Characteristics Analysis Reveals the Progress of Volvariella volvacea Mycelium Subculture Degeneration

Impact of the sterol O-acyltransferase gene (Cmare2) on morphology and stability of the mushroom Cordyceps militaris

Strain degeneration in mushroom cultivation can lead to significant commercial losses, yet the genetic factors remain elusive. This study identified the sterol O-acyltransferase gene, Cmare2, which is associated with colony sectorization in Cordyceps militaris, using a T-DNA insertion-mutant library. CmARE2 is conserved across Ascomycota and Basidiomycota. Deletion of Cmare2 via CRISPR/Cas9 resulted in degenerative phenotypes, including colony sectorization, hyphal adhesion, reduced conidia production, and abnormal fruiting body development. Scanning electron microscopy revealed surface perforations, cobweb-like filaments connecting the adhering hyphae, and eventual hyphal impairment. These phenotypes may be attributed to disturbance of sterol homeostasis, which impairs cell membrane fluidity and permeability. Overexpression of Cmare2 via CRISPR/Cas9 led to a more stable strain with consistent morphology, reduced reactive oxygen species level, and robust mycelia during successive subculturing. This research integrates forward and reverse genetics to unravel the molecular mechanisms behind strain degeneration, providing valuable insights for developing stable, non-degenerative mushroom strains.

The prospect of mushroom as an alterative protein: From acquisition routes to nutritional quality, biological activity, application and beyond

There is a need for new protein sources to sustainably feed the world. Mushroom proteins are regarded as a future protein alternative considering their low cost, high nutritional quality, and excellent digestibility, have attracted increasing attention. Proteins with multiple structural characteristics endow mushroom with various bioactivities, which has also broadened application of mushroom in nutrition, food fields, as well as in emerging industries. Therefore, the present review narrates the recent developments in nutritional quality of mushroom proteins, while paying considerable attention to cultivation technologies and preparation strategies of mushroom proteins. Moreover, the types, properties and biological benefits of mushroom proteins were summarized, herein the latest research on applications of mushroom or their proteins was highlighted. Eventually, the challenges confronting their widespread utility, despite their high nutritional content were discussed. This review would provide a new appreciation for the future use of mushroom proteins.

Transcriptional analysis provides molecular insights into degeneration of the edible fungus Flammulina filiformis

AIMS

Flammulina filiformis, a widely cultivated edible fungus, frequently suffers from strain degeneration, leading to reduce yield and quality, and causing significant economic losses in large-scale production. This study aimed to better understand degeneration mechanisms and to develop an assay for predicting degeneration.

METHODS AND RESULTS

This study investigates strain degeneration by comparing a cultivated strain (F1) and its subcultured derivative (F7). Although both strains display similar mycelial growth, F7 shows impaired fruiting body production, indicating that degeneration occurs prior to visible changes in mycelial growth. To uncover the molecular mechanisms underlying degeneration, transcriptome analysis was carried out. A total of 352 down-regulated and 280 up-regulated differentially expressed genes (DEGs) were identified in F7 compared to F1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed significant enrichment of DEGs in functional categories related to oxidoreductase activities and peroxisome pathway. Quantitative PCR further validated the regulation of certain DEGs associated with these enriched functions. A stress tolerance assay was developed to detect degeneration in strains with unchanged mycelial growth but reduced fruiting body production.

CONCLUSIONS

Results suggested that strain degeneration in F. filiformis is closely linked to oxidative stress regulation and occurs prior to observable mycelial impairment.

Adaptive Changes and Genetic Mechanisms in Organisms Under Controlled Conditions: A Review

