Fungal Ecology

Currently, the fungal class Paraglomeromycetes (phylum Glomeromycota) consists of one order, Paraglomerales, with two families: Paraglomeraceae, comprising the genera Paraglomus with ten species and Innospora with one species, and the monogeneric and monospecific Pervetustaceae represented by Pervetustus with Pe. simplex. However, our morphological analyses of these species and an undescribed specimen morphologically resembling other Paraglomeromycetes species, as well as analyses of sequences of these fungi and environmental sequences, indicated that the current taxonomic composition of this class should be updated. We did so here by creating in Paraglomeromycetes Pervetustales ord. nov. with Pervetustus and Opikia catenata gen. nov. and sp. nov., as well as transferring Innospora with In. majewskii to Innosporaceae fam. nov. These novelties were introduced primarily based on strong genetic divergences of the analyzed taxa, as many morphological and histochemical features of their spores and mycorrhizal structures overlap. Only Op. catenata possesses the unique trait of occasionally producing spores in chains. This mode of sporulation has also not been recognized in any other Glomeromycota species. Unlike species of Pervetustales and Innosporaceae, which produce single-walled spores, the subcellular spore structure of Paraglomus species contains one or two walls.

Sporulation is an integral process in the lifecycle of many fungal pathogens, including Histoplasma, a primary human pathogen that causes respiratory infections. Histoplasma conidia, or asexual spores, are the primary infectious particle but very little is known about them, in part due to the need for Biosafety Level 3 containment and inconsistency in generating viable conidia under laboratory conditions. Here, we identify media that consistently promote Histoplasma conidiation, yielding both micro- and macroconidia, and conditions that promote high levels of germination. We show that conidiation media and duration affect the proportion of macroconidia produced, and we demonstrate that Histoplasma strains vary in their response to these conidiation parameters. Finally, imaging studies of chitin, exposed chitin, and cell wall mannoproteins show that while micro- and macroconidia have similar cell wall compositions, strain type and conidiation media variation result in qualitative differences in staining. These optimized methods for Histoplasma conidial preparations will enable more detailed investigations into this understudied aspect of the biology of an important human fungal pathogen.

Mucormycosis is among the most lethal fungal infections in clinical medicine, with crude mortality rates between 50 and 90% that have improved little over decades of antifungal development. Alveolar macrophages constitute the primary cellular defense against inhaled Mucorales spores, yet quantitative comparative data on phagocytic outcomes across the taxonomic breadth of this fungal order are absent from the literature. We co-incubated 62 Mucorales strains drawn from nine phylogenetic groups and 12 countries with MH-S murine alveolar macrophages and with Dictyostelium discoideum amoeba, at multiplicities of infection (MOI) of 1 and 5 and at incubation times of 1.5 and 3 hours. Automated phagocytic index quantification was combined with spore morphometric measurements and geographic metadata. Macrophage phagocytic indices differed highly significantly among the nine phylogenetic groups across all experimental conditions (Kruskal-Wallis H = 394-780; p = 10^-163 to 10^-74). Group 1 (Absidia and Cunninghamella species) showed the lowest phagocytic index; Groups 5 (Rhizopus arrhizus) and 6 (Gilbertella persicaria and Mycotypha species) showed the highest. Larger spore area correlated negatively with macrophage phagocytic index. In the central comparative finding, Spearman rank correlations between macrophage and D. discoideum phagocytic indices were near zero across all four conditions (r = -0.07 to +0.11; all p > 0.8), demonstrating that protozoan phagocytosis does not predict the mammalian macrophage phagocytic hierarchy. Kinetic analysis further revealed, for the first time in any Mucorales or Mucormycotina species, evidence of vomocytosis in MH-S macrophages challenged with Group 8 (Mucor clade II) spores at MOI 1, and in D. discoideum across four groups at MOI 5 after 3 hours. These findings establish a quantitative, phylogenetically resolved framework for Mucorales innate immune recognition, demonstrate that the evolutionary training ground hypothesis does not hold at the order level for Mucorales, and identify vomocytosis as a previously unrecognised immune evasion mechanism in Mucormycotina.

