Culture Degeneration Reduces Sex-Related Gene Expression, Alters Metabolite Production and Reduces Insect Pathogenic Response in Cordyceps militaris

Metabolomics analysis reveals the changes of metabolites in Cordyceps militaris during subculture

Cordyceps militaris (C. militaris) strain is highly prone to degeneration during subculture. The morphological changes in colonies and fruiting bodies during subculture were observed and the metabolites changes were analyzed using metabolic profiling. The results showed that an obvious degeneration occurred in strain beginning from the fifth generation. Antioxidant enzymes activities gradually declined and MDA content slowly increased during subculture. LC-MS results indicated 121 metabolites were identified. K-means clustering analysis results suggested the 5th and 7th clusters had the greatest number of metabolites, mainly including organic acids and derivatives, nucleoside compounds, steroid compounds, fatty acids and their derivatives, and some peptide compounds. Furthermore, the characteristic metabolites levels progressively declined during subculture, which led to the degeneration. The reduced L-glutathione content in the 7th generations was significantly higher than that in the 1st generations, suggesting that C. militaris cells enhanced their synthesis capacity to counter oxidative damage during subculture.

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.

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.

Metabolomics and Transcriptomics Reveal the Effects of Different Fermentation Times on Antioxidant Activities of Ophiocordyceps sinensis

Ophiocordyceps sinensis is a fungus that is cultured through fermentation from wild Chinese cordyceps. While studies have examined its metabolites, the evaluation of its antioxidant capacity remains to be conducted. The antioxidant results of O. sinensis indicate that the ferric ion-reducing antioxidant power (FRAP), antioxidant capacity (2.74 ± 0.12 μmol Trolox/g), 2,2-diphenyl-1-picrylhydrazyl (DPPH•) free radical scavenging rate (60.21 ± 0.51%), and the hydroxyl free radical scavenging rate (91.83 ± 0.68%) reached a maximum on day 30. Using LC-MS/MS to measure the metabolites on D24, D30, and D36, we found that the majority of the differential accumulated metabolites (DAMs) primarily accumulate in lipids, organoheterocyclic compounds, and organic acids and their derivatives. Notably, the DAMs exhibiting high peaks include acetylcarnitine, glutathione, linoleic acid, and L-propionylcarnitine, among others. The transcriptome analysis results indicate that the differentially expressed genes (DEGs) exhibiting high expression peaks on D30 primarily included lnaA, af470, and ZEB1; high expression peaks on D24 comprised SPBC29A3.09c and YBT1; high expression peaks on D36 included dtxS1, PA1538, and katG. The combined analysis revealed significant and extremely significant positive and negative correlations between all the DAMs and DEGs. The primary enriched pathways (p < 0.05) included glutathione metabolism, tryptophan metabolism, carbon metabolism, biosynthesis of secondary metabolites, and phenylalanine metabolism. The metabolic pathway map revealed that the DAMs and DEGs influencing the antioxidant activity of O. sinensis were significantly up-regulated on D30 but down-regulated on D36. The correlation analysis suggests that an increase in the content of DEGs and DAMs promotes an increase in the levels of enzyme and non-enzyme substances, ultimately enhancing the antioxidant capacity of O. sinensis. These findings serve as a reference of how DAMs and DEGs affect the antioxidant activity of O. sinensis. This may contribute to the enhanced development and application of O. sinensis.

Effects of mating-type ratio imbalance on the degeneration of Cordyceps militaris subculture and preventative measures

The rapid degeneration of Cordyceps militaris strains during subculture represents a bottleneck problem that affects production stability. This study explored the mechanism underlying this degeneration in three production and three wild-type strains of Cordyceps militaris, isolating single-conidium strains from each. The effects of subculturing on fructification in both original and single mating-type strains were compared. Changes in the ratio of the two mating types were analyzed in both original and degenerated strains. Based on these findings, the two mating strains were paired in different ratios to determine their effects on fruiting. The resulting five strains were heterokaryotic strains with both MAT1-1 and MAT1-2 mating-type genes. Strain jb-2 was a single mating type (MAT1-1) mutant strain that produced stable fruiting bodies but failed to produce ascospores. It was found that the loss of or imbalance in mating types was the main reason for the rapid degeneration of fruiting traits during subculture and that this occurred randomly in the MAT1-1 and MAT1-2 types. The strains differed significantly in their stability during subculture. Fruiting was stable in the single mating-type Jb-2 strain, and the eleventh-generation fruited normally. There were differences in yield between the production and wild strains after inoculation with spawn containing different proportions of mating types. The production strain was more stable when inoculated with strains with mating-type ratios of 1:9 to 9:1 without affecting the yield. However, the yield of the wild-type strain xf-1 was positively correlated with the proportion of the MAT1-2 type, while the other two strains showed no correlations. Subculturing single mating-type mycelia separately and mixing them before production effectively mitigated degeneration during subculture. For Cordyceps militaris breeding, selecting strains containing both mating types, which are insensitive to the proportion of mating-type genes, enhanced stability in subculture and reduced the risk of mating-type loss. Direct breeding of specific single-mating type strains to induce fruiting is thus an effective breeding strategy.

