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Scanning electron micrograph of mycelia covering the outside of a fruiting bodies of natural Chinese Cordyceps.: (a) Anatomic structure of Chinese Cordyceps clearly showed the worm gut; (b) The spliced image of the Chinese Cordyceps segmentation using scanning electron microscopy (10×); (c) The sclerotia segmentation image shows that the lava was covered with mycelial cortices (10×); (d) The stromata segmentation image shows the fungal filaments on the surface of stromata (500×).
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Chinese Cordyceps, known in Chinese as “DongChong XiaCao”, is a parasitic complex of a fungus (Ophiocordyceps sinensis) and a caterpillar. The current study explored the endogenetic fungal communities inhabiting Chinese Cordyceps. Samples were collected from five different geographical regions of Qinghai and Tibet, and the nuclear ribosomal interna...
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... were much more complex than initially considered. Scanning electron microscopy (Hitachi S-3400N, Hitachi High Technologies, Japan) revealed that the surface of the fruit- ing bodies of Chinese Cordyceps are covered with a mycelia complex, indicating an abundant community of fungi on the surface of the fruiting bodies of Chinese Cordyceps (Fig. 5). However, because of the limitation of the available techniques, the diversity and the structure of the endogenetic fungal communities of Chinese Cordyceps remains unclear. In the present study, 787,002 high-quality reads from 65 genera were identified from the Chinese Cordyceps using Illumina Miseq sequencing (Table S2). Compared with ...
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Understanding the normal variation of the sugarcane rhizosphere fungal community throughout its life cycle is essential for the development of agricultural practices for fungal and ecological health associated with the microbiota. Therefore, we performed high-throughput sequencing of 18S rDNA of soil samples using the Illumina sequencing platform f...
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... The diversity of plant endophytes and the establishment of community structures are closely related to factors such as plant variety, growth environment, and geographic location [40]. Endophytic bacteria, which are associated with plant health and productivity, have become a focal point of interest in scientific and commercial realms worldwide in recent years [22,41,42]. However, the effects of VTM mining on the diversity and function of endophytic bacteria in the root systems of nearby plants, as well as the response strategies of root endophytes, have not been determined. ...
This study utilized 16S rRNA high-throughput sequencing technology to analyze the community structure and function of endophytic bacteria within the roots of three plant species in the vanadium–titanium–magnetite (VTM) mining area. The findings indicated that mining activities of VTM led to a notable decrease in both the biodiversity and abundance of endophytic bacteria within the root systems of Eleusine indica and Carex (p < 0.05). Significant reductions were observed in the populations of Nocardioides, concurrently with substantial increments in the populations of Pseudomonas (p < 0.05), indicating that Pseudomonas has a strong adaptability to this environmental stress. In addition, β diversity analysis revealed divergence in the endophytic bacterial communities within the roots of E. indica and Carex from the VTM mining area, which had diverged to adapt to the environmental stress caused by mining activity. Functional enrichment analysis revealed that VTM mining led to an increase in polymyxin resistance, nicotinate degradation I, and glucose degradation (oxidative) (p < 0.05). Interestingly, we found that VTM mining did not notably alter the endophytic bacterial communities or functions in the root systems of Dodonaea viscosa, indicating that this plant can adapt well to environmental stress. This study represents the primary investigation into the influence of VTM mining activities on endophytic bacterial communities and the functions of nearby plant roots, providing further insight into the impact of VTM mining activities on the ecological environment.
... Alpha diversity is a comprehensive index of microbial richness and evenness in the habitat [40]. Chao1 index and ACE index are used to compare community abundance [41], while Shannon index and Simpson index are used to compare community diversity [42]. As shown in Table S2, the coverage of all experimental samples is 1, indicating that the sequencing results can basically represent the actual situation of the samples [43]. ...
