Searching for Hidden Fungi in the Sonoran Desert

SAGUARO NATIONAL PARK, Ariz.—As the sprawl of homes begins to dissipate on the outskirts of Tucson, forests of saguaro cacti rise in its place, their arms twisting and twirling as if waving a welcome to the Sonoran desert. Fields of prickly pears and cholla cactuses, blooming creosote bushes and green-limbed palo verde trees spread beneath and between the beckoning icons of the Southwest. 

“We look like we’re on a movie set,” said Justin Stewart as he drove into Saguaro National Park, where the towering cacti, many older than the state of Arizona, are the charismatic stars of the scene. But Stewart and his colleague, Jinsu Elhance, weren’t there for the saguaros, but to see some tiny players with big roles growing in the soil beneath them: mycorrhizal fungi. 

Though invisible on the surface of the desert, researchers have found in recent decades that mycorrhizal fungi are a vital part of ecosystems around the world. The fungi form symbiotic relationships with most land plants, forming intimate relationships with root systems in which they trade water and nutrients like nitrogen and phosphorus for carbon that they use to grow farther out, expanding the highway delivering nourishment to the plant. It’s a useful system anywhere, but especially in arid deserts like that in Saguaro National Park, where the land can be unforgiving. And the relationship’s benefits spread far beyond deserts, forests and grasslands, as the fungi sequester over 13 billion tons of carbon that could otherwise be warming the climate. 

But despite their importance, how mycorrhizal fungi interact in various environments remains largely understudied, particularly in arid regions, where climate change is threatening those systems. 

Stewart, an ecologist, and Elhance, a data scientist, are with the Society for the Protection of Underground Networks (SPUN), an organization founded to map mycorrhizal fungi networks. The two arrived in Tucson in mid-March to learn what fungi support saguaros and how they help the cacti remain resilient to climate change and the rapid spread of invasive species. 

“People think we know stuff about these really well-densely populated ecosystems,” Stewart said. “It’s actually one of the least-sampled places on Earth.”

On the east side of Saguaro National Park, Stewart exited their vehicle, grabbed a rubber mallet, metal cylinder, test tubes and measuring tapes, and walked out into the desert toward an old saguaro with 16 limbs towering above the others. 

“How did you evolve!,” Stewart yelled at the cactus, then proceeded to get to work. He knelt at the base of the saguaro and collected a core sample by pounding a cylinder into the ground with the mallet, then placed the brown soil into a bag to be sent to a lab for analysis, stopping only to taste the soil. “This one doesn’t have much flavor,” he said. “But sometimes they taste crazy.” Ten meters away from the saguaro, Stewart collected another sample to see how the mycorrhizal fungi networks in the soil differ farther from the cactus. 

All the while, Elhance circled the saguaro, phone in hand, shooting a laser at it. It’s nothing like Dr. Evil from the Austin Powers movies, they explained, just LiDAR to create a 3D image showing how tall the cactus is and how many limbs it features, allowing the researchers to estimate its age.

Across the national park, the two collected samples around saguaros of all ages, from young ones just a few feet tall (though still decades old) to ones that have been growing for well over a century and rise 50 feet high. 

Towering size and unique limbs have made saguaros icons of the American West, even though they are only native to Arizona and northern Mexico. The cacti’s importance to the Sonoran desert goes far beyond their looks. Their fruit sustained generations of Indigenous communities across the Sonoran Desert. The Tohono O’odham see saguaros as people, and in 2021, the tribe formally passed a resolution granting them legal personhood.

For the desert itself, they are a keystone species without which the ecosystem would collapse. More than 100 other species rely on saguaros for survival. Gilded flickers and Gila woodpeckers make nests within the cactus, which other birds take over once they leave. Their flowers bloom in May and June, the driest time of year, when all the other vegetation has begun to brown, making them one of the few reliable sources of food for insects and, in turn, other species up the food chain.

