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Review

A Critical Review: Unearthing the Hidden Players—The Role of Extremophilic Fungi in Forest Ecosystems

by
Muhammad Talal
,
Xiaoming Chen
,
Irfana Iqbal
and
Imran Ali
*
Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Sciences and Agri-Forest, Southwest University of Science and Technology, Mianyang 621010, China
*
Author to whom correspondence should be addressed.
Forests 2025, 16(5), 855; https://doi.org/10.3390/f16050855
Submission received: 27 April 2025 / Revised: 12 May 2025 / Accepted: 19 May 2025 / Published: 20 May 2025
(This article belongs to the Section Forest Ecology and Management)
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Abstract

:
Often thought of as a mesic paradise, forest ecosystems are a mosaic of microhabitats with temporal oscillations that cause significant environmental stresses, providing habitats for extremophilic and extremotolerant fungi. Adapted to survive and thrive under conditions lethal to most mesophiles (e.g., extreme temperatures, pH, water potential, radiation, salinity, nutrient scarcity, and pollutants), these species are increasingly recognized as vital yet underappreciated elements of forest biodiversity and function. This review examines the current understanding of the roles of extremophilic fungi in forests, scrutinizing their presence in these ecosystems with a critical eye. Particularly under severe environmental conditions, extremophilic fungi play a crucial role in forest ecosystems, as they significantly enhance decomposition and nutrient cycling, and foster mutualistic interactions with plants that increase stress resilience. This helps to maintain ecosystem stability. We examine the definition of “extreme” within forest settings, survey the known diversity and distribution of these fungi across various forest stress niches (cold climates, fire-affected areas, acidic soils, canopy surfaces, polluted sites), and delve into their possible ecological functions, including decomposition of recalcitrant matter, nutrient cycling under stress, interactions with plants (pathogenesis, endophytism, perhaps mycorrhizae), bioremediation, and contributions to soil formation. However, the review stresses significant methodological difficulties, information gaps, and field-based natural biases. We recommend overcoming cultural constraints, enhancing the functional annotation of “omics” data, and planning investigations that clarify the specific activities and interactions of these cryptic creatures within the forest matrix to further advance the field. Here, we demonstrate that moving beyond simple identification to a deeper understanding of function will enable us to more fully appreciate the value of extremophilic fungi in forest ecosystems, particularly in relation to environmental disturbances and climate change.

1. Introduction

Despite occupying approximately 31% of the planet’s surface area, forests are essential habitats for biodiversity and biogeochemical cycles and provide critical ecosystem services [1,2]. Ecological research within forests has historically focused on the major vascular plants and the related communities of animals and mesophilic microbes, operating under either assumed optimal or near-optimal conditions. This viewpoint overlooks the dynamic character and inherent variation of forest settings [3]. Forests are not monolithic; they exhibit significant gradients of temperature, moisture, light, pH, and nutrient availability, both geographically, from the canopy top to deep soil, and from pole to equator, as well as temporally, through seasonal oscillations, diurnal cycles, and disturbance events such as fire, drought, or pollution [4]. These fluctuations create numerous microhabitats and temporary conditions that challenge life’s boundaries and favor species with specific adaptations, known as extremophiles [5,6,7].
Key participants in forest ecosystems, fungi famous for their metabolic adaptability and varied lifestyles, are mostly known for their functions as decomposers, mutualists (mycorrhizae, endophytes), and pathogens [8,9]. Although the great majority of research on forest fungi focuses on mesophilic species, a growing body of data suggests that extremophilic fungi—those able to grow and reproduce under conditions deemed extreme (e.g., 5 °C or >40 °C, pH < 3 or >9, low water activity, high salinity, high radiation, presence of heavy metals) [5,6,10,11]—are not only present but potentially have substantial ecological roles, particularly in modulating ecosystem responses to stress and disturbance [12,13,14].
The term “extremophile” itself merits scrutiny in a forest environment. Unlike the archetypal extremophiles investigated in hydrothermal vents, hypersaline lakes, or polar ice caps [15], the “extremes” encountered in many forest settings may be less severe in absolute terms but still pose substantial physiological challenges [16,17,18]. These factors may encompass the frigid temperatures of boreal or alpine forests, the heat and desiccation ensuing from forest fires or on exposed canopy surfaces, the acidity of podzolic soils or decomposing wood, the osmotic stress experienced during droughts, the anaerobic conditions in waterlogged soils, the elevated UV radiation in the upper canopy, or the presence of heavy metals and organic pollutants in anthropogenically altered forests [19,20,21,22,23,24,25]. Therefore, many fungi relevant in these circumstances would be better dubbed “extremophiles”, capable of surviving extreme conditions yet potentially preferring more moderate ones for optimal growth. For the sake of this review, extremophilic fungi will refer to both highly tolerant fungi discovered flourishing under conditions markedly different from mesophilic optima and obligate extremophiles [5,26].
Despite the potential importance of these organisms, the study of extremophilic fungi, specifically within forest ecosystems, remains a relatively embryonic and fragmented field. Much of our understanding is drawn from studies of fungi isolated from forests, but these studies are often conducted under laboratory conditions or in non-forest, harsh environments. The ability of extremophilic fungi to decompose recalcitrant organic matter, such as lignin-rich compounds, is vital for nutrient cycling, particularly in environments where conventional decomposers are less effective due to extreme conditions. These fungi facilitate carbon sequestration by metabolizing organic biomass and degrading complex carbon compounds, thereby reducing greenhouse gas emissions. Furthermore, the interaction between extremophilic fungi and specific tree species can affect decomposition rates, as the chemical composition of litter influences fungal colonization and activity. Understanding these dynamics is crucial for comprehending how forest ecosystems respond to environmental changes and for developing strategies to maintain ecosystem health under stressful conditions [25]. Recent research has underlined the prevalence of black yeasts—polyextremotolerant fungi renowned for their resistance to several stresses—in many terrestrial environments, including forest soils [27]. A significant paucity of integrated research directly examines the in situ activity, ecological relationships, and quantitative contributions of extremophilic fungi to essential forest processes such as decomposition, nutrient cycling, and plant health under naturally occurring stress conditions [12,28,29,30,31].
This study aims to provide a critical synthesis of the existing knowledge on the roles of extremophilic fungi in forest ecosystems by doing the following. (1) Define the spectrum of “extreme” circumstances relevant within forest ecosystems. (2) Survey the known diversity and distribution of fungi adapted to these conditions. (3) Critically analyze the evidence for their involvement in critical ecological processes (decomposition, nutrient cycling, plant interactions, bioremediation). (4) Discuss the adaptive mechanisms permitting their survival and highlight the considerable methodological obstacles and inherent biases preventing development in the subject. (5) Identify significant knowledge gaps and recommend directions for further study.

