Mycorrhizal Fungi, Heavy Metal Contamination, and Greenhouse Gas Fluxes in Forest Soils

Abstract

Heavy metals accumulate in forest soils worldwide, yet their effects on greenhouse gas dynamics remain poorly understood. Mycorrhizal fungi lie at the heart of this issue. These symbiotic organisms regulate carbon and nutrient flow between trees and soil, positioning them to influence fluxes of CO₂, N₂O, and CH₄. However, research on mycorrhizal ecology, metal toxicology, and greenhouse gas biogeochemistry has proceeded largely in isolation. This review bridges these fields through a conceptual framework built on three contamination scenarios and four mechanistic pathways. Our confidence in these mechanisms varies by gas: well-established for CO₂, developing for N₂O, and mostly inferential for CH₄. Critical gaps remain. Studies measuring mycorrhizal communities, metal availability, and gas emissions simultaneously are rare. Comparisons between ectomycorrhizal and arbuscular mycorrhizal systems are virtually absent. This framework establishes a basis for understanding how metal-contaminated forests regulate greenhouse gas exchange and identifies priority areas for future investigation.

1. Introduction

1.1. The Mycorrhiza–Metal–Greenhouse Gas Nexus

Forest soils play an outsized role in global biogeochemistry. They store roughly one-fifth of terrestrial soil carbon and regulate the exchange of CO₂, N₂O, and CH₄ with the atmosphere [1,2]. At the same time, these soils accumulate heavy metals from industrial emissions, mining, smelting, and traffic. Lead, cadmium, zinc, and copper have built up over decades, and they do not stay inert [3,4,5]. Instead, they reshape the biological communities that drive nutrient cycles, particularly in the rhizosphere where most of the action happens [6,7].

Mycorrhizal fungi make the rhizosphere what it is. These organisms form partnerships with nearly all forest trees, extending their hyphae far beyond root surfaces to capture water and nutrients. In return, they claim 10 to 30 percent of the carbon that trees fix through photosynthesis [8,9,10]. This arrangement makes mycorrhizae central players in forest nutrient cycling, but it also exposes them directly when metals contaminate the soil [11].

A surprising gap exists in the literature. We know a great deal about how mycorrhizae respond to metals and about how they shape carbon and nitrogen cycles. Yet few studies ask the obvious next question: when metals disrupt mycorrhizal communities, what happens to greenhouse gas emissions? Scattered studies address pieces of this question [11,12,13], but a comprehensive synthesis has been lacking. This review tackles that question head-on.

1.2. A Conceptual Framework: Three Contamination Scenarios

Studies of contaminated soils often report conflicting results. Some find large effects while others see almost none [14,15,16,17,18]. We propose that these differences reflect distinct contamination scenarios, each with its own trajectory (Figure 1, Figure 2 and Figure 3). Scenario A describes healthy forest soil, our baseline (Figure 1, left; Figure 2, left; Figure 3, left). Mycorrhizal communities are diverse and fully functional. Carbon flows steadily from trees through fungal networks into soil organic matter. Nitrogen cycles efficiently, and soils act as net methane sinks [8,14,15].

Scenario B represents adapted systems (Figure 1, middle; Figure 2, middle; Figure 3, middle). After chronic exposure, mycorrhizal communities have shifted toward tolerant species [6,16,17]. These fungi still function, though perhaps less efficiently. Metals become bound to glomalin and other organic compounds, reducing their bioavailability [18,19,20]. Decomposition slows, nitrogen cycling tightens, and greenhouse gas fluxes may actually fall below those of healthy soils because both substrates and microbial activity are constrained [21,22]. This scenario represents ecological adaptation in action.

Scenario C depicts degraded hotspots (Figure 1, right; Figure 2, right; Figure 3, right). Metal levels exceed what even tolerant species can handle [3,23]. Roots suffer direct damage. Mycorrhizal networks collapse. Without fungal hyphae and glomalin holding aggregates together, soil structure falls apart and waterlogged pockets expand [24,25]. Stressed plants increase their respiratory losses. Denitrification stalls partway through, releasing N₂O instead of harmless N₂. Methanotrophs decline while methanogens colonize newly anaerobic zones. This scenario captures acute contamination events and the persistent hotspots found even within otherwise stable landscapes.

The trajectory toward waterlogging versus erosion in Scenario C depends critically on site conditions. In humid climates with high water tables or concave topography, aggregate collapse leads to compaction, reduced infiltration, and anaerobic pocket expansion as described above. However, near smelters or in semi-arid regions with sparse vegetation, severe contamination often triggers a different pathway: vegetation dieback reduces canopy interception and root reinforcement, leading to drier, more eroded soils with enhanced physical degradation and carbon loss via runoff rather than waterlogging. Both pathways represent Scenario C outcomes but with divergent implications for greenhouse gas dynamics. Erosion-dominated sites may lose carbon physically before biological processes can act, while waterlogging-dominated sites shift microbial communities toward anaerobic metabolism. Climate, topography, and vegetation cover determine which trajectory predominates at any given contaminated site.

