Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields

RESEARCH ARTICLE Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields Xuhong Song1,2,3☯, Yuan Pan1,2,3☯, Longyun Li1,2,3¤*, Xiaoli Wu1,2,3, Yu Wang1,2,3 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 1 Chongqing Academy of Chinese Materia Medica, Chongqing, China, 2 Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China, 3 Chongqing Sub-center of National Resource, Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China ☯ These authors contributed equally to this work. ¤ Current address: Nan’an District, Chongqing Province, R. P. China * Abstract OPEN ACCESS Citation: Song X, Pan Y, Li L, Wu X, Wang Y (2018) Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields. PLoS ONE 13(3): e0193811. https://doi.org/10.1371/journal. pone.0193811 Editor: Daniel Cullen, USDA Forest Service, UNITED STATES Received: May 3, 2017 Accepted: February 19, 2018 Published: March 14, 2018 Copyright: © 2018 Song et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All raw sequences data are accessible in NCBI Sequence Reads Archive (SRA) database under the accession number SRR 5248582. Funding: This work was supported by China National Science and Technology Project of the 12th Five-Year Plan (2011BAI13B02-1), China Agriculture Research System (CARS-21), Basic Research Projects of Chongqing province (2015cstc-jbky-01904), National Key R & D Program, 2017YFC1702605, and Chongqing In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis. Introduction Coptis chinensis Franch. is one of the most important traditional medicinal plants in the family Ranunculaceae. The root of C. chinensis is regularly used for medicinal purposes, and has been prescribed alone or in combination with other traditional herbs for treating diabetes, PLOS ONE | https://doi.org/10.1371/journal.pone.0193811 March 14, 2018 1 / 14 Coptis chinensis rhizospheric soil fungal community and diversity Technical System of Chinese Medicinal Materials Industry, 2017-[5]. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. dysentery, jaundice, acute febrile and suppurative infections, seasonal febrile diseases, sore throat, reducing fever, and preventing diarrhea [1]. Previous phytochemical studies on C. chinensis, detected more than 30 alkaloids [2]. Among these alkaloids, berberine, epiberberine, palmatine, coptisine, and jatrorrhizine, which are isoquinoline alkaloids that are predominantly bioactive, have been confirmed as the main constituents, of the total alkaloid fraction, comprising more than 80%. Isoquinoline alkaloids obtained from herbal extracts of C. chinensis were found to display multiple biological activities, such as broad-spectrum antimicrobial [3], anti-inflammation [4–7], anti-cancer [8], anti-diabetes [9–12], attenuation depressive-like behaviors [13], Anti-adipogenesis [14], enhancement of osteogenic differentiation [15], reduction of oxidative stress [16] and anti-phototoxicity [17] effects. In China, C. chinensis is only distributed in Guizhou Province, Sichuan Province, Chongqing City, Shanxi Province, and Hunan Province. Currently, the most well-known crop area is Shizhu Tujia Autonomous County, which lies in Chongqing City. At present, the production of medicine from C. chinensis mainly depends on the field cultivation of the species. Given the increased demand for C. chinensis for medicinal purposes, continuous cropping of the herb has become increasingly common. Long-term continuous cropping of Chinese medicinal herbs often leads to a decrease in plant growth, serious root rot disease, and considerable yield loss [18]. Continuous cropping of C. chinensis resulted 70% to 80% reduction in yield. At the same time, root rot disease has become the major threat to the production of C. chinensis [19]. Soil microbial and biochemical properties are important soil health indicators because they are involved in soil organic matter decomposition and nutrient availability and cycling [20,21]. Soil enzyme activities and microbial biomass pools have also been proposed as integrative indicators of soil quality [21,22]. More recently, an increasing number of studies have speculated that continuous cropping or consecutive monoculture resulted in imbalances in soil microbial community diversity and structure [23–25]. Moreover, fungal pathogen populations increase rapidly in soil under continuous cropping [24,26–29]. Several molecular analytical technologies are used to analyze the diversity of soil microbes in continuous cropping systems, such as 454 pyrosequencing analysis [18,27], denaturing gradient gel electrophoresis [30,31], terminal restriction fragment length polymorphism [28], and fluorescence in situ hybridization [32]. However, these molecular technologies cannot ove (...truncated)