2. Forest Ecosystems in Extreme Environments

To critically analyze the significance of extremophilic fungi in forests, as shown in Figure 1, we must first define what constitutes an “extreme” environment within this context. Unlike the stark circumstances of deep-sea vents or Antarctic dry valleys, forest extremes are generally characterized by gradients, variations, and specialized micro-niches. Applying concepts drawn from fundamentally distinct biomes can be deceptive [6,32,33].

2.1. Physical vs. Chemical Extremes

Boreal, subalpine, and alpine forests undergo lengthy periods of sub-zero temperatures, snow cover, and freeze–thaw cycles. Soil and litter fungi must cope with lower metabolic rates, membrane fluidity difficulties, and ice crystal formation (psychrophiles/psychrotolerant fungi) mentioned in Table 1. Examples include fungi active under snowpack, digesting trash at near-freezing temperatures. [34,35,36,37,38,39]. Forest fires create extreme heat, sterilizing upper soil layers but potentially selecting for pyrophilous (heat-stimulated) or thermotolerant fungi that swiftly colonize post-fire habitats. Canopy surfaces and exposed rocks within forests can also reach high temperatures (>50–60 °C) throughout the summer, selecting for thermotolerant organisms, including melanized fungi. Decaying wood undergoing vigorous microbiological activity can generate interior heat. A recent investigation indicated that F. solani’s growth increased with mild temperature changes but decreased with larger fluctuations, demonstrating its adaptability to shifting thermal conditions. This illustrates the potential function of fungi in forest ecosystems experiencing temperature variability, such as during snowfall conditions, as mentioned in Table 1 [19,40,41,42]. Many forest soils, especially those that are ancient or highly weathered, are nutrient-poor, characterized by low nitrogen (N) and phosphorus (P) levels. Fungi that have developed to scavenge and recycle limited nutrients (oligotrophs) are vital, as shown in Figure 2. Examples of such fungi include Cenococcum geophilum, an ectomycorrhizal species recognized for its resistance in nutrient-poor soils, and Hydnellum ferrugineum, which is typically found in low-nutrient coniferous forests. These fungi play key roles in nutrient cycling and support forest ecosystem processes under oligotrophic conditions [9,43,44].