Like most species of the desert, saguaros grow at a leisurely pace. They take around 35 years to even begin flowering, decades longer to grow out their iconic arms, and more than 100 years to reach adulthood. The centuries-long lifespan makes the species resilient to changes to its environment, but climate change is throwing a wrench into their survival. Higher temperatures, drier landscapes, bigger and hotter wildfires and invasive species—which can outcompete saguaros by growing quickly and fueling fires that can kill native vegetation—have resulted in the deaths of thousands of saguaros in recent years. In some areas, the species is unlikely to recover without human intervention. 

“I get super excited about fungi that live with weird plants, because it just shows that, like life, you can’t live alone.”

— Justin Stewart, Society for the Protection of Underground Networks

Recent research published in Global Change Biology found that increasingly frequent and sustained heat and drought events are causing more scorching of the tissue of saguaros and other cacti, resulting in “a three-fold increase in mortality of giant cactus species across the region.” That may lead to “landscape-wide impacts that could fundamentally reshape populations of these keystone species and the communities that depend on them.”

Saguaros are all about numbers. As a succulent, it pulls in resources when it can—particularly during the wet monsoon seasons of the summer—and then stores them for months or even years. Each of its fruits has a couple of hundred seeds and disperse billions of them across the landscape, but few grow into new saguaros. That hasn’t been a hindrance to a species with such a long lifespan, but changing fire and drought patterns are making their infrequent reproduction a greater vulnerability. 

“You literally are really bad at being alive,” Stewart jokingly told the ungainly saguaro before him. “But the fungi are helping. I get super excited about fungi that live with weird plants, because it just shows that, like life, you can’t live alone. These plants aren’t living without fungi.”

But what exactly those fungi are—and how important they are to saguaros’ survival—remains somewhat of a mystery. Mycorrhizal fungi are incredibly endemic, Stewart said, meaning ecosystems often have their own unique species. As the climate changes, the SPUN team hopes to determine just how important mycorrhizal fungi are to making the iconic cactus resilient to adversity—and what lessons the resilient desert species can teach us in a hotter and drier world. 

Researching that connection, however, is dependent on having healthy ecosystems where the connection between mycorrhizal fungi and saguaros can be studied and provide a baseline for research—something national parks and other protected lands can provide in abundance, but are now under threat from the Trump administration as protected areas are threatened with dismantling, layoffs and funding cuts. National parks are refuges for biodiversity, Stewart said, and there are increasingly fewer places like them in the world.

“Once it’s gone and deleted, it’s gone,” he said. “The thing that upsets me is, if they’re gone before we actually know what’s there, we have no idea what we’ve lost. That’s an immeasurable loss to humanity.”

“The More We Look, The More We See”

For years, mycorrhizal fungi were like a black box, understudied because they were hidden below ground.

In 1983, Nancy Johnson found her first reference to mycorrhizal fungi in a one-and-a-half-page summary in a textbook after she began her master’s program in botany at the University of Wisconsin, Madison. She was interested in studying symbiosis and mutualism—the former concerned with the interaction between two species, and the latter focused on when both species benefit from the symbiosis—and the fungi piqued her interest. She checked out every book she could find on the subject and finished them in two weeks. 

It was the beginning of what would become a life’s work for Johnson, who is now a Regents professor at Northern Arizona University and on SPUN’s scientific advisory council. 

“The more we look, the more we see,” she said of the fungi. Studies in the decades since Johnson’s time in Wisconsin have revealed how vital a component they are in ecosystems. “We can tell that the fungus underground connects unrelated plants to each other,” she said. “The fungus makes this huge network under the soil. And, it’s pretty important. Every plant’s got maybe a dozen different fungi in it, and they come and go throughout the season.”

Over the years, researchers like Johnson have found that mycorrhizal fungi are nearly everywhere and in almost every ecosystem. For over 400 million years, they have shaped life on Earth. The fungi even predate plant roots.

