Fungi represent a diverse source of bioactive compounds with the potential to influence genomic stability in both harmful and beneficial ways. Some species produce metabolites capable of inducing DNA damage through direct interaction with genetic material or via metabolic activation, while others yield compounds that may protect against oxidative stress and mutagenesis. The scientific literature on this topic, however, contains notable contradictions, with discrepancies often stemming from differences in methodology, experimental models, and data interpretation. This review critically examines current evidence on the genotoxic and protective effects of fungi, while also addressing the challenges posed by inaccuracies and inconsistencies in published studies. Overall, fungal effects on genomic stability depend strongly on the chemical composition of fungal materials, the concentration and bioavailability of their constituents, and the experimental context. The reviewed evidence indicates that fungal compounds can exert both genotoxic and genoprotective effects, highlighting the need to distinguish direct genotoxicity from secondary DNA damage and antioxidant-mediated protection.
Alternative splicing (AS) is a fundamental post-transcriptional process that expands transcriptomic and proteomic diversity by generating multiple mRNA isoforms from a single gene. In fungi, AS not only contributes to proteome complexity but also appears to influence key biological processes, including development, morphogenesis, pathogenicity, stress responses, and environmental adaptation. Unlike animals and plants, in which exon skipping predominates, intron retention is the most prevalent AS mode in fungal species, suggesting unique evolutionary pressures and regulatory strategies. The spliceosome, along with splicing factors such as serine/arginine-rich proteins and heterogeneous nuclear ribonucleoproteins, orchestrates the precise selection of splice-sites. However, the mechanisms linking AS to cellular signaling and environmental cues remain largely unresolved. This review summarizes recent advances in our understanding of fungal AS and highlights its regulatory potential, adaptive significance, and evolutionary implications. Here, we discuss how stimulus-dependent splicing operates as a controlled response mechanism and provide a comprehensive perspective on the functional dimension of splicing in fungi. We propose that a landscape of splicing signal conservation/degeneration has been shaped in fungal genomes throughout evolution, which determines the intrinsic propensity for regulated AS events at individual splice sites.
Baudoinia compniacensis is a melanized saprobic fungus that causes blackening of surfaces in the vicinity of spirit maturation warehouses, commercial bakeries, or distilleries that are exposed to low levels of ethanol vapour; with the fungus growing on the ethanol in the vapour. The surfaces that are most affected are those that are highly exposed and undergo extreme diurnal temperature fluctuations. This review focuses on the currently available physiological and genomic data to facilitate a comparative analysis of Baudoinia compniacensis with the genomes of a panel of fungi representing a broad spectrum of lifestyles, stress-tolerance strategies, ecological specializations and convergent adaptations that parallel those of Baudoinia, together with fungi with ethanol tolerance. By anchoring Baudoinia within this rationally selected comparative framework, this review attempts to differentiate traits that are widely shared among melanized and extremotolerant fungi from those that are unique in helping to enable the fungus colonize ethanol-rich, anthropogenic surfaces. The review also provides insights into a number of potential adaptive genetic traits that are likely to underpin the ecological success of Baudoinia, including genes involved in carbon and pentose phosphate metabolism, carbohydrate-active enzymes, genes involved in peroxisome and mitochondrial fatty-acid metabolism, together with calcium signalling and in melanin biosynthesis. We place these traits in comparative perspective, noting that many are shared across the broader oligotrophic, melanized black-fungal guild and that ethanol appears to act as a multifunctional, concentration-dependent input — germination cue, carbon source and stressor — rather than as a uniquely defining resource, with wood- and plant-derived carbohydrates likely to supplement ethanol as carbon sources. We also identify priority avenues for future work, including the sequencing of confirmed B. compniacensis, systematic survey of natural (non-industrial) reservoirs, and experimental separation of the signalling and nutritional roles of ethanol, together with direct characterisation of carbon metabolism on lignocellulosic (wood-cask) substrates.