Sour bamboo shoot is a Chinese fermented vegetable with unique flavors and is favored by local consumers. In this study, at different fermentation times, the texture of bamboo shoots and the changing rules of pH, titratable acid (TA), reduced sugar, and nitrite in bamboo shoot fermentation broth were explored. Headspace solid-phase microextraction (HS-SPME) combined with gas chromatography-mass spectrometry (GC-MS) and orthogonal partial least squares discriminant analysis (OPLS-DA) were used to investigate the dominant aroma compounds. 16S rRNA high-throughput sequencing technology (HTS) was employed to investigate the core microbial communities. The results show that the chewiness, fracturability, hardness, and pH decreased, while TA increased during the 60-day fermentation. The contents of reducing sugar and nitrite peaked on the 14th day of fermentation and then decreased. A total of 80 volatile compounds were detected during sour bamboo shoot fermentation, with 2,4-Di-tert-butylphenol having the highest concentration. Among them, 12 volatile compounds (VIP ≥ 1) were identified as characteristic aroma substances of sour bamboo shoots. The dominant bacterial phyla in sour bamboo shoots were Firmicutes and Proteobacteria, while Bacillus and Acinetobacter were the dominant genus. Correlation analysis showed that Firmicutes exhibited a positive correlation with 3,6-Nonadien-1-ol, (E,Z)-, Oxalic acid, isobutyl hexyl ester, and (-)-O-Acetylmalic anhydride, whereas Bacillus exhibited a negative correlation with Silanediol, dimethyl-, and Oxime-, methoxy-phenyl-. A detailed picture of the microbial community of fermented bamboo shoots has been provided by this study, and it may provide insight into the Chinese traditional fermented vegetable microbial structure.
... Alpha diversity is a comprehensive index of microbial richness and evenness in the habitat [37]. Chao1 index and ACE index are used to compare community abundance [38], while Shannon and Simpson index are used to compare community diversity [39]. As shown in Table S2, the coverage of the experimental samples is all 1, indicating that the sequencing results can basically represent the actual situation of the samples [40]. ...
Fermented bamboo shoots are a distinctive ingredient in Southern cuisine. In this study, headspace solid-phase microextraction (HS-SPME) combined with gas chromatography-mass spectrometry (GC-MS), and 16S rRNA high-throughput sequencing technology (HTS) were employed to investigate the relationship among physicochemical properties, characteristic volatile compounds, and core microbial communities. The results show that the chewiness, fracturability, hardness, and pH decreased, while total acidity increased during 60d-fermentation. The contents of reducing sugar and nitrite reached the peak on the 14th day of fermentation and then decreased. A total of 80 volatile compounds were detected during sour bamboo shoot fermentation, with 2,4-Di-tert-butylphenol having the highest concentration. Among them, 12 volatile compounds (VIP ≥ 1) were identified as characteristic aroma substances of sour bamboo shoots. The dominant bacterial phyla in sour bamboo shoots were Firmicutes and Proteobacteria, while Bacillus and Acinetobacter were the dominant genus. Correlation analysis showed that Firmicutes positive correlation with 3,6-Nonadien-1-ol, (E,Z)-, Oxalic acid, isobutyl hexyl ester ,(-)-O-Acetylmalic anhydride, TA Bacillus was negative correlation with Silanediol, dimethyl-, and Oxime-, methoxy-phenyl-. This study provides a theoretical basis for screening flavor-enhancing microorganisms as fermentation agents in sour bamboo shoots, which can contribute to the improvement of their quality.
... In recent years, the 16S rRNA sequencing technology has been widely applied in the study of fungal diversity. Xia F studied the endophytic fungal community structure of Cordyceps Sinensis in five regions of Qinghai and Tibet by high-throughput sequencing (Xia et al. 2016). Shen et al. used high-throughput sequencing to analyze the community composition and its diversity of inter-rhizosphere soil fungi of wild and reintroduced Chinese wheatgrass (Shen et al. 2020). ...
The Ebinur Lake wetland in Xinjiang is a typical wetland, comprising a desert ecosystem with rich soil microbial resources, especially soil fungi in the inter-rhizosphere regions of the wetland plants. This study aimed to clarify the diversity and community structures of the inter-rhizosphere soil fungi of plants in areas of high salinity in the Ebinur Lake wetland and their correlations with environmental factors, as little is currently known on this topic. The diversity and differences in the community structures of fungi associated with 12 salt-tolerant plant species in the Ebinur Lake wetland were investigated using 16S rRNA sequencing. Correlations between the fungi and environmental factors, specifically, the physiochemical characteristics of the soil, were evaluated. The results showed that fungal
diversity was highest in the rhizosphere soil of Haloxylon ammodendron, followed by H. strobilaceum. The dominant fungal groups were found to be Ascomycota and Basidiomycota, and the dominant genus was Fusarium. Redundancy analysis revealed significant associations between total nitrogen, electrical conductivity, and total potassium in the soil and both the diversity and abundance of the fungi (P < 0.05). Furthermore, the abundance of fungi of all genera in the rhizosphere soil samples were found to be strongly correlated with environmental physicochemical factors such as available nitrogen and phosphorus. These findings provide data and theoretical support for a better understanding of the ecological resources of fungi in the Ebinur Lake wetland.
