Genome and Comparative Transcriptome Analysis of Growth and Developmental Changes in the Pileus of the Cyclocybe chaxingu

Black fungus is the second-most consumed edible fungus in China. The establishment of a risk assessment mechanism for heavy metals in black fungus is particularly critical to the safety of edible fungi. To clarify a risk assessment mechanism of heavy metal pollution of edible fungi in northeast China, in this study, the contents of Pb, Cr, CD and As in 415 samples were determined, and a total of 1660 valid data were obtained. Then, based on Monte Carlo simulation, a non-parametric probability assessment system for heavy metals in black fungus was established and improved. The results showed that the residual amounts of As, Pb, Cd and Cr in black fungus were in the order of Cr > Pb > As > Cd. The background content of four heavy metals in the main raw materials was preliminarily clarified. Among them, the content of As is between 0.010–0.320 mg·kg−1, Pb is between 0.051–0.792 mg·kg−1, Cd is between 0.019–0.236 mg·kg−1, and Cr is between 0.06–3.41 mg·kg−1. These results indicate that the dietary exposure risk of heavy metals ingested by dried black fungus in Chinese minors and adults is basically safe, but at the high exposure levels of 97.5% sites and 99% sites, Cr is at the light pollution level, and the comprehensive pollution of four heavy metals is at the moderate pollution level. In addition, this study found that raw materials can cause heavy metal accumulation in black fungus, mainly from sawdust, followed by rice bran and wheat bran.

Dynamic changes in pigmentation-related gene expression during morphogenesis in Plectropomus leopardus revealed by comparative transcriptome analysis

BackgroundBacillus cereus is a foodborne pathogen commonly found in nature and food and can cause food spoilage and health issues. Although the prevalence of B. cereus in foods has been reported worldwide, the extent of contamination in edible fungi, which has become increasingly popular as traditional or functional food, is largely unknown. Here we investigated the prevalence, toxin genes’ distribution, antibiotic resistance, and genetic diversity of B. cereus isolated from edible fungi in China.ResultsSix hundred and ninety-nine edible fungi samples were collected across China, with 198 (28.3%) samples found to be contaminated by B. cereus, with an average contamination level of 55.4 most probable number (MPN)/g. Two hundred and forty-seven B. cereus strains were isolated from the contaminated samples. Seven enterotoxin genes and one cereulide synthetase gene were detected. The detection frequencies of all enterotoxin genes were ≥ 80%, whereas the positive rate of the cesB gene in B. cereus was 3%. Most isolates were resistant to penicillins, β-lactam/β-lactamase inhibitor combinations, cephems, and ansamycins, but were susceptible to penems, aminoglycosides, macrolides, ketolide, glycopeptides, quinolones, phenylpropanol, tetracyclines, lincosamides, streptogramins, and nitrofurans. Meanwhile, 99.6% of all isolates displayed multiple antimicrobial resistance to three or more classes of antimicrobials. Using genetic diversity analysis, all isolates were defined in 171 sequence types (STs), of which 83 isolates were assigned to 78 new STs.ConclusionsThis study provides large-scale insight into the prevalence and potential risk of B. cereus in edible fungi in China. Approximately one-third of the samples were contaminated with B. cereus, and almost all isolates showed multiple antimicrobial resistance. Detection frequencies of all seven enterotoxin genes were equal to or more than 80%. These new findings may indicate a need for proper pre-/post-processing of edible fungi to eliminate B. cereus, thereby preventing the potential risk to public health.

Auricularia heimuer is one of the most popular edible fungi in China. It has high economic and medicinal value. The complete mitochondrial genome of A. heimuer is 40586 bp. It contains 48 genes, including 25 protein-coding genes, 22 tRNA genes, and 1 gene coding RNase P RNA. The G + C content is 37.92%. The phylogenetic relationships were constructed on the Bayesian inference method. It showed that A. heimuer was in distance to other species of Russulales, Polyporales, and Agaricales. The complete genome sequence of A. heimuer will provide a useful resource for the genetic and systematics studies.