Sustainable deployment of lignocellulosic biofuels hinges on enzyme cocktails that are efficient, robust and inexpensive. Trichoderma reesei remains the industrial workhorse, yet its low β-glucosidase activity, moderate thermostability and susceptibility to carbon catabolite repression limit performance. This review critically compares the secretomes, genomics and process attributes of established and emerging filamentous fungi including Penicillium spp., Aspergillus niger, Myceliophthora thermophila and, centrally, the thermophile Rasamsonia emersonii. Multi-omics analyses reveal that R. emersonii possesses a deeper repertoire of carbohydrate-active enzymes, especially high-temperature endoglucanases, β-glucosidases and AA9 lytic polysaccharide monooxygenases (LPMOs), and can operate optimally at high temperatures and lower pH, reducing viscosity and contamination in high-solids hydrolysis. Advances in strain engineering, soluble-inducer strategies and fed-batch cultivation are summarized, highlighting paths to enzyme costs below US $0.20/kg. We discuss synergistic formulations that pair R. emersonii activities with commercial T. reesei and A. niger products and outline remaining knowledge gaps in transport-mediated induction and redox regulation. Collectively, the review positions R. emersonii as a front-runner for next-generation, on-site enzyme manufacturing in second generation (2G) biorefineries.
The iconic networks of filamentous fungi are connected through hyphal fusions. While fusion is beneficial among hyphae from the same fungal individual, fusion between individuals (i.e., heterokaryon formation) risks infection by parasites or pathogens. Across fungi, multiple sets of genes, termed het genes, have evolved the capacity to prevent the formation of fused hyphae between individuals with incompatible allele combinations. The first het genes to be molecularly characterized function through triggering cell death pathways, forming a paradigm that cell death is the primary mechanism regulating heterokaryon formation. The originally described het genes in the Sordariomycete model fungi Neurospora and Podospora encode a small protein domain, called HET, that is essential in some cases for this cell death function. Since this initial description, the field of fungal self/nonself recognition has progressed in two directions. The experimental side has described het genes in various species, and with increasing mechanistic complexity. More than just cell death, the process of fusion itself has several described checkpoints prior to establishing fusion. These genes, as well as cell death-causing genes in other species, do not encode the characteristic HET domain. However, on the other hand many bioinformatics studies continue to use the HET domain as a primary marker for het genes. This reliance on a limited set of protein domains overlooks general evolutionary features of self/nonself recognition genes, including long-term balancing selection, that may be used to expand searches for undescribed self/nonself loci. We argue here that this singular focus on the HET domain is unproductive and ignores diverse allorecognition mechanisms, including those occurring pre-fusion. A more holistic, process-based view of self/nonself recognition provides a way forward in understanding this fundamental fungal trait, which in turn has cascading consequences for managing fungi in clinical and agricultural settings.
Sporidiobolaceae red yeasts, which produce diverse bioactive metabolites and thrive under multiple environmental stresses, are emerging as multifunctional members of plant-associated microbiomes, yet their plant growth-promoting roles remain less resolved than for bacterial and filamentous counterparts. These non-conventional basidiomycetous yeasts produce intra- and extracellular metabolites—including phytohormones, organic acids, siderophores, and volatile organic compounds—that support nutrient mobilization, hormone-like signaling, stress mitigation and pathogen suppression in plant-associated habitats. This review synthesizes advances on how the metabolic versatility and ecological traits of Sporidiobolaceae red yeasts underpin plant growth promotion. Taxonomy and ecological distribution across diverse environments are summarized, emphasizing traits that promote colonization, persistence and ecosystem functions. Metabolite-centered mechanisms are then dissected, encompassing direct effects on plant physiology, indirect modulation of plant immunity and microbiome structure, and environmental functions such as metal sequestration and pesticide degradation. Key research gaps that constrain translational use of these yeasts as biostimulants, biocontrol agents and remediation inoculants are highlighted, including incomplete understanding of stress- and host-responsive regulatory networks, strain- and context-dependent efficacy, severely limited field trials and strong methodological heterogeneity in IAA quantification and colonization assays among studies. Integrative multi-omics, functional genomics and ecology-informed strain and consortia design are identified as priorities to mechanistically resolve Sporidiobolaceae–plant–microbiome interactions and to overcome translational bottlenecks in developing red-yeast-based inoculants with predictable performance. Together, this review provides a framework that not only synthesizes current knowledge on the mechanisms and ecological roles of Sporidiobolaceae red yeasts, but also paves the way to harness the potential of these fungi.