... Furthermore, although effective in fungal enumeration, dilution plating may favor the most abundant species over the less abundant and slower growers, which may result in the underrepresentation of the latter (26)(27)(28). Hence, using HDSeq would likely give a more realistic picture of fungal diversity than plating methods (28)(29)(30)(31). Previous studies (26,27) similarly demonstrated a higher number of detected genera by HDSeq compared to plating. ...
The preharvest maize mycobiome may be crucial in defining the health of the crop in terms of potential disease burden and mycotoxins. We investigated the preharvest maize mycobiome structure, including the influence of weather patterns, in terms of rainfall intensity, on its composition. In addition, we investigated correlation of genera Fusarium and Aspergillus with maize fumonisin-B1 and aflatoxin. Forty maize fields from selected districts in the wetter northern (N) and drier southern (S) agroecological zones of Zambia were sampled twice over two seasons (1 and 2). The defined weather variables over the two seasons were low rainfall with dry spell (S1), low rainfall (S2), and high rainfall (N1 and N2). High-throughput DNA amplicon sequencing of internal transcribed spacer 1 (ITS1) was used to determine the mycobiome structure and the composition in relation to rainfall patterns. We detected 61 genera, with Fusarium and previously unreported Sarocladium in Zambia to have the highest frequency of detection on the maize. There was a significant difference in fungal genera composition between S1 and S2 but no difference between N1 and N2. The weather pattern with dry spell, S1, had a strong proliferation of Meyerozyma and xerophiles Penicillium, Kodamaea, and Aspergillus. The four genera drove the difference in composition between S1 and S2 and the significantly higher fungal diversity in S1 compared to N2. Of the mycotoxin-important fungi, dry conditions (S1) were a key driver for proliferation of Aspergillus, while Fusarium proliferation occurred irrespective of weather patterns. The relative abundance of Aspergillus and Fusarium resonated with maize aflatoxin and fumonisin-B1 levels, respectively. IMPORTANCE Fungi contaminate various crops worldwide. Maize, an important human staple and livestock cereal, is susceptible to contamination with fungi in the field. Fungi are drivers of plant disease and can compromise yield. Some species of fungi are known to produce chemical compounds (mycotoxins), which are cancer-causing agents in humans and impair livestock productivity. It is important to understand the spectrum of fungi on maize and how weather conditions can impact their abundance. This is because the abundance of fungi in the field can have a bearing on the health of the crop as well as potential for mycotoxins contamination. By understanding the spectrum of the preharvest fungi, it becomes possible to know the key fungi adapted to the maize and subsequently the potential for crop disease as well as mycotoxins contamination. The influence of weather conditions on the spectrum of preharvest fungi on maize has not been fully explored.
... And the establishment of plant endophyte diversity and community structure is closely related to plant varieties, genotypes, growth environment, geographical location and other factors (Rangjaroen et al., 2019). The plant endophyte is seemed to be an important determinant of plant health and productivity, and has attracted extensive attention worldwide in recent years as a subject of scientific and commercial interest (Gaiero et al., 2013;Xia et al., 2016;Wang et al., 2021). The tuber of G. elata, as an important part of human nutrition and drug, which are rich in microbial resources (Steinbrecher and Leubner-Metzger, 2016). ...
... Moreover, we found that the alpha and beta diversity of the endophytic bacteria of G. elata was the difference in different regions. The result demonstrated that many factors, including the level of oxygen, moisture and other environmental factors, could affect diversity levels of the endophytic bacteria community (Xia et al., 2016). This found is consistent with previous studies on endophytic bacteria communities in Camellia sinensis and saline-alkali tolerant rice, which also found that some key factors (e.g., salt, catechins, gallic acid and anthocyanidin etc.) determine the composition of endophytic bacteria (Wu et al., 2020;Wang et al., 2021). ...