Background Fungi in plant root systems are key to understanding the dynamics and functioning of terrestrial ecosystems. Whereas our knowledge of below-ground plant-fungus symbioses has derived mainly from studies of mycorrhizal and pathogenic fungi, recent studies have uncovered an unexpected diversity of ecological niches occupied by root-associated fungi. The fungal order Helotiales is conspicuous in this respect because this predominantly root-associated taxon encompasses a broad ecological spectrum, ranging from saprotrophic and pathogenic fungi to endophytic and mycorrhizal fungi with plant growth-promoting functions. In this study, we integrated a worldwide dataset of 1,996 Helotiales Species Hypotheses (i.e., species-level taxa tentatively defined based on DNA sequences) detected in roots of 362 plant genera representing 117 families and 47 orders, and systematically quantified the specificity of Helotiales-plant associations. Results The analysis of 37,688 unique occurrence records of Helotiales fungi across 1,940 global sampling locations revealed highly structured associations between Helotiales genera and plant lineages, exemplified by the strong specificity of Hyaloscypha, Oidiodendron, and Phialocephala for Pinales and that of Glutinomyces for Fagales, even after statistically controlling background biogeographic patterns. At the Species-Hypothesis-level analysis, major clades within the Helotiales phylogeny consistently exhibited high specificity for Pinaceae, whereas highly specific associations with other ectomycorrhizal, arbuscular mycorrhizal, and nonmycorrhizal plants were restricted to small terminal clades of the fungal phylogeny. Conclusions The integration of ecological specificity and phylogenetic analyses suggests the possibility that Helotiales fungi established close associations with Pinaceae early in their evolutionary history and subsequently underwent host shifts to diverse angiosperm lineages. Given the emerging evidence that Helotiales fungi play pivotal ecological and physiological roles in plant root systems, these statistical insights into Helotiales-plant associations provide a fundamental basis for understanding the evolutionary history and functioning of terrestrial ecosystems.

Forest-associated Saccharomycotina occur at low relative abundance, limiting inference about their diversity and dynamics. We sampled leaf litter weekly for 47 weeks across a subtropical forest in northern Taiwan. Enrichment, isolation and ITS sequencing recovered 687 isolates, including 613 Saccharomycotina representing 56 described species and 77 putatively novel operational taxonomic units. Rarefaction indicated unsampled culturable diversity. Among litter traps, community dissimilarity was high and dominated by taxon replacement, but neither topography nor geographic distance was associated with composition, and turnover matched randomised expectations. Richness peaked during warm, wet periods and declined in winter, and minimum temperature showed the strongest statistical association. Composition was associated with maximum temperature, minimum relative humidity, precipitation and solar radiation. Selected isolates' thermal optima covaried with collection-week temperatures, and two October Magnusiomyces magnusii isolates had higher optima than four winter isolates. Together, these findings reveal substantial culturable diversity and seasonal community restructuring consistent with temperature-related filtering.

Stemflow transports water and biological material from forest canopies to the stem base, yet fungal studies of this flux have largely relied on microscopy of conidia. We used ITS2 metabarcoding to characterize fungal environmental DNA (eDNA) in stemflow from 15 trees - five each of American beech (Fagus grandifolia), sugar maple (Acer saccharum), and tulip poplar (Liriodendron tulipifera) in a closed-canopy forest in northeastern Ohio, USA. Stemflow was sampled during eight rain events in the leafless season (November 2024-May 2025), along with simulated bark and gutter washes to assess near-collar and collector signals. Natural stemflow communities were compositionally distinct from both controls and occupied greater ordination space. Ascomycota dominated across all samples, with Parafenestella, Cytospora, Microcera, Nectria, and Aureobasidium among the most abundant resolved genera and 13 of the 25 most abundant taxa differed significantly among host species. Woody-plant-associated endophytes, canker fungi, and saprobes dominated ecological guild composition. Storm event explained 28.6% of taxonomic variation, host tree species 24.1%, and their interaction 10.0%. Guild composition was more strongly structured by host species (35.4%) than storm event (20.4%). Lichenized fungi and lichen-associated fungi were detected. Thus, leafless-season stemflow integrates broad bark-associated fungal eDNA, including recurrent lichen-derived material, beyond the morphologically distinctive conidia captured by traditional methods. Stemflow eDNA therefore offers a minimally invasive means of monitoring canopy fungal diversity and the strong host and temporal filtering of DNA exported from woody surfaces.

