Exploring the Species Diversity of Edible Mushrooms in Yunnan, Southwestern China, by DNA Barcoding

Blusher mushroom (Amanita rubescens Pers.): A Study of Mercury Content in Substrate and Mushroom Samples from Slovakia with Respect to Locality and Developmental Stages

The edible mushroom Amanita rubescens Pers., regularly collected and consumed in Slovakia, was assessed for health risk due to the mercury content in its fruiting body parts. For this purpose, 364 both from the soil/substrate and mushroom samples from 40 localities in Slovakia were evaluated. At the same time, 21 samples of 7 developmental stages of the fruiting body of A. rubescens were taken in the Žakýlske pleso locality. The total mercury content in the soil and mushroom samples was determined using an AMA-254 analyzer. The contamination factor (Cf) and index of geoaccumulation (Igeo) were used to detect the level of soil pollution by mercury. The ability of A. rubescens to accumulate mercury from the soil environment was evaluated using the bioconcentration factor (BCF), and the distribution of mercury in the mushroom body was evaluated using the translocation quotient (Qc/s). To determine the health risks resulting from mushroom consumption, the percentages of provisional tolerable weekly intake (%PTWI) and target hazard quotient (THQ) were used. The obtained results have confirmed serious content of mercury soil pollution, especially in former mining areas, where the situation is alarming from a health risk point of view. Consumption of A. rubescens was found to be risky, not only in former mining areas, but higher values of mercury were also detected in other parts of Slovakia. Evaluation of the developmental stages of the fruiting body of A. rubescens showed that the highest bioconcentration factor was determined at developmental stage no. VI for caps with a value of 2.47 mg kg-1 and developmental stage VII for stipes with a value of 1.65 mg kg-1 DW.

Complete mitochondrial genomes of edible mushrooms: features, evolution, and phylogeny

Edible mushrooms are an important food source with high nutritional and medicinal value. They are a useful source for studying phylogenetic evolution and species divergence. The exploration of the evolutionary relationships among these species conventionally involves analyzing sequence variations within their complete mitochondrial genomes, which range from 31,854 bp (Cordyceps militaris) to 197,486 bp (Grifolia frondosa). The study of the complete mitochondrial genomes of edible mushrooms has emerged as a critical field of research, providing important insights into fungal genetic makeup, evolution, and phylogenetic relationships. This review explores the mitochondrial genome structures of various edible mushroom species, highlighting their unique features and evolutionary adaptations. By analyzing these genomes, robust phylogenetic frameworks are constructed to elucidate mushrooms lineage relationships. Furthermore, the exploration of different variations of mitochondrial DNA presents novel opportunities for enhancing mushroom cultivation biotechnology and medicinal applications. The mitochondrial genomic features are essential for improving agricultural practices and ensuring food security through improved crop productivity, disease resistance, and nutritional qualities. The current knowledge about the mitochondrial genomes of edible mushrooms is summarized in this review, emphasising their significance in both scientific research and practical applications in bioinformatics and medicine.

Rapid and Accurate Authentication of Porcini Mushroom Species Using Fourier Transform Near-Infrared Spectra Combined with Machine Learning and Chemometrics

Porcini mushrooms have high nutritional value and great potential, but different species are easily confused, so it is essential to identify them rapidly and precisely. The diversity of nutrients in stipe and cap will lead to differences in spectral information. In this research, Fourier transform near-infrared (FT-NIR) spectral information about imparity species of porcini mushroom stipe and cap was collected and combined into four data matrices. FT-NIR spectra of four data sets were combined with chemometric methods and machine learning for accurate evaluation and identification of different porcini mushroom species. From the results: (1) improved visualization level of t-distributed stochastic neighbor embedding (t-SNE) results after the second derivative preprocessing compared with raw spectra; (2) after using multiple pretreatment combinations to process the four data matrices, the model accuracies based on support vector machine and partial least-square discriminant analysis (PLS-DA) under the best preprocessing method were 98.73-99.04% and 98.73-99.68%, respectively; (3) by comparing the modeling results of FT-NIR spectra with different data matrices, it was found that the PLS-DA model based on low-level data fusion has the highest accuracy (99.68%), but residual neural network (ResNet) model based on the stipe, cap, and average spectral data matrix worked better (100% accuracy). The above results suggest that distinct models should be selected for dissimilar spectral data matrices of porcini mushrooms. Additionally, FT-NIR spectra have the advantages of being nondevastate and fast; this method is expected to be a promising analytical tool in food safety control.

