Fungi: Key Players in Ecosystems and Nutrient Cycling

Fungi drive some of the most fundamental processes that keep ecosystems running, from recycling dead wood and leaves back into usable nutrients to feeding plants through underground partnerships that stretch across entire forests. Without them, dead organic matter would pile up, most land plants would struggle to access phosphorus and nitrogen, and soils would lose much of their structural integrity. Their roles span decomposition, mineral weathering, carbon storage, plant defense, and even the physical architecture of soil itself, making them arguably the most ecologically versatile kingdom of life on land.

Breaking Down What Nothing Else Can

The signature ecological trick of fungi is decomposition, and their most impressive feat in this department is dismantling lignin. Lignin is the tough, complex polymer that gives wood its rigidity and makes up roughly a quarter of terrestrial plant biomass. No animal digests it efficiently, and bacteria struggle with it. White-rot fungi, however, produce a suite of extracellular enzymes, including laccases, lignin peroxidases, and manganese peroxidases, that can oxidize and fragment lignin’s tangled molecular structure.¹ The process involves oxidative cleavage of specific chemical bonds within the polymer, essentially chewing through the molecule piece by piece.²

This ability matters far beyond forest floors. Without fungal lignin decomposition, the carbon locked inside woody plant material would remain sequestered almost indefinitely, and the nitrogen, phosphorus, and other nutrients bound within leaf litter and dead trunks would never return to the soil pool. The entire terrestrial nutrient cycle would slow to a crawl. This is not a hypothetical scenario: before white-rot fungi evolved their lignin-degrading enzymes (likely in the late Carboniferous period), dead plant material accumulated for millions of years, eventually forming the coal deposits we mine today. Fungi effectively ended that era of mass carbon burial.

Mycorrhizal Partnerships With Plants

The vast majority of land plants form intimate associations with mycorrhizal fungi, partnerships where fungal threads (hyphae) colonize plant roots and extend far into the surrounding soil. The basic deal is nutrient exchange: fungi provide the plant with soil minerals it cannot reach on its own, and the plant feeds the fungi sugars produced through photosynthesis. Two major types dominate. Arbuscular mycorrhizal fungi penetrate root cells and are associated with most grasses, crops, and tropical trees. Ectomycorrhizal fungi wrap around root tips without penetrating cells and are common partners of oaks, pines, birches, and other temperate and boreal trees.

Phosphorus is a nutrient that plants need in large quantities but that moves poorly through soil. Mycorrhizal fungi solve this problem by expressing specialized transport proteins that shuttle inorganic phosphate from distant soil pores into colonized roots through the fungal-plant interface.³ For nitrogen, ectomycorrhizal fungi go even further. They produce proteinases and other enzymes that break down proteins in soil organic matter, liberating nitrogen in forms the plant can absorb.⁴ Lab studies have shown ectomycorrhizal species like Paxillus involutus and Laccaria bicolor selectively taking up nitrogen-rich amide compounds from decomposing organic matter, effectively mining the soil for nitrogen on the plant’s behalf.⁵

These mycorrhizal networks do more than ferry nutrients. When fungal hyphae connect multiple plants, they create what researchers sometimes call a “common mycorrhizal network,” a physical web linking neighboring plants underground. Studies have demonstrated that these networks can transfer not just nutrients but also chemical defense signals between plants. When one plant is attacked by herbivores or pathogens, neighboring plants connected through the same fungal network can ramp up their own defense responses, altering gene regulation and physiology before the threat reaches them.⁶ The ecological implications are striking: individual plants are not truly isolated actors, and the fungal web beneath them creates a layer of community-level coordination.

Soil Carbon Storage and Physical Structure

Fungi do not just cycle carbon through ecosystems; they also lock substantial amounts of it away in soil. A study examining contributions of microbial remains to soil organic carbon found that fungal-derived carbon accounted for roughly 21% of the soil organic carbon pool on average, compared to about 5% from bacteria.⁷ Fungal cell walls contain chitin and melanin, molecules that resist decomposition and persist in soil long after the organism dies. This “necromass,” the accumulated remains of dead fungal tissue, turns out to be one of the larger reservoirs of stable carbon in many soils.

