Search Results (438)

Digital phenotyping is increasingly recognized as an essential tool for the quantitative analysis of fungal morphology, particularly in controlled indoor cultivation systems where large numbers of fruiting bodies must be assessed consistently and non-destructively. While YOLOv8-based deep learning approaches have previously been applied in phenotypic analyses of edible mushrooms, the applicability of newer YOLO architectures to fungal phenotyping remains largely unexplored. In this study, we present a controlled-environment digital phenotyping framework for indoor mushroom cultivation and conduct a systematic benchmarking evaluation of YOLOv11 for phenotypic segmentation in comparison with YOLOv8. Using bottle-cultivated Pleurotus ostreatus and Flammulina velutipes as representative edible basidiomycetes, we performed a controlled comparison of YOLOv8-seg and YOLOv11-seg using identical datasets, preprocessing pipelines, and hyperparameter configurations. The results demonstrate that YOLOv11 achieves segmentation performance comparable to that of YOLOv8 across all evaluated metrics (ΔmAP_50–95 < 0.01) while substantially reducing computational complexity, including fewer trainable parameters, lower FLOPs, and decreased gradient load. Validation against caliper-based physical measurements revealed moderate, trait-dependent agreement, whereas inter-model consistency between YOLOv8 and YOLOv11 remained consistently high across diverse morphological and segmentation scenarios. These findings suggest that recent developments in object detection architectures can improve computational efficiency without compromising phenotypic measurement fidelity. More broadly, this study highlights the importance of periodically evaluating emerging detection architectures within biological phenotyping pipelines to ensure scalable, sustainable, and high-throughput fungal phenotyping under controlled-environment cultivation systems. Full article

Antimicrobial metabolite production in basidiomycetes varies by strain and growing conditions. This study compared the antimicrobial activity of extracts from nine fungal strains at both their vegetative and reproductive stages. Wild-growing fungal fruiting bodies were collected and identified through both morphological characterization and molecular sequencing. Extracts from fruiting bodies, mycelia, and culture liquids were tested using the agar well diffusion method and by determining the minimum inhibitory concentration (MIC). Analysis revealed that the highest antimicrobial activity was associated with culture liquid extracts. Antimicrobial properties were detected in the submerged mycelium extracts of only two strains: Stereum hirsutum 1 and Flammulina rossica 16. For fruiting bodies, activity was restricted to extracts of strains from the genus Fomitopsis. The strain S. hirsutum 1 was determined to be the most effective producer of antibacterial compounds. The highest activity was exhibited by the S. hirsutum 1 culture liquid extract, with an MIC of 320 µg/mL against clinical Gram-positive strains (Staphylococcus aureus, S. epidermidis, S. haemolyticus, vancomycin-resistant Enterococcus faecium) and Gram-negative Proteus vulgaris. The studied strains demonstrated higher production of antimicrobial metabolites during vegetative growth, with the active compounds being primarily extracellular. Submerged cultivation of basidiomycetes offers an efficient method for obtaining antimicrobial metabolites, permitting their subsequent isolation, physicochemical characterization, and biomedical evaluation. Full article

This study investigated the secondary fermentation of cocoa beans using mushrooms to further improve the quality of beans. Cocoa beans were fermented using 42 species of basidiomycetes and ascomycetes. Mycelial growth was observed in 29 strains. When 75% cocoa chocolate was prepared using the cocoa beans in which mycelial growth was observed, theobromine concentration was higher in 17 strains compared with the control. Furthermore, caffeine concentration was similar to or lower than the control in all strains. Chocolate produced using cocoa beans fermented with particularly Polyporus arcularius, Peziza vesiculosa, and Urnula craterium exhibited significantly higher theobromine concentrations. Compared to the control theobromine concentration of 7.53 mg/g, P. arcularius showed 9.25 mg/g, 9.13 mg/g for P. vesiculosa, and 9.05 mg/g for U. craterium. Furthermore, the reducing sugar concentration and total polyphenol concentration increased, and the antioxidant activity was similar to or higher than that of the control. These results suggest that secondary fermentation using mushrooms could be used to develop chocolate characterized by high theobromine, low caffeine, and rich polyphenol content. Full article

Fungal fairy rings (FFRs) are circular patterns primarily formed by basidiomycete fungi. These structures significantly influence grassland ecosystems by mediating nutrient cycling, altering soil microbial communities, and driving shifts in plant community composition. The present study investigates FFR formed by Agaricus xanthodermus in a Pannonian sandy grassland, with a focus on vegetation structure, productivity, and diversity. Field surveys conducted along transects across FFR quantified plant species cover, height, and additional ecological parameters. The findings demonstrate that FFR alters species dominance, reduces diversity at the ring edge, and based on ecological indicator values of plant species it increases soil nitrogen, and modify the movement of water and nutrients within the soil. Collectively, these results suggest that FFRs function as ecosystem engineers, shaping ecological processes and affecting the agricultural potential of semi-natural grasslands. Full article