Morphology and Phylogeny of Lyophylloid Mushrooms in China with Description of Four New Species

The lyophylloid agarics are a group of ecologically highly diversified macrofungi, some of which are very popular edible mushrooms. However, we know little about lyophylloid species diversity in China. In this study, we described four new species from China: Lyophyllum atrofuscum, L. subalpinarum, L. subdecastes, and Ossicaulis sichuanensis. We conducted molecular phylogenetic analyses of Lyophyllaceae based on the nuclear ribosomal RNA gene (nLSU) and the internal transcribed spacer regions (ITS). Phylogenetic analyses by the maximum likelihood method and Bayesian inference showed that the four new species are unique monophyletic species. A key to the species of Lyophyllum from China and a key to Ossicaulis worldwide were given.

Systematic review of fungi, their diversity and role in ecosystem services from the Far Eastern Himalayan Landscape (FHL)

Fungi are morphologically and ecologically diverse kingdom but less explored in the global perspective. This systematic review of mainly higher fungi (mushrooms) and lichenized fungi (lichens) was aimed to convey comprehensive knowledge on these understudied taxa, especially considering diversity, research trends, taxonomic/geographic knowledge gaps, and their contribution to ecosystem services. We investigated literature from the Far Eastern Himalayas and adjacent areas. We followed the PRISM (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) framework for the evidence synthesis and reporting. Search strings were used to explore literature both in English and Chinese databases. Publications were validated examining the title, locality, abstract and full text. We included 75 eligible studies after screening 12,872 publications. The result on species diversity extrapolated from literature was consolidated as a species checklist and published on the Global Biodiversity Information Facility (GBIF) portal. This review demonstrates a significant shortage of research work on fungi, and a lack of quantitative data on diversity, ecology, and ecosystem services. Mycological inventories with multidisciplinary perspectives are urgent in the Landscape to better understand the importance of fungi in conservation and sustainable development science. This review is especially useful when global environmental and climate concerns are focused on the use of nature-based solutions, and fungi as integral part of all ecological processes, could play important role in enhancing ecosystem services and therefore benefits coming to people as natural solutions.

Automatic Mushroom Species Classification Model for Foodborne Disease Prevention Based on Vision Transformer

Mushrooms are the fleshy, spore-bearing structure of certain fungi, produced by a group of mycelia and buried in a substratum. Mushrooms are classified as edible, medicinal, and poisonous. However, many poisoning incidents occur yearly by consuming wild mushrooms. Thousands of poisoning incidents are reported each year globally, and 80% of these are from unidentified species of mushrooms. Mushroom poisoning is one of the most serious food safety issues worldwide. Motivated by this problem, this study uses an open-source mushroom dataset and employs several data augmentation approaches to decrease the probability of model overfitting. We propose a novel deep learning pipeline (ViT-Mushroom) for mushroom classification using the Vision Transformer large network (ViT-L/32). We compared the performance of our method against that of a convolutional neural network (CNN). We visualized the high-dimensional outputs of the ViT-L/32 model to achieve the interpretability of ViT-L/32 using the t-distributed stochastic neighbor embedding (t-SNE) method. The results show that ViT-L/32 is the best on the testing dataset, with an accuracy score of 95.97%. These results surpass previous approaches in reducing intraclass variability and generating well-separated feature embeddings. The proposed method is a promising deep learning model capable of automatically classifying mushroom species, helping wild mushroom consumers avoid eating toxic mushrooms, safeguarding food safety, and preventing public health incidents of food poisoning. The results will offer valuable resources for food scientists, nutritionists, and the public health sector regarding the safety and quality of mushrooms.