Arbuscular mycorrhizal fungi contribute to soil structure through a different mechanism. They produce a glycoprotein commonly referred to as glomalin-related soil protein (GRSP), which acts as a binding agent that helps glue soil particles together into aggregates.⁸ These aggregates physically protect organic carbon from being broken down by microbes, because the carbon is trapped inside clumps of soil particles that water and enzymes cannot easily penetrate. That said, the science around glomalin is still evolving. A review spanning 25 years of research noted that while the substance has been consistently associated with soil aggregation and carbon storage, the precise mechanisms behind these benefits have not been fully pinned down, and even the exact nature of glomalin remains debated.⁹ The association is real and robust, but the details are still being worked out.

Pioneers on Bare Rock

Fungi do not wait for soil to exist before they start working. Lichens, which are partnerships between fungi and photosynthetic algae or cyanobacteria, are among the first organisms to colonize bare rock surfaces. They break down rock through both physical and chemical means: hyphae physically penetrate cracks and pores, while the lichen secretes organic acids, especially oxalic acid, that dissolve minerals and chelate metal ions from the rock surface.¹⁰ This process creates pits and corrosion features on mineral surfaces and releases elements like silicon, calcium, and magnesium into the developing proto-soil.

Researchers studying lichen-mineral systems have proposed that fixed carbon from the photosynthetic partner fuels fungal growth, and the growing fungi then induce mineral disaggregation, hydration, dissolution, and the formation of secondary clay minerals.¹¹ Field studies of lichens and mosses on granitic gneiss in boreal forests confirmed that biological colonization produced intense chemical weathering and generated clay minerals directly, while rock surfaces without these organisms showed comparatively little weathering.¹² The clay minerals produced are the building blocks of fertile soil, so fungal weathering is quite literally soil creation from scratch.

Free-living soil fungi contribute to mineral weathering as well. Certain species secrete low-molecular-weight organic acids such as oxalic and citric acid at concentrations high enough to dissolve minerals that are otherwise considered quite stable. Some fungal isolates can even dissolve lead carbonate at remarkably high concentrations, a finding with implications for both natural geochemistry and the remediation of contaminated sites.¹³

Endophytic Fungi and Plant Resilience

Not all ecologically important fungi live in soil. Endophytic fungi reside inside plant tissues, leaves, stems, and roots, without causing visible disease. Many of these hidden residents turn out to be powerful allies when plants face environmental stress. Endophytic fungi can help plants tolerate drought, salinity, and extreme temperatures by triggering the plant’s own stress-response pathways, producing protective compounds like osmolytes and antioxidant enzymes, and directly altering gene expression related to water management and cell protection.¹⁴

Some of the most promising endophytes come from extreme environments. Fungi isolated from desert plants, already adapted to harsh conditions, have been tested on crop species with encouraging results. In one study, halotolerant (salt-tolerant) endophytic fungi recovered from desert plants were inoculated into tomato and cucumber plants subjected to drought and salt stress. The fungi increased chlorophyll concentrations and plant growth under every level of stress, and one species, Periconia macrospinosa, significantly boosted proline content and antioxidant enzyme activity across all stress levels compared to plants without the fungal partner.¹⁵ This kind of research hints at practical agricultural applications: inoculating crops with the right fungal endophytes could reduce irrigation needs and expand the range of land suitable for farming.

Shaping Biodiversity Above Ground

Fungi do not only support plant growth; they also regulate which plants thrive and where. One of the most elegant demonstrations of this involves the Janzen-Connell hypothesis, the idea that seedlings growing near their parent trees face higher mortality because species-specific pathogens accumulate in the surrounding soil. In a subtropical forest experiment, researchers found that seedling survival near a focal tree species increased with the evolutionary distance between the seedling species and the focal tree. When the soil was treated with fungicide, that pattern disappeared entirely, strongly suggesting that host-specific soil fungi were the agents driving the effect.¹⁶ In other words, soil fungi help maintain tree diversity by punishing any single species that tries to dominate a patch, forcing a mix of species to coexist.

