Aflatoxins and fungal community distribution during harvesting and processing of Platycladi Semen / 中国中药杂志

This study aimed to analyze aflatoxins content and fungal community distribution in the harvesting and processing of Platycladi Semen, and explore the key link that affects aflatoxins contamination. The related Platycladi Semen samples of different maturity periods(cone non-rupture period, early rupture, and complete rupture period) and different processing periods(before drying, during 2-d drying, during 7-d drying, before and after seed scale removal, before and after peeling, 1 d after color sorting, and 7 d after color sorting) were collected for identifying the fungal community composition on sample surface by ITS amplicon sequencing. Then the content of aflatoxins B_1, B_2, G_1 and G_2 was determined by HPLC-MS/MS. The results showed that during the harvesting of Platycladi Semen from cone non-rupture to complete rupture, aflatoxins were only detected in the seed scale and seed coat, with aflatoxin G_2 in the seed scale and aflatoxin B_1 in the seed coat. During the drying, with the prolongation of drying time, aflatoxins B_1 and G_2 were detected simultaneously in the seed scale, aflatoxin B_1 in the seed coat, and low-content aflatoxin B_1 in the seed kernel. During subsequent processing, the aflatoxin content in seed kernel during subsequent processing was slighted increased. As demonstrated by fungal detection, Aspergillus flavus was not present during the harvesting of Platycladi Semen, but present during the drying and processing. Its content in the seed coat during the drying process was relatively higher. In short, Platycladi Semen should be harvested as soon as possible after it becomes fully mature. Drying process is the key link of preventing aflatoxin contamination. It is advised to build a sunlight room or adopt similar settings, standardize the operations in other processes, and keep the surrounding environment clean to minimize aflatoxin contamination.

Comparison of endogenetic microbial community diversity between wild Cordyceps sinensis,artificial C. sinensis and habitat soil / 中国中药杂志

To obtain the difference of the fungal and bacterial community diversity between wild Cordyceps sinensis, artificial C. sinensis and their habitat soil, Illmina Hiseq high-throughput sequencing technology was applied. The results show that Proteobacteria was the dominant bacterial phylum in C. sinensis, Actinobacteria was the dominant bacterial phylum in soil microhabitat, Ophiocordyceps sinensis was the predominant dominant fungus of C. sinensis. The α diversity analysis showed that the fungal diversity of stroma was lower than other parts, and the fungal diversity of wild C. sinensis was lower than that of artificial C. sinensis. The β diversity analysis showed that the fungal and bacterial community diversity of soil microhabitat samples was significantly different from that of C. sinensis. The fungal community diversity was less different between wild and artificial C. sinensis, especially in sclerotia. LEfSe analysis showed a lot of species diversity between wild and artificial C. sinensis. Those different species between wild C. sinensis, artificial C. sinensis and their habitat soil provide ideas for further research on breed and components of C. sinensis.

Analysis of Rhizosphere Soil Fungal Community Composition and Diversity of Salvia miltiorrhiza Based on ITS Sequences / 中国实验方剂学杂志

Objective: To study rhizosphere soil fungal community composition and diversity of Salvia miltiorrhiza,in order to explain the changes of the rhizosphere microenvironment of S.miltiorrhiza,and provide theoretical basis for revealing the reasons for the formation of continuous obstacles.Method: Based on the high-throughput sequencing technology,three kinds of soil samples were collected,namely soil of non-plant (CK),soil for cultivating for one year (Y1) and soil for cultivating for two years (Y2),respectively.According to the sequencing of the internal transcribed space of nuclear ribosomal DNA (ITS) region of fungal rRNA gene,14 153,19 024 and 7 622 valid sequences were obtained and annotated as 1 027,1 095 and 712 varieties of OTUs.The diversity of fungal communities showed a trend of decreasing first and then increasing.Agaricomycetes,Leotiomycetes and Tremellomycetes were the dominant bacterial communities at the class level,their orders in three treatments were Y1 > CK > Y2,Y2 > Y1 > CK,CK > Y2 > Y1.At the genus level,Guehomyces was dominant species in CK,and both Y1 and Y2 had a decrease of 96.13% and 90.21%,respectively.Wickerhamomyces had a significantly increase in Y2(6.64%),250.59% and 564.00% compared with CK and Y1,respectively.Result: The results of cluster analysis showed that CK and Y1 had a higher similarity at the genus level in soil fungal community composition compared with Y2.Conclusion: Cryptosporiopsis and other pathogenic fungal communities were dominant genuses according to the heatmap analysis in Y2,suggesting a correlation with the incidence of S.miltiorrhiza.The findings provide theoretical basis for the formation of continuous cropping obstacle.

