5 Million Fungi

  • June 1, 2016

Fungus is growing in Brian Perry’s refrigerator — and not the kind blooming in someone’s forgotten lunch bag.

No, the Cal State East Bay assistant professor has intentionally packed his shelves with 1,500 Petri dishes, each containing a tiny sample of fungus from native and endemic Hawaiian plant leaves. The 45-year-old mycologist (a person who studies the genetic and biochemical properties of fungi, among many other things) figures hundreds of those containers hold heretofore-unknown species.

The professor’s work identifying and cataloguing fungal endophytes — microscopic fungi that live inside plants — carries several important implications. Scientists know little about the workings of these fungi, making them a particularly exciting frontier for examination: Learning about endophytes’ relationships to their host plants could save many endangered species; farmers have begun tapping into their power to help crops build resistance to pathogens; and researchers are interested in using them to unlock new compounds to make crucial medicines for people.

The only problem — finding, naming, and preserving them before it’s too late.


Perry’s search for fungi actually began locally in the East Bay, where he grew up fishing, hunting, backpacking and collecting mushrooms as a kid, although he was unable to name them at the time. After obtaining his bachelor’s and master’s degrees at SF State and a Ph.D. from Harvard — including a switch in majors from photography to biology along the way — he began uncovering mushrooms and endophytes across the globe. Throughout Tibet, Micronesia, on Borneo, and on São Tomé and  Príncipe (tiny islands off the coast of West Africa), Perry has surveyed “hotspots,” or regions with high levels of endemic, endangered plants and wildlife.

According to Conservation International, there are 35 total hotspots in the world that comprise just 2.3 percent of Earth’s landmass, yet these regions hold more than half of species that can’t be found anywhere else.

Along the way Perry’s also helped find and name five new species and one genus —including one that made international headlines and late-night comedy shows for its shape and name, and one glowing bioluminescent specimen. Each was the first fungus named to the annual Most Exciting New Discoveries list by the International Institute for Species Exploration (2010 and 2011, respectively).

Of late, with CSUEB graduate student Sean Swift under his wing, Perry has been scouring the Hawaiian archipelago — the most isolated island chain in the world, where more than 90 percent of plants are unique to their environment, and nearly 30 percent are threatened and/or endangered according to the state’s Division of Forestry and Wildlife.

“We’re collecting the baseline data,” Perry says. “We’re surveying the diversity of organisms and determining what’s there. In all these places,  we’re saying, ‘No one’s ever been to this place and done a full documentation of the fungal biodiversity that’s here.’ That’s the starting point.”

Perry has recently been awarded two National Science Foundation grants to study fungi. “He’s very accomplished,” says Simon Malcomber, program officer in the NSF’s Division of Environmental Biology. “He’s been making exciting discoveries, and we expect him to make even more.”

“With the endophyte project, we’re talking about big evolutionary questions,” Perry explains. “When we look at endophytes that are living in native plants, we want to know: Did they co-evolve with their host plants? Did they go through adaptive radiation (rapid evolutionary diversification of an organism)? Where did they come from?”

“The likelihood of the discovery of new species from this research is extremely high,” Malcomber adds. “(Perry and his team) will also make really important advances in understanding the pattern of relationships in the tree of life, and how this life is shaped and formed. This is basic information that we need. They are getting at this dark, unknown biodiversity.”


From tiny endophytes, Perry sees big potential. The microfungi hidden in leaves and stems may be doing more than meets the eye. For instance, the yew tree (an endangered species) was credited with producing the crucial compounds for the drug Taxol, a powerful chemotherapy treatment used for ovarian, breast, and prostate cancers. But it turns out the compounds actually derived from the yew’s endophytes — the fungi living inside it. Perry says endophytes might also be the reason some fruits and vegetables taste good and have health benefits. “The terroir (soil and climate conditions) of these things could be coming from the microbes that are associated with them,” he says, rather than the plants themselves.