Adaptive changes encompass physiological, morphological, or behavioral modifications occurring in organisms in response to specific environmental conditions. These modifications may become established within a population through natural selection. While adaptive changes can influence individuals or populations over short timeframes, evolution involves the inheritance and accumulation of these changes over extended periods under environmental pressures through natural selection. At present, addressing climate change, emerging infectious diseases, and food security are the main challenges faced by scientists. A comprehensive and profound understanding of the mechanisms of adaptive evolution is of great significance for solving these problems. The genetic basis of these adaptations can be examined through classical genetics, which includes stochastic gene mutations and chromosomal instability, as well as epigenetics, which involves DNA methylation and histone modifications. These mechanisms not only govern the rate and magnitude of adaptive changes but also affect the transmission of adaptive traits to subsequent generations. In the study of adaptive changes under controlled conditions, short-term controlled experiments are commonly utilized in microbial and animal research to investigate long-term evolutionary trends. However, the application of this approach in plant research remains limited. This review systematically compiles the findings on adaptive changes and their genetic foundations in organisms within controlled environments. It aims to provide valuable insights into fundamental evolutionary processes, offering novel theoretical frameworks and research methodologies for future experimental designs, particularly in the field of plant studies.

Glutathione peroxidase gene regulates substrate development and prevents strain aging in Volvariella volvacea

Degradation of Volvariella volvacea is associated with the accumulation of reactive oxygen species (ROS), and glutathione peroxidase (GPX) is one of the key antioxidant enzyme. The purpose of this research is to uncover the importance of the gpx gene in the degradation and revitalization of V. volvacea. In this study, a gpx-silenced strain of the primordial strain T0 and an overexpression strain of the degraded strain T19 of V. volvacea were constructed, and their antioxidant properties, matrix degradation ability, and production traits were determined. The results showed that the expression level of gpx altered the homeostasis of the V. volvacea redox system and affected the substrate degradation ability of V. volvacea, which altered the physiological traits of the V. volvacea mycelium. Most importantly, the primordial strain T0 was unable to produce fruiting bodies due to the silence of the gpx gene. On the other hand, the gpx gene overexpression promoted the regrowth of fruiting bodies in degenerated strains of V. volvacea T19. This study provides a new biotechnological strategy to control the degeneration of V. volvacea and other edible fungi.

Comparative transcriptomics and metabolomics provide insight into degeneration-related physiological mechanisms of Morchella importuna after long-term preservation

Ascomycetes fungi are often prone to degeneration. Agricultural production of the prized ascomycete mushroom Morchella importuna (black morel) typically suffers from reduced yield and malformed ascocarps owing to culture degeneration. This study compared M. importuna cultures subjected to five different long-term preservation treatments, using transcriptomics and metabolomics. Avoiding repeated subculturing in combination with nutrient-limited conditions was found to be the most beneficial method for maintaining the fruiting capability of morels. The expression of the gene sets involved in cysteine and methionine metabolism and nucleocytoplasmic transport was upregulated under nutrient-limited and nutrient-rich conditions, respectively. This increased expression was accompanied by differential accumulation of metabolites involved in nucleobase metabolism. Repeated subculturing triggered dissimilar changes in the functional modules under nutrient-rich and nutrient-limited conditions. A diverse set of cellular biochemical processes related to carbon metabolism were altered by repeated subculturing under nutrient-rich conditions, whereas glycerophospholipid and purine metabolism were key functions affected by repeated subculturing under nutrient-limited conditions. Altogether, metabolic alterations related to sulfur-containing amino-acid biosynthesis, DNA repair, and cellular structural maintenance contributed to improved preservation outcomes in terms of morel fruiting capability. Our findings contribute to a more detailed understanding of the molecular mechanisms related to subculturing and fruiting of ascomycete macrofungi after long-term preservation.

Molecular Mechanism During Mycelium Subculture Degeneration of Volvariella volvacea

Periodic mycelial subculture is a method commonly used for the storage of edible mushrooms, but excessive subculturing can lead to the degeneration of strains. In this study, the Volvariella volvacea strain V971(M0) was successively subcultured on PDA medium every 4 days, and one generation of strains was preserved every 4 months. Thus, five generations of subcultured strains (M1-M5) were obtained after 20 months of mycelial subculturing, their production traits were determined, and transcriptomic analysis was performed using RNA-seq; the differentially expressed genes were verified via RT-qPCR. The results showed that as the number of subcultures increased, the diameter of the mycelium and biological efficiency gradually decreased; in addition, the time in which the primordium formed increased and the production cycle was lengthened, while strains M4 and M5 lacked the ability to produce fruiting bodies. There were 245 differentially expressed genes between the M1-M5 and M0 strains, while the highest number of differentially expressed genes was between M3 and M0, at 1439; the smallest number of differentially expressed genes was between M2 and M0, at 959. GO enrichment analysis showed that the differentially expressed genes were mainly enriched in metabolic processes, organelle components, and catalytic activities. KEGG enrichment analysis showed that the differentially expressed genes were mainly enriched in metabolic pathways. The further annotation of differentially expressed genes showed that 39, 24, and 24 differentially expressed genes were related to substrate degradation, amino acid synthesis and metabolism, and reactive oxygen species metabolism, respectively. The downregulation of the related differentially expressed genes would lead to the excessive accumulation of reactive oxygen species, inhibit nutrient absorption and energy acquisition, and lead to the degradation of V. volvacea. These findings could form a theoretical basis for the degeneration mechanism of V. volvacea, and also provide a basis for the molecular function study of the genes related to strain degradation.

