Where Molecular Biology Meets the ‘Wood Wide Web’

Kabir Peay uses genetic sequencing tools to map the ‘grossly understudied’ world of fungal interactions.

At first glance, Kabir Peay’s lab in Stanford University’s glittering Bass Biology Building is nondescript. Rows of tables are lined with beakers. Students and postdocs rush around in lab coats. But if you look closely, there are clues that this isn’t a typical biology lab.

There’s a fridge full of samples of dirt from all over the world, each containing scores of different species of fungi waiting to be analyzed. In the basement, a muggy closet full of potted plants is the basecamp for innovative research into how fungi can help tree species grow faster. Behind a locked door, a research technician is poring over petri dishes filled with fungi, checking for signs of contamination. Kabir Peay walks around his lab confidently, his surf shop t-shirt, puffy jacket, and beanie matching his laid-back, unflappable vibe.

Kabir Peay’s mycology lab at Stanford University takes a “roots to biome” approach, exploring the interactions between plants and fungi at every scale. Photo provided.

Yet this California-born, San Francisco-based surfer has built a reputation as one of the foremost experts in fungal ecology, a relatively novel field of study that’s redefining the way we think of the natural world and illustrating how the smallest things can shape entire ecosystems.

Peay’s research centers on mycorrhizal fungi, a type of fungi that form mutual symbiotic relationships with plants. These organisms decompose organic matter into plant food like nitrogen and phosphorus, which they pass on to trees in exchange for the carbon trees suck out of the atmosphere. According to Peay, a whopping 99 percent of individual trees form this bond with mycorrhizal fungi. It’s one of the most widespread examples of a mutual symbiosis in the natural world, one that helps trees grow, provides a sink for carbon, and can potentially buffer plants from the effects of changing environmental conditions.

While researchers have been aware of mycorrhizal fungi and the relationships they form with trees for decades, scientists have only just begun to understand their critical role in ecosystems. Until recently, the definitive account of which symbiotic fungi live where came from hand-drawn maps made in the 1980s by Sir David Read, a botanist at the University of Sheffield and a pioneering researcher in the field of fungal symbiosis. Peay’s mycology lab at Stanford is at the cutting edge of redrawing those maps, enhancing our understanding of the world’s fungal communities. With new genetic sequencing techniques, their work is illuminating the vast, diverse kingdom of fungal organisms and how they prop up entire ecosystems by transporting nutrients from above ground to the roots below. Still, scientists are only beginning to scratch the surface of how these symbioses develop and what they can accomplish.

Peay puts it simply. “A lot of the things that we see are controlled by things we don’t,” he says.

An Accidental Ecologist

Although Peay is now one of the preeminent scholars in the field, he doesn’t have an obvious origin story as a fungal ecologist. In fact, he basically stumbled into the field. As an undergrad at UC Santa Barbara, Peay actually majored in Comparative Religions and East Asian Studies, moving to China and Taiwan for several years after graduation to work as a sustainability consultant. He returned to the US in 2001 to attend the Yale School of Forestry with every intention of pursuing a career in international environmental policy and trade. While in graduate school, Peay decided that he should learn a little about the science underpinning his interests in policy and economics. But one class in the foundations of ecology turned into a full course load.

“I just started taking more and more ecology classes and had this lightbulb moment where I realized that this wasn’t a means to an end,” Peay says. “It was the thing I really liked.”

After Yale, Peay didn’t move back to Asia as he originally intended. Instead, he returned to California to begin doctoral work in environmental sciences at UC Berkeley, which was followed by postdoctoral fellowships at Berkeley and Stanford. In 2012, he officially settled in at Stanford as a professor.

Peay takes what he calls a “roots to biome” approach to his work, exploring the interactions between plants and fungi at every scale.

Peay and his lab technician, Zhenyu “Amos” Lim, at a field mycology workshop in Malaysia. The research coming out of Peay’s lab highlighting the diversity and benefits of mycorrhizal fungi isn’t just challenging fundamental theories in ecology, it also has applications for managing forests. Photos provided.

Peay with his mushroom harvest at Salt Point State Park in Sonoma County, California. Even after all these years, it’s not the impressive potential applications of his work that most excites him; it’s the basic science.