Extremophilic fungi, especially those from polar and desert environments, are increasingly recognized as active, programmable systems rather than passive stress survivors. Capable of conditional gene activation and multi-stress sensing, these fungi exhibit shared molecular strategies, such as melanization, antioxidant production, and osmolyte synthesis under convergent environmental pressures. This review reframes them as climate-responsive organisms with potential roles in biosensing, synthetic biology, and ecological forecasting. It is herein proposed the Fungal Vulnerability Index, a modular tool that integrates multi-omics and environmental data to assess ecosystem sensitivity. Their metabolic efficiency, transcriptional plasticity, and environmental memory make fungi promising components for climate-adaptive technologies and Artificial Intelligence-integrated ecological systems in the Anthropocene.
Subphylum Saccharomycotina includes yeasts with broad ecological, manufacturing, medical and veterinary clinical significance and encompasses Candida spp. and related genera. While some, like Candida albicans, are frequently encountered as opportunistic pathogens in people, their ecological niches and significance beyond the clinical setting are unclear. However, evidence is emerging that transmission can occur between the three One-Health compartments of the human population, animal population and the environment. Using a One-Health approach, the presence of World Health Organization Saccharomycotina priority pathogens in these different niches is reviewed, including evaluation of evidence for genetic similarities between isolates from different ecological backgrounds. The Saccharomycotina yeasts that colonise healthy humans vary by anatomical site, age, ethnicity and geographic region. These same species of yeasts, including those of medical importance, colonise a diversity of vertebrate hosts, especially birds. Shorebirds, such as gulls, that feed on human refuse in urban environments can be carriers, reservoirs and disseminators of azole resistant isolates of yeasts including Candida tropicalis, C. parapsilosis and Nakaseomyces glabratus likely of anthropogenic origin. Saccharomycotina yeasts are also abundant in natural and built environments. Multilocus sequence typing (MLST) and other methods of genotyping combined with population analyses of C. albicans and non-albicans yeasts have revealed that human clinical isolates have some degree of separation from, but also significantly overlap with, animal and environmental isolates, supporting transboundary transmission. In conclusion, transmission of Saccharomycotina yeasts can occur between these niches. Further research into the directionality and risk of inter-niche transmission using a coordinated One Health approach is required.
This literature review explores how fungi, mycotoxins and yeast-based interventions may influence depressive disorders through the gut-brain axis. Although depression remains a highly prevalent and multifactorial condition, growing evidence shows that the intestinal microbiota plays an important role in its development and in shaping responses to treatment. Most of what is known today comes from studies focused on bacterial communities, which consistently reveal patterns of dysbiosis in individuals with Major Depression Disorder. However, recent findings suggest that the fungal component of the gut microbiota may also shift in depressive states, with alterations in species such as Candida, Penicillium, Saccharomyces and others, emerging across human and animal studies. From a pathological perspective, mycotoxins, particularly fumonisin B1, have also been implicated in the development of depressive-like symptoms in murine models. Beyond characterizing these associations, this review highlights experimental work demonstrating that fecal microbiota transplant from depressed individuals to germ-free rodents can reproduce metabolic and behavioral features of the disorder, reinforcing the relevance of the microbiota-gut-brain axis. In parallel, the review examines evidence on probiotic and postbiotic yeasts, from live Saccharomyces to heat-inactivated yeast cells and their structural components, which show potential to modulate inflammation, restore intestinal integrity, and alleviate stress-related behaviors. Together, these insights frame fungi and yeast-derived products as promising, yet underexplored, candidates for future therapeutic strategies targeting depression.
The cell wall is an essential structure in all fungi, providing structural, protective, and regulatory roles as their first line of contact with the environment. In terms of composition, the fungal cell wall is known to contain chitin as a major structural component, setting it apart from many other organisms because it is generally considered not to contain cellulose. Yet, studies in the past have shown that several species in the Ophiostomatales contain both chitin and cellulose in their cell walls. This review synthesises the historical and contemporary evidence for the presence of cellulose in the cell walls of fungi, focusing in particular on the unusual case of the Ophiostomatales. This is against the background that the presence of cellulose in this group of fungi has been largely overlooked due to taxonomic revisions of the Fungal Kingdom by applying molecular techniques and research efforts being substantially focussed on model organisms. As a result, an entire aspect of the ecology, evolution, and in some cases, pathogenicity of the Ophiostomatales has been obscured. By revisiting the unique cell wall composition of these non-model fungi, insights should provide a deeper understanding of their adaptations to their hosts, vectors and the environment.
