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Major CAZymes of M. importuna SCYDJ1-A1 involved in ENB decomposition. A supplemental figure showing all 88 CAZymes identified in ENB is provided in Fig. S5. Expression levels of transcripts and proteins were estimated by RNA-Seq and nanoLC-MS/MS, respectively. Steady-state transcript level (in RPKM) and protein relative abundance are the mean of three biological replicates. ND: not detected. Functions of CAZymes were predicted according to their nearest analogs whose activities had been characterized in previous studies, as provided by the CAZy database. Fold-change in RPKM between time-points, together with p-value of pairwise comparison, was calculated by the Baggerly’s proportion-based test (Baggerly et al., 2003) with a FDR correction for multiple testing (Benjamini and Hochberg, 1995). Fold-change values of protein relative abundance between time-points, together with p-value of pairwise comparison, were calculated by t-test with FDR correction. Significant up- and down- regulation were judged by fold-change > 2 and fold-change < 0.5, respectively, while FDR-corrected p-value < 0.05. Fold-change values and p-values are provided in Table S8.
Citations
... In the last decade, the artificial cultivation of morels has increased rapidly in China, reaching an area of 16,466 ha in 2021-2022 [12]. Cultivation methods are mainly based on the domestication of easy-to-fruit varieties, the utilization of exogenous nutrient bags, and suitable environmental conditions [11,13]. Despite remarkable breakthroughs in artificial cultivation, approximately half of morel cultivations experience low fruiting rates and difficulties in obtaining stable profits [9,12], caused by serious problems such as strain aging or degradation [9,14], fungal and bacterial diseases [12,[15][16][17], environmental fluctuations, and refined field management [11,13]. ...
... Cultivation methods are mainly based on the domestication of easy-to-fruit varieties, the utilization of exogenous nutrient bags, and suitable environmental conditions [11,13]. Despite remarkable breakthroughs in artificial cultivation, approximately half of morel cultivations experience low fruiting rates and difficulties in obtaining stable profits [9,12], caused by serious problems such as strain aging or degradation [9,14], fungal and bacterial diseases [12,[15][16][17], environmental fluctuations, and refined field management [11,13]. These problems place greater demands on understanding the developmental mechanism and biology of morels. ...
... The sufficient carbon and nitrogen sources in the nutrient bags provide energy for the growth of the mycelium network in the soil, meeting the needs for later reproductive growth. Of course, a portion of the nitrogen source in the soil is also absorbed [13]. In addition, our and others' studies have shown that primordium formation and fruiting body maturation are closely related to soil microbiota, which may promote morel growth [18][19][20][21][22]. ...
True morels (Morchella, Pezizales) are a popular edible and medicinal fungus with great nutritional and economic value. The dynamics and regulatory mechanisms during the morphogenesis and maturation of morels are poorly understood. In this study, the metabolomes and transcriptomes of the mycelium (MY), primordium differentiation (PR), young fruiting body (YFB), and mature fruiting body (MFB) were comprehensively analyzed to reveal the mechanism of the morphogenesis and maturation of Morchella sextelata. A total of 748 differentially expressed metabolites (DEMs) and 5342 differentially expressed genes (DEGs) were detected, mainly enriched in the carbohydrate, amino acid, and lipid metabolism pathways, with the transition from the mycelium to the primordium being the most drastic stage at both the metabolic and transcriptional levels. The integrated metabolomics and transcriptomics highlighted significant correlations between the DEMs and DEGs, and specific amino acid and nucleotide metabolic pathways were significantly co-enriched, which may play key roles in morphological development and ascocarp maturation. A conceptual model of transcriptional and metabolic regulation was proposed during morphogenesis and maturation in M. sextelata for the first time, in which environmental factors activate the regulation of transcription factors, which then promote metabolic and transcriptional regulation from vegetative to reproductive growth. These results provide insights into the metabolic dynamics and transcriptional regulation during the morphogenesis and maturation of morels and valuable resources for future breeding enhancement and sustainable artificial cultivation.
... However, this indoor morel cultivation method could not be applied on a large scale due to inconsistent harvesting yields. Based on the utilization of exogenous nutrients and successful domestication of easy-to-cultivate varieties since 2012, 16,466 ha of outdoor cultivation of morels has been achieved in mainland China during the 2021-2022 season (Tan et al., 2019;Shi et al., 2022). As morel cultivation is rapidly expanding, diseases are increasingly becoming the greatest threat to morel mushroom production (Tan et al., 2021a). ...