Application of DNA barcoding for ensuring food safety and quality

With increasing international food trade, food quality and safety are high priority worldwide. The consumption of contaminated and adulterated food can cause serious health problems such as infectious diseases and allergies. Therefore, the authentication and traceability systems are needed to improve food safety. The mitochondrial DNA can be used for species authentication of food and food products. Effective DNA barcode markers have been developed to correctly identify species. The US FDA approved to the use of DNA barcoding for various food products. The DNA barcoding technology can be used as a regulatory tool for identification and authenticity. The application of DNA barcoding can reduce the microbiological and toxicological risks associated with the consumption of food and food products. DNA barcoding can be a gold-standard method in food authenticity and fraud detection. This review describes the DNA barcoding method for preventing food fraud and adulteration in meat, fish, and medicinal plants.

A Contribution to Knowledge of Craterellus (Hydnaceae, Cantharellales) in China: Three New Taxa and Amended Descriptions of Two Previous Species

Species of Craterellus (Hydnaceae, Cantharellales) in China are investigated on the basis of morphological and molecular phylogenetic analyses of DNA sequences from nuc 28S rDNA D1-D2 domains (28S) and nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 region. Five species are recognized in China, of which three of them are described as new, viz. C. fulviceps, C. minor, and C. parvopullus, while two of them are previously described taxa, viz. C. aureus, and C. lutescens. A key to the known Chinese taxa of the genus is also provided.

A fast multi-source information fusion strategy based on deep learning for species identification of boletes

Wild mushroom market is an important economic source of Yunnan province in China, and its wild mushroom resources are also valuable wealth in the world. This work will put forward a method of species identification and optimize the method in order to maintain the market order and protect the economic benefits of wild mushrooms. Here we establish deep learning (DL) models based on the two-dimensional correlation spectroscopy (2DCOS) images of near-infrared spectroscopy from boletes, and optimize the identification effect of the model. The results show that synchronous 2DCOS is the best method to establish DL model, and when the learning rate was 0.01, the epochs were 40, using stipes and caps data, the identification effect would be further improved. This method retains the complete information of the samples and can provide a fast and noninvasive method for identifying boletes species for market regulators.

Genetic Differentiation and Widespread Mitochondrial Heteroplasmy among Geographic Populations of the Gourmet Mushroom Thelephora ganbajun from Yunnan, China

The mitochondrial genomes are generally considered non-recombining and homoplasmic in nature. However, our previous study provided the first evidence of extensive and stable mitochondrial heteroplasmy in natural populations of the basidiomycete fungus Thelephora ganbajun from Yunnan province, China. The heteroplasmy was characterized by the presence of two types of introns residing at adjacent but different sites in the cytochrome oxidase subunits I (cox1) gene within an individual strain. However, the frequencies of these two introns among isolates from different geographical populations and the implications for the genetic structure in natural populations have not been investigated. In this study, we analyzed DNA sequence variation at the internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA gene cluster among 489 specimens from 30 geographic locations from Yunnan and compared that variation with distribution patterns of the two signature introns in the cox1 gene that are indicative of heteroplasmy in this species. In our samples, evidence for gene flow, abundant genetic diversity, and genotypic uniqueness among geographic samples in Yunnan were revealed by ITS sequence variation. While there was insignificant positive correlation between geographic distance and genetic differentiation among the geographic samples based on ITS sequences, a moderate significant correlation was found between ITS sequence variation, geographical distance of sampling sites, and distribution patterns of the two heteroplasmic introns in the cox1 gene. Interestingly, there was a significantly negative correlation between the copy numbers of the two co-existing introns. We discussed the implications of our results for a better understanding of the spread of stable mitochondrial heteroplasmy, mito-nuclear interactions, and conservation of this important gourmet mushroom.

