Fungi

Lead Summary

Fungi occupy a singular position in terrestrial ecosystems: they are neither plant nor animal, yet life on land as we know it depends on them. As the principal decomposers of dead plant matter, fungi recycle carbon and nutrients on timescales of years to decades. As mycorrhizal partners, they extend the reach of plant roots and channel a staggering ~13 gigatonnes of carbon per year from forests into soil. And across millennia, humans have domesticated select fungal species—for bread, cheese, sake, soy sauce, and, since 1985, industrial-scale protein production—in a partnership that continues to expand into biomaterials and biofabrication.

This article draws on supported research across fungal ecology, mycorrhizal biology, domestication genomics, climate-driven pathogenicity, and ethnomycology to survey what is robustly known about fungi: how they work, how they partner with plants and humans, and how cultural attitudes toward them vary across the world.

Historical Development

Ancient origins

Arbuscular mycorrhizal fossils appear in the earliest known land plants, from the Devonian period approximately 450–400 million years ago. The discovery of arbuscules and nonseptate hyphae in the Early Devonian land plant Aglaophyton major provides unequivocal evidence that mycorrhizal associations were established over 400 million years ago—with arbuscule morphology identical to modern arbuscular mycorrhizae. This fossil evidence strongly supports the hypothesis that mycorrhizal fungi played a critical role in enabling plants to colonize terrestrial environments.

The Carboniferous coal question

The fungal gap hypothesis proposes that a temporal lag existed between the evolution of abundant lignin production in woody plants and the subsequent evolution of lignin-degrading Agaricomycetes fungi. According to this hypothesis, this evolutionary lag resulted in a period when vast amounts of lignin-rich plant material accumulated without being decomposed—offering an explanation for the massive coal deposits formed during the Carboniferous period (~360–300 million years ago). The hypothesis remains actively discussed; subsequent analyses have challenged whether it fully accounts for Carboniferous coal production patterns.

Millennia of human domestication

The human-fungal partnership stretches back thousands of years through fermentation. Koji (Aspergillus oryzae) has been central to Japanese sake, soy sauce, and miso production for centuries, and was officially designated Japan's "national microbe" by the Brewing Society of Japan in 2006. Indigenous Mesoamerican peoples used psilocybin mushrooms ritually for at least 3,000 years. The modern frontier of fungal domestication—mycoprotein production since 1985, mycelium-based biomaterials since the early 2000s—represents, as researchers have characterized it, "a quiet but real expansion of the human-fungal partnership beyond its agrarian origins."

Mechanism & Process

Saprotrophic decomposition

Saprotrophic fungi are the largest functional guild of decomposers in terrestrial ecosystems. They degrade complex polymers—lignin, cellulose, hemicellulose, and chitin—by secreting mixtures of extracellular enzymes (both oxidative and hydrolytic) directly into dead organic matter. These enzymes break large, insoluble biopolymers into smaller, soluble units that are then absorbed and metabolized by the fungal hyphae.

The specialists of lignin degradation are white-rot fungi (Agaricomycetes), which accomplish this through secretion of class II peroxidases—lignin peroxidase, manganese peroxidase, and versatile peroxidase—that catalyze oxidative cleavage of the phenolic and non-phenolic aromatic bonds in the lignin macromolecule. Without this capability, dead plant matter would accumulate indefinitely in the biosphere rather than cycling carbon back to bioavailable forms.

Mycorrhizal symbiosis

The fungal partner in mycorrhizal symbiosis extends the effective absorptive surface area of plant roots through an extensive hyphal network that penetrates soil beyond the reach of the root alone. Through this network, fungi acquire phosphorus, nitrogen, and water that are transported to the plant host, while receiving photosynthetically fixed carbon in return.

