The analysis of the developmental stages of Agaricus bisporus, a major edible and medicinal mushroom, has always been an important focus in this research area. The process of the growth and development of edible mushrooms is complex and involves the regulation of multiple genes and metabolic pathways. Less data exist on the mechanism of their growth and development at the overall level. In this study, RNA sequencing analyses (RNA-Seq) and data-independent acquisition (DIA) proteomic analyses were carried out at the button phase (BP), harvesting phase (HP), and opening phase (OP) stages of Agaricus bisporus ‘Shuangbao 106’ to reveal the changes in gene expression during the different growth periods of its substrates. The authors screened and explored 3351 differentially expressed genes (DEGs) with a difference factor of ≥2.0, including 2080 up-regulated and 1271 down-regulated genes. After proteome sequencing, 1156 differentially expressed proteins (DEPs) were screened, including 524 up-regulated and 632 down-regulated genes. The expression in TPM of glycoside hydrolase, catalytic core, and chitinase II decreased during both the HP and OP compared with the BP. This may be because mushrooms require higher levels of glycoside hydrolase, catalytic core, and chitinase II activity during the BP to cope with external threats and the need for cell wall remodeling. Conversely, the growth of mushrooms slowed down and the need for cell wall remodeling decreased during the HP and OP, leading to a decrease in the expression of glycoside hydrolase, catalytic core, and chitinase II. This change is related to the need for environmental adaptation, immune defense, and cell wall remodeling, and may regulate the post-growth process of A. bisporus via the hydrolysis of cell wall chitin and glycoside hydrolase. It may also inhibit the growth of mushroom pilei.

Morchella rotation and intercropping is a new and efficient ecological planting mode, which not only contributes to economic growth, but also promotes the sustainable development of agriculture and has high ecological benefits. Morchella sextelata is an edible mushroom that relies on soil-based cultivation. Understanding the composition and dynamics of soil fungal communities under different cropping systems is crucial for optimising its cultivation. This study investigated the fungal community characteristics of Morchella spp. under different rotation and intercropping patterns, together with the associated environmental factors. Using Illumina NovaSeq high-throughput sequencing coupled with ecological and statistical analyses, the relative abundance, alpha diversity index, beta diversity, and intergroup differences in fungal communities were assessed. Additionally, key soil physical and chemical properties were evaluated across four cultivation systems: conventional Morchella spp. cultivation, Morchella sextelata—ginger rotation, vine—Morchella sextelata intercropping, and mulberry tree—Morchella sextelata intercropping. Our results indicate that Morchella spp. cultivation leads to a significant decline in soil fungal diversity compared to uncultivated soils This indicates that cultivation with Morchella spp. simplifies the soil fungal community structure to some extent. Furthermore, distinct variations in fungal community structure were observed across the different cropping systems. Regarding major pathomycete, the relative abundance of Paecilomyces penicillatus increases in vine intercropping soil (VIS), whereas Botryotrichum atrogriseum and Paecilomyces sp. are more abundant in ginger rotation soil (GRS). Similarly, Fusarium solani and Mortierella sp. exhibit higher relative abundance in mulberry tree intercropping soil (MTIS) and fallow soil (FS) compared to natural soil (NS). Functional prediction analysis indicated a general increase in the relative abundance of potential animal and plant pathogenic fungi across all the soil samples, excluding the VIS. This increase was most pronounced in GRS. Further study revealed that the physical and chemical properties of covering soil, including pH, available potassium (AK), available phosphorus (AP), and total phosphorus (TP), significantly influence fungal community diversity and structure. A significant negative correlation was observed between pH and the relative abundance of Fusarium fungi. These findings provide valuable data for further exploration of the ecological mechanisms underlying Morchella spp. cultivation, including rotation constraints and disease dynamics. Ultimately, this research aims to support the development of sustainable and high-quality Morchella spp. production.

Morchella spp. is a type of valuable and rare edible fungi cultivated in soil. Optimization of the cultivation medium for Morchella spp. is key to obtaining high-efficiency production in an ecologically friendly manner. Recently, the sustainable resource utilization of agricultural waste has gathered attention. Specifically, reusing tomato substrate, mushroom residues, and coconut shells can lower the production costs and reduce environmental pollution, demonstrating remarkable ecological and economic benefits. To determine the soil microbial communities of Morchella spp. using different culture medias and influencing factors, this study analysed the relative abundance of bacterial and fungal communities in natural soil, soil with 5% tomato substrate, soil with 5% mushroom residues, and soil with 5% coconut shells using Illumina NovaSeq high-throughput sequencing. In addition, intergroup differences, soil physiochemical properties, and product quality were also determined. Results demonstrated that agricultural waste consisting of mushroom residues, waste tomato substrate, and coconut shells can improve the efficiency of Morchella spp. cultivation. When considering yield and quality, mushroom residue achieved the highest yield (soil nutrient enrichment), followed by tomato substrate (water holding + grass carbon nutrient). All three types of agricultural waste promoted early fruiting, significantly increased polysaccharide, crude protein, and potassium content, and lowered crude fat and fibre. In regard to soil improvement, the addition of different materials optimized the soil’s physical structure (reducing volume weight and increasing water holding capacity) and chemical properties (enrichment of nitrogen, phosphorus, and potassium, regulating nitrogen and medium trace elements). For microbial regulation, the added materials significantly increased the abundance of beneficial bacteria (e.g., Actinomycetota, Gemmatimonadota and Devosia) and strengthened nitrogen’s fixation/nitration/decomposition functions. In the mushroom residue group, the abundance of Bacillaceae was positively related to yield. Moreover, it inhibited pathogenic fungi like Mortierella and Trichoderma, and lowered fungal diversity to decrease ecological competition. In summary, mushroom residues have nutrient releasing and microbial regulation advantages, while tomato substrate and coconut shells are new high-efficiency resources. These increase yield through the “physiochemical–microorganism” collaborative path. Future applications may include regulating the function of microorganisms and optimizing waste preprocessing technologies to achieve sustainability.

Based on transcriptome and proteome sequencing technologies, this study aims to preliminarily reveal the molecular mechanisms of growth and development and related metabolic regulation in Morchella sextelat. A total of 42.31 GB of Clean Data was acquired from the transcriptome sequencing (RNA-seq) of six samples in two development phases (n = 3) of M. sextelata. In the young phase (YP) and harvest phase (HP), there were 2887 differentially expressed genes (DEGs), including 1910 up-regulated genes and 977 down-regulated genes. In YP and HP, there were 987 differentially expressed proteins (DEPs), including 417 up-regulated ones and 570 down-regulated ones. Based on GO and KEGG analysis, significant differences in the transcriptomes and proteins in metabolic pathways are disclosed. Glycometabolism, especially starch, saccharose, and polysaccharide metabolism, plays a crucial role in the growth of M. sextelata. In addition, expression changes in the genes related to selenium metabolism are here recognized. These research results not only offer strong support for further exploration of the biological significance and functional differences of M. sextelata, but are also conducive to discovering key genes and understanding their regulation network during growth.