1.3. Four Mechanistic Pathways

How exactly do mycorrhizae shape greenhouse gas fluxes? We identify four main pathways, each vulnerable to metal disruption.

The first is carbon allocation (Figure 1). The carbon that trees send to their fungal partners does not simply vanish. It fuels fungal respiration, builds persistent structures like glomalin, and feeds associated microbes [26,27,28,29]. When metals impair fungi, this flow diminishes. Interestingly, some plants respond to moderate stress by sending more carbon belowground, apparently investing in protection [11,30]. The net effect depends on how severe contamination becomes.

The second pathway involves nutrient acquisition (Figure 2). Mycorrhizal fungi actively compete with free-living soil bacteria for available nitrogen. By acquiring nitrogen before denitrifying bacteria can access it as a substrate, mycorrhizae reduce the pool available for denitrification. Additionally, mycorrhizae recruit bacteria that possess nitrous oxide reductase (encoded by the NosZ gene), which catalyzes the final step of denitrification: the reduction of N₂O to inert N₂. Through these complementary mechanisms, mycorrhizal fungi help minimize N₂O emissions from forest soils [8,15,31]. Heavy metal contamination disrupts these processes by impairing fungal nutrient transport systems and directly inhibiting denitrification enzymes, particularly nitrous oxide reductase [6].

Third, mycorrhizae shape soil structure (Figure 1, Figure 2 and Figure 3). Fungal hyphae bind particles together while glomalin acts as biological glue [32,33]. Together they create the aggregates and pore networks that control oxygen distribution [24,34]. These redox gradients determine whether microsites produce or consume methane and whether denitrification finishes or stops short. When metals reduce hyphal density and glomalin production, structure degrades [35,36].

Finally, mycorrhizae cultivate their own hyphosphere microbiome. The zone around fungal hyphae hosts distinct bacterial communities sustained by fungal exudates [8,31,37,38]. These communities include nitrifiers, denitrifiers, methanotrophs, and methanogens. Metals disrupt these assemblages both directly through toxicity and indirectly by changing what fungi release [5,39].

It is important to distinguish the hyphosphere from the broader mycorrhizosphere. The hyphosphere refers specifically to the micro-environment influenced by a single hypha and its exudates, characterized by highly localized microbial processes. In contrast, the mycorrhizosphere encompasses the entire root–fungus–soil interface. Metal toxicity may differentially affect these zones: in the bulk mycorrhizosphere, contamination drives general community shifts, while in the hyphosphere, metals can disrupt specific, intimate fungal-bacterial partnerships critical for processes such as N2O reduction or CH4 oxidation. This spatial distinction adds precision to understanding mechanistic pathways of metal effects on gas fluxes.

1.4. Metal-Specific Considerations

Different metals cause different problems. Cadmium strongly inhibits spore germination and hyphal growth, cutting colonization by 30 to 70 percent depending on fungal species [16]. Lead is less acutely toxic but accumulates near the surface, creating steep gradients that complicate interpretation [6,40]. Despite being common near roads and smelters, lead’s specific effects on gas fluxes remain poorly characterized [3,40].

Copper deserves special attention. Unlike cadmium and lead, copper is an essential nutrient. Both plants and fungi need it, and so does the methane-oxidizing enzyme pMMO [41,42]. This creates a narrow window: too little copper impairs methanotrophs, while too much poisons them. Mercury, though less studied in mycorrhizal systems, appears devastating to methanotrophs even at low levels [43]. Most real contamination involves mixtures, which complicates assigning blame to any single metal.

Table S1 (Supplementary Materials) summarizes metal-specific effects, including: (a) primary toxicity mechanism for fungi, (b) key effect on target GHG process, and (c) interaction notes. For example, cadmium inhibits hyphal growth, reducing C allocation and disrupting NosZ to increase the N₂O:N₂ ratio. Copper is notable for being essential to both mycorrhizal laccase and methanotroph pMMO, creating competition for this micronutrient. Zinc at high concentrations disrupts membrane integrity and enzyme function. Lead accumulates in organic horizons and cell walls but has less acute toxicity than cadmium.

1.5. Mycorrhizal Guild Identity and Ecosystem Context

The two main mycorrhizal types use fundamentally different strategies. Ectomycorrhizal (ECM) fungi dominate temperate and boreal forests. They produce enzymes that break down organic nitrogen directly and invest heavily in extensive hyphal networks [44,45,46]. ECM fungi employ multiple metal immobilization strategies that extend beyond simple interception. Their dense mantles provide physical barriers, but ECM hyphae also actively exude metal-chelating compounds including organic acids (such as oxalic and citric acid) and metallothioneins that complex metals extracellularly. Additionally, ECM fungi sequester metals internally within vacuoles and bind them to fungal cell walls through melanin and chitin [47,48]. Arbuscular mycorrhizal (AM) fungi take a different approach. They lack enzymes for organic matter breakdown but scavenge inorganic nitrogen efficiently. They cycle nutrients faster and produce glomalin, which binds both soil particles and metals [27,49,50]. Thus, AM fungi rely heavily on glomalin-mediated extracellular metal stabilization, while ECM fungi employ hyphal surface binding, internal sequestration in vacuoles, and complexation by exudates. These different strategies have implications for metal bioavailability and long-term stability of metal–organic complexes in forest soils.