Morel mushroom ( Morchella spp.) is a rare edible and medicinal fungus distributed worldwide. It is highly desired by the majority of consumers. Bacterial diseases have been commonly observed during artificial cultivation of Morchella sextelata . Bacterial pathogens spread rapidly and cause a wide range of infections, severely affecting the yield and quality of M. sextelata . In this study, two strains of bacterial pathogens, named M-B and M-5, were isolated, cultured, and purified from the tissues of the infected M. sextelata . Koch’s postulates were used to determine the pathogenicity of bacteria affecting M. sextelata , and the pathogens were identified through morphological observation, physiological and biochemical analyses, and 16S rRNA gene sequence analysis. Subsequently, the effect of temperature on the growth of pathogenic bacteria, the inhibitory effect of the bacteria on M. sextelata on plates, and the changes in mycelial morphology of M. sextelata mycelium were analyzed when M. sextelata mycelium was double-cultured with pathogenic bacteria on plates. The results revealed that M-B was Pseudomonas chlororaphis subsp. aureofaciens and M-5 was Bacillus subtilis . Strain M-B started to multiply at 10–15°C, and strain M-5 started at 15–20°C. On the plates, the pathogenic bacteria also produced significant inhibition of M. sextelata mycelium, and the observation of mycelial morphology under the scanning electron microscopy revealed that the inhibited mycelium underwent obvious drying and crumpling, and the healthy mycelium were more plump. Thus, this study clarified the pathogens, optimal growth environment, and characteristics of M. sextelata bacterial diseases, thereby providing valuable basic data for the disease prevention and control of Morchella production.
... By contrast, the six variables (d 13 C, dD, d 18 O, d 15 N, C%, and N%) in different stages of the current study may also provide a reference for the cultivation of G. lucidum. These variables could not only be used to trace geographical origin but also for tracking the migration of the flux of nutritional elements such as N during cultivation (Tan et al., 2019). ...
Rationale
Ganoderma lucidum ( G. lucidum ) is a popular medicinal fungus that has been used in traditional medicine for decades, with its provenance influencing its medicinal and commercial worth. The amount of active ingredients and the price of G. lucidum from different origins vary significantly; hence, fraudulent labeling is common. Reliable techniques for G. lucidum geographic verification are urgently required to safeguard the interests of consumers, producers, and honest dealers. A stable isotope is widely acknowledged as a useful traceability technique and could be developed to confirm the geographical origin of G. lucidum .
Methods
G. lucidum samples from various sources and in varying stages were identified by using δ ¹³ C, δ D, δ ¹⁸ O, δ ¹⁵ N, C, and N contents combined with chemometric tools. Chemometric approaches, including PCA, OPLS-DA, PLS, and FLDA models, were applied to the obtained data. The established models were used to trace the origin of G. lucidum from various sources or track various stages of G. lucidum .
Results
In the stage model, the δ ¹³ C, δ D, δ ¹⁸ O, δ ¹⁵ N, C, and N contents were considered meaningful variables to identify various stages of G. lucidum (bud development, growth, and maturing) using PCA and OPLS-DA and the findings were validated by the PLS model rather than by only four variables ( δ ¹³ C, δ D, δ ¹⁸ O, and δ ¹⁵ N). In the origin model, only four variables, namely δ ¹³ C, δ D, δ ¹⁸ O, and δ ¹⁵ N, were used. PCA divided G. lucidum samples into four clusters: A (Zhejiang), B (Anhui), C (Jilin), and D (Fujian). The OPLS-DA model could be used to classify the origin of G. lucidum . The model was validated by other test samples ( Pseudostellaria heterophylla ), and the external test ( G. lucidum ) by PLS and FLDA models demonstrated external verification accuracy of up to 100%.
Conclusion
C, H, O, and N stable isotopes and C and N contents combined with chemometric techniques demonstrated considerable potential in the geographic authentication of G. lucidum , providing a promising method to identify stages of G. lucidum .
... Morels (Morchella spp.) are highly prized mushrooms known for their exceptional taste and nutritional composition, which includes amino acids, polysaccharides, and trace elements (Liu et al., 2017Tietel and Masaphy, 2018). With the growing demand for morel mushrooms that exceeds the availability of wild resources, the cultivation of black morel species (such as M. sextelata, M. importuna, and M. exima) in China has expanded rapidly in recent decades (Zhang et al., 2023a) because of the widespread application of exogenous nutrient bag (ENB) technology, a special type of organic substrate enriched in plant polysaccharides (Tan et al., 2019). Previous studies have demonstrated the presence of complex microbiota associated with morels under natural conditions and production systems (Orlofsky et al., 2021). ...