2.2. Water Availability

Forests in dry and semi-arid regions, or those experiencing seasonal droughts, often face osmotic stress and desiccation issues. Soil, litter, and epiphytic ecosystems can become extremely water-limited. In forest ecosystems, soil moisture and temperature are therefore fundamental elements controlling microbial activity and community composition. Reduced soil moisture in arid and semi-arid areas, or in forests suffering seasonal droughts, can cause osmotic stress and desiccation, profoundly affecting microbial processes. Due to reduced substrate dispersion and microbial movement, microbial activity typically decreases under low moisture levels. On the other hand, excessive moisture can lead to anaerobic conditions, thereby preventing aerobic microbial activities and altering community structures. To retain moisture in the face of strong sunshine and wind, canopy epiphytes often rely on water storage adaptations, such as succulent leaves and specialized structures [45,46]. On the other hand, soil fungi typically rely on the buffering capacity of their surroundings and utilize metabolic changes and spore generation to survive periods of limited water availability [47,48]. Xerotolerant fungi, capable of thriving at low aW (<0.85), are vital in these settings. Canopy fungi, exposed to rapid drying cycles, also require desiccation tolerance [23,49,50]. Conversely, swamps, bogs, floodplains, and poorly drained forest soils can become waterlogged, leading to anaerobic or microaerobic conditions. While fungi are usually considered aerobes, some demonstrate facultative anaerobic capabilities or tolerance, which is necessary for breakdown in specific habitats [48,51].

2.3. pH

Forest soils are generally naturally acidic due to the decomposition of litter, which releases organic acids, and leaching, as mentioned in Table 1. Podzolic soils under coniferous woods can have pH values that range from 3.5 to 4. Acid rain can worsen this. Decaying wood also forms acidic microenvironments. Acidophilic and acidotolerant fungi are abundant and crucial for nutrient cycling in these environments [8,21,22,52]. While less common, certain places with calcareous bedrock or specific anthropogenic impacts could exhibit alkaline conditions, selecting for alkalitolerant fungi [53].

2.4. Radiation

Fungi inhabiting exposed surfaces, such as the upper canopy (phyllosphere), rock outcrops, or freshly burned ground, suffer high levels of UV-B radiation. Many of these fungi manufacture melanin, a pigment that absorbs a broad spectrum of UV wavelengths, therefore shielding cellular components from radiation-induced damage and so reducing the negative consequences of UV exposure. In these settings, this melanization is an essential adaptation for radiotolerance. In places contaminated with radioactive isotopes, such as the Chernobyl Nuclear Power Plant, certain melanized fungi have been discovered to not only resist high amounts of ionizing radiation but also to exhibit accelerated growth in their presence. Radioactive species, such as Cladosporium sphaerospermum, have demonstrated how melanin can be utilized to convert gamma radiation into chemical energy. This phenomenon suggests that melanin may function similarly to chlorophyll in photosynthesis, enabling these fungi to utilize radiation as their primary energy source [42,54,55,56]. Although the specific biochemical pathways underpinning radiosynthesis remain under investigation, the potential of melanized fungi to survive in high-radiation conditions highlights the remarkable adaptability of these organisms. These discoveries have significant implications for the bioremediation of radioactive sites and the production of radiation-resistant materials [57].

2.5. Chemical Stressors

Coastal woods or those influenced by deicing salts can experience higher salinity, selecting for halotolerant fungi [58]. Forests near industrial regions, mines, or roadsides can gather heavy metals (Pb, Cd, Zn, Cu) or organic pollutants (PAHs, pesticides) [59]. Metallotolerant and pollutant-degrading fungi serve potential roles in detoxification and bioremediation [60,61]. Wood contains phenolic chemicals and extractives that are inhibitory to many microorganisms [62]. Fungi colonizing wood, especially heartwood, must tolerate these natural toxins.

2.6. Diversity and Distribution

Identifying the extremophilic fungal players in forests relies on both traditional culture-based approaches and current culture-independent molecular tools, such as metabarcoding and metagenomics [63,64].

2.7. Culture-Based Studies

Isolation using selective media that mimic severe conditions (low pH, low aW, high temperature, and the presence of toxins) has revealed several examples of extremotolerant fungi in forest soils, litter, wood, and the phyllosphere. Psychrotolerant yeasts (e.g., Mrakia, Leucosporidium) and filamentous fungi (e.g., Penicillium, Cladosporium, Antarctomyces) have been isolated from cold-temperature forest soils [65]. Thermotolerant Ascomycetes have been isolated from post-fire soils (e.g., Pyronema, Morchella, Aspergillus fumigatus), acidotolerant Ascomycetes and Basidiomycetes in acidic forest soils and peatlands, xerotolerant Aspergillus and Penicillium species in dry litter or canopy surfaces.Melanized microfungi (‘black yeasts’ and relatives, e.g., Exophiala, Hortaea, Knufia) have been isolated from rock surfaces, canopy leaves, and in stressful soil environments [10,48]. Metallotolerant fungi (e.g., Trichoderma, Penicillium, some ectomycorrhizal fungi) have been isolated from polluted sites [40,49,52,60,66,67]. Culturing captures only a small, often easily culturable part of the total fungal diversity (‘the big plate count anomaly’) [68]. It picks for organisms that can thrive under specified lab conditions, not necessarily those most abundant or active in situ. It often leans towards fast-growing spore formers, such as Penicillium and Aspergillus [69]. Obligate extremophiles, or those with specialized dietary requirements, may be overlooked entirely [70,71].