Edible Mushrooms for Sustainable and Healthy Human Food: Nutritional and Medicinal Attributes

Global food production faces many challenges, including climate change, a water crisis, land degradation, and desertification. These challenges require research into non-traditional sources of human foods. Edible mushrooms are considered an important next-generation healthy food source. Edible mushrooms are rich in proteins, dietary fiber, vitamins, minerals, and other bioactive components (alkaloids, lactones, polysaccharides, polyphenolic compounds, sesquiterpenes, sterols, and terpenoids). Several bioactive ingredients can be extracted from edible mushrooms and incorporated into health-promoting supplements. It has been suggested that several human diseases can be treated with extracts from edible mushrooms, as these extracts have biological effects including anticancer, antidiabetic, antiviral, antioxidant, hepatoprotective, immune-potentiating, and hypo-cholesterolemic influences. The current study focuses on sustainable approaches for handling edible mushrooms and their secondary metabolites, including biofortification. Comparisons between edible and poisonous mushrooms, as well as the common species of edible mushrooms and their different bioactive ingredients, are crucial. Nutritional values and the health benefits of edible mushrooms, as well as different biomedical applications, have been also emphasized. Further research is needed to explore the economic sustainability of different medicinal mushroom bioactive compound extracts and their potential applications against emerging diseases such as COVID-19. New approaches such as nano-biofortification are also needed to supply edible mushrooms with essential nutrients and/or to increase their bioactive ingredients.

Green Biotechnology of Oyster Mushroom (Pleurotus ostreatus L.): A Sustainable Strategy for Myco-Remediation and Bio-Fermentation

The field of biotechnology presents us with a great chance to use many organisms, such as mushrooms, to find suitable solutions for issues that include the accumulation of agro-wastes in the environment. The green biotechnology of mushrooms (Pleurotus ostreatus L.) includes the myco-remediation of polluted soil and water as well as bio-fermentation. The circular economy approach could be effectively achieved by using oyster mushrooms (Pleurotus ostreatus L.), of which the substrate of their cultivation is considered as a vital source for producing biofertilizers, animal feeds, bioenergy, and bio-remediators. Spent mushroom substrate is also considered a crucial source for many applications, including the production of enzymes (e.g., manganese peroxidase, laccase, and lignin peroxidase) and bioethanol. The sustainable management of agro-industrial wastes (e.g., plant-based foods, animal-based foods, and non-food industries) could reduce, reuse and recycle using oyster mushrooms. This review aims to focus on the biotechnological applications of the oyster mushroom (P. ostreatus L.) concerning the field of the myco-remediation of pollutants and the bio-fermentation of agro-industrial wastes as a sustainable approach to environmental protection. This study can open new windows onto the green synthesis of metal-nanoparticles, such as nano-silver, nano-TiO2 and nano-ZnO. More investigations are needed concerning the new biotechnological approaches.

Immunosuppressive Sesquiterpenoids from the Edible Mushroom Craterellus odoratus

The aim of this work was to comprehensively understand the chemical constituents of the edible mushroom Craterellus ordoratus and their bioactivity. A chemical investigation on this mushroom led to the isolation of 23 sesquiterpenoids including eighteen previously undescribed bergamotane sesquiterpenes, craterodoratins A–R (1–18), and one new victoxinine derivative, craterodoratin S (19). The new structures were elucidated by detailed interpretation of spectrometric data, theoretical nuclear magnetic resonance (NMR) and electronic circular dichroism (ECD) calculations, and single-crystal X-ray crystallographic analysis. Compounds 1 and 2 possess a ring-rearranged carbon skeleton. Compounds 3, 10, 12–15, 19, 20 and 23 exhibit potent inhibitory activity against the lipopolysaccharide (LPS)-induced proliferation of B lymphocyte cells with the IC₅₀ values ranging from 0.67 to 22.68 μM. Compounds 17 and 20 inhibit the concanavalin A (ConA)-induced proliferation of T lymphocyte cell with IC₅₀ values of 31.50 and 0.98 μM, respectively. It is suggested that C. ordoratus is a good source for bergamotane sesquiterpenoids, and their immunosuppressive activity was reported for the first time. This research is conducive to the further development and utilization of C. ordoratus.