Exogenous MnSO4 Improves Productivity of Degenerated Volvariella volvacea by Regulating Antioxidant Activity

Manganese is one of the trace elements necessary for organisms to maintain normal biological activities and is also a cofactor for manganese superoxide dismutase (Mn-SOD) and manganese peroxidase (MnP). In order to find a simple and effective method to rejuvenate the degenerated V. volvacea strains, we explored the effect of the exogenous addition of MnSO4 on the antioxidant vigour and productivity of degenerated strains of V. volvacea. The results showed that the exogenous MnSO4 had no significant effect on the non-degenerated strain T0, but it could effectively increase the mycelial growth rate, mycelial biomass, and LBL decolouring ability of the degenerated strains T10 and T19, and reduce the production cycle and increased the biological efficiency of T10; it helped the severely degenerated T19 to regrow its fruiting body; and it also significantly increased the viability of the matrix-degrading enzymes such as EG, Lac, Xyl, etc. of T10 and T19. Meanwhile, exogenous MnSO4 significantly increased the activity of GPX, GR, CAT, SOD, and the content of GSH, polyphenols, minerals, and polysaccharides in T10 and T19 strains, which resulted in a significant decrease in the accumulation of ROS, such as O2- and H2O2 in T10 and T19. The correlation analysis showed that there was a significant correlation between antioxidant activity and the production ability of V. volvacea. This study can provide theoretical reference and technical support for the rejuvenation research of degenerated strains of V. volvacea and other edible fungi.

Metabolomics Combined with Physiology and Transcriptomics Reveal the Response of Samsoniella hepiali to Key Metabolic Pathways and Its Degradation Mechanism during Subculture

During the subculture of filamentous fungi, obvious signs of degradation occur which affect the growth and development of the strain, change the content of metabolites, and interfere with gene expression. However, the specific molecular mechanism of filamentous fungi degradation is still unclear. In this study, a filamentous fungus Samsoniella hepiali was used as the research object, and it was continuously subcultured. The results showed that when the strain was subcultured to the F8 generation, the strain began to show signs of degradation, which was manifested by affecting the apparent morphology, reducing the growth rate and sporulation, and destroying the antioxidant system. Further transcriptome and metabolomics analyses were performed, and the results showed differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) that were mainly enriched in four metabolic pathways: ABC transporters; fatty acid degradation; alanine, aspartate, and glutamate metabolism; and purine metabolism. Many of the metabolites that were significantly enriched in different pathways may mainly be regulated by genes belonging to proteins and enzymes, such as Abcd3, Ass1, and Pgm1. At the same time, in the process of subculture, many genes and metabolites that can induce apoptosis and senescence continue to accumulate, causing cell damage and consuming a lot of energy, which ultimately leads to the inhibition of mycelial growth. In summary, this study clarified the response of S. hepiali strains to key metabolic pathways during subculture and some reasons for the degradation of strains.