Root-associated fungal (RAF) communities can influence tree nutrient acquisition and performance, yet their structuring factors and relationship with tree growth remain poorly understood, particularly near environmental treelines. We characterized root-associated fungal (RAF) communities on fine roots of white spruce (Picea glauca [Moench] Voss) in paired forest and treeline plots across two elevational and one moisture-limited treeline ecotones in Alaska. Using ITS2 DNA metabarcoding of fine root tips, we characterized individual RAF community alpha and beta diversity and tree growth based on basal area increment (BAI) over 5-30 years. As a result, sampling site was the strongest predictor of RAF composition, explaining 19.6% of variation, while soil pH explained an additional 11.7%. Treeline effects on RAF communities were weaker and context-dependent, with treeline trees showing distinct community composition in the Alaska Range, lower alpha diversity across all Hill numbers in Interior Alaska, and higher ECM relative abundance in the Brooks Range. RAF composition did not differ between fast- and slow-growing trees within sites. In contrast, alpha diversity was negatively associated with tree growth: OTU richness, Shannon and Inverted Simpson indices significantly predicted BAI over the previous 5, 10 and 15 years, with fast-growing trees supporting less diverse RAF and ECM communities. This relationship was strongest for recent growth and weakened with longer BAI averaging periods. Our results suggest that high growth of mature P. glauca is not necessarily associated with greater RAF or ECM diversity or specific taxa but may instead rely on fewer dominant or functionally effective fungal partners.

The obscure life histories of many kickxellalean genera remain a bottleneck for comprehensive taxon sampling and phylogenetic reconstruction of the order. While Kickxellales has long been regarded as saprobes inhabiting soil or dung, the discovery of "amphibious fungi" such as Unguispora, which exhibits dimorphic growth between the animal gut and feces, suggests a cryptic gut-dwelling stage within these genera. Given its phylogenetic proximity to Unguispora, ecophysiological traits of Linderina were investigated to evaluate its potential association with the animal gut. Two isolates of L. macrospora were obtained from Japanese soil, representing the first record of this species in Japan. Physiological assays revealed that the optimal temperature for both vegetative growth and sporulation was 25-30 {degrees}C. Furthermore, comparative growth assays on different media demonstrated that sporocladium abundance per sporangiophore is sensitive to nutrient availability, and nutrient-poor media were determined to be the most suitable for evaluating morphological characterization. Under anaerobic, nutrient-rich conditions which are known to induce yeast-like growth in Unguispora, sporangiospores of L. macrospora produce arthrospores. Although marked morphological plasticity was observed during the arthrospore formation, the occurrence of yeast-like unicellular proliferation suggests a potential relationship with the animal gut. Additionally, vegetative growth and sporulation were markedly inhibited by white light exposure; notably, a lethal effect on growth was observed during incubation at 20 {degrees}C, indicating that the natural niche of the species is restricted to light-shielded environments. Our findings will help to elucidate the cryptic life cycles and evolutionary trajectories within Kickxellales.

BACKGROUNDBlackleg, caused by Leptosphaeria maculans, is a major disease limiting oilseed rape production worldwide, and its management increasingly requires sustainable alternatives to chemical fungicides. In this study, we evaluated the antagonistic activity and plant growth-promoting potential of three endophytic bacteria, Bacillus velezensis Bro5, Bacillus subtilis Bro11, and Pantoea agglomerans Bru13, against a geographically diverse collection of 139 L. maculans isolates from five oilseed rape-producing regions of Argentina. RESULTSDual culture assays revealed strong inhibitory activity by Bro5 and Bro11, with mean inhibition rates of [~]80% across isolates, while Bru13 showed variable inhibition (<75% for most isolates). Greenhouse and growth chamber assays confirmed the protective potential of these strains. At the cotyledon stage, Bro11 and Bro5 reduced lesion size by 47% and 28%, respectively, while their combination achieved a 51% reduction. In greenhouse trials, combined application of Bro5 and Bro11 reduced stem base necrosis by 45% and increased the proportion of plants with [&le;]50% damage to 98%, compared to only 70% in controls. Key disease metrics, including disease index, incidence, and severity, decreased by 60%, 23%, and 26%, respectively. Beyond pathogen suppression, inoculation with the Bro5-Bro11 consortium enhanced plant growth, increasing shoot biomass by 89% at early stages, and improving stem dry weight and diameter by 10% and 35%, respectively, at maturity. CONCLUSIONThese findings highlight the robustness of Bacillus endophytes as biocontrol agents, their capacity to suppress diverse pathogen isolates, and their dual role in plant growth promotion, supporting their potential integration into sustainable blackleg management programs.