Historical Differentiation and Recent Hybridization in Natural Populations of the Nematode-Trapping Fungus Arthrobotrys oligospora in China

Maintaining the effects of nematode-trapping fungi (NTF) agents in order to control plant-parasitic nematodes (PPNs) in different ecological environments has been a major challenge in biological control applications. To achieve such an objective, it is important to understand how populations of the biocontrol agent NTF are geographically and ecologically structured. A previous study reported evidence for ecological adaptation in the model NTF species Arthrobotrys oligospora. However, their large-scale geographic structure, patterns of gene flow, their potential phenotypic diversification, and host specialization remain largely unknown. In this study, we developed a new panel of 20 polymorphic short tandem repeat (STR) markers and analyzed 239 isolates of A. oligospora from 19 geographic populations in China. In addition, DNA sequences at six nuclear gene loci and strain mating types (MAT) were obtained for these strains. Our analyses suggest historical divergence within the A. oligospora population in China. The genetically differentiated populations also showed phenotypic differences that may be related to their ecological adaptations. Interestingly, our analyses identified evidence for recent dispersion and hybridization among the historically subdivided geographic populations in nature. Together, our results indicate a changing population structure of A. oligospora in China and that care must be taken in selecting the appropriate strains as biocontrol agents that can effectively reproduce in agriculture soil while maintaining their nematode-trapping ability.

The Effect of Amanita rubescens Pers Developmental Stages on Aroma Profile

The dichloromethane extraction was applied to extracted volatile compounds of the six developmental stages of caps and stipes of an Amanita rubescens mushroom and the relative contents were measured with the gas chromatography-mass spectrometry. The number of identified compounds ranged between 53 and 52, respectively, with a high ratio of alkane volatiles. The significant differences between the aroma compounds were determined in caps to identify their stages of development. The fully mature stage caps were characterized by 4,6-dimethyl-dodecane (7.69 ± 1.15%), 2-hexyl-1-decanol (11.8 ± 1.61%), 1,3-di-tert-butylbenzene (11.4 ± 1.25%), heptadecyl pentadecafluorooctanoate (2.16 ± 0.31%), and 2-hexyl-1-dodecanol (13.5 ± 1.33%). Niacinamide (3.90 ± 0.07%) and glycerol (3.62 ± 1.27%) was present in the caps in the early-stage of the rotting mushroom, which represented the 10th-12th day of fructification. The caps and stipes from the 12th-15th day of fructification were characterized by 2,3-butanediol (11.7 ± 0.13% and 8.00 ± 0.10%, respectively). Moreover, the caps from this developmental stage were characterized by 2-methyl- and 3-methyl butanoic acids (0.18 ± 0.03% and 0.33 ± 0.02%, respectively) which are typical for the rotting stage. In this study, we confirmed the effect of A. rubescens developmental stages on the aroma profile.

Evidence for Persistent Heteroplasmy and Ancient Recombination in the Mitochondrial Genomes of the Edible Yellow Chanterelles From Southwestern China and Europe