There are four main types of mycorrhizal fungi—arbuscular, ectomycorrhizal, ericoid and orchid-specific mycorrhizal fungi. Arbuscular is by far the most common, making up 70 percent of global plant biomass, but they do not grow mushrooms, and are rarely seen. So they draw far less attention—of the total samples of mycorrhizal fungi eDNA, those collected in their natural environment, there are ten-fold fewer samples of arbuscular fungi. 

It’s a huge blind spot that’s especially pronounced in places like the Sonoran Desert, despite the fact that about a third of the world’s population lives in arid regions. 

Studies, Johnson said, are often focused on areas near major research institutions, typically not found in the vicinity of deserts. That’s left more arid regions understudied, she said. And, given they are found underground, mycorrhizal fungi are understudied everywhere. 

But mycorrhizal fungi are most certainly in the desert, and perhaps especially crucial to plant life in the region. “Water is the most limiting resource by far” in the desert, Johnson said, making nutrients harder for plants to get by themselves. Mycorrhizal fungi can make up for that. 

“The threads that come out of the fungus are super, super thin, and so they can get into these tiny, tiny nooks and crannies and increase the surface area tremendously for the uptake of all kinds of things,” she said. “There are mechanisms showing how they actually do help with water uptake in that physical way and actually, they improve drought tolerance.”

Threats to Public Lands Also Undercut Research

Living underground with few sprouting mushrooms made mycorrhizal fungi difficult to study. But modern technology has finally provided the tools to truly measure them at scale, researchers said, paving the way to understand how they work with plants and bacteria, and in turn, whole ecosystems. 

But studying the fungi requires those ecosystems to be intact, with soil that has not been disturbed, which is increasingly rare in the modern world. That’s made protected areas like national parks vital for that work.

“It’s irreplaceable, undisturbed ecosystems where the soil has not been disturbed, the vegetation, it is preserved as a whole ecosystem,” said Johnson. “Those are super important.” 

The Trump administration, however, has put those areas at risk, all while attacking science. 

In February, the National Park Service fired 1,000 employees, only for two U.S. District Court judges to order them reinstated, destabilizing parks across the country as they prepared for the busy summer season. The Trump administration’s Department of Government Efficiency has slashed workforces at national parks, monuments, forests and other public lands. And federal funding freezes have stalled vital conservation work. 

Now, Department of the Interior Secretary Doug Burgum has touted the idea of selling off public lands to address the nation’s housing crisis. To that end, Republican members of the House of Representatives in May added a late-night amendment to the budget reconciliation bill to do exactly that in Nevada and Utah. Public outcry led to the amendment being stripped, but Republicans in the Senate are negotiating how to add public lands sales back into the bill. 

Fewer workers can deteriorate visitors’ experiences in national parks, but the impacts of staff cuts extend far beyond tourists. Researchers like the SPUN team and others rely on staff scientists at the park service to coordinate their visits, provide valuable resources on where to go for the best results, serve as conduits to existing studies that may be relevant to new work and point them towards other research projects in the park. Those staffers’ departure will hinder research projects.

Perhaps most concerning, though, is direct threats to protected areas. Places like Saguaro National Park will likely stay protected, even if resources supporting those protections dwindle. But national monuments and some other public lands used for research may not remain protected. 

In March, the Trump administration announced it would eliminate California’s Chuckwalla and Sáttítla Highlands national monuments before removing language from a White House fact sheet publicizing the decision. The administration has also reported that it is considering shrinking six other monuments across the West. The Department of Justice in June issued an opinion saying the president has the power to undo national monuments, reversing the department’s previous position and going against existing case law.

“It really is the heritage of our nation being preserved in these parks and short-sighted leaders and others just want to make a profit off of it,” Johnson said.

Grand Staircase-Escalante is one of the nation’s largest national monuments, with 1.87 million acres of public land under the protection and management of the Bureau of Land Management. The first Trump administration shrank it by half, but the Biden administration quickly restored its size. The current Trump administration has signaled it may shrink that monument once again.