These differences should produce distinct responses to contamination and different gas flux patterns. Remarkably, the controlled comparisons needed to test this expectation barely exist. This stands out as one of the clearest gaps in the field.

Context matters too. Soil pH, clay content, and organic matter all affect metal availability [22,51,52]. Climate shapes both mycorrhizal function and metal mobility [12,53]. Findings from one system may not transfer to another.

2. Search Strategy and Conceptual Synthesis

This review was developed through a systematic multi-platform approach combining generative artificial intelligence (AI) tools with traditional academic practices. Literature acquisition was conducted primarily through SciSpace (https://scispace.com) and Consensus (https://consensus.app), which enabled efficient identification and retrieval of relevant publications at the intersection of mycorrhizal ecology, heavy metal contamination, and greenhouse gas dynamics. These platforms facilitated advanced search functionality and rapid synthesis of key findings across approximately 150 collected references, helping identify mechanistic connections between traditionally separate research domains. The conceptual framework, including the three-scenario model (healthy soil, metal-buffered, and metal-disrupted systems), emerged through iterative refinement using Claude AI Opus 4.5 (Anthropic) and ChatGPT 5.1 (OpenAI). NotebookLM (Google) was employed for organizing and cross-referencing literature sources, supporting consistent terminology and structure across sections. The scientific diagrams illustrating N₂O, CO₂, and CH₄ cycling pathways under each scenario were generated using Gemini 2.5 (Google) with specialized prompting, producing publication-quality figures with consistent styling based strictly on mechanisms described in the cited literature and the conceptual framework developed by the authors. The original narrative text was composed in Slovak and subsequently translated into English using Claude AI. Following translation, Claude AI was also used to systematically improve sentence clarity and readability for an international audience while preserving scientific precision. In summary, generative AI tools were used exclusively to assist with: (1) literature search, organization, and synthesis; (2) drafting, translation, and language editing of the text; and (3) conceptualization and design of schematic figures. No generative AI tools were used to generate, modify, or statistically analyze empirical data. All responsibility for the scientific content, interpretation, and final wording rests fully with the authors.

3. Carbon Cycling and CO₂ Dynamics

3.1. Mycorrhizal Carbon Transfer

Trees invest heavily in their fungal partners, sending 10 to 30 percent of fixed carbon belowground [27,54]. This represents a major flux in forest carbon budgets, sustaining hyphal growth, maintenance, and networks that reach meters beyond root tips (Figure 1, left) [9,28,44]. What happens to this carbon determines its atmospheric importance. A large fraction, perhaps 30 to 70 percent, gets respired [29,55]. Fungi burn carbon for energy just like other organisms, and this CO₂ contributes directly to soil efflux. The rest follows a different path. It accumulates as dead hyphae, glomalin, and chitin-rich cell walls. These materials can persist for years or decades, protected inside aggregates or bound to minerals [28,29,56]. Lower relative abundance of ectomycorrhizal fungi under a warmer and drier climate is linked to enhanced soil organic matter decomposition

Through this route, mycorrhizae contribute meaningfully to long-term carbon storage.

3.2. Metal-Induced Alterations in Carbon Allocation

When metals enter the picture, carbon dynamics get complicated. The obvious prediction is that toxicity should reduce carbon flow to fungi, and this often proves true. Metal-stressed plants photosynthesize less and produce fewer fine roots. The fungi themselves suffer directly as spore germination slows, hyphae extend less, and colonization drops [6,16,39,57]. But biology is rarely simple. Under moderate contamination, some plants actually boost their belowground investment [58]. This makes sense as a protective strategy since mycorrhizae help with nutrient uptake, exclude certain metals, and sequester others in their own tissues [11,59,60,61]. The complication is that fungi receiving extra carbon may spend it on detoxification rather than growth [18]. Even when allocation rises, functional benefits may not follow.

3.3. Respiratory Responses to Metal Stress

Soil respiration has multiple sources. In forests, roots and their fungal partners typically account for 40 to 60 percent of total CO₂ efflux [55,62]. Metal contamination pushes these sources in opposite directions, making net outcomes hard to predict (Figure 1).

On one hand, fungal respiration drops. Fewer hyphae and lower metabolic activity mean less CO₂ from fungi (Figure 1, middle). On the other hand, stressed roots work harder. They spend extra energy making detoxification compounds, producing antioxidants, and repairing damage [3,63]. Meanwhile, free-living decomposers often decline because many are more sensitive to metals than mycorrhizae [64].

The balance among these shifts determines what happens to total CO₂ flux. Often it decreases, but not uniformly across sources [55]. In Scenario C (Figure 1, right), elevated stress respiration and breakdown of protected carbon can push total flux up despite reduced fungal activity. Sorting out these components requires careful experimental design and is rarely attempted.