Research on relationship between occurrence of root rot and changes of fungal communities in rhizosphere of Panax quinquefolius / 中国中药杂志

The root rot disease is a common disease during the cultivation of Panax quinquefolius. In order to provide some clues for solving the root rot disease of P. quinquefolius, the relationship between rhizosphere soil fungal communities and root rot of P. quinquefolius was investigated in this study. The diversities and the changes of fungal communities structure in blank control group (group C), rhizosphere soil of healthy P. quinquefolius (group N) and occurrence of root rot in rhizosphere soil of P. quinquefolius (group R)were analyzed byusing the Illumina MiSeq high-throughput sequencing technology. A total of 505 968 high-quality sequences were obtained through high-throughput sequencing and the rare faction curves analysis showed that the sequencing depth was sufficient and the sampling was reasonable. The fungal communities structure of rhizosphere soil samples mainly belonged to 9 phylums including Ascomycota(54.9%), Basidiomycota(5.6%), etc., and the dominant specie was Ascomycota of the total fungal identified, respectively. The 115 genera of fungi were tested, including Monographella (3.9%), Archaeorhizomyces (3.9%), Mortierella, etc., and the dominant specie was Monographella. At the genus level, the abundance of Monographella and Mortierella in group R increased significantly compared with the abundance in groups C and N. Alpha diversity index of species showed that the diversity index of fungal communities reduced and the numbers of fungi reduced in group N and R, compared with group C, and reaching the minimum in group R. Beta diversity index of species showed that there was a significant difference in the fungal communities structure in each sample. In addition, the heat map analysis revealed that the dominant fungal genera were significantly different among the each sample. The proportion of Monographella and Mortierella in group R was significantly higher than that in group C and N, while the proportion of Trichoderma,Penicillium and Cadophora in group R was extremely low. The proportion of Phoma and Gibberella in group R increased significantly compared with group C. This study clarified the decline of diversity index and the imbalance of community structure in fungi may lead to the occurrence of root rot in P. quinquefolius by analysis of fungal diversity and community composition in the rhizosphere soil of P. quinquefolius in this study, which provided a theoretical basis for the prevention and treatment of occurrence of root rot in P. quinquefolius.

Illumina high-throughput sequencing reveals fungal community composition and diversity in root rot of Coptis chinensis in rhizosphere soil / 中草药

Objective To reveal fungal community composition and diversity in health and root rot of Coptis chinensis in rhizosphere soil. Methods High-throughput sequencing technology was used to characterize the fungal community composition, richness, and diversity of health and root rot Coptis chinensis in rhizosphere soil in Shizhu County of Chongqing Province. Spearman analysis was used to evaluate the correlation between soil physicochemical parameters and the first 35 most abundant fungal genera. Results More than 106 267 effective tags were obtained, and the community was composed of six phyla (Ascomycota, Zygomycota, Basidiomycota, Glomeromycota, Chytridiomycota, and Neocallimastigomycota). The fungal community diversity showed no significant difference in healthy and root rot samples. The relative abundance of Ascomycota, Basidiomycota and Chytridiomycota in root rot soil was significantly higher than that in healthy soil. Moreover, the relative abundance of Zygomycota, Glomeromycota, and Neocallimastigomycota in root rot soil was significantly lower than in healthy soil. The relative abundance of Fusarium was significantly higher in root rot samples than in healthy samples. Spearman analysis showed that the relative abundance of Fusarium was significantly positively correlated with pH and available phosphorus, but negatively correlated with alkali-hydrolyzable nitrogen. Conclusion Changes in soil physicochemical characteristics were related to the changes in soil fungal diversity.