2.8. Culture-Independent Studies (Metabarcoding/Metagenomics)

High-throughput sequencing of environmental DNA (eDNA) from forest materials, including soil, litter, roots, and leaves, provides a deeper understanding of fungal diversity, including unculturable taxa [71,72]. These investigations consistently reveal a high level of fungal diversity in forests, often characterized by the predominance of Ascomycota and Basidiomycota [73,74]. Sequences related to species known to survive in harsh habitats (e.g., some Archaeo-rhizomycetes, Geomyces [associated with frigid environments], melanized fungal orders like Dothideomycetes, Chaetothyriales) [75,76] are typically identified in challenging forest habitats, including cold soils [77], dry canopy surfaces [42], acidic horizons, or post-fire environments [21]. Metagenomics offers insights into functional genes related to stress tolerance, including those involved in the synthesis of suitable solutes, heat shock proteins, melanin formation, and detoxification enzymes [76,78]. The presence of DNA does not equate to metabolic activity or ecological value. Dormant spores or relic DNA may contribute to increased diversity estimates [71,79]. The choice of PCR primers for metabarcoding can lead to distorted community profiles [80]. Many sequences discovered, especially from less-studied taxa or habitats, lack near matches in public databases, making taxonomic and functional annotation difficult (‘dark matter’ fungi) [81,82]. Functional predictions from metagenomes are often questionable due to the limited annotation of fungal genes compared to those of bacteria [81]. ITS metabarcoding, the standard marker, frequently yields limited phylogenetic resolution, especially for specific taxa. Correlating variations in community composition along stress gradients with ecosystem function remains challenging [28,30]. Detecting extremophile DNA does not show that it is performing a particular purpose.

3. Speculation vs. Substantiated Function

The probable roles ascribed to extremophilic fungi in forests are varied, matching those of their mesophilic relatives [41], but are performed under challenging conditions, as shown in Figure 3 [83]. However, convincing data explicitly linking the in situ activity of individual extremophilic organisms to ecosystem-level processes is generally limited [30].

3.1. Decomposition and Nutrient Cycling

Fungi are the primary decomposers of plant debris and wood [84,85]. In severe forest conditions (e.g., cold, acidic, dry, post-fire), extremophilic/tolerant fungi endowed with specialized enzymes (extremozymes: cold-active, acid-stable, thermostable, salt-tolerant cellulases, ligninases, etc.), as summarized in Table 1 [86,87], are considered to be crucial for sustaining decomposition and nutrient release [25,88]. Psychrotolerant fungi may continue decomposing beneath snow [39]; acidotolerant fungi break down trash in acidic soils [89]; and pyrophilous fungi begin breakdown of charred material post-fire [90]. Many fungi isolated from severe forest habitats demonstrate appropriate extremozyme activity in laboratory trials (e.g., cold-active enzymes from psychrotolerant forest soil fungi; acid-stable enzymes from peatland fungi) [91]. Some studies revealed a direct link between extracellular enzyme activity and mass loss from decaying plant litter in boreal forests. Similarly, fungal traits, including enzyme activity, are correlated with litter decomposition rates; however, a limited number of studies have directly linked laboratory-based enzyme activity assays to field-based decomposition rates, particularly under extreme environmental conditions. This gap highlights the need for further integrated research that combines laboratory and field methodologies to better understand the ecological roles of extremophilic and extremotolerant fungi in forest ecosystems [92]. Genes encoding hydrolytic enzymes are identified in metagenomes from stressed forest soils [78]. Metatranscriptomic studies are rare in this specific scenario and could potentially link enzyme expression to specific taxa under stress in situ [93].
Decomposition rates are known to be regulated by temperature, moisture, and pH, which implicitly suggests a role for adaptable fungi. Post-fire investigations often reveal rapid colonization by pyrophilous fungi, followed by decomposition [94,95].