3.4. Decomposition Dynamics: The Gadgil Effect and Beyond

Mycorrhizae influence soil carbon not just through their own respiration but through their effects on other decomposers. In many ECM forests, extensive fungal networks suppress saprotrophs by monopolizing nitrogen, water, and space. This Gadgil effect slows litter breakdown and lets carbon accumulate [65,66,67]. Under other conditions, especially when nutrients are more available, mycorrhizal exudates can instead stimulate decomposers and accelerate mineralization of old organic matter [26,68,69]. Which outcome prevails depends on context [70].

Metals add another layer. Because many decomposers are more sensitive than mycorrhizae, contamination can shift competitive dynamics and suppress decomposition overall [21,71,72]. In Scenario B (Figure 1, middle), this might paradoxically enhance carbon storage as reduced decomposition leaves more carbon in soil. In Scenario C (Figure 1, right), structural collapse exposes previously protected organic matter to whatever decomposers remain. Stressed roots may also prime old carbon for breakdown. Outcomes are not straightforward.

The modulation of the Gadgil effect by metals deserves closer examination. While metals may disproportionately harm saprotrophs, thereby reinforcing ECM competitive dominance and suppressing decomposition, an alternative trajectory is also possible. Metals may impair the ECM fungi’s ability to produce inhibitory compounds or compete effectively for resources, potentially reversing the Gadgil effect. This could lead to non-linear outcomes for decomposition: initial suppression as sensitive saprotrophs decline, followed by acceleration if metal-tolerant saprotrophs proliferate in the absence of effective ECM competition. Understanding which trajectory predominates requires attention to metal speciation, exposure history, and the relative metal tolerances of competing fungal guilds.

There is an intriguing twist. Some metal-tolerant mycorrhizae retain significant ability to decompose organic matter [56,73,74]. In heavily contaminated soils where other decomposers have died off, these fungi may become the main agents of carbon mineralization. The usual functional categories start to blur.

3.5. Long-Term Carbon Sequestration: Glomalin and Necromass

Two mycorrhizal products deserve special attention for long-term storage. AM fungi produce glomalin, a glycoprotein that builds aggregates and shields organic matter from microbial attack [8,75,76]. In many soils, glomalin accounts for 5 to 15 percent of total organic carbon and turns over far more slowly than typical plant residues [77]. ECM fungi contribute differently through melanized cell walls that resist decomposition and persistent necromass in organic horizons [28,55,56].

Metals may have a counterintuitive effect here. Glomalin binds lead, cadmium, zinc, and copper [11,19,20]. The resulting complexes may be more stable than either component alone [35]. This raises the possibility that moderate contamination could actually enhance carbon persistence under some conditions (Figure 1, middle). The catch is that severe metal stress inhibits fungal growth and cuts glomalin production in the first place. Whether contamination ultimately increases or decreases long-term storage likely depends on site history and severity.

The long-term stability of these metal-glomalin complexes warrants careful consideration. While initially more recalcitrant than unbound glomalin, these complexes may be vulnerable to future environmental changes. Shifts in soil pH, whether from acid deposition recovery or liming amendments, can alter metal speciation and potentially destabilize metal–organic bonds. Similarly, changes in redox conditions during flooding or drainage can remobilize metals and release associated carbon. This raises the concerning possibility that contaminated soils functioning as apparent carbon sinks under current conditions could become slow-release sources of both metals and CO₂ if environmental conditions shift. The metal-glomalin pool may therefore represent a conditional rather than permanent carbon store, with stability contingent on maintaining the geochemical conditions under which complexation occurred. Long-term monitoring studies tracking both metal speciation and carbon dynamics through environmental fluctuations are needed to assess this risk.

Table 1. Carbon cycling characteristics across contamination scenarios (see Figure 1).

Parameter	Scenario A	Scenario B	Scenario C
C transfer to fungi	10–30% of NPP	Reduced	Severely diminished
Fungal respiration	Major CO2 source	Reduced	Fungal: reduced; Plant stress: elevated
Decomposition	Balanced	Suppressed	Old C exposed
Glomalin/necromass	5–15% of SOC	Metal-stabilized	Production impaired
Net CO2 flux	Balanced	Low	Elevated

summarizes the key carbon cycling parameters across these three contamination scenarios, illustrating how metal stress progressively alters carbon transfer, respiration, decomposition, and long-term storage dynamics in forest soils.

4. Nitrogen Cycling and N₂O Emissions

4.1. Mycorrhizal Regulation of Nitrogen Availability

The fate of nitrogen in forest soils depends heavily on mycorrhizal activity (Figure 2). Consider ECM fungi first. These organisms produce enzymes that break down organic nitrogen compounds directly, effectively bypassing the mineralization step that would release ammonium into solution [44,45,78]. By keeping nitrogen in organic forms longer, ECM fungi shrink the pool available to nitrifiers and denitrifiers, the bacteria that ultimately produce N₂O [79]. AM fungi work differently. They lack enzymes for organic matter breakdown but extend hyphae that efficiently scavenge inorganic nitrogen from soil (Figure 2, left) [8,80].

Both types tend to reduce N₂O emissions, though through different routes. ECM fungi starve the system of mineral nitrogen substrate. AM fungi also intercept nitrogen, but they seem to do something more. They recruit bacteria that finish denitrification completely, converting N₂O to harmless N₂ rather than letting it escape [15,31]. Studies show that the AM hyphosphere is enriched in organisms carrying nosZ, the gene for the enzyme that catalyzes this final step (Figure 2, left) [31,81]. The mycorrhizal hyphosphere appears to be a better home for complete denitrifiers.