Cutaneotrichosporon dermatis (formerly Trichosporon dermatis) is a basidiomycetous yeast-like fungus known to cause summer-type hypersensitivity pneumonitis, although its virulence in humans remains poorly understood. We performed morphological and molecular identification of an isolate from the sputum and blood cultures of an immunocompromised patient, together with pathogenicity assessment using a Galleria mellonella model, biofilm formation/eradication assays, antifungal susceptibility testing, drug combination effects, and the post-antifungal effect (PAFE), compared with Trichosporon asahii. The isolate was identified as C. dermatis by ITS/IGS1 sequencing, supported by phylogenetic analysis. Growth of C. dermatis increased more at 37 than at 25. In the Galleria mellonella assay, C. dermatis, T. asahii, and Candida albicans each showed dose-dependent pathogenicity at sufficiently high inocula, although Rhizopus oryzae was the most potent pathogen on a per-CFU basis. C. dermatis formed biofilms that were more completely inhibited by terbinafine (TRB) and amphotericin B (AmB) than azole agents, which showed only partial inhibitory activity even at high concentrations. Susceptibility testing showed relatively strong susceptibility to AmB and azole agents. In the TRB and azole combination assay, the fractional inhibitory concentration index (FICI) was below 0.5, indicating synergy. Isavuconazole (ISC) showed a markedly stronger PAFE than the other azole agents tested. These findings indicate that although azoles show only partial efficacy against its biofilm, C. dermatis can still cause invasive infection, and that azole monotherapy or TRB and azole combination therapy, aided by the potent PAFE of ISC, may represent effective treatment options.

Pseudogymnoascus destructans is a psychrophilic ascomycete fungus that causes White-Nose Syndrome in North American hibernating bats. P. destructans invades the tissue present in bats' noses and wing membranes, causing the characteristic white nose and cupping erosion in the wings. P. destructans exhibits characteristics of a hemibiotrophic fungal pathogen, in which P. destructans can invade the host cells without inducing damage. During this stage, P. destructans hyphae assume a morphology similar to fungal plant pathogens during the biotrophic stage of infection. However, the mechanism by which P. destructans regulates its morphology and virulence is not fully understood. The phosphatase calcineurin is a key regulator of fungal stress response and virulence and could play a role in P. destructans virulence. Calcineurin can be inhibited using FK506 or Cyclosporin A (CSA). FK506 interacts with FKBP12, while CSA interacts with Cyclosporin A, and the protein-drug complex then inhibits calcineurin activity. Here, we show that P. destructans is intrinsically resistant to one calcineurin inhibitor (FK506), possibly because P. destructans FKBP12 has a lysine instead of the conserved arginine at position 89, which has been shown to reduce the affinity of the FKBP12-FK506 complex for calcineurin. Using cyclosporin A, we found that calcineurin is important for fungal growth. Additionally, calcineurin inhibition increases voriconazole inhibition. In contrast, calcineurin inhibition was antagonistic to the anti-cell wall drug micafungin. Taken together, calcineurin's role in fungal growth and response to voriconazole is conserved in P. destructans but may play a unique role in P. destructans response to micafungin.

Colletotrichum graminicola causes significant losses of the staple crop maize worldwide. The fungus produces two distinct asexual spore types, oval and falcate conidia, which show unique processes in development and plant interaction. Based on genome resequencing of our laboratory strain (CgM2/ M1.001), we investigated the gene expression profiles of oval and falcate conidia during development and early leaf infection using RNA-seq. Our results reveal specific gene expression profiles between the two spore types, indicating fundamental differences in their developmental programs that reflect different modes of infection. We identified expression patterns discriminating both conidia types from mycelium and spore type-specific ones for genes encoding transcription factors, conserved fungal developmental genes, transporters, genes of secondary metabolite clusters, and pathogenicity-related functions, including effectors and carbohydrate-active enzymes (CAZymes). Our study shows that despite the identical genomic basis, oval and falcate conidia show unique transcriptomes across vegetative development and early plant interaction. Taking together, these results provide new insights into the molecular mechanisms determining the biology of C. graminicola and its interaction with the plant host.

