there.

If you could look inside just one teaspoon of forest soil, you’d witness a strange, secret society. Among the microscopic pools, mountains, deserts, and winds in that spoon, something remarkable is going on: up to 1 billion bacteria, 40 miles of fungi, several hundred thousand amoebae, and hundreds of tiny microscopic worms—all hard at work, shredding, grazing, preying, and decomposing so we can live.

Faculty and staff referenced in this article include Jean-Marc Bollag, professor of soil microbiology and director of Penn State’s Center for Bioremediation and Detoxification; Mary Ann Bruns, assistant professor of agronomic soils and microbiology; Kate Butler, senior lecturer in agronomy; Jon Chorover, associate professor of environmental soil chemistry; Steve Knabel, associate professor of food science; Roger Koide, professor of horticultural ecology; Sridhar Komarneni, professor of clay minerology; and Rick Stehouwer, assistant professor of environmental soil science.

Jon Chorover recently joined the Department of Soil, Water and Environmental Science at the University of Arizona as an associate professor of environmental chemistry.

Research in this article was supported by the A. W. Mellon Foundation, the National Geographic Society, the National Science Foundation, the Pennsylvania Department of Environmental Protection, the Sweden America Foundation, the U.S. Department of Agriculture, and the U.S. Environmental Protection Agency.