BackgroundThe black cutworm, Agrotis ipsilon, is a serious global underground pest. Its distinct phenotypic traits, especially its polyphagy and ability to migrate long distances, contribute to its widening distribution and increasing difficulty of control. However, knowledge about these traits is still limited.ResultsWe generated a high-quality chromosome-level assembly of A. ipsilon using PacBio and Hi-C technology with a contig N50 length of ~ 6.7 Mb. Comparative genomic and transcriptomic analyses showed that detoxification-associated gene families were highly expanded and induced after insects fed on specific host plants. Knockout of genes that encoded two induced ABC transporters using CRISPR/Cas9 significantly reduced larval growth rate, consistent with their contribution to host adaptation. A comparative transcriptomic analysis between tethered-flight moths and migrating moths showed expression changes in the circadian rhythm gene AiCry2 involved in sensing photoperiod variations and may receipt magnetic fields accompanied by MagR and in genes that regulate the juvenile hormone pathway and energy metabolism, all involved in migration processes.ConclusionsThis study provides valuable genomic resources for elucidating the mechanisms involved in moth migration and developing innovative control strategies.

Pathogenicity and transcriptome analysis of a strain of Vibrio owensii in Fenneropenaeus merguiensis

Safety assessment of the fermented Phylloporia ribis (Lonicera japonica Thunb.) mycelia by oral acute toxicity study in mice and 90-day feeding study in rats

Pleurotus nebrodensis is a popular edible fungus in China. In December 2009, soft rot disease appeared on fruiting bodies of P. neberodensis in greenhouses located at Haidian District of Beijing, China. Early symptoms were water-soaked lesions on the pilei of the fruiting bodies. Lesions then spread and purulent tissues were formed. Severe soft rot induced production of deformed fruiting bodies and offensive odor. Diseased fruiting bodies stopped growth and commercial losses were estimated at 5 to 10%. Internal sections of the diseased pilei about 0.5 × 0.5 cm were suspended in 0.85% NaCl and the suspension was spread on trypticase soy agar (TSA) media. After incubation at 30°C for 2 days, dominant bacterial colonies were yellow, smooth, round, and convex. Cells were gram-negative, short rods, non-capsulated, motile, and non-spore forming. The 16S rRNA gene (1,408 bp, GenBank Accession No. KF849293) was amplified by using the universal forward primer P1 (5'-AGAGTTTGATCCTGGTCAGAACGCT-3') and the universal reverse primer P6 (5'-TACGGCTACCTTGTTACGACTTCACCCC-3'). Neighbor-joining tree analysis based on 16S rRNA gene sequences demonstrated the isolates belonged to the genus Pantoea and showed highest similarity with Pantoea beijingensis LMG 27579T (99.9% similarity, 2 base pair differences), which was isolated from the diseased fruiting bodies of P. eryngii in China. Pantoea sp. PA4, reported to be the pathogen of soft rot disease of P. eryngii in Korea (1), showed 99.8% similarity with P. ananatis ATCC 33244T, which suggested our isolates belonged to a different species with Pantoea sp. PA4 (supported by 97.9% similarity between the present isolates and Pantoea sp. PA4) (2). Results of physiological properties and enzyme activities determined by the API 20E, API 20NE, API 50CH, API ZYM (bioMérieux), and GN2 MicroPlate (Biolog) system showed that there was no difference between the present isolates and P. beijingensis LMG 27579T. Pathogenicity tests for these isolates were performed with bacterial suspensions (approximately 1 × 106 CFU/ml) that were grown for 24 h in trypticase soy broth (TSB). Fruiting bodies of P. nebrodensis were induced after spawn was run for 30 days in plastic bags. When the young fruiting bodies were forming, the prepared bacterial suspension was sprayed onto the surface of the pilei. Sterilized TSB media was used as a negative control. All inoculated fruiting bodies were then incubated at 16°C with 80 to 95% relative humidity. Assays were conducted twice and five fruiting bodies were used each time. Results were observed after 5 to 10 days of incubation. The symptoms that developed were similar to those observed in the original samples. The negative control remained symptomless. Koch's postulates were fulfilled by re-isolating bacteria, which were identical to the original isolates based on 16S rRNA gene sequence analysis, physiological properties and enzyme activities. Pantoea ananatis was first reported as a pathogen of Pleurotus eryngii, causing soft rot disease (1), but to the best of our knowledge, this is the first report of P. beijingensis- induced soft rot disease of P. nebrodensis in China. This disease may be an emerging disease problem in the near future and information on this pathogen will be useful in the development of management practices.