This exchange is not passive. Arbuscular mycorrhizal symbiosis is established through specific molecular signaling pathways between fungal and plant partners. Compatible recognition between plant and fungal partners requires specific molecular interactions, and plant genetic mutations affecting symbiotic signaling can prevent colonization entirely even when compatible fungi are present. Once established, arbuscule-containing cortical cells undergo comprehensive transcriptional reorganization, including coordinated upregulation of nutrient transporter genes and sugar transporter genes (SWEET family), localized to cells in direct contact with fungal arbuscules.

Plants allocate approximately 13 gigatonnes of CO₂-equivalent carbon per year to their mycorrhizal fungal partners — roughly one-third of annual fossil-fuel emissions.

Carbon allocation to mycorrhizal fungi is quantitatively significant at the global scale: approximately 13 Gt CO₂-equivalent per year flows from plants to their mycorrhizal partners, combining contributions from arbuscular (~3.93 Gt CO₂e/year), ectomycorrhizal (~9.07 Gt CO₂e/year), and ericoid (~0.12 Gt CO₂e/year) fungi. This figure represents roughly one-third of annual fossil-fuel emissions and constitutes a climate-relevant carbon flux that has historically been undercounted in biogeochemical models.

This allocation is not constant: field studies using ¹³C isotope tracing in boreal pine forests found 500% higher below-ground carbon allocation in late growing season (August) compared to early season (June), tied to the reproductive biology of ectomycorrhizal fungi. Nitrogen additions reduce below-ground allocation to mycorrhizal fungi by approximately 60% within one year.

Fungal necromass as carbon sink

Beyond living mycelium, dead fungal biomass (necromass) contributes substantially to soil carbon storage. Microbial necromass accounts for approximately 35% of total soil organic carbon in forest soils, 47–54% in grassland soils, and 24–51% in cropland soils, with two-thirds of that microbial necromass being of fungal origin. Fungal cell wall compounds decompose slowly, meaning fungal necromass persists longer in soil than bacterial necromass—making it a disproportionately important pathway for long-term carbon storage.

Variants & Subtypes

Mycorrhizal types and connectivity

Common mycorrhizal networks (CMNs) physically connect roots of multiple trees and plants through fungal hyphae, demonstrated by microscopy, DNA sequencing, and stable isotope tracing. Their existence as a structural feature of forest belowground architecture is not scientifically contested; what remains actively debated is the ecological significance and mechanisms of resource transfer among trees.

A 2025 study further expanded this picture: dark septate endophytes (DSEs) and other non-mycorrhizal fungi can also form common fungal networks between plants, enabling resource transfer and water movement. Underground fungal connectivity appears to be more diverse than the original mycorrhizal-centric framework proposed.

Agricultural impacts on mycorrhizal communities

Nutrient enrichment through mineral fertilization causes declines in arbuscular mycorrhizal fungal (AMF) populations and agroecosystem diversity. Excessive phosphorus and nitrogen availability reduce the mutualistic dependence of plants on mycorrhizal partners, leading to reduced fungal colonization and lower species richness in fungal communities. Organic fertilizer produces less severe reductions in AMF diversity compared to mineral-only fertilization.

Mycorrhizal fungal diversity directly determines plant biodiversity, ecosystem variability, and overall productivity: greater diversity of arbuscular mycorrhizal fungi colonizing plant roots correlates with increased plant community diversity and enhanced ecosystem functioning.

Notable Examples

Fungi domesticated for fermentation

Koji (Aspergillus oryzae) is a domesticated ecotype of the wild, toxin-producing species Aspergillus flavus. Comparative genomic analysis shows 99.5% genomic similarity between the two species yet significant functional differences, particularly in genes encoding saccharifying enzymes, amino acid metabolism, and sugar uptake. The domestication process also involved the loss of aflatoxin biosynthesis capacity—a deliberate selection against toxin production. In A. oryzae RIB strains, the key regulatory gene aflR shows extremely low or absent expression; in A. sojae, specific mutations in aflR (including an HAHA motif and a premature stop codon) reduce transcription-activating activity to approximately 15% of that found in the toxin-producing A. parasiticus.