Gastrodia elata f.glauca (G. elata) is a commonly used Chinese Medicinal Materials with great medicinal value. The medicinal plant and its endophytic bacteria are a symbiotic whole, and the endophytic bacteria are rich in species, and their metabolites are a treasure trove of natural compounds. However, there is a relative lack of analysis on the diversity, flora composition and network interactions of the endophytic bacteria of G. elata. In this study, high-throughput sequencing technology based on the Illumina Miseq platform was used to reveal the core microbiota by examining the diversity and community structures of tuber endophytic bacteria in G. elata grown under different regions and exploring the effect of region on its endophytic bacteria. Here, 1,265 endophytic ASVs were found to coexist with G. elata tuber in Guizhou and Hubei. At the phylum level, the dominant phyla were Proteobacteria, Actinobacteria and Acdobacteriota. At the family level, the dominant family were Comamonadaceae, Nocardicaece, Xanthobacteraceae, and Burkholderiaceae. At the genus level, Delftia and Rhodococcus were represented the core microbiota in G. elata tuber, which served as the dominant genera that coexisted in all samples tested. Moreover, we found that the beta diversity of endophytic bacteria in G. elata tuber was higher level in the Guizhou region than Hubei region. Overall, this study results to provide a reference for screening active strains and interaction between plants and endophytic bacteria.
... Furthermore, a comparison of the fungal communities of O. sinensis and O. nujiangensis showed that they had different community compositions. However, Trichothecium and Microdochium could not be found among the top 19 genera in fungal communities of O. sinensis reported (Xia et al. 2016). Consequently, the differences in the microbial community composition of closely related species might be suitable as further evidence for identifying species. ...
Ophiocordyceps contains the largest number of Cordyceps sensu lato , various species of which are of great medicinal value. In this study, a new entomopathogenic fungus, Ophiocordyceps nujiangensis , from Yunnan in southwestern China, was described using morphological, phylogenetic, and mitogenomic evidence, and its fungal community composition was identified. It was morphologically characterized by a solitary, woody, and dark brown stromata, smooth-walled and septate hyphae, solitary and gradually tapering conidiogenous cells with plenty of warty protrusions, and oval or fusiform conidia (6.4–11.2 × 3.7–6.4 µm) with mucinous sheath. The phylogenetic location of O. nujiangensis was determined based on the Bayesian inference (BI) and the maximum likelihood (ML) analyses by concatenating nrSSU, nrLSU, tef-1a , rpb1 , and rpb2 datasets, and ten mitochondrial protein-coding genes (PCGs) datasets ( atp6 , atp9 , cob , cox2 , nad1 , nad2 , nad3 , nad4 , nad4L , and nad5 ). Phylogenetic analyses revealed that O. nujiangensis belonged to the Hirsutella sinensis subclade within the Hirsutella clade of Ophiocordyceps . And O. nujiangensis was phylogenetically clustered with O. karstii , O. liangshanensis , and O. sinensis . Simultaneously, five fungal phyla and 151 fungal genera were recognized in the analysis of the fungal community of O. nujiangensis . The fungal community composition differed from that of O. sinensis , and differences in the microbial community composition of closely related species might be appropriate as further evidence for taxonomy.
... The application of DNA metabarcoding could overcome this limitation and better reveal the fungal diversity. For example, Xia et al. found that 55 genera in Chinese Cordyceps that were not observed by culture-dependent methods were identified through Illumina Miseq sequencing [45]. Similarly, another study indicated that the number of fungi in Coix Seed detected by HTS was considerably greater than that by potato dextrose agar medium [46]. ...