Mitochondrial genes and genomes have patterns of inheritance that are distinctly different from those of nuclear genes and genomes. In nature, the mitochondrial genomes in eukaryotes are generally considered non-recombining and homoplasmic. If heteroplasmy and recombination exist, they are typically very limited in both space and time. Here we show that mitochondrial heteroplasmy and recombination may not be limited to a specific population nor exit only transiently in the basidiomycete Cantharellus cibarius and related species. These edible yellow chanterelles are an ecologically very important group of fungi and among the most prominent wild edible mushrooms in the Northern Hemisphere. At present, very little is known about the genetics and population biology of these fungia cross large geographical distances. Our study here analyzed a total of 363 specimens of edible yellow chanterelles from 24 geographic locations in Yunnan in southwestern China and six geographic locations in five countries in Europe. For each mushroom sample, we obtained the DNA sequences at two genes, one in the nuclear genome and one in the mitochondrial genome. Our analyses of the nuclear gene, translation elongation factor 1-alpha (tef-1) and the DNA barcode of C. cibarius and related species, suggested these samples belong to four known species and five potential new species. Interestingly, analyses of the mitochondrial ATP synthase subunit 6 (atp6) gene fragment revealed evidence of heteroplasmy in two geographic samples in Yunnan and recombination within the two new putative species in Yunnan. Specifically, all four possible haplotypes at two polymorphic nucleotide sites within the mitochondrial atp6 gene were found distributed across several geographic locations in Yunnan. Furthermore, these four haplotypes were broadly distributed across multiple phylogenetic clades constructed based on nuclear tef-1 sequences. Our results suggest that heteroplasmy and mitochondrial recombination might have happened repeatedly during the evolution of the yellow chanterelles. Together, our results suggest that the edible yellow chanterelles represent an excellent system from which to study the evolution of mitochondrial-nuclear genome relationships.

Description of the Fifth New Species of Russula subsect. Maculatinae from Pakistan Indicates Local Diversity Hotspot of Ectomycorrhizal Fungi in Southwestern Himalayas

Russula subsect. Maculatinae is morphologically and phylogenetically well-defined lineage of ectomycorrhizal fungi associated with arctic, boreal, temperate and Mediterranean habitats of Northern Hemisphere. Based on phylogenetic distance among species, it seems that this group diversified relatively recently. Russula ayubiana sp. nov., described in this study, is the fifth in the group known from relatively small area of northern Pakistan situated in southwestern Himalayas. This is the highest known number of agaric lineage members from a single area in the world. This study uses available data about phylogeny, ecology, and climate to trace phylogenetic origin and ecological preferences of Maculatinae in southwestern Himalayas. Our results suggest that the area has been recently colonised by Maculatinae members migrating from various geographical areas and adapting to local conditions. We also discuss the perspectives and obstacles in research of biogeography and ecology, and we propose improvements that would facilitate the integration of ecological and biogeographical metadata from the future taxonomic studies of fungi in the region.

Building of an Internal Transcribed Spacer (ITS) Gene Dataset to Support the Italian Health Service in Mushroom Identification

This study aims at building an ITS gene dataset to support the Italian Health Service in mushroom identification. The target species were selected among those mostly involved in regional (Tuscany) poisoning cases. For each target species, all the ITS sequences already deposited in GenBank and BOLD databases were retrieved and accurately assessed for quality and reliability by a systematic filtering process. Wild specimens of target species were also collected to produce reference ITS sequences. These were used partly to set up and partly to validate the dataset by BLAST analysis. Overall, 7270 sequences were found in the two databases. After filtering, 1293 sequences (17.8%) were discarded, with a final retrieval of 5977 sequences. Ninety-seven ITS reference sequences were obtained from 76 collected mushroom specimens: 15 of them, obtained from 10 species with no sequences available after the filtering, were used to build the dataset, with a final taxonomic coverage of 96.7%. The other 82 sequences (66 species) were used for the dataset validation. In most of the cases (n = 71; 86.6%) they matched with identity values ≥ 97–100% with the corresponding species. The dataset was able to identify the species involved in regional poisoning incidents. As some of these species are also involved in poisonings at the national level, the dataset may be used for supporting the National Health Service throughout the Italian territory. Moreover, it can support the official control activities aimed at detecting frauds in commercial mushroom-based products and safeguarding consumers.