Sporothrix schenckii, Sporothrix brasiliensis, and Sporothrix globosa are thermodimorphic fungi responsible for sporotrichosis, an emerging subcutaneous mycosis with increasing zoonotic transmission. The innate immune response plays a fundamental role in the early recognition and control of infection by these species. Recent studies have provided insights into how innate immune cells, including neutrophils, human peripheral blood mononuclear cells, natural killer cells, macrophages, and dendritic cells, detect and respond against Sporothrix spp., through the activation of pattern recognition receptors (PRRs) and the release of proinflammatory mediators. The fungal cell wall, particularly its glycan composition and structure, has emerged as a key determinant in immune recognition, showing significant variation between the mycelial and yeast phases of these organisms, as well as among species within the Sporothrix pathogenic clade. These structural differences modulate interaction with the host and influence immune evasion strategies. Moreover, the morphological dimorphism of Sporothrix spp., an important virulence trait, affects immune recognition by exposing or concealing immunostimulatory epitopes during the transition between environmental and parasitic forms. This review integrates current knowledge on species-specific innate immune responses, highlighting how cell wall architecture and fungal dimorphism determine the immune system activation. Finally, therapeutic perspectives based on these findings are addressed, including vaccine development, passive immunization, and modulation of trained immunity, which represent promising strategies for controlling sporotrichosis in humans and animals.
The genus Exophiala, a group of black yeasts, exemplifies the resilience of polyextremotolerant fungi, which thrive in diverse habitats, including polluted industrial sites, saline waters, and human-associated environments. Characterized by their ability to overcome fluctuations in pH, high salinity, temperature extremes, chaotropic conditions, and nutrient scarcity, Exophiala species serve as models for understanding fungal adaptations to polyextreme conditions. This perspective article reviews current knowledge on the Exophiala genus, highlighting key adaptations, including melanin-mediated protection against radiation and oxidative stress, the emerging role of extracellular vesicles in cellular communication, the influence of polymorphic transitions on environmental resilience and pathogenicity, and the molecular basis of Exophiala's adaptability and resilience. A central focus of this work is E. dermatitidis, which we propose as a model species for studying fungal adaptation to both natural and anthropogenic environments. Here, we introduce the concept of “urban oligotrophic specialist” to describe E. dermatitidis, emphasizing its ability to thrive in nutrient-limited human-made environments, including kitchens, dishwashers, bathrooms, and hydrocarbon-polluted sites. This unique ecological positioning reflects its adaptation to the Anthropocene, where increasing urbanization, pollution, and climate change are creating novel habitats for fungi. Its thermotolerance, biofilm formation ability, and hydrocarbon metabolism place E. dermatitidis at the intersection of polyextremotolerance and pathogenicity, raising concerns about its potential expansion in response to global environmental challenges. Understanding the biology of the genus Exophiala not only enhances our knowledge of fungal polyextremotolerance but also provides new perspectives into its implications for bioremediation, pathogenicity, and survival in extreme and anthropogenic environments.
Fungal diseases represent a growing global health crisis, exacerbated by limited therapeutic options and the rise of antifungal resistance. A deeper understanding of the molecular mechanisms governing host-pathogen interactions is crucial for developing novel strategies. Small non-coding RNAs (sncRNAs), a diverse class of regulatory molecules under 200 nucleotides, have emerged as critical players in modulating the host immune response to infection. This article bridges traditional review with emerging perspectives to comprehensively explore sncRNAs in fungal pathogenesis. We highlight how microRNAs (miRNAs), such as miR-155 and miR-146a, act as first responders to balance pro and anti-inflammatory signaling and serve as promising clinical biomarkers. Futhermore, we examine the biotechnological and therapeutic potential of piwi-interacting RNAs (piRNAs) and small interfering RNAs (siRNAs) as novel antifungal agents, alongside the complex dynamics of cross-kingdom RNAi (ckRNAi) as mechanism of virulence. Finally, we propose novel functional roles for understudied classes, suggesting that small nucleolar RNA (snoRNAs) regulate immune cell differentiation and small nuclear RNA (snRNAs) drive alternative splicing during fungal adaptation. By defining these specific mechanisms and identifying critical knowledge gaps, this review outlines actionable future directions for exploiting sncRNAs in the diagnosis and the targeted treatment of fungal infections.