As Charles Bacon, research leader and supervisory microbiologist of the Department of Agriculture’s Toxicology and Mycotoxin Research Unit says, “The biggest thrust (in this field of research) is to use these organisms for biochemicals — medicinals — for anything from headaches to cancer. Some of these endophytes are very talented at making and transforming exotic metabolites (byproduct compounds), which cannot be manufactured or synthesized in a laboratory by a chemist.”

Conceivably, endophytes could be put to work doing anything from replicating the qualities of a rare wine to bolstering drought tolerance in water-greedy plants — so long as scientists can document, harvest, and study the minute capacities of fungi before it’s too late.  

Additionally, millions of dollars have been spent on sterile greenhouses in which scientists grow endangered plants. However, Perry says many of these plants die once transferred into their natural habitats, likely because they haven’t been inoculated by beneficial endophytes and are too fragile to survive.

Much like how humans are now discovering the importance of their microbiomes, Perry believes scientists are coming to appreciate plants’ microbiomes. “We’re thinking of probiotics for plants,” he says. “How do you build up the endophytic community in your plant to make it as healthy as it can be in its environment? As we learn more and more about these systems and truly understand the biology of these endophytes, they become a very important factor in plant conservation.”

“The likelihood of the discovery of new species from this research is extremely high.”



In his lab today, Perry maintains the appearance of an outdoorsman in a plaid shirt and hiking boots. He looks like he’d rather be in a muddy forest, reaching into logs, braving leeches and spiders — or as he recalls, a four-foot green cobra dangling at head level from a tree branch — to find a new mushroom.

A mycological Indiana Jones, if you will.

In that vein, though Perry’s work does include sophisticated laboratory equipment to replicate and sequence fungal DNA, he uses startlingly mundane tools — a garden-variety hole-puncher to gather samples and plain vials to transport them from the field. Once the samples are carried and/or shipped from the Hawaiian Islands to Cal State East Bay, they go into a fridge that looks like something straight out of student housing. That fridge smells funky, but it’s doing what the USDA regards as critical work.

“It’s necessary to do this because no one else has,” Bacon says. “We’re now aware that there’s no such thing as a single entity on this planet. Every living thing is made up of a conglomerate of organisms that is contributing to its success.”

“We’re creating a living library of all these fungi,” Perry explains. “We’ll identify them, then we’ll send them off to the USDA, about 1,000 species. They’ll grow them and then cryopreserve them. Essentially, once you freeze-dry these things, they’ll last forever, as far as we know.”

Ready and waiting for some scientist of the future — perhaps Perry down the road or one of his students — to extract the compounds and solve another scientific mystery in the evolutionary tale of life on earth. “Our estimate is that global fungal diversity ranges from 3.5 to 5 million species,” he says. “So far we’ve only documented about 100,000 of those. That tells you how much there is out there to be done. To me, that’s incredibly exciting.”


When Cal State East Bay graduate student Devin Schaefferkoetter needed a project, Assistant Professor Brian Perry gave him an assignment that represented the perfect blend of science and nature.

“My background is in ecology and conservation, so I wanted to be outside as much as possible,” Schaefferkoetter says. “I chose (Perry’s) lab to get more hands-on experience.”

Perry, whose work surveying fungi has taken him around the world, is finding opportunities for CSUEB students to contribute to the research here at home, too.

He sent Schaefferkoetter to catalog the diversity of mushrooms at the Pepperwood Preserve in Sonoma County, a 3,120-acre wildlife and plant sanctuary. “I knew the preserve,” Perry says. “They had never done a comprehensive fungal diversity study. There are still huge portions of California that we’ve never done a thorough survey of.”

 In his first two trips to Pepperwood, Schaefferkoetter found 25 species of fungi.

At the preserve, Shaefferkoetter is also teaming up with a UC Berkeley professor who’s been collecting data there to study the impact of the weather on large woody plants. By including fungi, they can search for correlations in each other’s work, and possibly draw some conclusions about the effects of climate change on the environment.

Perry says the work with the nature preserve can ramp up over time. “We hope we can maintain a relationship with Pepperwood and go every year for sampling. If we go to the same site year after year for five, 10 or 15 years, they’ll develop data that will enable them to draw important conclusions about the health of the property.”