Many insects rely on symbiotic fungi to occupy specialized ecological niches, yet the evolutionary dynamics of these partnerships remain poorly resolved for most lineages. The beetle family Ptinidae, split into the morphologically distinct Spider beetles and Deathwatch beetles, has long been known to harbor fungal endosymbionts based on early microscopy, but few associations have been confirmed with molecular methods. Here, we combined ultra-conserved element (UCE) phylogenomics with ITS amplicon sequencing to test whether fungal endosymbionts are conserved across Ptinidae and whether they have cospeciated with their hosts. Our UCE phylogeny supports Spider beetles and Deathwatch beetles as monophyletic clades but indicates that some aspects of subfamily-level taxonomy may merit closer examination. Screening for three known symbiotic fungal genera (Symbiotaphrina, Meyerozyma, Nakazawaea) revealed Symbiotaphrina in most Deathwatch beetles but no Spider beetles, while the other two genera were present but uncommon. Despite widespread Symbiotaphrina infection, we found no phylogenetic mirroring between host and symbiont trees, indicating an absence of codiversification. Instead, distantly related hosts frequently shared closely related symbionts, consistent with diffuse, mixed-mode transmission involving both vertical and horizontal symbiont exchange. This pattern parallels those documented in fungus-farming termites, ambrosia beetles, ants, and woodwasps, suggesting that diffuse, mixed-mode symbiosis may be a general hallmark of long-term insect-fungal associations. We further identify an unidentified Helotiales group as a candidate novel endosymbiont, recovered consistently within a clade comprising Anobium, Hemicoelus, and Ptilinus. Together, these findings reframe Deathwatch beetle-fungal associations as a dynamic, evolutionarily labile symbiosis rather than a fixed partnership.

Fire-dependent or fire-influenced ecosystems harbor species with diverse response strategies, such as smoke-stimulated germination and dormancy release through heat shocks. Although these cues influence germination in many fire-prone ecosystems, their effects on seeds of woody species from tropical dry forests (TDFs) remain poorly understood. We evaluated the germination response of twelve TDF woody species to three heat-shock temperatures (80, 120, and 160C), two exposure times (3 and 5 min), and two smoke conditions (with and without smoke water), plus dry and wet controls. We also assessed the relationship between germination and functional seed traits, including permeability, seed-coat thickness, mass, and shape index. Of the eleven species that germinated, four showed broad tolerance, with no significant reduction in germination even at 160C for 5 min, which was associated with lower permeability, thicker seed coats, and greater mass. Four other species showed restricted tolerance to heat, with significant declines in germination at higher temperatures or longer exposure times, and were associated with higher permeability, thinner seed coats, and lower seed mass. The remaining three species showed heat-stimulated germination between 80 and 120C and tended to have lower shape-index values. Smoke treatments significantly increased germination in three species, Ceiba pentandra, Guazuma ulmifolia, and Samanea saman. In the remaining species, significant differences were either absent or attributable to moisture or imbibition effects rather than to smoke itself. Overall, germination responses to heat were associated with variation in functional seed traits, whereas responses to smoke were less widespread and showed a less consistent functional pattern.

