By 2019, Harte Singer wanted a mushroom cheat code. Singer, a professional chef, had been mushroom-hunting for more than a decade—at first with dinner in mind, and then out of growing curiosity about the kingdom of fungi. But a lot of mushrooms look alike. Identifying them can require intense study of photographs, keys, spore prints, or microscopic cells. Getting really good at it can take a lifetime.

Listening to mycologist Alan Rockefeller at Counter Culture Labs in Oakland, Singer thought maybe he’d found a shortcut. Rockefeller was explaining to the audience how, with just a few hours of lab work, you could extract a mushroom’s DNA. Once you got a machine to read out the sequence of that DNA, you could be one quick search through a genetic database away from the mushroom’s name. No field guides, and few microscopes, necessary.

Singer stayed for hours after the talk to watch Rockefeller at work. He thought it seemed like magic. “You could… mix a few potions together and send something off and then get a result,” he says. 

Today, the search for fungal answers has taken over Singer’s life—and his garage in Santa Rosa, which he’s now converted into a full laboratory dedicated to fungal DNA. Centrifuges, sterile cabinets, pipette tips, and piles of ziploc bags filled with dried fungi abut shelves of camping equipment and duvet covers. Cooking is now strictly personal for Singer. He is completing a master’s degree in mycology at California State University East Bay, runs his own fungal DNA sequencing business, and leads sequencing for the California Fungal Diversity Survey (CA FUNDIS)—a community science project that aims to collect, preserve, and sequence as much of the state’s dizzying fungal diversity as possible. 

These spooky fingers were found near redwoods on the north coast of California. Mandy Hackney’s iNat observation includes a provisional taxonomy and a DNA barcode, thanks to changes in iNaturalist’s database prompted by fungal enthusiasts’ advocacy. Mandy Hackney via iNaturalist, CC-BY

Singer helped launch CA FUNDIS in 2022 to take advantage of new, cheap DNA technologies—and a growing cohort of obsessive amateur mycologists. “They’re doing something which I think a lot of us have dreamed about,” says Kabir Peay, a mycologist at Stanford University who has not worked on the project. 

More than 90 percent of fungi across the world remain undescribed, Peay notes. That’s because people tend to study—and protect—fluffy, charismatic, or large plants and animals. “We love those things, but they’re not necessarily the most important,” says Daniel Gluesenkamp, the executive director of the California Institute of Biodiversity, which supported CA FUNDIS along with the state of California. “We need the organisms that keep soil healthy, that eat the pathogens, that sequester carbon.” CA FUNDIS, he says, has helped expand and complicate our understanding of that biodiversity.

It didn’t take long for Singer to realize DNA sequences offered more questions than answers. Between shifts waiting tables, Singer devoted hours—and much of his money—to the painstaking art of DNA. “I was spending all my discretionary income on sequencing mushrooms,” he says. The careful, methodical work, where a single break in protocol would ruin the final product, felt similar to high-end cooking—minus the loud, sweaty restaurant kitchen. 

Singer would mail test tubes of liquid DNA he’d extracted and amplified to a San Francisco lab that provided overnight sequencing. Buzzing with excitement, sometimes he would stay up all night, waiting for the email with the sequencing results. But often it matched few, if any fungi, in existing genetic libraries. “That was even more exciting,” he says. 

Get Bay Nature’s Free Weekly Newsletter

Singer had company in his excitement. “What we’re realizing is that we’ve got all these mushrooms in California that have the wrong names on them,” says Damon Tighe, a leading Bay Area community scientist who specializes in fungi, and who volunteered as a collector with CA FUNDIS. Several local fungi had been given the European names of their cross-pond lookalikes. As DNA became easier, quicker, and cheaper to work with through the 2010s, more California mycologists started sequencing their hauls out of sheer curiosity. In the process, many discovered that mushrooms they thought had come from Europe might, in fact, be California natives. “Everyone was looking around going like, ‘Oh, maybe it’d be cool if we did that at a big scale,’” says Tighe. 

By 2022, those conversations became CA FUNDIS. New portable DNA sequencing technology, refined by Michigan-based mycologist Stephen Russell, had transformed the world of mail-order sequencing. The national nonprofit Russell had helped found, the Fungal Diversity Survey, offered an institutional home for the project. To scale up sequencing, Singer took over an annex in the mycology lab of his advisor, CSU professor Bryan Perry, and bought and borrowed equipment to establish his garage lab. The CA FUNDIS project managers planned and got permits for surveys on lands across the state, recruited collectors to find and document fungi, and then sent them mushroom-hunting.