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.

Ethanolic extract from fruiting bodies of Cordyceps militaris HL8 exhibits cytotoxic activities against cancer cells, skin pathogenic yeasts, and postharvest pathogen Penicillium digitatum

Cordyceps militaris is a well-known medicinal mushroom in Asian countries. This edible fungus has been widely exploited for traditional medicine and functional food production. C. militaris is a heterothallic fungus that requires both the mating-type loci, MAT1-1 and MAT1-2, for fruiting body formation. However, recent studies also indicated two groups of C. militaris, including monokaryotic strains carrying only MAT1-1 in their genomes and heterokaryotic strains harboring both MAT1-1 and MAT1-2. These strain groups are able to produce fruiting bodies under suitable cultivating conditions. In previous work, we showed that monokaryotic strains are more stable than heterokaryotic strains in fruiting body formation through successive culturing generations. In this study, we report a high cordycepin-producing monokaryotic C. militaris strain (HL8) collected in Vietnam. This strain could form normal fruiting bodies with high biological efficiency and contain a cordycepin content of 14.43 mg/g lyophilized fruiting body biomass. The ethanol extraction of the HL8 fruiting bodies resulted in a crude extract with a cordycepin content of 69.15 mg/g. Assays of cytotoxic activity on six human cancer cell lines showed that the extract inhibited the growth of all these cell lines with the IC50 values of 6.41-11.51 µg/mL. Notably, the extract significantly reduced cell proliferation and promoted apoptosis of breast cancer cells. Furthermore, the extract also exhibited strong antifungal activity against Malassezia skin yeasts and the citrus postharvest pathogen Penicillium digitatum. Our work provides a promising monokaryotic C. militaris strain as a bioresource for medicine, cosmetics, and fruit preservation.

Molecular mechanisms underlying phenotypic degeneration in Cordyceps militaris: insights from transcriptome reanalysis and osmotic stress studies

Phenotypic degeneration in Cordyceps militaris poses a significant concern for producers, yet the mechanisms underlying this phenomenon remain elusive. To address this concern, we isolated two strains that differ in their abilities to form fruiting bodies. Our observations revealed that the degenerated strain lost the capacity to develop fruiting bodies, exhibited limited radial expansion, increased spore density, and elevated intracellular glycerol levels. Transcriptome reanalysis uncovered dysregulation of genes involved in the MAPK signaling pathway in the degenerate strain. Our RT-qPCR results demonstrated reduced expression of sexual development genes, along with upregulation of genes involved in asexual sporulation, glycerol synthesis, and MAPK regulation, when compared to the wild-type strain. Additionally, we discovered that osmotic stress reduced radial growth but increased conidia sporulation and glycerol accumulation in all strains. Furthermore, hyperosmotic stress inhibited fruiting body formation in all neutralized strains. These findings indicate dysregulation of the MAPK signaling pathway, the possibility of the activation of the high-osmolarity glycerol and spore formation modules, as well as the downregulation of the pheromone response and filamentous growth cascades in the degenerate strain. Overall, our study sheds light on the mechanisms underlying Cordyceps militaris degeneration and identifies potential targets for improving cultivation practices.

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.

Special Issue on "Entomopathogenic Fungi: Ecology, Evolution, Adaptation": An Editorial

Entomopathogenic endophytic ascomycetes are the most widespread and commercially promising fungi and are used to solve many problems in basic and applied research in ecology, evolution, and agricultural sciences [...].

Changes of the gene expression in silkworm larvae and Cordyceps militaris at late stages of the pathogenesis

Cordyceps militaris is an entomopathogenic fungus that forms its fruiting body. The gene expression change in C. militaris and silkworm larvae were analyzed using RNA-seq to investigate the relationship of C. militaris with the host, silkworm larvae before the death by mycosis. At 144 h after the injection of C. militaris conidia, genes encoding proteases, protease inhibitors, and cuticle proteins in the fat body of silkworm larvae were upregulated, but genes encoding lipoproteins and other proteins in hemolymph were downregulated. On the other hand, at 168 h after the injection of C. militaris conidia, genes encoding amino acid and oligopeptide transporters and permeases in C. militaris were upregulated, suggesting that C. militaris may use peptides and amino acids in silkworm larvae as a nutrient to grow in vivo. Additionally, one gene cluster composed of genes putatively involved in the degradation of phenolic substrates was also upregulated. The addition of 4,5-dichlorocatechol, an inhibitor of catechol 1,2-dioxygenase, inhibited the in vivo growth of C. militaris, Beauveria bassiana and Metarhizium anisopliae. These results also suggest that the expression of the gene cluster may be crucial for the in vivo growth of C. militaris and entomopathogenic fungi. This study will clarify how C. militaris grows in insect hosts by avoiding host's immune systems.