There are fungi in our oceans and our prestige television shows, in our pharmaceuticals and designer furniture, in our newspapers and our tumors. Wherever we look these days we seem to find more, like the morning after fall rain on a global scale. Yet, according to a recent estimate from the Royal Botanic Gardens in England, most of the world’s fungal population—and, by extension, most of what we mean when we talk about fungi—remains mysterious to us.

A vast majority of the world’s fungal species have, so far, eluded conventional scientific identification. Some of these species can be discerned by the presence of their DNA in soil samples, but we don’t really know what they are. These unidentified life-forms, what researchers sometimes call “dark fungi,” might be thought of as the world’s secret fabric: the dark matter of life. They hold together our ecosystems in ways we are only starting to fathom. And in this age of mass extinction, their elusiveness has become an ecological concern.

What do we know about this invisible universe? And why does it remain so stubbornly mysterious?

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It starts with the number. The question of how many fungal species exist in the world has vexed researchers for over a century. In 1902, the most comprehensive taxonomy of fungi then in existence, Pier Andrea Saccardo’s multi-volume Sylloge Fungorum, listed over 52,000 species. They hailed from around the globe, although identifications tended to be densest where mycologists, the students of fungi, were densest: Europe (especially England, France, and Germany) and North America.

There was reason to believe, at the time, that the number was inflated. Despite Saccardo’s best efforts, there were duplicates and misidentifications—the result of researchers working in different places and languages, overlooking each other’s writings, seeking to make a name for themselves by giving their names to fungi.

Saccardo believed his list was only a fraction of the global population, predicting the actual number of different fungi to be closer to 150,000. Today, after more than a century of additional work using high-tech genetic sampling techniques and global collection, researchers have cataloged almost exactly that many species. And still, there are strong indications that Saccardo’s estimate was conservative. In 2011, mycologist Meredith Blackwell calculated that there might be nearly five million total species of fungi, and others have offered numbers as high as ten or twenty million, with more sober guesses around three million. We have found only a small fraction of the world’s fungal diversity.

There are more fungi than plants and mammals combined, a diversity and extent matched only by insects and bacteria. A growing body of research has also revealed the essential role fungi play in maintaining ecosystems at nearly every level. They are decomposing chemical spills, turning ants into zombies, cycling nutrients, and weaving intricate webs of hyphal threads that transmit vital signals beneath the skin of the earth. Many of these species are threatened by a warming world, and we may not even know what they are or do.

But why is there so much uncertainty about the number itself, and why does it matter? Here the question gets deeper, and somewhat stranger, bringing us to one of the more curious paradoxes of modern taxonomy, one which unsettles our very definition of a “species.” Many unidentified fungi have in fact already been collected—they just cannot be visualized or cultured in laboratories. They are, in multiple senses, invisible, even as they represent a vast portion of our ecological tapestry.

What does it mean if some living things simply cannot be brought into the light?

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To get a sense of all that is hiding in the shadows, one must first appreciate what fungi we can see—and how we got to know them. Throughout the early nineteenth century, when mycology began to don the garb of a conventional scholarly discipline, the work of identifying new species focused on macrofungi, such as brilliantly colored fly agarics and delicious boletes. Research relied heavily on experience and direct observation. Those interested in finding fungi—which were still considered “plants”—took extended strolls through quiet woods, picked scandalously phallic mushrooms, ate a few of the safer ones, and dried their most unusual spoils for later observation.

Unfortunately, in contrast to flowering plants, paper turned out to be a poor host for mushrooms, which lost their lively colors and shriveled, offering little insight into vital processes. Drawing and painting were therefore essential, and many early fungal experts (or their wives and assistants) were remarkably capable artists, enabling colleagues in distant lands to witness their discoveries.