The mechanistic basis for NosZ enrichment in the AM hyphosphere remains an active research question. Two non-exclusive hypotheses merit consideration. First, AM fungi may actively recruit complete denitrifiers through specific exudate signals. Fungal hyphae release diverse organic compounds including sugars, organic acids, and amino acids that could selectively favor nosZ-carrying bacteria capable of utilizing these substrates while completing the denitrification pathway. Second, the enrichment may be a byproduct of microhabitat conditions rather than targeted recruitment. The hyphosphere offers unique microenvironmental characteristics: elevated carbon availability, specific pH and redox gradients, and physical refugia that may coincidentally favor the ecological niche of complete denitrifiers. Distinguishing between active recruitment and passive habitat filtering has practical implications. If specific exudates drive NosZ enrichment, identifying and applying these compounds could inform mitigation strategies for N₂O emissions in contaminated soils where mycorrhizal function is compromised.

4.2. Metal Impacts on the Denitrification Pathway

Denitrification is not one reaction but a chain: nitrate to nitrite to nitric oxide to nitrous oxide to dinitrogen (NO₃⁻ → NO₂⁻ → NO → N₂O → N₂). Each step needs its own enzyme, and each enzyme contains metal cofactors that contaminating metals can displace or block [82]. What matters for the atmosphere is whether the chain runs to completion. If it does, the end product is harmless N₂. If it stalls at the second-to-last step, N₂O builds up and escapes.

Here is the problem. The enzyme that runs that final step, N₂O reductase encoded by nosZ, is more sensitive to metals than the upstream enzymes [83,84]. So when metals contaminate soil, denitrification may keep going but tends to stop short. The N₂O:N₂ ratio shifts the wrong way (Figure 2, right).

Different metals inhibit NosZ through distinct mechanisms. Copper, while essential as a cofactor, can be displaced from the active site by competing metals. Cadmium preferentially binds to thiol groups in the enzyme, disrupting its structure. Silver targets the electron transport chain that supplies reducing equivalents to NosZ. Furthermore, the sensitivity of different NosZ clades to metals is an emerging research question. Clade I and clade II NosZ carriers differ in their phylogenetic distribution and ecological niches, and may exhibit differential metal sensitivity with implications for N₂O emissions in contaminated soils. This clade-specific response represents a frontier for understanding metal impacts on denitrification completion.

Copper plays an especially important role because N₂O reductase needs it as a cofactor. Lead, cadmium, and zinc can kick copper out of binding sites or compete for uptake, creating functional copper deficiency even when total copper is adequate [41,83]. This helps explain a puzzling observation: sites with metal mixtures often emit more N₂O than sites with equivalent amounts of single metals. Multiple metals hit multiple steps at once.

4.3. Mycorrhiza–Denitrifier Interactions Under Metal Stress

Metal stress compounds these effects by disrupting the functional partnership between mycorrhizal fungi and denitrifying bacteria. Denitrification requires organic carbon as an electron donor [85]. In forest soils, mycorrhizal exudates represent a primary carbon source for hyphosphere-associated denitrifiers. When metal toxicity reduces carbon allocation to fungal symbionts, less organic carbon reaches hyphosphere denitrifiers. This creates a dual constraint: carbon limitation may reduce overall denitrification rates, while concurrent metal inhibition of nitrous oxide reductase shifts the end-product ratio toward N₂O accumulation [15,31].

There is more. Healthy mycorrhizae recruit nosZ-carrying bacteria to their hyphospheres (Figure 2, left and middle). Metal contamination seems to selectively wipe out these complete denitrifiers. Studies find reduced NosZ gene abundance in contaminated soils [81,86]. The very bacteria best equipped to reduce N₂O are the ones that decline under metal stress. This compounds direct enzyme inhibition, pushing the N₂O:N₂ ratio further toward emission. Under Scenario C (Figure 2, right), these reinforcing effects can create hotspots where N₂O fluxes far exceed those from healthy or moderately contaminated soils.

4.4. Structural Controls on Denitrification Microsites

Denitrification needs anaerobic conditions, yet most forest soils are aerobic overall. How does it happen at all? The answer lies in microsites, small pockets where oxygen gets used up faster than it can diffuse in [32,33]. Mycorrhizae strongly influence where these pockets form. Hyphal networks and glomalin stabilize aggregates that create oxygen gradients, with aerobic surfaces surrounding anaerobic cores [75]. The architecture determines whether denitrification products pass through aerobic zones where N₂O can be reduced, or escape directly to the atmosphere.

When metals damage mycorrhizal communities, this organization breaks down. Lower hyphal density and less glomalin mean weaker aggregates [35,87]. Outcomes can be paradoxical. Collapse creating larger anaerobic zones with longer diffusion paths might allow more N₂O reduction before escape. Collapse creating compacted layers with poor gas exchange might let shallow N₂O escape before reduction. Evidence suggests contamination more often produces the second outcome, expanding the effective source area (Figure 2, right) [24,34].