A Review Delving into the Factors Influencing Mycelium-Based Green Composites (MBCs) Production and Their Properties for Long-Term Sustainability Targets

Mycelium-based green composites (MBCs) represent an eco-friendly material innovation with vast potential across diverse applications. This paper provides a thorough review of the factors influencing the production and properties of MBCs, with a particular focus on interdisciplinary collaboration and long-term sustainability goals. It delves into critical aspects such as fungal species selection, substrate type selection, substrate preparation, optimal conditions, dehydrating methods, post-processing techniques, mold design, sterilization processes, cost comparison, key recommendations, and other necessary factors. Regarding fungal species selection, the paper highlights the significance of considering factors like mycelium species, decay type, hyphal network systems, growth rate, and bonding properties in ensuring the safety and suitability of MBCs fabrication. Substrate type selection is discussed, emphasizing the importance of chemical characteristics such as cellulose, hemicellulose, lignin content, pH, organic carbon, total nitrogen, and the C: N ratio in determining mycelium growth and MBC properties. Substrate preparation methods, optimal growth conditions, and post-processing techniques are thoroughly examined, along with their impacts on MBCs quality and performance. Moreover, the paper discusses the importance of designing molds and implementing effective sterilization processes to ensure clean environments for mycelium growth. It also evaluates the costs associated with MBCs production compared to traditional materials, highlighting potential cost savings and economic advantages. Additionally, the paper provides key recommendations and precautions for improving MBC properties, including addressing fungal strain degeneration, encouraging research collaboration, establishing biosecurity protocols, ensuring regulatory compliance, optimizing storage conditions, implementing waste management practices, conducting life cycle assessments, and suggesting parameters for desirable MBC properties. Overall, this review offers valuable insights into the complex interplay of factors influencing MBCs production and provides guidance for optimizing processes to achieve sustainable, high-quality composites for diverse applications.

Nondestructive detection of Pleurotus geesteranus strain degradation based on micro-hyperspectral imaging and machine learning

In the production of edible fungi, the use of degraded strains in cultivation incurs significant economic losses. Based on micro-hyperspectral imaging and machine learning, this study proposes an early, nondestructive method for detecting different degradation degrees of Pleurotus geesteranus strains. In this study, an undegraded strain and three different degradation-level strains were used. During the mycelium growth, 600 micro-hyperspectral images were obtained. Based on the average transmittance spectra of the region of interest (ROI) in the range of 400-1000 nm and images at feature bands, feature spectra and images were extracted using the successive projections algorithm (SPA) and the deep residual network (ResNet50), respectively. Different feature input combinations were utilized to establish support vector machine (SVM) classification models. Based on the results, the spectra-input-based model performed better than the image-input-based model, and feature extraction improved the classification results for both models. The feature-fusion-based SPA+ResNet50-SVM model was the best; the accuracy rate of the test set was up to 90.8%, which was better than the accuracy rates of SPA-SVM (83.3%) and ResNet50-SVM (80.8%). This study proposes a nondestructive method to detect the degradation of Pleurotus geesteranus strains, which could further inspire new methods for the phenotypic identification of edible fungi.

Effects of MAT1-2 Spore Ratios on Fruiting Body Formation and Degeneration in the Heterothallic Fungus Cordyceps militaris

The medicinal mushroom Cordyceps militaris is widely exploited in traditional medicine and nutraceuticals in Asian countries. However, fruiting body production in C. militaris is facing degeneration through cultivation batches, and the molecular mechanism of this phenomenon remains unclear. This study showed that fruiting body formation in three different C. militaris strains, namely G12, B12, and HQ1, severely declined after three successive culturing generations using the spore isolation method. PCR analyses revealed that these strains exist as heterokaryons and possess both the mating-type loci, MAT1-1 and MAT1-2. Further, monokaryotic isolates carrying MAT1-1 or MAT1-2 were successfully separated from the fruiting bodies of all three heterokaryotic strains. A spore combination of the MAT1-1 monokaryotic isolate and the MAT1-2 monokaryotic isolate promoted fruiting body formation, while the single monokaryotic isolates could not do that themselves. Notably, we found that changes in ratios of the MAT1-2 spores strongly influenced fruiting body formation in these strains. When the ratios of the MAT1-2 spores increased to more than 15 times compared to the MAT1-1 spores, the fruiting body formation decreased sharply. In contrast, when MAT1-1 spores were increased proportionally, fruiting body formation was only slightly reduced. Our study also proposes a new solution to mitigate the degeneration in the heterokaryotic C. militaris strains caused by successive culturing generations.