Few garnered envy quite like Charles and Louis René Tulasne, two brothers who left law and medicine to dedicate themselves to mushrooms and lichen. Charles’ careful drawings of life histories, symbioses, and microscopic structures are photorealistic and fantastically alive, dispatches from a vibrantly alien world. Mycology was at once an art and a science, and the enduring appeal of fungal illustrations, whether on notebooks or totes, confirms the lasting power of that amalgam. Saccardo was also a talented artist, known for meticulously cataloging the tree trunks or leaves he found fungi on, but by the end of the nineteenth century, few could afford the exacting detail of the Tulasnes. Drawings were diminished; lists, figures, and photographs predominated. As mycologist Louis Krieger bemoaned in 1922, “I think it is safe to say that never again will such hand-work appear as we find reproduced in the stupendous monographs issued by these two unassuming brothers. Commercialism has killed the possibility; men are no longer training their minds, eyes, and hands for such work—the art is dead!”

If the art was dying, replaced partially by a desire to “let nature speak for itself” through photographs (what Lorraine Daston and Peter Galison call “mechanical objectivity”), mycologists were still being trained in new modes of seeing. The widespread accessibility of powerful microscopes took them closer to their objects of fascination than ever before. In his first book, Saccardo described feeling “almost drowned” in a “great sea” of microscopic life-forms. He and others like him could see what earlier eyes could not, and the total number of identified species exploded.

Technology was only one piece of the puzzle. Mycology’s charming curmudgeon, Curtis Gates Lloyd, who funneled part of a Cincinnati pharmaceutical fortune into his passion for puffballs, blamed the narcissism of other researchers. Foragers insisted on attaching their name to every little fungus they found, a “fever” he named “species-making.” Men looked at the world’s plant diversity, Lloyd thought, and mostly saw themselves.

The acceleration of species identification could hardly be ignored, but Saccardo’s near drowning indexed an irony: few mycologists were extending their search to the world’s great seas. One exception was Frederick Sparrow, a warm-hearted Michigander with a hearty mustache, who in the late 1920s submerged twigs and soggy apples, sealed sea moss within waxed cardboard containers, and subjected the results to microscopic examination. By 1950, dozens of studies revealed an immense array of aquatic fungi, many adapted to saltwater conditions. Identification required new approaches to an increasingly central mode of mycological inquiry, the so-called “pure culture,” which allowed living organisms to be maintained over longer durations in specially fabricated containers. Culturing solved part of the preservation dilemma that plagued earlier generations—drawings are less critical if one can see the fungus itself—and revealed the unbelievable diversity of substrata on which fungi could survive. They existed on insect skeletons, onion skins, pollen grains, algae, shrimp skeletons, snake skin, eel worms, ferns, and almost everything in between.

“We have the tools and we have the fungi,” Frederick Sparrow exclaimed in a 1950 article on the “Expanding Horizon of Mycology.” But what was out there, at the edge of that horizon?

For one, a billowing wave of species identifications and an explosion of fungal data that made life as difficult as it was exciting for working mycologists. The electron microscope, for example, which uses a thin beam of energetic electrons to magnify miniscule things like cellular components, allowed mycologists to peer ever deeper into the microscopic world, illuminating the ultrastructure of hyphae, the tubular threads by which many fungi explore their environments. If visualization remained essential, here was a powerful new way to see.

Yet with new tools came new problems: the known fungal world was growing, but so were the horizons of what mycologists didn’t know. In a lecture to University of Wisconsin bacteriologists in 1962, mycologist and historian Geoffrey Clough Ainsworth noted that fungal information was “increasing exponentially,” published in “more languages and scattered through more publications than ever before.” Even the most industrious researchers had to wonder how they could stay afloat. In the 1980s, the introduction of DNA sequencing would further exacerbate those concerns while fundamentally reshaping ideas about how to name and classify fungi.

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Long before DNA transformed mycology, researchers noticed major inconsistencies in how they arranged and classified organisms.