This review explores physical treatment methods for the inactivation of spoilage molds in the food industry. Focus is placed on sustainable, chemical-free technologies that offer safe, effective, and environmentally friendly solutions for improving food safety and extending shelf life. A total of eight physical treatment categories were evaluated for their antifungal activity and inactivation mechanisms, namely ultraviolet light, pulsed light, gamma irradiation, microwave, ultrasound, cold plasma, high pressure, and pulsed electric fields.Ultraviolet and pulsed light treatments demonstrate promising results in rapidly inactivating fungal spores on surfaces as well as in liquids. Gamma irradiation offers a reliable means of achieving deep penetration and extended shelf life. Microwave and ultrasound technologies provide innovative approaches to disrupt fungal cell structures. Cold plasma and high-pressure treatments emerge as alternative options, capable of inactivating a broad spectrum of spoilage fungi without compromising food integrity while pulsed electric fields enhance permeability in fungal cells, leading to effective inactivation. The use of different physical treatments having different modes of actions could be of interest in agreement with the “hurdle” technology concept. Finally, a critical evaluation of the advantages and limitations of these approaches serves as a base for exploring new research perspectives.The comparative analysis revealed that while ultraviolet and pulsed light are the most cost-effective and rapid for surface decontamination, High-Pressure Processing (HPP) and cold plasma offer the best efficacy for preserving organoleptic quality. From an environmental perspective, UV-LEDs and cold plasma stand out for their low energy consumption and mercury-free operation, suggesting that the most efficient technique is application-dependent or achieved through synergistic hurdle combinations.
As the primary trophic resource for giant pandas, bamboo forms the ecological and nutritional basis of their survival. In sharp contrast, phytopathogenic fungi undermine this foundation by degrading the structural and biochemical integrity of bamboo, thereby precipitating a nutritional cascade that directly affects panda health. This review positions itself at the interface between microbial ecology and conservation biology to discuss the mechanistic interactions between fungal pathogens and their bamboo hosts, with an emphasis on the enzymatic degradation of lignocellulosic biomass and the mechanisms by which fungal pathogens evade the plant defense systems. Despite the urgent ecological imperatives, symbiotic and pathogenic interactions within the bamboo-fungus system remain understudied, particularly regarding species-specific virulence patterns and bamboo resilience. Furthermore, we discuss how anthropogenic climate change and pollution redefine pathogen-host synchrony, reshape microbial community structures, and sometimes increase disease severity. A critical assessment of the current spectrum of control paradigms from chemical fungicides to biological antagonists reveals an urgent need for integrated approaches balancing disease mitigation with ecological sustainability. Finally, we propose a cross-disciplinary conservation framework grounded in Integrated Disease Management (IDM) and suggest that harmonizing microbial ecology with biodiversity conservation can provide sustainable, evidence-based solutions. This integrative model clarifies how fungal pathogenesis in bamboo triggers nutritional decline in pandas, and outlines ecosystem-based management strategies to restore bamboo health and ensure panda survival.
Plants mutually associate with different taxonomic groups of endophytic fungi. Endophytic fungi can promote plant growth through increased micronutrient acquisition, nitrogen uptake, activity of proton pumps, shoot branching, leaf number, root development and hair formation, metabolism, anti-insect activity, and suppressing plant cell death. They produce volatile organic compounds with a wide range of activities. Endophytic fungi induce plant immune responses to fight against viruses. Plants defend themselves against herbivores through salicylic acid (SA) and jasmonic acid (JA) signaling, regulated by endophytic fungi. They can improve growth under arsenic stress by modulating anti-oxidative enzymes and reducing mobilization from root to shoot and reproductive organs. Endophytic fungi reduce the translocation of arsenic, cadmium, and chromium to the upper parts of plants by chelating them and producing indole-3-acetic acid and gibberellic acid to combat toxic metal and metalloid stress. The molecular mechanisms employed by a taxonomically diverse group of endophytic fungi for conferring toxic metal and metalloid tolerance and enhancing plant growth are discussed.