Cheese Penicillium species. Both Penicillium roqueforti (blue cheese) and P. camemberti (camembert) show clear genomic and phenotypic signatures of domestication. P. roqueforti comprises at least four to five genetically distinct populations, each showing adaptation to specific cheese-making contexts, likely emerging through independent domestication events. Selection against toxin production is evident here too: the non-Roquefort P. roqueforti population cannot produce mycophenolic acid due to a 174 bp deletion in the mpaC gene.

Mycoprotein: industrial fungal domestication

Fusarium venenatum has been a commercial alternative-protein product marketed as Quorn since 1985. Production employs continuous submerged fermentation in large-scale bioreactors; harvested fungal biomass is heat-treated at 90°C to reduce ribonucleic acid content and increase digestibility, then centrifuged to produce a concentrated mycelial paste.

The nutritional profile is notable: mycoprotein contains all nine essential amino acids with a Protein Digestibility Corrected Amino Acid Score (PDCAAS) of 0.996—higher than soy (0.91) and very close to egg (1.18) and milk (1.21). It contains 6% dietary fiber by dry weight (two-thirds β-1,3 and -1,6 glucans, one-third chitin) which may function as a prebiotic. Life-cycle analyses demonstrate substantially lower greenhouse gas emissions, land use, and water consumption compared to equivalent beef production.

Components & Structure

Mycelium as material

Mycelium-based biomaterials represent a recent domestication wave, with companies including Ecovative, MycoWorks, and Mogu cultivating fungal hyphae on agricultural waste substrates to produce packaging, leather alternatives, acoustic and structural panels, and construction materials. The mycelium packaging market alone is projected to grow significantly from approximately $68 million in 2024.

Life cycle assessments find that mycelium packaging has a better climate change impact than expanded polystyrene, foam concrete, rockwool, and quadcore sandwich panels when measured by cumulative energy demand and global warming potential. (Caveats exist: electricity requirements for production and hemp cultivation contribute significantly to environmental impacts, and mycelium materials show higher impacts in stratospheric ozone depletion and marine eutrophication compared to some alternatives.)

Controversies & Debates

Fungal pathogenicity and temperature

The rarity of fungal human pathogens is not coincidental. Analysis of 4,802 fungal strains across 144 genera found that most fungi cannot grow at mammalian body temperature (37°C), and less than 1% of described fungal species operate as opportunistic human pathogens. Mammalian endothermy provides a thermal barrier that restricts most fungi from successfully infecting endothermic vertebrates.

However, growth at 37°C is a necessary but not sufficient condition for pathogenicity. Tens of thousands of nonpathogenic fungal species are also thermotolerant at this temperature; additional virulence traits—adhesion factors, immune evasion, and metabolic capabilities—are required for successful invasion.

Thermal dimorphism is a key mechanism among pathogens that have crossed this barrier. Thermally dimorphic fungi exhibit temperature-dependent morphological switching between hyphal form (optimal at 22–25°C) and yeast form (optimal at 37°C), with conversion to yeast upon entering a mammalian host constituting a critical virulence mechanism.

Pseudogymnoascus destructans, the causative agent of white-nose syndrome in bats, represents the opposite extreme: a psychrophilic (cold-loving) fungus with optimal growth at 12.5–15.8°C and a maximum critical growth temperature around 19–20°C. Its thermal constraint confines disease to the hibernation period when bat body temperature drops.

Candida auris and climate-associated emergence

Candida auris displays exceptional thermotolerance compared to phylogenetically related Candida species, thriving at temperatures above 37°C and in elevated salt concentrations—traits rare among environmental fungi. Three genetically distinct clades of C. auris emerged nearly simultaneously on three continents (South Africa, India, and Venezuela) in 2016–2017, each representing an independent genetic lineage separated by thousands of single-nucleotide polymorphisms. This pattern of parallel emergence has been proposed as consistent with thermal adaptation in environmental reservoirs driven by climate warming.