Yeasts, rusts, and smuts, for example, are all fungi (and among the most alluringly named subgroups). But yeasts were classified by their morphological characteristics and ability to assimilate carbon compounds, while rust and smut species eluded morphological resolution and were instead often named for the plants they parasitized. Thus brewer’s yeast, Saccharomyces cerevisiae, literally the sugar fungus of beer, is named for its use of sugar as a carbon source, while Ustilago maydis is the smut of corn, or maize. Drawing taxonomic connections on the basis of DNA sequences seemed to offer a better solution, leaving each species division “a product of nature rather than the creation of the taxonomist,” in the words of yeast taxonomist Cletus Kurtzman in 1985. Molecular objectivity seemed to offer a solution to the limits of mechanical guesswork.

The usage of genetic tools caused a radical redistricting of the fungal kingdom. Longstanding taxonomic groups fell apart, as things so often do, and phylogenetic studies drew new lines across traditional classifications. Many organisms were found to be, in fact, fungi, while others long studied as fungi, such as the late potato blight, were decisively determined to be nothing of the sort. Some single species even turned out to be immensely multiple, like a lichenized fungus in the genus Cora, which DNA studies recently revealed to be several hundred distinct species. At the highest level, fungi, associated for centuries with plants rather than animals, were shown to share, to the mild discomfort of many vegetarians, far more with chickens than roses.

The application of advanced genetic methods to fungi was expensive and time-consuming at first. It could not be done willy-nilly on whatever potentially exciting speck of earth one found: the first fungal genome, that of brewer’s yeast, was sequenced in 1996, but another important laboratory species, Neurospora crassa, followed only in 2003, and the results revealed major divergences in the genetic makeup of fungal families. A decade later, however, an expanded array of approaches allowed researchers to collect large environmental samples, like tropical soils and vials of ocean water, gather DNA and RNA sequences, and find evidence of numerous, previously unidentified organisms. 

There was, however, a problem: many of these organisms were so small or fragmentary that they could neither be visualized by conventional devices nor cultured in laboratories. As mere read-outs of DNA printed on computer screens, they were difficult to interpret—the invisible obverse of the known and named world: dark taxa, or dark fungi.

For mycologists, the existence of such cryptic, invisible, and “voucherless” organisms represents a multiform dilemma: a “staggering limitation” to communicating and interpreting fungal ecology and evolution, according to a recent study. The reasons are various, but they concern an ongoing reevaluation of how we decide what is and is not a species.

At a basic level, taxonomists name and classify organisms. The name Candida albicans, for example, coined by mycologist Christine Marie Berkhout, tells us the genus and species, respectively, of the yeast commonly responsible for skin infections. Etymologically, it’s a goofy name, since both albicans and Candida come from Latin words for “white,” making Candida albicans something like “white whitening,” the Wonder Bread of fungi. There are around two hundred other species within the genus Candida, including C. antarctica (found in a lake you’ll never guess where, as well as on polished rice in Japan) and C. krusei, which limits the bitterness in chocolate.

Species and genus names frequently differ in reference, from places and characteristics to the discoverer’s name, but the key point for working taxonomists is that each name has been published, usually in a scientific journal, along with a description. Under the terms set out by the International Code of Nomenclature for algae, fungi, and plants, each also requires a “type” specimen, a kind of standard representative, which might be a dried sample, an illustration, or a metabolically inactive culture. As Adam once gave names to the animals, so traditionally have mycologists given names to the fungi.

Dark fungi do not have names. For much of recent mycological history, the path to a name went via study of an organism’s morphology and phylogenetic placement: how it behaves, develops, and forms relationships. But because dark fungi can neither be seen nor cultured, the task of conventional description is all but hopeless. Rather than isolated individual entities, they remain ghostly, fluorescently labeled presences in environmental samples. Still, they are significant, because their numbers appear monumental and their possible ecosystem roles immeasurable.

One way of getting around this unnameability is DNA “barcoding,” in which a small fragment of an organism’s genome is used as a standard of comparison for its taxonomic group. (There is, to wit, a “Consortium for the Barcode of Life.”) For fungi, such comparisons are usually based on internal transcribed spacer (ITS) groups, which readers are invited to research at their own leisure. According to a 2018 study, of the nearly one billion fungal ITS regions collected in a large database known as the Sequence Read Archive, operated by the National Library of Medicine, the vast majority are known only by their sequence: tens or even hundreds of thousands of novel taxonomic groups. Naming fungi by their codes would eliminate some of the poetry of old names, but it could offer a way of getting a handle on these beings.