Mitochondria play a pivotal role in fungal growth, development, and metabolic regulation, yet their significance has often been overlooked in traditional breeding programs. Auricularia heimuer, the second most widely cultivated edible fungus in China, has attracted increasing attention due to its nutritional and health-promoting properties, underscoring the urgent need for the development of functional cultivars and the elucidation of mitochondrial regulatory mechanisms. In this study, we constructed isonuclear alloplasmic strains with identical nuclear genotypes but distinct mitochondrial backgrounds. Comparative analyses of mycelial growth, fruiting body morphology, and nutritional composition were conducted, alongside transcriptomic profiling. The results showed no significant morphological differences on sawdust-based medium; however, on PDA medium, the strains exhibited notable differences in growth rate, melanin content, β-glucan levels, iron ion concentration, and amino acid content. Transcriptomic analysis identified 3385 differentially expressed genes (DEGs), which were enriched in pathways related to lysine biosynthesis, purine metabolism, DNA replication, and repair. Key DEGs involved in lysine biosynthesis were found to encode aminoadipate reductase (AAR) and saccharine dehydrogenase (SDH), with AAR localized in the cytoplasm and potentially regulating lysine synthesis through its enzymatic activity. This study highlights the critical influence of mitochondrial genes on the metabolic composition and transcriptional landscape of A. heimuer, providing a theoretical foundation for genetic improvement and the development of functional fungal cultivars.

ABSTRACTMorchella sextelata is a valuable and popular commercial edible fungus in China. Hot‐air drying can enhance the flavor and quality of edible mushrooms; however, the resulting changes in volatile and non‐volatile metabolites have not been investigated for M. sextelata. In the present study, we used a widely targeted metabolomics approach combining ultra‐high‐performance liquid chromatography–tandem mass spectrometry (UHPLC–MS/MS) and gas chromatography–mass spectrometry (GC–MS) to explore the dynamic variations in metabolites after hot‐air drying and the influence of drying treatment on the flavoromics of different sections of the fruiting bodies of M. sextelata. In total, we identified 1419 non‐volatile and 270 volatile metabolites. Based on multivariate statistical analysis, we identified 511 metabolites with significant differences between fresh and dry products, revealing that hot‐air drying resulted in more nutty, toasty, and fatty flavors, particularly in the pileus. Moreover, hot‐air drying enriched the beneficial dietary components of the pileus. Through the elucidation of the metabolite changes that occur in M. sextelata after hot‐air drying, this study provides theoretical support for the higher commercial value of the pileus after drying and can be applied to improve the quality of dried morels.