The successful large-scale cultivation of morel mushrooms ( Morchella sextelata ) requires a comprehensive understanding of the soil bacterial communities associated with morel-farming beds, as the interactions between fungi and bacteria play a crucial role in shaping the soil microbiome. In this study, we investigated the temporal distribution and ecological characteristics of soil bacteria associated with morel fruiting bodies at different stages, specifically the conidial and primordial stages, under two cropping regimes, non-continuous cropping (NCC) and continuous cropping (CC). Our findings revealed a significant reduction in the yield of morel primordia during the third year following 2 years of CC (0.29 ± 0.25 primordia/grid), in comparison to the NCC regime (12.39 ± 6.09 primordia/grid). Furthermore, inoculation with morel mycelia had a notable impact on soil bacterial diversity, decreasing it in the NCC regime and increasing the number of generalist bacterial members in the CC regime. The latter regime also led to the accumulation of nutrients in the soil beds, resulting in a shift from a stochastic to a deterministic process in the composition of the bacterial community, which differed from the NCC regime. Additionally, mycelial inoculation had a positive effect on the abundance of potential copiotrophic/denitrifying and N-fixing bacteria while decreasing the abundance of oligotrophic/nitrifying bacteria. Interestingly, this effect was more pronounced in the NCC regime than in the CC regime. These results suggest that the increase in potential copiotrophic/denitrifying and N-fixing bacteria facilitated the decomposition of nutrients in exogenous nutrient bags by morel mushrooms, thereby maintaining nitrogen balance in the soil. Overall, our study provides valuable insights into the interactions between morel mycelia and the associated soil bacteriome as well as the influence of different cultivation regimes on these interactions. These findings contribute to our understanding of the complex dynamics of the soil microbiome and can inform strategies for optimizing morel mushroom cultivation.
... In recent years, basic research on Morchella has made some progress in terms of life cycle, sclerotium development mechanisms, exogenous nutrition utilization, characteristic of mitochondrial genome, etc. (Tan et al., 2019;Liu et al., 2020Liu et al., , 2021aDu and Yang, 2021;Chai et al., 2022). However, there is still a lack of understanding of conidial production, working mechanisms of exogenous nutrition bags, primordium formation, and fruiting body development mechanisms , so basic research should be continued. ...
... Recent experiments have found that filter paper coated with exogenous nutrients can play the same role as polypropylene bags , suggesting that it is possible for environmentally friendly materials to replace polypropylene plastics. Based on the basic principle of exogenous nutrient bags delivering nutrients to soil (Tan et al., 2019), more materials should be tried to replace plastics or make more efficient use of exogenous nutrients and reduce environmental pressure. ...
... With the boosting of morel field cultivation, multi-disciplinary basic biological research has gained increased attention, mainly that involving cultivation schemes, cultivation management, appropriate strains, integrative taxonomy of species suitable to be cultivated, mating type gene structure, sclerotia development, nutrient metabolism, ascomata development, and life cycle [27][28][29][30][31][32][33][34][35][36][37][38][39][40]. Studies related to "multiomics" and molecular biology technologies have also been encouraged. ...
... However, with the boosting of research related to the growth and development of sclerotia as a model for morel cultivation, it is possible to trace back the basic principles of the success of this technology [1,[16][17][18][19]26,29]. First, studies on sclerotia formation showed that sclerotia mostly occurred in nutrient-poor environments and that sclerotia was an important lipid reservoir [16][17][18][19]29]. Second, during the cultivation process, no ascomata can be produced without the addition of external nutrient bags or nutrients added directly to the soil [36]. Additionally, it is currently known that the number of sclerotial cells and the lipid contents of the soil increase significantly with time when exogenous nutrition is added. ...
... Nutrients can be stored in sclerotial cells in the soil in "rich" and "poor" areas to satisfy the appropriate amounts of energy reserve necessary for sexual reproduction in the last stage of cultivation [1]. The knowledge of these basic principles related to the differential nutrient distribution in space and their consequent energy transfer and storage in the different fungal compartments is of fundamental relevance for successful morel cultivation [1,36]. ...