Table 2. Nitrogen cycling characteristics across contamination scenarios (see Figure 2).

Parameter	Scenario A	Scenario B	Scenario C
N acquisition	ECM: organic; AM: inorganic	Reduced efficiency	Severely impaired
Mineral N pool	Low	Moderate	Elevated
NosZ community	Enriched	Reduced	Depleted
NosZ activity	Active	Inhibited	Severely inhibited
N2O:N2 ratio	Low	Elevated	High
Net N2O emission	Low	Variable	Elevated; hotspots

summarizes how nitrogen cycling parameters shift across the three contamination scenarios, highlighting the progressive disruption of mycorrhizal nitrogen regulation, NosZ community function, and the resulting changes in N₂O emission patterns.

5. Methane Cycling and CH₄ Dynamics

5.1. Mycorrhizal Influences on Methane Balance

Well-drained forest soils usually consume more methane than they produce, acting as net atmospheric sinks (Figure 1, left) [88,89]. This happens because methanotrophic bacteria in aerobic surface layers oxidize CH₄ faster than methanogens in deeper anaerobic zones can make it. The balance hinges on oxygen supply, moisture, and the abundance of these opposing groups. Mycorrhizae influence all of these factors, though the connections are less direct than for CO₂ or N₂O, and the evidence is thinner.

The strongest link runs through soil structure. Healthy mycorrhizal networks maintain aggregate stability and preserve the pores that let gases move between soil and atmosphere [32,33,35]. In well-drained forests, this keeps surface soils aerobic enough to support methanotrophs (Figure 3, left) [90]. Mycorrhizal water uptake helps too. By pulling moisture from soil, fungi may keep surface layers from waterlogging during wet spells.

There may be more direct ties as well. The hyphosphere offers carbon-rich habitat that could support methanotroph populations [37,38]. Some evidence suggests methanotrophs prefer to associate with mycorrhizal hyphae (Figure 1, left) [88], though this is less well documented than for other groups. If true, healthy networks would create not just favorable physical conditions but actual microsites of enhanced methane oxidation.

5.2. Metal Effects on Methanotroph–Methanogen Balance

Heavy metals do not hit methane cyclers equally. Methanotrophs seem relatively sensitive, partly because their key enzyme, particulate methane monooxygenase (pMMO), needs copper and can be blocked by competing metals (Figure 3, right) [41,42]. Methanogens, tucked away in strictly anaerobic niches, may be somewhat shielded [91]. When contamination collapses soil structure and expands anaerobic zones, methanogen habitat actually grows even as methanotroph activity falls (Figure 3, right) [89].

In principle, this could flip soils from net CH₄ sinks to net sources. Under Scenario C, with severe structural damage, expanded anaerobic pockets, and stressed methanotrophs, this shift might actually happen (Figure 3, right). We should be cautious, though. The mycorrhizal connection to these processes remains mostly inferential. We expect healthy mycorrhizal communities to maintain structure and perhaps support methanotrophs directly, keeping fluxes negative. We expect disruption to tip the balance positive. But few studies have tested these ideas with the integrated measurements needed to show causation [60,61].

5.3. Copper: A Special Case for Methane Cycling

Copper holds a unique position. It is essential for methanotrophy since pMMO cannot work without it, yet toxic at high levels. Some methanotrophs go to great lengths to get copper, producing specialized scavenging compounds called methanobactins [41,42]. This underscores how critical copper availability is for methane oxidation.

This shared copper requirement suggests a potential direct mechanistic link between mycorrhizal activity and CH₄ flux: the copper competition hypothesis. Both mycorrhizal fungi and methanotrophs require copper for key enzymes—fungi for laccase and other oxidases, methanotrophs for pMMO. In soils where copper is limiting or where mycorrhizal biomass is high, fungal copper uptake could act as a competitive sink that directly limits methanotroph activity. This hypothesis provides a testable mechanistic focus beyond the indirect structural controls discussed above, and could explain why mycorrhizal abundance correlates with reduced methane oxidation capacity in some systems.

Mycorrhizae also use copper and regulate its uptake [11]. In contaminated soils, fungal sequestration could cut both ways. It might protect plants and microbes from toxicity. But it might also starve methanotrophs that need copper. The outcome probably depends on how severe contamination gets and which fungi are present. At moderate levels, mycorrhizal copper management might help maintain the narrow window methanotrophs need. At severe levels, sequestration may fail to prevent toxicity while creating copper-poor zones elsewhere.

5.4. Evidence Gaps and Inferential Connections

We must be honest: the mycorrhiza–metal–CH₄ connection is the weakest part of our framework. The individual pieces are reasonably well documented in isolation. Mycorrhizae affect soil structure [32,33]. Metals inhibit methanotrophs [41,42]. Structural collapse shifts methane balance [24,34]. But integrating these through mycorrhizal mediation remains largely hypothetical. Most of what we have is correlation rather than demonstrated mechanism.