3.2. Plant Interaction and Pathogenesis

Mycorrhizal symbiosis is vital for plant nutrient uptake in most forests [9]. Can extremophilic fungi create functional mycorrhizae, potentially benefiting plant life under stress (e.g., drought, cold, high metal concentrations) as mentioned in Table 1 and Figure 2 [96]. Some fungi developing ectomycorrhizae (EM) or ericoid mycorrhizae (ErM) demonstrate tolerance to various stressors, including freezing, drought, acidity, and heavy metals (e.g., certain Piloderma, Cadophora, Oidiodendron, and Wilcoxina species) [96,97,98]. Studies indicate alterations in mycorrhizal communities along stress gradients [99]. Some experimental studies imply that tolerant symbionts can boost host plant performance under stress [100]. There is limited evidence to support the development of broad, functional mycorrhizae by obligate extremophilic fungi. Most tolerant mycorrhizal fungi are likely extremotolerant generalists [101]. Demonstrating that the fungal stress resistance immediately translates into a meaningful symbiotic advantage for the plant in the field under relevant stress levels is tough and seldom achieved [102]. Numerous studies have shown a correlation [96]. Although correlations exist between fungal presence and plant stress tolerance, defining causation remains challenging due to the complex interplay of factors in natural environments [103]. The relative impact of fungal tolerance vs. host plant physiological adjustments is often unclear. Endophytic fungi (living asymptomatically within plant tissues) are ubiquitous in forest plants [104,105]. Extremotolerant endophytes residing in leaves, stems, or roots can confer stress tolerance to their host plants against heat, drought, salinity, and herbivory [105,106]. Numerous studies have isolated endophytes from plants thriving in complex forest habitats, such as cold-adapted endophytes in boreal trees [103] and drought-tolerant endophytes in dry forests [104]. Some inoculation experiments under controlled conditions show that specific endophytes (often Aspergillus, Penicillium, Cladosporium-related taxa, known for tolerance) can enhance host plant growth or survival under abiotic stress (e.g., by producing phytohormones, antioxidants, or altering host physiology) [105,107,108]. Melanized endophytes in roots, specifically dark septate endophytes (DSE), are abundant in stressed situations, as mentioned in Table 2 [103]. Although their function remains uncertain, it ranges from harmful to mutualistic [109]. Some forest pathogens possess extremotolerant properties, which enable them to infect or cause disease when environmental stressors, such as drought, heatwaves, or frost damage, weaken host plants [110]. Furthermore, allowing pathogens to live in demanding conditions between infection intervals is a form of stress tolerance. Some fungal infections affecting forests are known to resist pertinent challenges (e.g., certain canker fungi survive cold winters, root rot pathogens, such as Armillaria, tolerate various soil conditions, and needle cast fungi survive desiccation on foliage) Table 3 [8,111]. Stress related to climate change is sometimes linked to increased susceptibility to illness or epidemics [110,112], indirectly suggesting a role for tolerant pathogens. Although logical, specific research is necessary to link the extremotolerance of a pathogen (beyond general hardiness) to its virulence or epidemiology under particular forest stress circumstances [110]. Is the main driver the pathogen’s tolerance or the host’s stress-induced susceptibility? While characterizing the pathogen’s specific extremophilic adaptations and their significance in the host-pathogen-environment triangle under stress, research typically focuses on the pathogen’s lifespan or host responses [113].