Woody tissue diseases of avocado (Persea americana Mill. var. Hass) pose a major phytosanitary threat due to their chronic progression, late symptom expression, and severe impact on tree stability and productivity. Although white rot has traditionally been attributed to saprobic basidiomycetes, increasing evidence suggests corticioid fungi may act as facultative pathogens in agricultural systems. This study examined corticioid basidiomycetes associated with white rot in stems and branches of avocado in Michoacán, Mexico. Field surveys revealed consistent symptoms of structural weakening, branch dieback, and wood decay. Fungal isolates obtained from symptomatic tissues and sporomes were characterized morphologically and identified through ITS-based phylogenetic analyses. Representative isolates of Grammothele spp. and Dentocorticium portoricense were evaluated in pathogenicity assays under controlled conditions. All isolates reproduced field symptoms, confirming pathogenicity, though aggressiveness varied. D. portoricense exhibited the highest incidence, severity, and AUDPC values, indicating greater virulence, while Grammothele isolates showed slower, moderate progression. Phylogenetic analyses provided robust support for D. portoricense, whereas Grammothele was resolved at genus level. Integration of field, pathogenicity, and molecular data demonstrates corticioid fungi are not merely secondary saprotrophs but relevant pathogens in avocado white rot. These findings highlight the need to include corticioid fungi in diagnostic, monitoring, and management strategies for trunk and branch diseases. Full article

Amylocorticiales forms a well-supported clade within Agaricomycetes, Basidiomycota, and most of the species have resupinate basidiomes and cause brown rot on wood. It is one of the smallest orders of the basidiomycetes, with the species diversity and phylogeny being understudied. In the present study, we conduct phylogenetic analyses based on the concatenated ITS + nLSU sequence dataset of the order with an emphasis on the samples from southern China. As a result, ten new lineages were found. Combined with the morphological evidence, two new genera and six new species are described and illustrated, and four new combinations are proposed. Amylophanerochaete hainanense gen. et sp. nov. is closely related to Serpulomyces but differs in having smooth hymenophores with rhizomorphs and narrowly cylindrical to slightly sigmoid amyloid basidiospores. The new genus Pseudoathelia is proposed to accommodate Leptosporomyces linzhiense and Athelia septentrionalis, two athelioid species. Four new species, viz. Amylocorticium athelioides, A. bisporum, A. guangxiense, and A. luteolum, collected from southern China, formed distinct lineages within the Amylocorticium clade. Serpulomyces borealis, the only species of the genus, is proven to be a species complex, while one new species, S. subborealis, and two new combinations, S. rhizomorphus and S. yunnanensis, transferred from Ceraceomyces, are found in the lineage. An identification key to all the known genera is provided. Full article

The present study explores the treatment and valorization of carbon-rich, low-cost waste streams—sugar beet molasses, expired rice, and wheat cereal hydrolysates—as substrates for submerged shake-flask cultures of edible ascomycetes (Morchella elata AMRL 63, Tuber aestivum AMRL 364) and basidiomycetes (Lentinula edodes AMRL 126, Agaricus bisporus AMRL 209) within a circular bioeconomy framework. Cultures were conducted under different C/N ratios (20 and 50) with or without the addition of olive oil or its emulsion. Among the tested species, the ascomycetes M. elata AMRL 63 and T. aestivum AMRL 364 outperformed the basidiomycetes in biomass production and substrate utilization. Supplementation with olive oil or its emulsion enhanced mycelial growth and lipid accumulation, while a higher C/N ratio (50) favored exopolysaccharide (EPS) synthesis. Lipid profiles were dominated by oleic (Δ⁹C18:1) and linoleic (Δ^9,12C18:2) acids, with greater unsaturation observed in C/N = 20 cultures. Volatile analysis revealed species-specific aroma signatures, including characteristic truffle and morel compounds. The results underscore the feasibility of using waste streams for sustainable mushroom cultivation. Full article

The Amazon Forest harbors one of the largest fungal diversities on the planet, occupying a wide variety of ecological niches comprising terra firme (non-flooded forest), várzea (white-water floodplains), and igapó (black-water floodplains). In this review article, we examine Amazonian fungal diversity based on three complementary approaches—culture-based surveys, in situ inventories of macrofungi, and environmental DNA/metagenomic analyses—discussing advances, limitations, and contributions to regional mycological knowledge. Subsequently, we present a critical synthesis of the potential of Amazonian basidiomycetes regarding the production of metabolites with antimicrobial activity, highlighting the main genera reported in the literature, the chemical classes involved (e.g., terpenes, steroids, quinones, and bioactive peptides), and the metabolic pathways responsible for their biosynthesis. The integration between biodiversity and bioprospecting underscores the importance of Amazonian fungi both for understanding ecological processes and for the development of new solutions to the antimicrobial resistance challenge. This work seeks to fill current gaps in the academic literature and to contribute to future strategies for the conservation and sustainable use of regional mycobiota. Full article