Several questions need answers. Do methanotrophs actually prefer mycorrhizal hyphae, and why? How does metal contamination change these associations? At what thresholds does structure degrade enough to shift CH₄ balance? Does mycorrhizal copper sequestration help or hurt methanotrophs at different contamination levels? We flag these as priorities. Until they are addressed, our predictions about CH₄ remain tentative.

Of the four mechanistic pathways proposed in this framework, soil structure modification and hyphosphere microbiome cultivation appear most likely to drive the predicted CH₄ flux shifts under metal contamination. Soil structure controls the distribution of aerobic and anaerobic microsites that determine methanotroph and methanogen habitat availability. The hyphosphere microbiome pathway may directly influence methanotroph populations through habitat provisioning and potential copper competition. Carbon allocation and nutrient acquisition pathways likely exert secondary, indirect effects on CH₄ dynamics. This proposed hierarchy of pathway importance for methane cycling requires empirical validation.

Table 3. Methane cycling characteristics across contamination scenarios (see Figure 3).

Parameter	Scenario A	Scenario B	Scenario C
Soil structure	Well-aggregated	Degraded	Collapsed
Anaerobic microsites	Limited	Expanding	Extensive
Methanotroph activity	Active	Suppressed	Inhibited
Methanogen habitat	Restricted	Expanding	Expanded
Net CH4 flux	Sink	Potential weakened sink	Source possible
Evidence quality	Moderate	Limited	Inferential

summarizes methane cycling characteristics across the three contamination scenarios, reflecting the progressive shift from net CH₄ sink to potential source as mycorrhizal-mediated soil structure degrades and the methanotroph–methanogen balance tips under metal stress.

6. Synthesis and Future Directions

6.1. Putting the Pieces Together

What emerges from this review is that heavy metals affect forest soil greenhouse gas fluxes mainly through mycorrhizae. Direct toxicity to gas-cycling bacteria matters, but the bigger story is disruption of fungal networks that control carbon flow, nutrient availability, soil structure, and microbial community composition (Figure 1, Figure 2 and Figure 3) [8,27,29]. When these networks break down, the consequences ripple outward and often amplify emissions.

The three-scenario framework helps make sense of seemingly contradictory findings. In Scenario B, adapted systems with tolerant fungi (Figure 1, Figure 2 and Figure 3, middle), we expect dampened fluxes. Both carbon supply and microbial activity are constrained. Metal binding to glomalin may even stabilize some carbon [24,29,35]. In Scenario C, degraded hotspots where tolerance has failed (Figure 1, Figure 2 and Figure 3, right), feedbacks turn positive. Stress respiration raises CO₂. Incomplete denitrification releases N₂O. Structural collapse tips CH₄ balance toward emission. The same contamination can produce either outcome depending on severity, history, and context.

The scenarios presented here (A, B, C) represent states, but the transitions between them are dynamic and may exhibit hysteresis. A system moving from Scenario A to Scenario C under increasing contamination may not recover to Scenario B via the same path when contamination is reduced. Recovery of gas fluxes may lag substantially behind remediation due to persistent changes in microbial community composition. Metal-tolerant communities that establish during contamination may resist displacement even as metal availability declines, and the loss of key functional groups (such as complete denitrifiers or efficient methanotrophs) may create long-lasting legacy effects on greenhouse gas dynamics. This temporal dimension deserves explicit attention in future research and management planning.

6.2. How Strong Is the Evidence?

Our confidence varies substantially across gases. For CO₂ (Figure 1), we stand on solid ground. Carbon allocation to fungi [27,54], fungal respiration [55,62], mycorrhizal effects on decomposition [65,66,67], and glomalin-mediated stabilization [28,75,77] all have strong empirical support. Metal effects on these processes are also well documented [6,11,16]. What we lack are studies that trace the complete chain from contamination through mycorrhizal disruption to altered CO₂ flux.

For N₂O (Figure 2), the picture is developing but incomplete. We have good evidence that mycorrhizae reduce emissions [8,15,31] and that metals inhibit denitrification enzymes, especially NosZ [82,83,84]. The proposed link between mycorrhizal disruption and increased N₂O under contamination has been tested directly only a handful of times [81,86]. The idea that hyphosphere communities lose complete denitrifiers is plausible but not firmly established.

For CH₄ (Figure 3), we remain in the realm of inference. Mycorrhizal effects on structure [32,33], metal effects on methanotrophs {Formatting Citation} and structural controls on methane cycling [88,89,90] have each been studied independently. Their integration through mycorrhizae has not been tested. This is the biggest gap in our framework and the area where new work could be most transformative.

6.3. Critical Research Gaps

Several gaps stand out. First and foremost, we need studies that measure mycorrhizal communities, metal availability, and all three gases in the same system at the same time. The literature is full of paired comparisons, but comprehensive three-way studies are essentially absent.

Second, we lack controlled experiments comparing ECM and AM systems under equivalent metal exposure. These fungi differ fundamentally in how they acquire nitrogen, allocate carbon, and tolerate metals [44,45,46,47,48,49,50]. They should respond differently. But this remains prediction, not observation.