3.3. Bioremediation and Biogeochemical Transformations

In forests contaminated with pollutants, such as heavy metals and organic compounds, specialized extremotolerant fungi can facilitate bioremediation through biodegradation, biosorption, or biotransformation [59,60]. They may also play roles in mineral weathering and soil formation on difficult substrates [114]. Fungi isolated from disturbed forest soils often demonstrate resistance to heavy metals and the ability to destroy persistent organic pollutants (POPs) in lab experiments, as mentioned in Table 2 [59,115]. Some EM fungi can limit the uptake of heavy metals by host trees [67]. Melanized fungi and rock-colonizing fungi play a role in mineral weathering and the participation of elements from rock surfaces within forests through the production of acids and ligands [114,116]. Potential exists, particularly for mycoremediation applications [56,114], although in situ efficacy in complex forest soils is generally substantially lower than in controlled laboratory settings [117]. The bioavailability of contaminants, competition with other microbes, and environmental variations all limit the practical success of these methods in real-world applications. The contribution of fungi to total weathering rates in forests, compared to abiotic processes or bacteria, is difficult to measure [75]. While fungi are ubiquitous on rock surfaces, demonstrating a significant contribution to soil formation requires long-term investigations and quantification, which are lacking [115].
Table 1. Extreme conditions of the forests and their influence.
Table 1. Extreme conditions of the forests and their influence.
Stress VerityMetricExtreme BoundariesTypical FrequencySignificant InfluenceReferences
Soil pHpH in units More than 8.0/less than 4.5 Site-based,
rare		Trap nutrients,
Root destruction 		[118]
SalinitySoil EC
(dS/m)		More than 4 dS/mOffshore/roadside stopsDecline in seed germination/osmotic stress[119]
FireIgnited area
(% of stand)		More than 30% in one incidentWildfire:
10–20 years		Soil sterilization/replacing fire[120,121]
WaterSoil moisture (%)More than 80% (flood)
Less than 10% (extreme drought)		Floods: variable
Drought: 5–10 years 		Root anoxia, Hydraulic collapse[122]
Wind Max blowMore than 30 m/sTyphoon: annual/several yearsBranch cracking, extreme wind throw mortality, and uprooting[123]
LightUv-B flux
(kJm−2 day−1)		Less than 5 kJm−2
(spike event)		Sporadic Damage to DNA,
photoinhibition		[124,125]
TemperatureMaximum daily temperature (°C)More than 15 °C (cold)
Less than 35 °C
(heatwave)		Cold snaps: decadal; heatwaves annual Cold forest cracks, leaf scorch, and cambial damage[126,127]
Table 2. Different Fungal species showing Cd removal rates.
Table 2. Different Fungal species showing Cd removal rates.
Fungal SpeciesCd Removal Rate (%)Cd Removal Rate (%)References
Beauveria bassiana T758.7% over 7 days100 μg/mL Cd in liquid medium[128]
Trametes pubescens53.13%10 mg/L Cd concentration[129]
Penicillium sp. XK1032.2% over 4 days0.1 mM Cd at pH 6[130]
Table 3. Distributions and adaptations of Halophilic Fungi in Forests.
Table 3. Distributions and adaptations of Halophilic Fungi in Forests.
Species/GenusNaCl % RangeTypes of HabitatGeographic Occurrence Famous Adaptations References
Aspergillus spp.5 to 20Mangrove sediments; solar salternes(Mangrove) Pakistan; (Pattani salterns) ThailandSurvival in extreme saline environments, halotolerance [11,131,132]
Penicillium spp.5 to 20Salt marshes, brines, and mangrove soils Europe (salterns); Pakistan (Lasbela)Efficient metabolites production, halotolerance [108,133]
Alternaria spp.5 to 15Coastal hypersoliter soilsMediterranean coast, Pakistan mangroves Co-isolation along halotolerant Fungi; osmolyte melanin[134]
Cladosporium spp.5 to 15 Hypersaline soils; solar salterns Europe; ThailandOsmoprotectant synthesis; pigmentation in conidia for UV protection [131,135]
Debaryomyces hansenii0 to 25Salted foods, brines, saline soils Huge coverage
(Asia, Europe, America)		Antiporters Na+/H+ for osmotolerance; excessive glycerol production [135]
Wallemia ichthyophage10 to 32
optimum 20		Hypersaline habitats, solar salternsSalted cured foods, Black Sea, Mediterranean salternsEpic halophilic fungi are known; cell wall thickening, compatible solute accumulation[136]
Hortaea werneckii0 to 32Hypersaline brine, salt marshesSalted foods, Indian Ocean, Red Sea, Mediterranean HOG pathway development, multiple gene transformations for osmoregulation, highly melanized[135,137]

4. Mechanisms of Adaptation

Understanding how these fungi survive requires looking at their physiological and biochemical adaptations, partly clarified by studies on extremophiles from varied locales as summarized in Table 3 and shown in Figure 3 [10,11,138,139].
Modifying the composition of lipids (e.g., increasing unsaturated fatty acids at low temperatures; altering sterol content) to maintain optimal membrane fluidity [83,140]. Producing proteins with changed structures (e.g., different amino acid content, additional salt bridges, chaperones) that stay functional at severe temperatures, pH, or salinity. Cold-active enzymes often have more structural flexibility [87,141]. Accumulating low-molecular-weight organic molecules (e.g., glycerol, mannitol, trehalose) to maintain osmotic balance during drought or excessive salinity without interfering with cellular activities [10,142]. Producing melanin pigments in cell walls protects against UV radiation, desiccation, severe temperatures, heavy metals, and oxidative stress [10,39,48]. Melanin acts as a critical protective component in extremophilic fungi, enabling them to live and grow in situations with intense ultraviolet (UV) radiation. These fungi produce melanin using mechanisms such as the dihydroxynaphthalene (DHN) pathway, incorporating the color into their cell walls and membranes, as shown in Figure 3. A renowned example is Cryomyces antarcticus, an extremophilic fungi isolated from the Antarctic desert. Studies have shown that its melanin-rich cell walls give significant protection against UV-B radiation, contributing to its amazing persistence in one of Earth’s most severe environments. Similarly, Knufia petricola, another black fungus, demonstrates melanin-mediated UV protection, although the degree of protection differs between species. These findings underline the following mechanisms. Melanin is a significant adaptation characteristic for fungi inhabiting high-radiation settings [143,144,145,146]. Efficient proton pumps and buffering mechanisms help maintain a near-neutral intracellular pH even in strongly acidic or alkaline environments [91,147]. Enzymes (e.g., P450 monooxygenases, laccases, peroxidases) and transport mechanisms enable fungi to break down or sequester harmful substances, heavy metals, or reactive oxygen species (ROS) created under stress [148,149,150]. Fungi may develop resistant structures like thick-walled spores, chlamydospores, or sclerotia to withstand unfavorable periods (desiccation, heat, cold) [41]. Specific growth types (e.g., compact colonies, biofilm development) can establish protective microenvironments [75]. While these fundamental mechanisms are recognized, studies explicitly documenting the dominant adaptation strategies adopted by key extremophilic fungi taxa within specific forest habitats are less common. Furthermore, trade-offs certainly exist; adaptations to one stress might degrade performance under other contexts [151]. Understanding these trade-offs is critical for anticipating fungal responses to complicated environmental changes [12,81,152].