The Registration Situation and Use of Mycopesticides in the World

Mycopesticides are living preparations that use fungal cells, such as spores and hyphae, as active ingredients. They mainly include mycoinsecticides, mycofungicides, mycoherbicides and nematophagous fungi. The utilization of fungi for controlling agricultural pests can be traced back to approximately 1880, when entomopathogenic fungi were initially employed for this purpose. However, it was not until 1965 that the world's first mycopesticide, Beauveria bassiana, was registered as Boverin® in the former Soviet Union. In past decades, numerous novel mycopesticides have been developed for their lower R&D costs, as well as the environmentally friendly and safe nature. In this review, we investigated the mycopesticides situation of registration in USA, EU, China, Canada and Australia. Superisingly, it was found that the registered mycopesticides are extremely raised in recent years. Currently, the insecticides, fungicides (nematocides) and herbicides were respectively registered 27, 53 and 8 fungal strains. This paper also analyzes the main problems currently faced by mycopesticides and offers suggestions for their future development.

Analysis and modification of central carbon metabolism in Hypsizygus marmoreus for improving mycelial growth performance and fruiting body yield

Hypsizygus marmoreus is one of the main industrially cultivated varieties of edible fungi, with a delicious taste and high nutritional value. However, the long harvest period of 130-150 days greatly limits its large-scale expansion. This study aimed to investigate the effects of central carbon metabolism (CCM) on the mycelial growth performance and fruiting body formation of H. marmoreus. Nine edible fungi with different harvest periods were collected and used to evaluate their intracellular carbon metabolic differences in the CCM, which revealed that the imbalanced distribution of intracellular carbon metabolic levels in the CCM of H. marmoreus might be one of the key factors resulting in a slow mycelial growth rate and a long harvest period. Further analysis by three strategies, including metabolomics, adaptation of different carbon sources, and chemical interference, confirmed that low carbon flux into the pentose phosphate pathway (PPP) limited the supply of raw materials, reduced power, and thus influenced the mycelial growth of H. marmoreus. Furthermore, four transformants with increased expression levels of glucose-6-phosphate dehydrogenase (G6PDH), a key rate-limiting enzyme in the PPP of H. marmoreus, were developed and showed more extracellular soluble protein secretion and higher sugar assimilation rates, as well as improved mycelial growth rates in bottle substrate mixtures. Finally, cultivation experiments indicated that the maturation periods of the fruiting body with ~4-5 days in advance and the maximum fruiting body yield of 574.8 g per bag with an increase of 7.4% were achieved by improving the G6PDH expression level of the PPP in H. marmoreus. This study showed that CCM played an important role in the mycelial growth and development of H. marmoreus, which provided new insights for future advancements in cultivating and breeding edible fungi.

Oxidative damage from repeated tissue isolation for subculturing causes degeneration in Volvariella volvacea

The fungal fruiting body is the organized mycelium. Tissue isolation and mycelium succession are common methods of fungal species purification and rejuvenation in the production of edible mushrooms. However, repeated succession increases strain degeneration. In this study, we examined the effect of repeated tissue isolation from Volvariella volvacea fruitbodies on the occurrence of degeneration. The results showed that less than four times in succession improved production capacity, however, after 12 successions, the traits indicating strain degeneration were apparent. For instance, the density of aerophytic hyphae, hyphal growth rate and hyphal biomass were gradually reduced, while the hyphae branching was increased. Also, other degenerative traits such as prolonged production cycles and decreased biological efficiency became evident. In particular, after 19 successions, the strain degeneration became so severe no fruiting bodies were produces anymore. Meanwhile, with the increase in successions, the antioxidant enzyme activity decreased, reactive oxygen species (ROS) increased, the number of nuclei decreased, and the mitochondrial membrane potential decreased along with morphological changes in the mitochondria. This study showed that repeated tissue isolation increased oxidative damage in the succession strain due to the accumulation of ROS, causing cellular senescence, in turn, degeneration in V. volvacea strain.