Morindae Officinalis Radix (MOR) and Alpiniae Oxyphyllae Fructus (AOF) have been widely used as dietary supplements and traditional herbal medicines for centuries. Fungal and mycotoxin contamination in MOR and AOF has been reported recently. In this study, fungi in MOR and AOF are first investigated using DNA metabarcoding, and the differences in fungal microbiome between moldy and non−moldy samples are analyzed. The results show that Ascomycota is the most prevailing fungus at the phylum level in MOR and AOF with relative abundances of 49.53–94.32% and 14.81–81.85%, respectively. Penicillium (1.86–76.14%), Cladosporium (1.82–56.65%), and Trichoderma (0.12–19.71%) are the dominant genera in MOR. Penicillium (0.27–56.06%), Papiliotrema (0.04–51.71%), and Cladosporium (3.08–44.41%) are the dominant genera in AOF. Two potential toxigenic fungi were detected, namely, Trichoderma atroviride and Fusarium equiseti. Moreover, the differences in fungal communities between moldy and non−moldy samples were monitored. In conclusion, DNA metabarcoding can be used to assess the fungal microbiome in edible medicinal herbs, thereby providing a basis for ensuring food safety and drug efficacy.
... Bacteria and fungi serve major roles in processing raw materials, minimizing fungal competitors, and inducing fructification [3,123,136]. Multiple bacteria and fungi play important roles in the population differentiation, environmental suitability, infection mechanism, and quality of Ophiocordyceps sinensis [16,[137][138][139]. Proteobacteria, Firmicutes, Verrucomicrobia, and Deltaproteobacteria are the most relatively abundant bacteria detected during the life cycle of O. highlandensis [17]. ...
Lignocellulosic materials commonly serve as base substrates for mushroom production. Cellulose, hemicellulose, and lignin are the major components of lignocellulose materials. The composition of these components depends upon the plant species. Currently, composted and non-composted lignocellulosic materials are used as substrates in mushroom cultivation depending on the mushroom species. Different substrate compositions can directly affect the quality and quantity of mushroom production yields. Consequently, the microbial dynamics and communities of the composting substrates can significantly affect mushroom production. Therefore, changes in both substrate composition and microbial diversity during the cultivation process can impact the production of high-quality substrates and result in a high degree of biological efficiency. A brief review of the current findings on substrate composition and microbial diversity for mushroom cultivation is provided in this paper. We also summarize the advantages and disadvantages of various methods of mushroom cultivation by analyzing the microbial diversity of the composting substrates during mushroom cultivation. The resulting information will serve as a useful guide for future researchers in their attempts to increase mushroom productivity through the selection of suitable substrate compositions and their relation to the microbial community.
... Currently, the comparison between wild and cultivated O. sinensis predominantly focuses on the detection of components' contents (Zheng-Ming et al., 2016), differences in identification , and research on the pharmacological effects of certain types of biologically active ingredients (Zhou et al., 2008); however, such comparisons do not fundamentally explain the formation mechanism of these differences. With the rapid development of high-throughput technologies, applying omics methods to study differences in biological characteristics has become an effective method (Zhu et al., 2014;Xia et al., 2016;Xia et al., 2017). For instance, using mRNA sequencing data of cultivated and wild tomatoes, wild tomatoes were shown to have better salt tolerance and drought resistance based on the molecular levels (Dai et al., 2017). ...
Background:
Ophiocordyceps sinensis is a species endemic to the alpine and high-altitude areas of the Qinghai-Tibet plateau. Although O. sinensis has been cultivated since the past few years, whether cultivated O. sinensis can completely replace wild O. sinensis remains to be determined.
Methods:
To explore the differences of O. sinensis grown in varied environments, we conducted morphological and transcriptomic comparisons between wild and cultivated samples who with the same genetic background.
Results:
The results of morphological anatomy showed that there were significant differences between wild and cultivated O. sinensis, which were caused by different growth environments. Then, a total of 9,360 transcripts were identified using Illumina paired-end sequencing. Differential expression analysis revealed that 73.89% differentially expressed genes (DEGs) were upregulated in O. sinensis grown under natural conditions compared with that grown under artificial conditions. Functional enrichment analysis showed that some key DEGs related to fatty acid metabolism, including acyl-CoA dehydrogenase, enoyl-CoA hydratase, 3-ketoacyl-CoA thiolase, and acetyl-CoA acetyltransferase, were upregulated in wild O. sinensis. Furthermore, gas chromatography-mass spectrometry results confirmed that the fatty acid content of wild O. sinensis was significantly higher than that of cultivated O. sinensis and that unsaturated fatty acids accounted for a larger proportion.
Conclusion:
These results provide a theoretical insight to the molecular regulation mechanism that causes differences between wild and cultivated O. sinensis and improving artificial breeding.