In doing so, however, barcoding threatens another death for the art of mycology, and some wonder whether there is danger in sequence-based naming. An emphasis on this practice could, for instance, diminish support for international culture collections, which often maintain a tenuous hold on institutional funding. A future sequence-based mycology might also stack the deck in favor of large laboratories with access to the most advanced sequencing tools.

There is debate about the validity of these criticisms, but few dispute the fundamental challenge that dark fungi represent to the work of mycology. “The fungal kingdom may be almost exclusively dark,” noted a summary of a recent study. It no longer appears feasible, as it once did at the dawn of the DNA era, to apply a single, universal approach to identifying fungi. The future of mycology looks stranger than many could have imagined.

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We tend to think that we know a great deal about the workings of the biological world. But despite the omnipresence of fungi today, there is so much we still don’t understand. Even assuming a limited estimate of the total existing species, mycologists David Hawksworth and Robert Lücking argue that a complete inventory would take 680 more years at our current rate of discovery. For the more expansive estimate of 3.8 million species, the full catalog would be finished only in the year 3848—and who can envision the challenges facing mycology then?

“Imagine a census of a population of three million people,” wrote Lücking and fellow mycologist Conrad Schoch recently. “Now consider that only 150,000 of these people had a name and a valid, government-issued document connecting that name to the corresponding person. Imagine further that many of those people had more than one name, having been married one or several times or just because they felt like changing their name every once in a while. You end up with 150,000 people having 300,000 different names, while the remaining 2.85 million have none.”

We could take their science fiction further: imagine that those 2.85 million people are dying, en masse and at an accelerated rate, leaving behind vital jobs that none of the survivors know how to perform. Many are unlikely to ever be identified before it’s too late, and the plausible toll of such ongoing extinction is, in an era of climate catastrophe, monumental. Already vulnerable ecosystems may be further undermined, while the difficulty of accounting for this vast world of dark life leaves many of our geo-ecological models fundamentally unstable. With so many medicines and industrial products reliant on fungi, there is good reason to worry that humans are destroying organisms with vital importance for the future of worldly life. How does a discipline with such a tight focus approach such a huge task?

In a 2011 lecture, “Dreams and Nightmares of Neotropical Ascomycete Taxonomists,” the delightfully eccentric Cornell scientist Richard Korf worried about the social utility of fungal taxonomy. Looking back over centuries of research, Korf fretted that the old conditions enabling taxonomic inquiry, such as supportive museum posts and an academic environment of open-ended inquiry, were disappearing. The ivory tower, he noted, had ceased to offer such a climate, and granting agencies now held exaggerated sway over what studies could be done and how.

But Korf, who passed away in 2016, remained optimistic. Taxonomists seek the truth about relationships, he affirmed. Even more important than naming, which Korf had dedicated much of his life to, was the work of saving. Mycologists were in the business of preserving that which was being lost far too quickly, of “saving whatever we can of our natural diversity.” This was, Korf concluded, in what he called his “final sermon,” mycology’s continuing moral duty.

What we colloquially call scientific progress is, in reality, a seesawing expansion of both the known and the unknown. A good experiment, after all, typically raises as many new questions as it answers. Although taxonomic debates, often derided as the quibbles of biological stamp collectors, have long seemed like footnotes to the more thrilling tales of scientific discovery, they have a vital role to play in grappling with climate destruction: indexing loss and identifying what might be preserved.

If the work of naming and organizing species was once a mark of human mastery over the natural world, it might be seen as something else today, in an era in which that mastery finds itself so clearly upended: a form of attention, care, and consideration. Making sense of the darkness has its challenges and perils, but if we don’t start looking closely now, we may only see some of the light after it has already gone. ♦