Influence of Peanut Cultivars and Environmental Conditions on the Diversity and Community Composition of Pod Rot Soil Fungi in China

Peanut yield and quality are seriously affected by pod rot pathogens worldwide, especially in China in recent years. The goals of this study are to analyze the structure of fungal communities of peanut pod rot in soil in three peanut cultivars and the correlation of pod rot with environmental variables using 454 pyrosequencing. A total of 46,723 internal transcribed spacer high-quality sequences were obtained and grouped into 1,706 operational taxonomic units at the 97% similarity cut-off level. The coverage, rank abundance, and the Chao 1 and Shannon diversity indices of the operational taxonomic units were analyzed. Members of the phylum Ascomycota were dominant, such as Fusarium, Chaetomium, Alternaria, and Sordariomycetes, followed by Basidiomycota. The results of the heatmap and redundancy analysis revealed significant variation in the composition of the fungal community among the three cultivar samples. The environmental conditions in different peanut cultivars may also influence on the structure of the fungal community. The results of this study suggest that the causal agent of peanut pod rot may be more complex, and cultivars and environmental conditions are both important contributors to the community structure of peanut pod rot fungi.

Soil pretreatment and fast cell lysis for direct polymerase chain reaction from forest soils for terminal restriction fragment length polymorphism analysis of fungal communities

Abstract Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high purity DNA from soil microbiota, five prewashing agents were compared in terms of their efficiency and effectiveness in removing soil contaminants. Residual contaminants were precipitated by adding 0.6 mL of 0.5 M CaCl2. Four cell lysis methods were applied to test their compatibility with the pretreatment (prewashing + Ca2+ flocculation) and to ultimately identify the optimal cell lysis method for analyzing fungal communities in forest soils. The results showed that pretreatment with TNP + Triton X-100 + skim milk (100 mM Tris, 100 mM Na4P2O7, 1% polyvinylpyrrolidone, 100 mM NaCl, 0.05% Triton X-100, 4% skim milk, pH 10.0) removed most soil humic contaminants. When the pretreatment was combined with Ca2+ flocculation, the purity of all soil DNA samples was further improved. DNA samples obtained by the fast glass bead-beating method (MethodFGB) had the highest purity. The resulting DNA was successfully used, without further purification steps, as a template for polymerase chain reaction targeting fungal internal transcribed spacer regions. The results obtained by terminal restriction fragment length polymorphism analysis indicated that the MethodFGB revealed greater fungal diversity and more distinctive community structure compared with the other methods tested. Our study provides a protocol for fungal cell lysis in soil, which is fast, convenient, and effective for analyzing fungal communities in forest soils.

Sugarcane trash levels in soil affects the fungi but not bacteria in a short-term field experiment

Abstract The sugarcane in Brazil is passing through a management transition that is leading to the abolition of pre-harvest burning. Without burning, large amounts of sugarcane trash is generated, and there is a discussion regarding the utilization of this biomass in the industry versus keeping it in the field to improve soil quality. To study the effects of the trash removal on soil quality, we established an experimental sugarcane plantation with different levels of trash over the soil (0%, 50% and 100% of the original trash deposition) and analyzed the structure of the bacterial and fungal community as the bioindicators of impacts. The soil DNA was extracted, and the microbial community was screened by denaturing gradient gel electrophoresis in two different seasons. Our results suggest that there are no effects from the different levels of trash on the soil chemistry and soil bacterial community. However, the fungal community was significantly impacted, and after twelve months, the community presented different structures among the treatments.

First Report of Mortierella alpina (Mortierellaceae, Zygomycota) Isolated from Crop Field Soil in Korea

A new recorded species of Mortierella was recovered during the investigation of fungal communities in soil samples collected from different locations of Gangwon-do, Korea. The species was identified and described as Mortierella alpina on the basis of phylogenetic analysis of internal transcribed spacer sequences and morphological characteristics. This species has not been officially reported from Korea thus far.

Effect of Organic Farming on Spore Diversity of Arbuscular Mycorrhizal Fungi and Glomalin in Soil

In this study, eight soil samples were collected from organic and conventional farms in a central area of South Korea. Spore communities of arbuscular mycorrhizal fungi (AMF) and glomalin, a glycoprotein produced by AMF, were analyzed. Spores of Glomus clarum, G. etunicatum, G. mosseae, G. sp., Acaulospora longula, A. spinosa, Gigaspora margarita, and Paraglomus occultum were identified at the study sites, based on morphological and molecular characteristics. While Acaulospora longula was the most dominant species in soils at organic farms, Paraglomus occultum was the most dominant species in soils at conventional farms. Species diversity and species number in AMF communities found in soils from organic farms were significantly higher than in soils from conventional farms. Glomalin was also extracted from soil samples collected at organic and conventional farms and was analyzed using both Bradford and enzyme-linked immunosorbent assays. The glomalin content in soils from organic farms was significantly higher than in soils from conventional farms. These results indicate that agricultural practices significantly affect AMF abundance and community structure.