采用改良的QuEChERS方法,结合超高效液相色谱-串联质谱(UHPLC-MS/MS)建立了银耳和木耳中米酵菌酸含量测定的分析方法。对QuEChERS方法的提取、净化条件进行了优化,发现提取液中乙酸含量对米酵菌酸的提取效率影响很大,最终采用5%(v/v)乙酸乙腈为提取溶剂,盐析分层,再用200 mg C18分散固相萃取净化。对UHPLC-MS/MS分析条件也进行了优化,以含0.01%(v/v)甲酸、0.05%(v/v)氨水的水溶液和甲醇为流动相,在Waters HSS T3柱(100 mm×2.1 mm, 1.8 μm)上分离,以电喷雾电离、多反应监测负离子模式进行检测。在优化好的条件下,银耳和木耳中米酵菌酸检测的基质效应分别为-6.3%和-11.5%,表明该方法具有很好的净化效果,样品基质不会对米酵菌酸的检测产生影响。进一步对方法学进行了考察,在1~200 μg/L范围内,线性方程回归系数的平方(R2)大于0.999,以信噪比的3倍和10倍计算的方法检出限和定量限分别为0.15 μg/kg和0.5 μg/kg。银耳中3种添加水平0.5、10、50 μg/kg下的加标回收率为92.4%~102.6%,日内和日间相对标准偏差(RSD)分别为4.3%~4.9%和3.2%~3.5%;木耳的加标回收率为89.6%~102.3%,日内和日间RSD分别为2.4%~9.5%和3.6%~4.1%,表明该方法具有很好的准确度和精密度。最后,将该方法应用于实际样品中米酵菌酸的分析,取得了很好的效果。该工作为银耳和木耳中米酵菌酸的风险防控提供了一种有效的检测技术。

Hericium caput-medusae (Bull.:Fr.) Pers. fermentation concentrate polysaccharides improves intestinal bacteria by activating chloride channels and mucus secretion

Qingyuan County, Zhejiang, China is recognized as a source of mushrooms around the world and as Mushroom City in China. Because of a favorable ecological environment and abundant forest resources, mushroom farmers in Qingyuan have engaged in mushroom production for 800 years and continued to form unique mushroom production systems where people and nature live in a harmonious way, and a rich and colorful mushroom culture. The Qingyuan Mushroom Culture System was named the Nationally Important Agricultural Heritage systems of China in 2014. Based on analysis of the importance of agricultural heritage and the necessity and urgency of protection, here we examine the agricultural heritage of the Qingyuan mushroom culture system as a research case study and comprehensively describe its heritage values, including supply materials and production, ecosystem services, cultural inheritance and multi-function agricultural development. These results provide reference values for agricultural heritage protection and inheritance of edible fungi in China, agricultural sustainable development and extension of agricultural function.

Identification of phytochemicals from Lentinus edodes and Auricularia auricula with UPLC-Q-Exactive Orbitrap MS

Pleurotus ostreatus is a widely cultivated edible fungus in China. Green mold disease of P. ostreatus which can seriously affect yield is a common disease during cultivation. It occurs mostly after P. ostreatus mycelia have been subjected to high temperatures. However, little information is available on the relationship between high temperature and green mold disease. The aim of this study is to prove that extracellular metabolites of P. ostreatus affected by high temperature can promote the growth of Trichoderma asperellum. After P. ostreatus mycelia was subjected to high temperature, the extracellular fluid of P. ostreatus showed a higher promoting effect on mycelial growth and conidial germination of T. asperellum. The thiobarbituric acid reactive substance (TBARS) content reached the maximum after 48 h at 36°C. A comprehensive metabolite profiling strategy involving gas chromatography-mass spectrometry (GC/MS) combined with liquid chromatography-mass spectrometry (LC/MS) was used to analyze the changes of extracellular metabolites in response to high temperature. A total of 141 differential metabolites were identified, including 84.4% up-regulated and 15.6% down-regulated. Exogenous metabolites whose concentrations were increased after high temperature were randomly selected, and nearly all of them were able to promote the mycelial growth and conidial germination of T. asperellum. The combination of all selected exogenous metabolites also has the promotion effects on the mycelial growth and conidial germination of T. asperellum in a given concentration range in vitro. Overall, these results provide a first view that high temperature affects the extracellular metabolites of P. ostreatus, and the extensive change in metabolites promotes T. asperellum growth.