Lichens as multi-partner systems

Lichens are obligate symbiotic associations between a fungal partner (mycobiont) and one or more photosynthetic partners (photobionts)—green algae, cyanobacteria, or both. The fungal partner provides structural support, mineral uptake, and UV protection; the photobiont provides fixed carbon; cyanobacterial partners also contribute fixed nitrogen.

In 2016, Spribille and colleagues discovered that many macrolichens contain a stable secondary fungal symbiont: a basidiomycete yeast (order Cystobasidiomycetes) embedded in the lichen cortex—previously invisible to standard culturing and sequencing methods. Related lineages of these yeasts have been found in 52 genera of lichens worldwide across six continents. Their abundance positively correlates with previously unexplained phenotypic variation, particularly production of secondary metabolites like vulpinic acid.

However, subsequent surveys of 339 lichen species spanning 57 families demonstrate that cystobasidiomycete yeasts are not uniformly distributed across all lichen taxa—they occur selectively within particular lichen families and genera, representing a specialized adaptation present in some lineages but not others.

Cultural Significance

Ethnomycology and the Wasson framework

Ethnomycology is an inherently multidisciplinary field spanning the humanities, fine arts, and social and natural sciences. It examines fungi across cultural domains including diet, medicine, spirituality, economics, and cognition, drawing on anthropology, history, mycology, chemistry, pharmacology, ecology, and religious studies.

R. Gordon Wasson is widely recognized as the founder of ethnomycology as an academic discipline. His 1957 Life magazine article documenting the Mazatec psilocybin mushroom ceremony with curandera María Sabina—and his 1957 book Mushrooms, Russia and History, co-authored with Valentina Wasson—established the field's foundational framework.

That framework introduced the concepts of mycophilia and mycophobia: mycophilic cultures (Slavic, Italian, Catalan, Japanese, and many East and Central European traditions) treat wild mushroom gathering as routine and cherished, while mycophobic cultures (notably Anglo-American) historically associated fungi with poison, decay, and witchcraft.

Contemporary ethnomycological research has challenged this binary as oversimplifying culturally nuanced relationships with fungi. Empirical studies find that mycophilia-mycophobia does not follow a bimodal distribution; sociocultural variables explain cultural differences better than ecological region alone.

Indigenous Mesoamerican traditions

Archaeological and historical evidence documents ritual use of psilocybin mushrooms by indigenous Mesoamerican peoples for at least 3,000 years. More than twenty mushroom species in the genus Psilocybe were recognized as sacred across multiple cultures including the Chatino, Chinantec, Matlatzinca, Mazatec, Mixe, Mixtec, Nahua, and Zapotec peoples.

Mesoamerican languages developed names reflecting the sacred status and perceived agency of these fungi. In Mazatec, psilocybin mushrooms are called ndi xijtho ("the little ones that sprout") or "holy children"; in Nahuatl/Aztec, teunanácatl means "flesh of the gods". These names treat mushrooms not as inert substances but as entities capable of communication and wisdom-sharing during ritual use.

Misconceptions & Disputed Claims

"Fungal networks are like the internet of the forest." While common mycorrhizal networks physically connect plants, the popular framing that fungi intentionally route resources between trees as a form of communication exaggerates the evidence. Positive citation bias in the CMN literature has created a perception of robust evidence for "wood-wide-web" mechanisms that exceeds the actual empirical base. The scientific consensus accepts CMNs as physical structures; it does not support attributions of intentionality or coordinated behavior.

"Fungi will become more dangerous as temperatures rise." The relationship between climate change and fungal pathogenicity is more nuanced than often portrayed. Fungal thermotolerance has been revisited, and thermotolerance alone is neither necessary nor sufficient for pathogenicity: tens of thousands of non-pathogenic species already tolerate 37°C. Additional virulence traits are required for successful mammalian infection.

"Lichens are two-organism systems." The 2016 discovery of basidiomycete yeasts as stable third partners in many macrolichens revised this model, demonstrating that many lichen "holobionts" are in fact multi-partner systems. However, this does not apply universally: subsequent surveys confirmed that secondary fungal symbionts are not present in all lichen families.