Morels are one of the most highly prized edible and medicinal mushrooms worldwide. Therefore, historically, there has been a large international interest in their cultivation. Numerous ecological, physiological, genetic, taxonomic, and mycochemical studies have been previously developed. At the beginning of this century, China finally achieved artificial cultivation and started a high-scale commercial development in 2012. Due to its international interest, its cultivation scale and area expanded rapidly in this country. However, along with the massive industrial scale, a number of challenges, including the maintenance of steady economic profits, arise. In order to contribute to the solution of these challenges, formal research studying selection, species recognition, strain aging, mating type structure, life cycle, nutrient metabolism, growth and development, and multi-omics has recently been boosted. This paper focuses on discussing current morel cultivation technologies, the industrial status of cultivation in China, and the relevance of basic biological research, including, e.g., the study of strain characteristics, species breeding, mating type structure, and microbial interactions. The main challenges related to the morel cultivation industry on a large scale are also analyzed. It is expected that this review will promote a steady global development of the morel industry based on permanent and robust basic scientific knowledge.
... Sowing methods and soil conditions are also crucial for successful cultivation. Common sowing methods include furrow, spreading, and hole sowing, as shown in Figure 3, and nutrient bags are typically spaced 20-30 cm apart after 7-15 days of sowing [58][59][60]. In Chongqing, Li, et al. [61] found that the content of HMs in edible fungi collected in different seasons was also different. ...
Morel is a popular edible mushroom with considerable medicinal and economic value which has garnered global popularity. However, the increasing heavy metal (HM) pollution in the soil presents a significant challenge to morels cultivation. Given the susceptibility of morels to HM accumulation, the quality and output of morels are at risk, posing a serious food safety concern that hinders the development of the morel industry. Nonetheless, research on the mechanism of HM enrichment and mitigation strategies in morel remains scarce. The morel, being cultivated in soil, shows a positive correlation between HM content in its fruiting body and the HM content in the soil. Therefore, soil remediation emerges as the most practical and effective approach to tackle HM pollution. Compared to physical and chemical remediation, bioremediation is a low-cost and eco-friendly approach that poses minimal threats to soil composition and structure. HMs easily enriched during morels cultivation were examined, including Cd, Cu, Hg, and Pb, and we assessed soil passivation technology, microbial remediation, strain screening and cultivation, and agronomic measures as potential approaches for HM pollution prevention. The current review underscores the importance of establishing a comprehensive system for preventing HM pollution in morels.
... These edible ascomycetous mushrooms are of high economic and scientific value [2,3]. In recent years, several black morel species have been "domesticated" and used in large-scale production of highly prized mushroom crops [4]. The black morel agroindustry is now expanding rapidly, both in China and around the world [3,5,6], but a severe decline in morel yields and resistance to soil-borne diseases have been observed as a result of continuous cropping, hampering the full development of the morel agroindustry [1,7]. ...
... The addition of the morel spawn and ENBs, containing large amounts of wheat seeds and corn cobs, likely explained these striking changes in soil nutrient levels. It is known that the saprotrophic M. sextelata secretes a diverse set of degrading enzymes involved in the substrate decomposition [4]. This leads to a rapid increase in the organic carbon content in the surface soil of the mushroom bed, which is thereafter catabolized during mycelial growth to sustain fruiting body yield [33]. ...
... Solicoccozyma aeria is involved in biodegradation in agricultural soils [41]. Humicola grisea and Trichocladium are known as cellulolytic fungi [42], and they may be favored by the high cellulose content of the ENBs and spawn substrates [4]. Importantly, M. sextelata itself is a strong decomposer of substrates found in ENBs and spawn substrates, resulting in a rapid increase in the organic carbon content in inoculated soils. ...