Basidiomycete mushrooms contain complex β-D-glucans which act as immunomodulator, immune stimulants and anti-cancer agents, which can be either free or bound to proteins. The present report consists of a novel and intrinsic synchronous fluorescence and phosphorescence assay method for β-D-glucans. This analytical technique was carried out by a spectrofluorometer in the range of 250 to 750 nm with a Δλ range of 5–30 nm which exhibited peaks at 492, 540 and 550 nm by using β-D-glucan from Euglena gracilis as a standard. A micro and high-throughput method based on a microplate fluorescence reader was devised with a excitation and emissions λ of 420 nm and 528 nm, respectively. This assay method revealed some advantages over the reported colorimetric methods, since it is a non-destructive assay method of β-D-glucans in samples with a linearity range of 0–14 μg/well, correlation coefficient (r2) of 0.9961, LOD of 0.973 μg/well, LOQ of 2.919 μg/well, greater sensitivity, fast, a high-throughput method and very economical. β-D-glucans of several mushrooms (i.e., Poria coccus, Auricularia auricula, Ganoderma lucidium, Pleurotus ostreatus, Cordyceps sinensis, Agaricus blazei, Polyporus umbellatus, Inonotus obliquee) were purified by using a sequence of various solvent extractions, quantified by either spectrofluorometer or fluorescence microtiter plate reader assay and compared with Congo red assay method. Three-dimensional spectra measurements were carried out on β-D-glucans from commercial sources and medicinal mushroom strains. FTIR spectroscopy was selected to investigate the structural properties of β-D-glucans in these mushroom samples. Therefore, the present assay method is simple, fast, cheap and non-destructive for β-D-glucans from medicinal mushrooms as well as from commercial sources. Full article

Shanxi Province, located in northern China, characterized by a warm-temperate monsoon climate, complex mountainous topography, and vegetation dominated by trees of Fagaceae and Pinaceae, provides diverse habitats for Russula diversity. Recent investigations on macrofungi in this region revealed nine new Russula species based on integrated morphological and multi-locus phylogenetic analyses (ITS, nrLSU, rpb2, tef1), which are described and illustrated in this paper. These new taxa are classified into three subgenera of Russula: one species of subgen. Brevipes, four of subgen. Heterophyllidia, four of subgen. Russula. This work enhances the understanding of Russula resources in China’s temperate zone. Full article

Mitochondrial genomes play a central role in fungal physiology and adaptation, yet their evolutionary dynamics during domestication remain poorly understood. Here, we performed a comparative mitogenomic and gene-expression analysis of three Pleurotus ostreatus dikaryotic strains differing in origin and degree of adaptation to laboratory conditions: the long-term commercial strain dkN001, the laboratory-maintained wild isolate dkF515, and the recently collected wild strain dkN009. High-throughput Illumina sequencing enabled complete assembly of circular mitochondrial genomes, revealing substantial size variation among strains, where the dkN001 strain exhibited the second smallest mitogenome reported for the genus Pleurotus. Comparative analyses showed >99% sequence identity between wild isolates and ~95% identity relative to the commercial strain. Variations in genome size among strains were associated with intron dynamics in the cox1 and rnl genes, as well as intron loss predominantly in the commercial strain dkN001, consistent with mitochondrial genome streamlining during domestication. Expression profiling of mitochondrial protein-coding genes (PCGs) under multiple culture conditions revealed conserved transcriptional responses in dkN001 and dkF515 that contrasted sharply with those of dkN009. The differences observed, which affected components of the electron transport chain, suggested shifts in energy metabolism associated with long-term laboratory maintenance. Therefore, our results demonstrate that domestication in P. ostreatus involves both structural remodelling of the mitogenome and changes in regulation of mitochondrial PCGs, highlighting the importance of mitonuclear interactions in fungal adaptation to controlled environments. Full article

A huge amount of waste is produced annually by the food processing industry which must be valorized into high-value products. Therefore, the aim of this work involves the use of such wastes for production of β-glucans from medicinal basidiomycete strains which are powerful biological response modifiers in several clinical disorders. The production of β-glucans from basidiomycete strains in submerged fermentation was monitored by using monoclonal antibodies of the IgG and IgM classes as well as by Congo red assay in the presence of several agro-industrial waste products such as milk permeate, waste coffee grounds, orange peels and rice husks. Subsequently, these β-glucans were purified by using gel filtration and ion-exchange chromatography. FTIR analysis of several β-glucans was carried out to investigate their structural properties. The adsorption of β-glucans on microtiter plates was dependent on the temperature as well as on the time period of immobilization for ELISA. These mAbs can be used in a competitive ELISA for detection and quantification of β-glucans from basidiomycete mushrooms. Full article

