High-throughput sequencing-based analysis of endogenetic fungal communities inhabiting the Chinese Cordyceps reveals unexpectedly high fungal diversity.

Fei Xia,Yan Liu,Xin Chen,Juan Lin,Meng-Yuan Guo,Yu-Ling Li,Xiao-Hui Bai,Guang-Rong Shen,Xuan-Wei Zhou

doi:10.1038/srep33437

Abstract

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 internal transcribed spacer-1 sequences from each sample were obtained using Illumina high-throughput sequencing. The results showed that Ascomycota was the dominant fungal phylum in Chinese Cordyceps and its soil microhabitat from different sampling regions. Among the Ascomycota, 65 genera were identified, and the abundant operational taxonomic units showed the strongest sequence similarity to Ophiocordyceps, Verticillium, Pseudallescheria, Candida and Ilyonectria Not surprisingly, the genus Ophiocordyceps was the largest among the fungal communities identified in the fruiting bodies and external mycelial cortices of Chinese Cordyceps. In addition, fungal communities in the soil microhabitats were clustered separately from the external mycelial cortices and fruiting bodies of Chinese Cordyceps from different sampling regions. There was no significant structural difference in the fungal communities between the fruiting bodies and external mycelial cortices of Chinese Cordyceps. This study revealed an unexpectedly high diversity of fungal communities inhabiting the Chinese Cordyceps and its microhabitats.

Highlights

IntroductionThe nuclear ribosomal internal transcribed spacer (ITS) region is widely used as a DNA molecular marker for the analysis of fungal communities using high-throughput sequencing[19]
The Chao[1] index and Accumulated Cyclone Energy (ACE) estimator indicated that, in Chinese Cordyceps collected from Qumarlêb County, the richness of the fungal community was higher in the fruiting bodies of Chinese Cordyceps than in the external mycelial cortices and soil microhabitats
As a mysterious material for traditional Chinese medicine, endogenetic fungal communities have been studied by many researchers, and many fungi have been isolated from Chinese Cordyceps using culture-dependent methods

Summary

Introduction

The nuclear ribosomal internal transcribed spacer (ITS) region is widely used as a DNA molecular marker for the analysis of fungal communities using high-throughput sequencing[19]. With continuing improvements in sequencing techniques and the development of dedicated DNA databases, recent studies have demonstrated the potential of large-scale sequencing of ITS regions for quantifying and characterizing the fungal diversity in special biological samples, such as the pile-fermentation of puer tea[20], plant endophytic fungi[21] and rhizospheric fungi[22]. The diversity of the Chinese Cordyceps endogenetic fungal communities has not been evaluated using high-throughput sequencing. We used Illumina MiSeq sequencing to assess the fungal diversity in Chinese Cordyceps samples collected from five different geographical regions in the Tibet and Qinghai provinces. High-throughput sequencing will accelerate studies of the microbial diversity and community structure of Chinese Cordyceps and is beneficial for screening novel bioactive metabolites from different endogenetic fungal species

Methods

Results

Conclusion