5. Methodological Hurdles and Biases

Methodological obstacles greatly limit progress in understanding the role of extremophilic fungi in forests.
As indicated, many fungi, potentially including critical extremophiles, are difficult or impossible to culture in the laboratory, which restricts their physiological and functional characterization [68]. The lack of exact, ecologically appropriate limits for establishing tolerance makes comparisons problematic [153]. Fungal tolerance in one forest habitat could be deemed mesophilic in another. While powerful, metagenomics, metatranscriptomics, etc., confront limitations shown in Table 1, DNA/RNA extraction efficiency from specific substrates (e.g., wood, refractory soil organic matter), primer/probe biases [154], incomplete databases for annotation exceptionally functional genes [155], and distinguishing active from inactive organisms (DNA vs. RNA/protein) [79] represent the biggest challenge, as shown in Figure 4. Finding the presence or even expression of genes, through approaches such as metabarcoding, metagenomics, and metatranscriptomics, does not directly quantify the rate or ecological relevance of the activity in situ [30]. Laboratory research (enzyme tests, microcosm studies) often does not scale up accurately to varied outdoor environments and ecosystem-level processes [156]. Techniques to detect the activity of individual microbial groups directly in undisturbed forest soil, litter, or inside plants under stress are restricted. Stable isotope probing (SIP) paired with sequencing has potential but is technical and expensive [93]. Poor taxonomic resolution for many fungal families, especially from environmental sequences, limits ecological interpretation [82].

6. Future Directions

Despite increased attention, our understanding of extremophilic fungi in forests remains superficial in many aspects. Integrating extremotolerant fungal features into ecosystem models is a promising method to expand our understanding of ecosystem resilience and function under changing environmental circumstances. There are concrete project concepts that address this integration, together with considerations for resource allocation and model parameterization [30,71]. The temporal dynamics of fungi community structure and function following wildfire disturbances in boreal forests can be explored by identifying boreal forest stands that represent a chronosequence of time since fire (e.g., 1, 5, 10, 20, and 50 years’ post-fire). Soil samples, collected annually over 5 years from each site, could then be subjected to RNA sequencing to measure active fungal gene expression related to stress tolerance, decomposition, and nutrient cycling, and to correlate gene expression profiles with environmental factors and ecological processes. Approximately $1.5–2 million over 5 years is needed to cover fieldwork, sequencing, bioinformatics, and labor costs [157]. The growing popularity of metatranscriptomics, metaproteomics, and metabolomics, preferably combined with techniques such as SIP, is necessary to link specific taxa to active processes in situ under relevant stress conditions [93]. To develop better functional predictions using ‘omics’ data, significant efforts are needed to improve fungal genome annotation and reference databases [158]. This includes developing and implementing methodologies to directly assess extremophilic fungi’s contribution to specific processes (e.g., decomposition rates of distinct litter types under stress, nutrient mobilization, pollutant degradation) in the field [159]. Further research should investigate the unique relationships between extremophilic fungi and plants, mechanisms of endophyte-mediated stress tolerance, function of tolerant mycorrhizae, and interactions with other microbes (bacteria, archaea) under stress [96]. It is also essential to explore how expected changes in temperature, precipitation patterns, and disturbance regimes (fire, drought frequency/intensity) may affect the prosperity, distribution, and activity of extremophilic fungi and their subsequent impact on forest resilience and carbon cycling [160]. While ecologically focused, continuous investigation of forest extremophiles for novel extremozymes and bioremediation capacities is valuable, ecological relevance should be the primary driving force for forest studies [87]. Integrating extremotolerant fungal communities’ functional features and responses into forest ecosystem models can improve forecasts under stress and climate change scenarios [13].