Cyclocybe chaxingu is a well-known edible fungus in China, in which pileus size and color are key traits determining its commercial value. However, the molecular genetic mechanisms underlying the morphological development of its pileus remains limited at present. To address this, our study first completed the high-quality genome assembly of the monokaryotic strain Ag.c0002-1 of albino C. chaxingu, anchoring it to 13 chromosomes via Hi-C technology. The final genome size was 51.7 Mb with a GC content of 51.06%, and 11,332 protein-coding genes were annotated. Phenotypic observations and comparative transcriptome analyses were then conducted on the pilei of the brown cultivar Ag.c0067 and the white cultivar Ag.c0002 at the primordium, elongation, and mature stages. Phenotypic analysis revealed continuous pileus expansion accompanied by progressive color lightening in both cultivars during development. Comparative transcriptomic analyses revealed significant differences in gene expression patterns between the two cultivars across developmental stages. KEGG enrichment analysis indicated that pileus expansion is closely associated with pathways related to DNA replication, cell cycle of yeast, carbon metabolism, and carbohydrate digestion and absorption. Among these, differentially expressed genes involved in cell division tended to be downregulated, whereas genes associated with energy metabolism and substance transport were upregulated, providing the necessary energy and material support for pileus growth. Changes in pileus pigmentation were primarily associated with tyrosine metabolism, betalain biosynthesis, tryptophan metabolism, and melanogenesis pathways. Notably, the downregulation of tyrosinase genes and the upregulation of glutathione S-transferase genes during development may represent major molecular mechanisms underlying pileus color lightening. Overall, this study provides important insights into the molecular mechanisms regulating pileus development and pigmentation in C. chaxingu, while also offering valuable theoretical support for genetic analysis of basidiomycete morphogenesis and the molecular breeding of edible mushrooms. Full article

One of the global challenges is the deficit of food. Food production is highly dependent on the productivity of agricultural plants used by humans and livestock. Various chemical and natural compounds are used to stimulate plant growth and increase their resistance to stress. The aim of our study was to analyze the chemical composition of extracts of the most common Ural tinder fungi and their effect on the early stages of wheat growth. Water–alcohol extracts from five wood-destroying fungi contained biologically active compounds (BACs), such as phenolics, free amino acids and reducing sugars. F. pinicola was characterized by the smallest amount of extracted substances. F. fomentarius has the largest amount of phenolic compounds and sugars, and I. obliquus had the highest concentration of free amino acids. Qualitative analysis revealed alkaloids in P. betulinus, and anthraquinones in F. fomentarius. Saponins were found in all tested species, except F. fomentarius. The extracts stimulated the early stages of wheat development at concentrations of 1.0–0.2 g of fungal biomass per liter. Seed germination rate was comparable to the control samples or exceeded it, and the length of roots and shoots increased. Thus, extracts from fruiting bodies of studied fungi can be recommended for priming wheat seeds, and for biotechnological cultivation. Full article

The recently described genus Candolleomyces (Basidiomycota, Agaricales, Psathyrellaceae) is now recognized as a distinct taxonomic group separate from Psathyrella. Currently, no fully assembled and accurately annotated genomes of Candolleomyces species are available, limiting our understanding of their physiological traits and biotechnological potential. Numerous tools exist for fungal genome assembly and annotation, each using different algorithms, resulting in substantial variation in gene content and distribution within the same genome. In this work, a hybrid assembly and annotation of the genome of strain CMU-8613 were performed using pipelines that combine different assembly and annotation tools. Phylogenetic analysis showed that the analyzed strain CMU-8613 belongs to Candolleomyces candolleanus. The assembled genome size ranged from 46.8 Mb (NECAT + Racon) to 59.3 Mb (Canu + Coprinellus micaceus genome assembly), depending on the assembly and polishing strategy. The analysis identified 15–25 secondary metabolite gene clusters (BGCs), depending on the genome assembly and the tools used for BGC prediction. In strain CMU-8613, CAZyme-encoding genes varied across assemblies: 494 genes were detected in the Flye assembly and 453 in NECAT; in both cases, the AA (Auxiliary Activities) and GH (Glycoside Hydrolases) families were the most represented. The diversity of CAZymes observed among Candolleomyces species suggests differences in their saprophytic capacities. Analysis of the MAT-A/MAT-B loci revealed that C. candolleanus possesses a tetrapolar mating system. This study provides the first annotated genome of C. candolleanus, highlighting its enzymatic potential to degrade plant biomass and its capacity to synthesize diverse secondary metabolites. The combination of assembly and annotation tools employed here offers robust alternative strategies for characterizing non-model fungi or species lacking high-quality reference genomes. Full article