After a long day of mushroom hunting in the critically undersampled Klamath Mountains, Justin Paulin, Stuart Pickell, and Thea Chesney sit around a table at their base camp (a rented house) to process their collections and photos. Harte Singer

Almost immediately, people started pulling up surprises. When collecting started, Tighe was in Southern California, far from his usual damp fungal-foraging climes. The only place nearby where CA FUNDIS had a permit was a hot, dusty mile of Bureau of Land Management-owned chaparral. He tried his luck in the dry chemise—and stumbled upon a Hygrophorus, a kind of waxcap mushroom he had only ever seen in redwood forests. “I was like, ‘Oh crap, there’s this huge biozone we just haven’t been looking at in California,’” Tighe says. “We pulled so many new species out of the chaparral that it’s just jaw-dropping.” 

In the first year alone, 17 percent of the 2,000 fungi Singer sequenced for CA FUNDIS had no match with a known species. To make the data accessible, nearly all of the sightings, along with their DNA sequences, were uploaded onto iNaturalist, the free community science platform. The FUNDIS organizers hoped taxonomists—the scientists who describe the world’s diversity—would use the observations to find and name the new species. 

This raised an issue: how to flag mystery mushrooms for taxonomists. Normally, iNaturalist only recognizes new species after taxonomists give them an official Latin name. But there are few taxonomists, “and more work than we can keep up with,” says Peay. Singer and other mycologists asked the platform for the ability to give potential new fungi temporary names tied to their DNA sequences, to speed up taxonomists’ Sisyphean task, and help mycologists know whether their sequenced fungus was a new mystery, or an old one. 

This flame-colored mushroom collected in the Marin Water District has a DNA barcode is labeled with a provisional taxonomy in iNaturalist: Hygrocybe sp. ‘CA08’. Andrew Abballo via iNaturalist, CC-BY-NC

At first, the request was “vehemently denied,” Singer says. At the time, iNaturalist was part of the California Academy of Sciences. But after it became an independent nonprofit, iNaturalist finally accepted the longstanding feature request and launched a pilot letting users use temporary names for any fungi with DNA sequences attached. “This is a great example of community-led innovation on iNaturalist,” wrote Scott Loarie, iNaturalist’s executive director, in an email. 

One Thursday evening, Singer logs onto a Zoom call. He’s been running these for the last couple of years to teach people how to analyze fungal DNA. Some 15 people join. One has a psychedelic mushroom-filled Zoom background. Some attendees are PhD students; others may work as rocket scientists or middle school teachers, and pursue fungal fanaticism in their free time. You can’t tell who’s who. Singer hosts these calls nine times a month. Sharing his screen, Singer starts clicking from iNaturalist through other websites to show how you can compare a sequence across different genetic libraries to narrow down what a mushroom might be. 

Singer has learned over the past half-decade that the DNA identification of fungi is “more of an art than a science.” For certain groups of fungi, a difference of five DNA letters, say, from one sequence to another means it’s a whole different species. For other groups, that’s just normal variation. “Evolution doesn’t necessarily make things convenient for us,” he says.

To date, Singer has sequenced more than 10,000 different fungi for CA FUNDIS. This work has flagged up to 1,000 potential new species for taxonomists to eventually get around to. And after three years of work, the team has begun to wrap up. Funding for CA FUNDIS has shrunk, and other sequencing efforts, like Russell’s MycotaLab, are also sequencing people’s fungal finds. The nationwide nonprofit that housed CA FUNDIS has seen leadership turnover in recent years. “We delivered on all the metrics we promised,” wrote Singer over email. This year’s smaller grant from the California Institute of Biodiversity supports people to go to unique habitats in California to look for rare species but doesn’t support much sequencing. Singer has promised CA FUNDIS collectors that he’ll sequence any fungi they find for free.

In the eastern Sierra, Damon Tighe collects soil for the California Institute for Biodiversity. Harte Singer

But the example set by CA FUNDIS and the researchers who’ve supported it, Tighe says, have “lit a fire” for amateur mycologists. “You’re seeing this ripple effect that’s spreading out,” he says. Most amateur groups of mushroom-hunters are now trying to sequence their fungi, says Perry. Several send their samples to Singer’s DNA sequencing business. He gets through about 900 specimens a month. “As a side gig, it’s doing quite well,” he says. 

Personally, after five years hunched over minute amounts of liquid in test tubes, Singer wants to get beyond just identifying mushrooms. DNA sequences only begin to explain what fungi actually get up to in the world. His master’s thesis—long-delayed because of the CA FUNDIS work—unravels the relationships between the microscopic fungi that live in the leaves of one pink flower. “If I could understand the ecosystem in the soil under one tree, I would die happy,” Singer says.