7. Conclusions

Extremophilic and extremotolerant fungi are essential components of forest ecosystems, occupying niches characterized by environmental extremes such as boreal cold, post-fire heat, peatland acidity, canopy dryness, and soil toxicity. Their evolutionary adaptations enable them to perform critical ecological functions, including decomposition, nutrient cycling, plant interactions, and biogeochemical transformations, especially under conditions where mesophilic organisms may be less effective. Despite growing documentation of their existence and potential capabilities, a significant gap remains in the comprehension of their actual, quantitative contributions to forest ecosystem processes in situ. Methodological limitations, particularly in linking taxonomic identity to functional activity within complex forest environments, restrict this understanding. Recognizing the global significance of these fungi, their practical applications are manifold. In agriculture, extremophilic fungi can be implemented to develop biofertilizers and biocontrol agents, enhancing crop resilience and reducing reliance on chemical inputs. Their enzymatic machinery provides solutions for bioremediation, facilitating the detoxification of polluted environments. Furthermore, their role in carbon sequestration positions them as useful supporters in climate change mitigation strategies. To fully realize these applications, future research must adopt functionally oriented, analytically robust, and ecologically integrative approaches. By bridging the gap between identification and functional understanding, extremophilic fungi can be potentially unlocked to contribute to sustainable ecosystem management and global environmental resilience. Bringing the lab and the field together will revolutionize our understanding of how forests are responding to climate extremes.

Author Contributions

M.T. and I.I.; writing—original draft preparation, X.C. and I.A.; supervision. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Natural Science Foundation of China (12275227).

Conflicts of Interest

The authors declare no conflicts of interest.

Abbreviations

The following abbreviations are used in this manuscript:
DESDark septate endophytes
POPsPersistent organic pollutants
ROSReactive oxygen species
SIPStable isotope probing
EMEctomycorrhizae
ErMEricoid mycorrhizae

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Figure 1. Recent development status of utilizing various extremophilic fungi in forests and publication percentages in different journals. (A) Total publications from 2010 to 2025, (B) percentage of countries working on the topic over the last 15 years, (C) percentage of extremophilic fungi in the forests, (D) quantitative role of extremophilic fungi in ecological processes. (These statistics have been taken from Science Direct, Scopus journals, and Google Scholar).
Figure 1. Recent development status of utilizing various extremophilic fungi in forests and publication percentages in different journals. (A) Total publications from 2010 to 2025, (B) percentage of countries working on the topic over the last 15 years, (C) percentage of extremophilic fungi in the forests, (D) quantitative role of extremophilic fungi in ecological processes. (These statistics have been taken from Science Direct, Scopus journals, and Google Scholar).
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Figure 2. Schematic diagram showing decomposition, plant interaction, protection from pathogens, and bioremediation powers of extremotolerant fungi in the forest.
Figure 2. Schematic diagram showing decomposition, plant interaction, protection from pathogens, and bioremediation powers of extremotolerant fungi in the forest.
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Figure 3. Schematic diagram showing adaptive changes in extremophilic fungi brought about by extreme forest conditions.
Figure 3. Schematic diagram showing adaptive changes in extremophilic fungi brought about by extreme forest conditions.
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Figure 4. A flowchart diagram presenting the identification of biases and proposing methods.
Figure 4. A flowchart diagram presenting the identification of biases and proposing methods.
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Talal, M.; Chen, X.; Iqbal, I.; Ali, I. A Critical Review: Unearthing the Hidden Players—The Role of Extremophilic Fungi in Forest Ecosystems. Forests 2025, 16, 855. https://doi.org/10.3390/f16050855

AMA Style

Talal M, Chen X, Iqbal I, Ali I. A Critical Review: Unearthing the Hidden Players—The Role of Extremophilic Fungi in Forest Ecosystems. Forests. 2025; 16(5):855. https://doi.org/10.3390/f16050855

Chicago/Turabian Style

Talal, Muhammad, Xiaoming Chen, Irfana Iqbal, and Imran Ali. 2025. "A Critical Review: Unearthing the Hidden Players—The Role of Extremophilic Fungi in Forest Ecosystems" Forests 16, no. 5: 855. https://doi.org/10.3390/f16050855

APA Style

Talal, M., Chen, X., Iqbal, I., & Ali, I. (2025). A Critical Review: Unearthing the Hidden Players—The Role of Extremophilic Fungi in Forest Ecosystems. Forests, 16(5), 855. https://doi.org/10.3390/f16050855

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