Aims In forest ecosystems, tree species composition and diversity are fundamental drivers of biodiversity and many species are closely associated to specific tree species as hosts. Saproxylic diversity across tree species may be shaped by interactions between ecological and environmental factors, such as resource availability. However, a throughout and unbiased quantification of diversity across tree species is missing. We investigated patterns an drivers of saproxylic beetle diversity across European tree genera while accounting for differences in sampling effort. Location Europe Methods We used a large dataset, of 25 studies, comprising 500,000 deadwood-dependent beetles, representing 1041 saproxylic beetle species, sampled from 29 tree genera. We accounted for sampling effort by estimating diversity using coverage-based standardization across Hill numbers. We than used linear models to identify drivers of saproxylic beetle diversity across tree genera and assessed differences in community composition using Nonmetric Multidimensional Scaling (NMDS). Additionally, the most abundant beetle families were identified for a subset of 14 genera. Results Quercus supported the highest richness of infrequent, frequent, and highly frequent species, while Fagus exhibited the highest observed (unstandardized) species richness. Beetle communities were less differentiated when focusing on infrequent species, whereas tree genera were separated when focusing on frequent and highly frequent species. In addition, we found that resource availability and maximum tree height best predicted infrequent beetle diversity, whereas resource availability was the main driver of frequent species. In contrast, the same analyses for unstandardized data indicated postglacial occurrence as an important factor for infrequent species. Main conclusions Although resource availability supported the species area hypothesis, standardized data revealed higher richness on smaller trees, partly contradicting this pattern. Our results highlight the importance of accounting for sampling bias and promoting tree diversity, particularly oaks, to sustain saproxylic beetle diversity.

Deadwood is a common ephemeral resource in boreal forests, but arthropod succession across the full decay gradient and transition into soil remains poorly understood. We analyzed the successional trajectory of arthropods in deadwood to soil. Further, we investigated whether the succession pattern differed in previously clear-cut and near-natural forests in southeastern Norway. This was done by DNA metabarcoding analyses of arthropod communities in collected deadwood and soil samples. We detected 741 arthropod OTUs, with 565 OTUs in deadwood and 291 in organic soil layers, of which 115 were found in both deadwood and organic soil layers. Arthropod richness increased with deadwood decay stage and organic soil layers supported higher richness than all deadwood decay stages. Community composition of arthropods changed significantly along the decay gradient, with late-decay stages sharing more OTUs with organic soil layers than with earlier decay stages. This suggests a gradual transition between communities in highly decayed deadwood and organic soil layers. Forest type (previously clear-cut vs. near-natural forest) had limited effects on overall richness and community composition, although previously clear-cut and near-natural forests supported partially distinct species pools and differed in co-occurrence patterns in late decay and organic soil layers. Our results show that arthropod communities are strongly structured along the decay gradient from freshly dead wood to organic soil layers. This highlights the importance of retaining deadwood across different decay stages for maintaining arthropod diversity and community convergence between deadwood and soil in boreal forests.

Diverse ecological communities can reduce pathogen transmission; a phenomenon known as the dilution effect of biodiversity. This effect, in turn, depends on variation in host species' ability to spread disease (i.e., host competence) and which host species persist under biodiversity loss. Mutualistic symbionts can influence host competence and are sensitive to variation in host biodiversity; yet whether mutualists can modify dilution effects is unknown, partially because quantifying host competence during epidemics remains challenging. We experimentally tested whether mutualists could modify dilution effects by establishing gradients of host species richness, community competence, and access to the below-ground arbuscular mycorrhizal fungus (AMF), Rhizoglomus irregulare. Plant hosts were then exposed to the fungal root pathogen, Rhizoctonia solani, and disease spread was monitored over the course of an epidemic. Overall, host richness did not affect epidemic outcomes. Instead, AMF inoculation increased disease risk via species-specific increases in host competence. Moreover, communities containing highly competent host species experienced more disease, but only in the presence of mutualistic AMF. These results underscore the importance of plant community composition in mycorrhiza-mediated disease dynamics and suggest that predicting disease in our changing world might require a deeper understanding of host-symbiont and pathogen-symbiont interactions under global change.

Candida auris (currently Candidozyma auris) is an emerging fungal pathogen responsible for dramatic global increase in invasive candidiasis with high mortality. Most concerning, C. auris has a high propensity to colonize patients and persist and develop multidrug resistance to main classes of antifungals. In this study, we investigated the genetic and phenotypic diversity and resistance mechanisms of C. auris clinical isolates recovered from hospitalized infected patients. A total of 53 isolates from 38 unique patients were recovered from various clinical sources and evaluated for susceptibility to routine antifungal drugs. Whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) analysis were performed to generate a phylogenetic network to infer population structure and identify mutations associated with drug resistance development. Isolates were also phenotypically evaluated for ability to form biofilms and aggregate, and cell wall adhesins gene expression studies were performed to provide mechanistic insights into C. auris phenotypic plasticity. Except for one clade III isolate, all isolates belonged to clade I and all were resistant to fluconazole with incidence of resistance to amphotericin B, echinocandins or both. Non-synonymous SNPs were found in genes associated with antifungal resistance including ERG11, TAC1B, CDR1 and FKS1. Phenotypically, isolates varied in their ability to form biofilm and aggregate which correlated with expression of the Scf1 and Als4112 cell wall adhesins genes highlighting C. auris phenotypic plasticity in circulating clinical strains. These findings underscore the growing clinical threat posed by C. auris and reinforce the need for optimized surveillance and treatment strategies for controlling its spread.