Successive mycelial subculturing decreased lignocellulase activity and increased ROS accumulation in Volvariella volvacea

Strain degradation is a common problem in many artificially-cultivated edible mushrooms. As a fungus with poor tolerance to low-temperature, Volvariella volvacea cannot delay its degradation by long-term low temperature storage like other fungi, so its degradation is particularly severe, which hinders industrial applications. Periodic mycelial subculture is a common storage method for V. volvacea, but excessive subculturing can also lead to strain degeneration. After 20 months of continuous subculturing every 3 days, V. volvacea strains S1–S20 were obtained, and their characteristics throughout the subculture process were analyzed. With increasing number of subculture, the growth rate, mycelial biomass, the number of fruiting bodies and biological efficiency gradually decreased while the production cycle and the time to primordium formation was lengthened. Strains S13–S20, obtained after 13–20 months of mycelial subculturing, also lacked the ability to produce fruiting bodies during cultivation experiments. Determination of reactive oxygen species (ROS) content as well as enzyme activity showed that decreased lignocellulase activity, along with excessive accumulation of ROS, was concomitant with the subculture-associated degeneration of V. volvacea. Reverse transcription polymerase chain reaction (RT-PCR) was eventually used to analyze the gene expression for lignocellulase and antioxidant enzymes in subcultured V. volvacea strains, with the results found to be consistent with prior observations regarding enzyme activities. These findings could form the basis of further studies on the degeneration mechanism of V. volvacea and other fungi.

Strain Degeneration in Pleurotus ostreatus: A Genotype Dependent Oxidative Stress Process Which Triggers Oxidative Stress, Cellular Detoxifying and Cell Wall Reshaping Genes

Strain degeneration has been defined as a decrease or loss in the yield of important commercial traits resulting from subsequent culture, which ultimately leads to Reactive Oxygen Species (ROS) production. Pleurotus ostreatus is a lignin-producing nematophagous edible mushroom. Mycelia for mushroom production are usually maintained in subsequent culture in solid media and frequently show symptoms of strain degeneration. The dikaryotic strain P. ostreatus (DkN001) has been used in our lab as a model organism for different purposes. Hence, different tools have been developed to uncover genetic and molecular aspects of this fungus. In this work, strain degeneration was studied in a full-sib monokaryotic progeny of the DkN001 strain with fast (F) and slow (S) growth rates by using different experimental approaches (light microscopy, malondialdehyde levels, whole-genome transcriptome analysis, and chitosan effect on monokaryotic mycelia). The results obtained showed that: (i) strain degeneration in P. ostreatus is linked to oxidative stress, (ii) the oxidative stress response in monokaryons is genotype dependent, (iii) stress and detoxifying genes are highly expressed in S monokaryons with symptoms of strain degeneration, (iv) chitosan addition to F and S monokaryons uncovered the constitutive expression of both oxidative stress and cellular detoxifying genes in S monokaryon strains which suggest their adaptation to oxidative stress, and (v) the overexpression of the cell wall genes, Uap1 and Cda1, in S monokaryons with strain degeneration phenotype indicates cell wall reshaping and the activation of High Osmolarity Glycerol (HOG) and Cell Wall Integrity (CWI) pathways. These results could constitute a hallmark for mushroom producers to distinguish strain degeneration in commercial mushrooms.

Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in Pleurotus ostreatus

Pleurotus ostreatus is one of the widely cultivated edible fungi across the world. Mycelial subculture is an indispensable part in the process of cultivation and production for all kinds of edible fungi. However, successive subcultures usually lead to strain degeneration. The degenerated strains usually have a decrease in stress resistance, yield, and an alteration in fruiting time, which will subsequently result in tremendous economic loss. Through proteomic analysis, we identified the differentially expressed proteins (DEPs) in the mycelium of Pleurotus ostreatus from different subcultured generations. We found that the DNA damage repair system, especially the double-strand breaks (DSBs), repairs via homologous recombination, was impaired in the subcultured mycelium, and gradual accumulation of the DSBs would lead to the strain degeneration after successive subculture. The TUNEL assay further confirmed our finding about the DNA breaks in the subcultured mycelium. Interestingly, the enzyme activity of laccase, carboxylic ester hydrolase, α-galactosidase, and catalase directly related to passage number could be used as the characteristic index for strain degeneration determination. Our results not only reveal for the first time at the molecular level that genomic instability is the cause of degeneration, but also provide an applicable approach for monitoring strain degeneration in process of edible fungi cultivation and production.