Fungi also regulate insect populations, though their role here is subtler than that of predators or parasitic wasps. Entomopathogenic fungi, species that infect and kill insects, are found in species-rich assemblages within most insect populations. A meta-analysis found a median infection prevalence of about 8% across surveyed insect populations, which is lower than mortality caused by predators and parasitoids. Epidemic-level fungal outbreaks in insect populations are rare, but the steady background pressure of fungal infection adds a persistent source of mortality that helps shape insect community dynamics.¹⁷

Fungal Highways and Cross-Kingdom Cooperation

Soil is a physically discontinuous environment, full of air pockets, mineral grains, and water films that bacteria struggle to cross. Fungal hyphae bridge these gaps, and in doing so, they create highways for bacteria to travel on. This phenomenon, known as “fungal highways,” involves bacteria riding along the surfaces of fungal filaments to reach nutrient patches, water pockets, or new habitats they could never access on their own.¹⁸ The interaction is regulated by both physical properties of the hyphae and biological factors, meaning not every bacterium can hitch a ride on every fungus. But the general pattern is widespread enough that it shapes microbial community assembly in soils globally, effectively allowing fungi to act as architects of bacterial geography.

Fungi in Water

Although we tend to associate fungi with terrestrial environments, they are active in aquatic ecosystems as well. A large-scale molecular survey of marine and freshwater habitats found that fungal sequences, while a small fraction of total microbial diversity (an overall mean of about 1.35% of sequences), were present across a wide range of aquatic settings. The surprise was in the composition: chytrid-like fungi, an ancient and often overlooked lineage, dominated fungal sequences in nearly every sample type, accounting for 38 to 93% of fungal reads depending on the habitat.¹⁹ Chytrids are microscopic, often single-celled, and many are parasites of algae and zooplankton. Their ecological roles in aquatic nutrient cycling are only beginning to be understood, but their sheer prevalence suggests they are far more important than previously recognized.

At the other extreme of aquatic environments, deep-sea fungi survive under crushing hydrostatic pressure, near-freezing temperatures, and scarce nutrients. These extremophile fungi represent a largely unexplored frontier, but early research indicates they have evolved distinct survival strategies and may play roles in organic matter processing on the ocean floor that have not yet been quantified.²⁰

Fungi in Drylands and Biological Soil Crusts

Arid and semi-arid landscapes cover a large fraction of the Earth’s surface, and fungi play roles there that are easy to overlook. In drylands, biological soil crusts, thin living layers of microorganisms, mosses, and lichens on the soil surface, are critical for preventing erosion and cycling nutrients. Fungi appear to contribute more to biocrust function than has been broadly appreciated. Research in the Kalahari found that fungi in biocrusts are candidates for processing complex organic compounds, provisioning resources to neighboring organisms, and translocating water through what has been called the “fungal loop model,” where fungal hyphae move water and nutrients between soil layers and crust organisms.²¹

In Chinese arid regions, researchers tracked how fungal communities change during long-term vegetation recovery. Early successional stages had lower fungal biomass but were dominated by resilient species whose vigorous hyphal growth could decompose tough organic compounds like lignin and physically wrap around soil particles, promoting crust formation. As the ecosystem matured, more complex fungal communities emerged, including species forming symbioses with lichens and mosses. Increasing fungal diversity and network complexity over time contributed to soil stabilization, nutrient cycling, and overall ecosystem recovery.²² These findings reframe drylands as places where fungi are not just surviving but actively rebuilding ecosystem function.