Collecting samples from a burn area in California’s Big Basin Redwoods State Park. The lab is also looking at the distribution of microbes across California’s redwood forests and how the symbiotic relationships fungi form with trees might help forests recover from wildfires.

On a microscopic level, Peay and Tadashi Fukami, a Stanford biology professor who he trained under and now shares lab space with, have researched the interactions between different species of yeast within the nectar of a single flower. Elsewhere in Peay’s lab, Caroline Daws, a recently-graduated PhD student, focused on entire forests, examining the distribution of microbes across California’s redwood forests and how the symbiotic relationships fungi form with trees might help forests recover from wildfire.

Peay has even been involved in research spanning continents. In 2019, he and several collaborators launched an ambitious project to create a global map of the so-called “wood wide web.” Evaluating more than 28,000 tree species across more than a million sites, the team mapped where mycorrhizal fungi interactions occur, what kinds of fungi dominate in different forests, and the environmental drivers that shape or upset those patterns.

Peay confessed that having a research agenda that spans the micro to the macro is partly a function of his curiosity. “I have a hard time restraining my interests,” he says. But he also sees practical value in having a broad research agenda.

“I think there are important connections between them that you don’t see otherwise,” he says. Case in point: By examining which fungi form bonds with trees, where those fungi are found, and how those relationships function, his lab has been able to show that fungi are as diverse and geographically unique as any other species. That realization is a significant paradigm shift from the long-held view that microbes are so small and prolific that they’re basically the same everywhere.

The DNA Revolution

The research coming out of Peay’s lab highlighting the diversity and benefits of mycorrhizal fungi isn’t just challenging fundamental theories in ecology, it also has applications for managing forests.

“We’re really just starting to understand how this whole system is propped up by these kinds of interactions,” says Daws, the former-PhD student. “If we can’t understand them, then we can’t make conservation decisions.”

Peay believes his lab’s research can help foresters combat invasive fungal pathogens like those that wiped out chestnut trees in the Northeast and are devastating California’s oak forests. Understanding natural barriers to these pathogens — and how human activity can break those barriers — can inform how we prevent the movement of invasives across ecosystems.

Similarly, understanding which microbes thrive where, and how they affect plant growth, may also inform future forestation and carbon capture projects to mitigate climate change. “Mycorrhizal fungi really are critical for plant success and establishment,” Peay says.

Much of Peay’s work has been made possible by a methodological revolution in the field, where new techniques in DNA sequencing have allowed ecologists to genetically map ecosystems as never before.

For fungal ecologists, these techniques have opened “a new age of discovery,” says Brian Steidinger, a postdoc at the University of Konstanz in Germany and a former postdoc in Peay’s lab.

Previously, fungal ecologists had to rely on mushrooms, using only the parts of the fungi that are visible and above-ground, to characterize which species were present. But studying mushrooms, Peay says, “is like trying to study plants by only looking at their flowers.”

With sequencing, Peay’s team can extract DNA from soil samples to pinpoint all the species of fungi present, where they’re found, and the symbiotic relationships they form with different species of plants. “Before, we weren’t really even able to say what microbes live in a teaspoon of soil,” he explained. “Now we can also know that and say a lot about what genes they have and what those genes might be doing.” Advances in sequencing is what made their efforts to map global distributions of mycorrhizal fungi possible, he says.

“The ability to see what’s out there and to start to pick apart what they’re doing and how they’re behaving has just blown the field open,” says Tom Bruns, a professor emeritus of plant biology at Berkeley and one of Peay’s mentors.

But it’s not just the new tools that have contributed to the research success of the Peay lab. It’s Peay himself. His colleagues and the postdocs working under him describe him as a mentor and friend who creates a space for everyone to pursue their passions and grow as researchers. Daws says she probably wouldn’t have gotten through graduate school without such a supportive advisor. Fukami jokes that the benefit he gets from sharing lab space with Peay is greater than what he could ever pay back.

“He’s the person that I admire the most, just overall as a person, a researcher, an ecologist,” Fukami says.

In Peay’s view, the lab’s success is due to the excitement of working at the frontier of an important, exciting field. Even after all these years, it’s not the impressive potential applications of his work that most excites him; it’s the basic science.

“There’s such fundamental value in understanding the shape of the universe we inhabit,” he says. “My god, these organisms are just so amazing!”

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