A powerful approach to address this gap would be common garden experiments with paired tree species—one ECM-associated (such as oak or pine) and one AM-associated (such as maple or ash)—grown on the same metal-contaminated soil. Simultaneous measurement of gas fluxes, fungal community composition, and metal speciation across both mycorrhizal types would provide the controlled comparisons needed to test whether guild identity predicts contamination responses.

Third, time matters. Chronic and acute contamination should produce different trajectories as communities adapt or collapse [21,22]. Is Scenario B stable, or just a stop on the way to Scenario C? Time-series studies could answer this but are rarely done.

Fourth, we need trait-based approaches that link specific fungal characteristics to gas flux outcomes. Which taxa maintain function under metal stress? Do they differ in carbon efficiency, glomalin production, or microbial recruitment? Correlating community composition with fluxes will only get us so far. Understanding why some fungi matter more would enable prediction.

Specific traits most promising for linking to GHG flux outcomes include fungal exploration types (contact, short-distance, medium-distance, and long-distance explorers), which determine hyphal extent and thus the spatial scale of carbon allocation and microbiome recruitment. Melanization of hyphal walls affects both metal tolerance and necromass persistence. Glomalin production rates and molecular composition influence aggregate stability and metal binding capacity. Host specificity determines which plant communities can support mycorrhizal function under contamination. On the plant side, root exudate profiles, particularly the balance of organic acids, sugars, and secondary metabolites, shape both metal bioavailability and hyphosphere community assembly. Root architecture traits like specific root length and branching intensity affect the extent of mycorrhizal colonization potential. Measuring these traits alongside gas fluxes across contamination gradients would transform our ability to predict ecosystem responses from community composition data.

Fifth, linking active microbial populations to process rates requires techniques that go beyond correlation. Stable isotope probing (SIP) coupled with gas flux measurements offers a powerful approach to identify which methanotrophs and denitrifiers are actually active in the hyphosphere under metal stress. By tracing 13C or 15N through microbial communities while simultaneously measuring gas production, researchers could directly connect community function to ecosystem fluxes in contaminated systems.

6.4. What This Means for Management

Despite uncertainties, our framework suggests practical guidance. The main message is that maintaining mycorrhizal function should be a priority, not just for plant health or contaminant stabilization but for greenhouse gas mitigation too [12,53]. Practices that boost mycorrhizal resilience, like adding organic matter, managing pH, and maintaining diverse host plants, may provide climate co-benefits in contaminated systems.

However, organic matter amendments in contaminated soils require careful consideration of timing and quality. Adding fresh, labile organic matter can initially stimulate microbial activity through priming effects, potentially releasing a short-term pulse of CO₂ and N₂O before long-term stabilizing benefits materialize. The magnitude and duration of this pulse depends on amendment characteristics. Biochar, with its high recalcitrance and sorptive capacity, may minimize priming while providing immediate metal immobilization and habitat for beneficial microbes. In contrast, fresh manure or green waste, while eventually beneficial for mycorrhizal recovery, supplies readily available carbon that can fuel rapid decomposition and denitrification. Composted materials offer an intermediate option with reduced labile carbon content. Amendment timing also matters: applications during cool, dry periods when microbial activity is naturally suppressed may reduce initial GHG pulses. A phased approach, beginning with recalcitrant amendments like biochar for immediate stabilization followed by more labile materials once mycorrhizal communities establish, may optimize both short-term emission control and long-term ecosystem recovery. Site-specific trials are essential given the strong context-dependence of these dynamics.

Spatial heterogeneity matters. Even in landscapes that mostly look like Scenario B, Scenario C hotspots may dominate the gas budget. Managing these hotspots through amendments that immobilize metals, drainage improvements, or revegetation could yield outsized benefits.

7. Conclusions

This review establishes mycorrhizal fungi as critical but underappreciated mediators of heavy metal effects on forest soil greenhouse gas fluxes. Our three-scenario, four-pathway framework (Figure 1, Figure 2 and Figure 3) provides structure for interpreting the literature and identifying what we still need to learn. The main conclusions are as follows.

Heavy metals affect greenhouse gas fluxes primarily by disrupting mycorrhizal function rather than through direct toxicity to gas-cycling bacteria. Carbon allocation, nutrient acquisition, soil structure, and hyphosphere communities all respond to metal stress in ways that cascade to CO₂, N₂O, and CH₄ emissions.

Severity determines outcomes. Moderate contamination with adapted fungi may produce modest or even reduced fluxes (Scenario B). Severe contamination that overwhelms tolerance creates emission hotspots (Scenario C).

Evidence quality varies by gas. For CO₂ (Figure 1), mechanisms are well established. For N₂O (Figure 2), the picture is emerging. For CH₄ (Figure 3), connections remain mostly inferential. Integrated studies are the critical need.

ECM and AM systems likely respond differently based on their distinct strategies, but controlled comparisons are almost entirely lacking.

Managing for mycorrhizal resilience offers potential greenhouse gas co-benefits. Maintaining the fungal networks that regulate carbon cycling, nitrogen retention, and soil structure may help moderate emissions under stress.

Future research should prioritize comprehensive multi-gas studies across contamination gradients that include both mycorrhizal types. Only through such integrated approaches can we move from the conceptual framework presented here toward the predictive understanding that forest managers need.