“The current administration is really interested in coal production and energy production, and there’s a really gigantic nine billion ton coal deposit right in the central part [of the monument] because it used to be a big swamp,” said Jackie Grant, the executive director of Grand Staircase Escalante Partners, which was founded in 2004 to protect and preserve the national monument. “That’s why it’s so scientifically valuable, because there are amazing dinosaur and other fossil discoveries on the monument because of this historic swampiness.”

Before her role at Grand Staircase Escalante Partners, Grant spent almost 13 years at Southern Utah University, where she first became acquainted with the monument when she took students there for research projects every summer. She studied bees and native plants, and collected native seeds for the BLM to aid in restoration projects, like wildfire recovery efforts.

“When we’re looking at the migration of the animals from climate change, we need to look at landscape-scale movement of those animals,” she said. “So when we have 1.87 million acres under a single jurisdiction, that’s going to be really helpful for designing studies related to climate change and looking at how animals and plants change over time in response to a changing climate.”

Research efforts often go far beyond just biology, she added, with Grand Staircase-Escalante and other parks and monuments providing study opportunities for both sociological and archeological studies. 

“One of my biggest points of fostering science on public lands is that public land science is often an incubator for applied science,” Grant said. Unlike research conducted in a lab, she said, research on public lands can support the actual restoration and management of the areas where the studies are conducted.

A Shifting Landscape

At the western end of Saguaro National Park near the edge of Tucson, Stewart and Elhance descended again into a field of saguaros.

Rather than collect soil at the base of a saguaro to analyze what fungi grow with it, this time they measured out rectangles on the land with their tape measure to take bulk samples, the equivalent of a census of the general biodiversity of the area, they said.

SPUN was founded not just to raise awareness of mycorrhizal fungi, but to map those fungal networks around the world in its Ground Truthing project. Researchers with SPUN like Elhance and Stewart take samples at understudied locations like Saguaro National Park, and then use machine learning to summarize how many species of the fungi are found in an area. 

The project has used DNA samples from ecosystems around the world, both taken at SPUN-supported projects and drawn from other research papers, and aggregates them into one big study. 

“A lot of scientists are moving towards trying to be able to draw scientific conclusions at larger, regional, even global scales, interpolating the individual point data that scientists typically collect when they’re doing environmental research into predictions across the landscape,” Elhance said.

As global warming expands arid regions around the world, it’s vital to understand the role mycorrhizal fungi networks play in those areas, and how they make native vegetation more resilient in the face of the changing climate. It’s important the work not slow down, the SPUN team said, but the Trump administration’s slashing of federal funding for research, attacks on universities and threats to protected areas nonetheless threaten to delay it. 

While ecosystems have never been stagnant, Stewart said, climate change is increasing the degree and speed of the changes they are enduring, shifting the borders of biomes. So it is crucial to get these baseline studies that tell researchers what exists in native communities before the climate can transform them.

The Sonoran Desert is younger than other arid regions, which is what makes it much wetter and greener, and has given it its famed biodiversity. 

But hotter temperatures and less rainfall threaten to change that. And highly flammable invasive plants like buffelgrass and fountain grass, introduced for cattle grazing and landscaping. are fueling bigger and hotter wildfires in an ecosystem not adapted for them, killing saguaros that are tolerant of less-intense fires and speeding the spread of the combustible exotics. 

Wildfires impact fungal networks, too, studies have found. But researchers have determined that if plants have their native mycorrhizal fungi systems in the soil, the networks can help negate some of the negative impacts of a changing environment. The fungi help anchor those native species thanks to their interplay with a plant’s root systems. That anchoring, Stewart said, may prove to be vital as the climate shifts. 

“This is such a unique desert because it really changes shape. It’s like a blob. Every year, the climate changes a little bit, so it expands or contracts a tiny amount,” he said. “So if you think of these fungi as things that stabilize plant communities, can they help make sure that these deserts don’t grow or contract?”