The Agaricus genus represents the most popular edible mushroom in the world. Wheat straw often is used as the substrate for mushroom cultivation following pretreatment to degrade the lignocellulosic biomass in agricultural waste. In this study, we investigated the changes in bacterial and fungal microflora of wheat straw substrate during different phases of composting. We collected samples of the raw material (M1), phase I aerobic fermentation (F1, F2, F3), and phase II after-fermentation (AF1) for high-throughput 16S rRNA and internal transcribed spacer (ITS) sequencing to analyze the microbial diversity in the substrate during composting. Our data revealed that among the five stages, 365 operational taxonomic units (OTUs) were shared, with Firmicutes , Proteobacteria , and Actinobacteria being the predominant bacterial phyla. In addition, Thermobispora , Thermopolyspora , Ruminiclostridium , Thermobacillus , and Bacillus were the predominant genera in F3 and AF1, with the species Thermobispora bispora and Pseudoxanthomonas taiwanensis being predominant in F2. Both principal component analysis (PCA) and nonmetric multidimensional scaling (NMDS) plots showed that the bacterial communities of five stages could be distinguished from each other based on their composting time. The Shannon and Simpson indexes of F2 were lower than M1 ( P < 0.05), and the clustering dendrogram showed that the bacterial communities in AF1 were similar to F3, with Micromonosporaceae , Streptosporaceae , Thermomonosporaceae , and Vulgatibacteraceae representing the differential bacterial families by linear discriminant analysis with effect size (LEfSe) analysis. The analysis of fungal communities showed that 384 OTUs were common among the five stages, with 1054 and 454 OTUs unique to M1 and AF1, respectively. Ascomycota and Basidiomycota were the two predominant phyla in all stages, and Chytridiomycota was predominant in F2, F3, and AF1 stages. PCA and NMDS plots showed that the clusters of F2 and AF1 were more dispersed than the other stages. No differences were observed in alpha diversity between the stages, and samples of F1, F2, and F3 were closer to AF1 in the clustering dendrogram. By LEfSe analysis, Mycothermus thermophilus , Gonapodya polymorpha , and Phaeophleospora_eugeniae were identified as the predominant fungal species in AF1.

Agaricus bisporus growth alters the lignocellulosic composition and structure of compost. However, it is difficult to differentiate the enzyme activities of A. bisporus mycelia from the wider microbial community owing to the complication of completely speareting the mycelia from compost cultures. Macrogenomics analysis was employed in this study to examine the fermentation substrate of A. bisporus before and after mycelial growth, and the molecular mechanism of substrate utilization by A. bisporus mycelia was elucidated from the perspective of microbial communities and CAZymes in the substrate. The results showed that the relative abundance of A. bisporus mycelia increased by 77.57-fold after mycelial colonization, the laccase content was significantly increased and the lignin content was significantly decreased. Analysis of the CAZymes showed that AA10 family was extremely differentiated. Laccase-producing strains associated with AA10 family were mostly bacteria belonging to Thermobifida and Thermostaphylospora, suggesting that these bacteria may play a synergistic role in lignin decomposition along with A. bisporus mycelia. These findings provide preliminary evidence for the molecular mechanism of compost utilization by A. bisporus mycelia and offer a reference for the development and utilization of strains related to lignocellulose degradation.

Sanghuangporus sanghuang (SS) is a rare medicinal polypore fungus that grows solely on Morus trees. In this study, seven grains (oats, barley, millet, rice, buckwheat, corn, and coix seed) were used as solid substrates for SS fermentation and characterized in their nutrition, functional composition, and antioxidant activities. After fermentation, the nutrient compositions of crude protein (F_1,41 = 111.1, P < 0.01), soluble protein (F_1,41 = 595.7, P < 0.01), soluble sugar (F_1,41 = 51.4, P < 0.01) and ash (F_1,41 = 227.3, P < 0.01) increased significantly. Oats were one of the best grains for SS fermentation, SS-Oat produced 6.23 mg QE/g polyphenols, 21.8 mg rutin/g flavonoids, and 2.3% triterpene. In addition, the antioxidant capacities of the seven grains all increased. Principal component analysis analysis shows that the antioxidant properties of the grains were similar after SS fermentation. The changes of antioxidant activity due to SS fermentation were corrected with corresponding grain and remarked as ΔT-AOC/ABTS⁺/DPPH/DNAp, that was correlated to part of changes in polyphenol, carotenoid, triterpenoids, and flavonoid contents. In summary, oats have the greatest potential for use as a fermentation substrate for health food development.

Introduction: Cordyceps cicadae is a traditional Chinese medicinal fungus known for its rich production of bioactive substances, particularly cyanidin, an anthocyanin commonly found in plants with notable anti-inflammatory, anti-tumor, antiviral, and antibacterial properties. This study revealed two key genes, CcDFR and CcOMT9, affecting cyanidin biosynthesis in C. cicadae.Methods: The roles of these genes in cyanidin production, growth, and development were elucidated through the gene knockout method, phenotypic analysis, transcriptomics, and metabolomics.Results: CcDFR deletion led to reduced cyanidin-3-O-glucoside (C3G), suppressed expression of cyanidin biosynthesis genes, impaired synnemata formation, decreased polysaccharide and adenosine content, and diminished chitinase activity. Meanwhile, the ΔCcOMT9 mutant exhibited an increase in C3G production, promoted expression of cyanidin biosynthesis genes and rising bioactive compounds, suppressed RNA methylation, and led to phenylalanine accumulation with no effect on fruiting body formation.Discussion: We revealed a distinct anthocyanin biosynthesis pathway in C. cicadae and identified two genes with opposite functions, laying the foundation for future genetic modification of cyanidin-producing strains using modern biological techniques. This will shorten the production period of this valuable compound, facilitating the industrial-scale production of cyanidin.