How Nitrogen Pollution and Climate Change Threaten Fungal Communities

Fungal communities are not immune to the environmental pressures humans impose, and two of the largest threats are nitrogen deposition and rising temperatures. Excess nitrogen from agriculture and fossil fuel combustion settles into forests and soils around the world, and it does not treat all fungi equally. Research has found that fungal biomass and species richness increase with added nitrogen at sites where background nitrogen levels are already low, but decrease at sites where ambient nitrogen deposition is already high, suggesting that fungal communities can be pushed past a stress threshold beyond which diversity collapses.²³ One casualty is oxidative enzyme production, the very enzymatic machinery that drives decomposition of tough organic matter.

Ectomycorrhizal fungi appear particularly vulnerable. Studies in forests exposed to nitrogen deposition have found that the enzyme activities involved in ectomycorrhizal mobilization of organic nitrogen decrease as nitrogen availability rises.²⁴ In broader surveys, increased nitrogen deposition correlates with shifts from ectomycorrhizal to arbuscular mycorrhizal tree dominance and with the decline of key ectomycorrhizal taxa, particularly species with the capacity to forage widely through soil and break down organic nitrogen.²⁵ Since ectomycorrhizal fungi are the main players in organic nitrogen cycling in temperate and boreal forests, losing them could fundamentally alter how these forests obtain and recycle nutrients.

Temperature is the other lever. A global field survey identified temperature thresholds that control the distribution of soil fungal decomposers: small increases past a mean annual air temperature of about 9°C led to abrupt reductions in the proportion of decomposer fungi in soil communities, mirroring a similar threshold for soil carbon content.²⁶ The effect is more pronounced in arid conditions, meaning drylands face a double vulnerability. If warming pushes fungal decomposer communities below these thresholds, decomposition rates could drop, altering carbon fluxes between soil and the atmosphere.

At the same time, warming accelerates the activity of wood-decomposing fungi in ways that do not appear to diminish over time. A study of key wood-decay species found that the effect of temperature on fungal respiration actually increased over medium-term incubation, with no evidence of compensation or adaptation. The researchers concluded that carbon loss through respiration of wood-decomposing fungi will likely increase beyond the direct effect of temperature on metabolic rates, potentially creating a positive feedback loop: warming accelerates fungal respiration, releasing more carbon dioxide, which drives further warming.²⁷ The tension between declining decomposer abundance in warming soils and increased per-organism activity makes predicting net outcomes genuinely difficult, and it is one of the more unsettling open questions in climate science.

Applied Uses and Remediation

The same enzymatic firepower that lets fungi dismantle lignin and dissolve minerals has caught the attention of people trying to clean up pollution. Mycoremediation, the use of fungi to degrade or immobilize environmental contaminants, is an active area of research. Fungal enzymes capable of breaking down polycyclic aromatic hydrocarbons (PAHs), toxic compounds from fossil fuel combustion and industrial spills, are being explored alongside fungal-bacterial co-cultures that combine the broad enzymatic reach of fungi with bacterial metabolic versatility.²⁸ Similarly, the ability of some fungi to dissolve and mobilize heavy metals through organic acid secretion could be harnessed for cleaning contaminated soils, though the same property also means fungi can make metals more mobile in ways that are not always desirable.

An Evolutionary Perspective on Terrestrial Life

Fungi were not always the soil-dwelling, wood-rotting organisms we know today. Over a billion years ago, they were unicellular marine microbes. Their evolution toward multicellularity, filamentous growth, and powerful carbohydrate-degrading enzymes paralleled and enabled the colonization of land by plants. Fungi were likely among the earliest organisms to form mutualistic relationships with the first land plants, trading mineral nutrients for photosynthetic carbon in a deal that made terrestrial vegetation viable. Those ancient interactions changed not just ecology but geology and atmospheric chemistry, reshaping the surface of the Earth.²⁹ The relationships fungi forged with plants hundreds of millions of years ago are essentially the same ones operating in every forest, grassland, and crop field today: a trade network underground that makes life above ground possible.