Basidiomycete fungi are an underexplored source of specialized metabolites with significant biotechnological potential. However, the environmental cues that activate their biosynthetic pathways remain poorly understood. Here, we investigated the response of the wood-decaying fungus Fomitopsis betulina, to nutritional competition using co-cultures with Escherichia coli. On solid medium, F. betulina inhibited the bacterial growth. Using a mass spectrometry-based metabolomics approach, we identified a Sumikis acid derivative, calcium diformate, and sulfuric acid among the compounds enriched within the inhibition zone and hypothesized that these compounds were associated with the acidification of the medium. Although F. betulina has previously been reported to produce the antibacterial compound piptamine, neither piptamine nor related derivatives were detected under our experimental conditions. In liquid medium, the co-culture with E. coli caused the rapid depletion of the available glucose, resulting in the establishment of carbon-starvation conditions and a 44% reduction in fungal biomass. Transcriptomic analyses revealed extensive metabolic reprogramming in response to bacterial competition, including the induction of genes involved in carbon acquisition, nutrient transport, redox homeostasis, and stress adaptation. Notably, a homolog of the Velvet regulatory complex, a central regulator of fungal development and specialized metabolism, was upregulated. The co-culture induced the expression of genes associated with multiple biosynthetic gene clusters, including terpene, polyketide, and fungal RiPP. Taken together, our results demonstrate that bacterial competition acts as a potent trigger of nutritional stress and secondary metabolism in F. betulina. More broadly, fungal-bacterial co-culture represents a promising alternative to extractions to identify high-value added metabolites pathways from basidiomycetes.

Deadwood is a fundamental component of forest ecosystem, supporting biodiversity and driving multiple ecological processes. However, structures that may develop on downed coarse woody debris (CWD) create additional microhabitats that are used by numerous organisms and contribute to small-scale habitat heterogeneity. To date, quality of CWD is commonly characterized by its volume, diameter, tree species or stage of decomposition, while fine-scale structures occurring there remain not surveyed and their role in ecosystem is rarely quantified. Here, we introduce the novel concept of microhabitats on CWD. i.e. Deadwood-related Microhabitats (DreMs), defined as distinct features occurring on CWD that may provide shelter, breeding or foraging sites for forest-dwelling organisms. Using an original catalogue comprising 14 groups and 30 types, we inventoried DreMs on 6,003 CWD across 423 study plots located in best-preserved old-growth forests in Poland. We quantified the frequency and richness of DreMs and assessed the link between CWD characteristics and DreM richness in spruce, beech, willow-poplar, fir-beech and oak-lime- hornbeam forests. All inventoried DreMs occurred on both deciduous and coniferous taxa. The most frequent DreM included bryophyte mats, loose bark patches, insect galleries, fungal fruiting bodies and polypores. DreM richness increased with CWD diameter, more complex architecture and the presence of multiple decay classes within single debris. DreM richness peaked at intermediate decay classes and was higher on deciduous than on coniferous taxa. Our study is the first large-scale qualitative and quantitative assessment of DreMs in temperate forests. By focusing on forests characterized by ecological continuity and minimal human-related disturbance, the results provide a reference for downed deadwood-associated structures. By complementing inventory of tree-related microhabitats, DreMs extend potential monitoring schemes of habitat quality and contribute to biodiversity-oriented forest management. Highlights* Downed coarse woody debris (CWD) hosts Deadwood-related microhabitats (DreMs) * Higher DreM richness is associated with CWD diameter * DreM richness peak at intermediate stages of wood decay * CWD of deciduous taxa support more DreMs than coniferous * Diversified CWD and DreMs increase habitat heterogeneity for forest-dwelling taxa