The black morel Morchella sextelata (Morchellaceae, Pezizales) is a valuable edible mushroom that can be cultivated on a large scale, but a severe yield decline is observed during continuous cropping. The effect of long-term cropping on soil-borne diseases and the dysbiosis of the microbiome and how these biotic factors affect the morel yield are not well understood. To help fill this knowledge gap, we designed an indoor experiment to investigate the influence of black morel cropping regimes on soil physicochemical properties, richness and distribution of fungal community, and morel primordial production. In this study, we employed rDNA metabarcoding and microbial network analysis to evaluate the effect of non-continuous and continuous cropping regimes on the fungal community during three developmental stages of black morel production, namely, the bare soil mycelium, mushroom conidial, and primordial stages. The results showed that during the first year, M. sextelata mycelium overwhelmed the resident soil fungal community by reducing the alpha diversity and niche breadth of soil fungal patterns by a greater amount compared to the continuous cropping regime, leading to high crop yield of 12.39 ± 6.09/quadrat but less complex soil mycobiome. To sustain continuous cropping, exogenous nutrition bags and morel mycelial spawn were consecutively added to the soil. The additional nutrient input stimulated the growth of fungal saprotrophic decomposers. The degrading activity of soil saprotrophs, including M.sextelata, caused a significant increase in soil nutrient content. This led to an inhibitory effect on the formation of morel primordia, resulting in a sharp decline to 0.29 ± 0.25/quadrat and 0.17 ± 0.24/quadrat, respectively, in the final morel cropping. Our findings provided a dynamic overview of the soil fungal community during morel mushroom production, allowing us to identify beneficial and detrimental fungal taxa in the soil mycobiome involved in morel cultivation. The information acquired from this study can be applied to mitigate the adverse impact of continuous cropping on the yield of black morel.
... Morel cultivation has achieved significant breakthroughs in China since 2012, with an area of 16,466 ha during the 2021-2022 season [11]. Meanwhile, morel biology has been recently extensively studied with important findings on its reproductive modes [7,[12][13][14][15][16], nuclear and mitochondrial genome sequence and function [9,[16][17][18][19][20][21], microbial community dynamics [22][23][24][25][26], nutrient metabolism [27], and fruiting body development [28][29][30][31]. ...
The cultivation of true morels (Morchella spp., Morchellaceae, Ascomycota) has rapidly expanded in recent years, especially in China. Red stipe is a symptom wherein the stipe of morel fruiting bodies becomes red–gray, resulting in the gradual death of the affected fruiting bodies. The impact of red-stipe symptom occurrence on the development and nutritional quality of morel fruiting bodies remains unclear. Herein, morel ascocarps with the red-stipe symptom (R) and normal (N), artificially cultivated in the Fujian Province of China, were selected for the transcriptome and metabolome analysis to study the physiological and biochemical responses of morel fruiting bodies to the red-stipe symptom. Transcriptome data revealed several differentially expressed genes between the R and N groups significantly enriched in the tyrosine, riboflavin, and glycerophospholipid metabolism pathways. Similarly, the differentially accumulated metabolites were mainly assigned to metabolic pathways, including tyrosine, the biosynthesis of plant secondary metabolites, and the biosynthesis of amino acids. Moreover, the transcriptome and metabolome data combination revealed that tyrosine metabolism was the most enriched pathway, which was followed by ATP-binding cassette (ABC) transport, alanine, aspartate, and glutamate metabolism. Overall, the integration of transcriptomic and metabolomic data of M. sextelata affected by red-stipe symptoms identified several important genes, metabolites, and pathways. These findings further improve our understanding of the mechanisms underlying the red-stipe symptom development of M. sextelata and provide new insights into how to optimize its cultivation methods.
... Differences in soil nutrients can affect the yield of black morel [31], and the diversity and homogeneity of soil microorganisms can affect morel production [32]. Multi-omic analyses have revealed the nutrient acquisition and transfer of black morel [33]. The characteristics of soil microbiota can be used to predict the potential of Fusarium wilt occurrence [34]. ...
Gastrodia elata is a valuable traditional Chinese medicinal plant. However, G. elata crops are affected by major diseases, such as brown rot. Previous studies have shown that brown rot is caused by Fusarium oxysporum and F. solani. To further understand the disease, we studied the biological and genome characteristics of these pathogenic fungi. Here, we found that the optimum growth temperature and pH of F. oxysporum (strain QK8) and F. solani (strain SX13) were 28 °C and pH 7, and 30 °C and pH 9, respectively. An indoor virulence test showed that oxime tebuconazole, tebuconazole, and tetramycin had significant bacteriostatic effects on the two Fusarium species. The genomes of QK8 and SX13 were assembled, and it was found that there was a certain gap in the size of the two fungi. The size of strain QK8 was 51,204,719 bp and that of strain SX13 was 55,171,989 bp. Afterwards, through phylogenetic analysis, it was found that strain QK8 was closely related to F. oxysporum, while strain SX13 was closely related to F. solani. Compared with the published whole-genome data for these two Fusarium strains, the genome information obtained here is more complete; the assembly and splicing reach the chromosome level. The biological characteristics and genomic information we provide here lay the foundation for further research on G. elata brown rot.
