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Martin-Pozas T, Nováková A, Jurado V, Fernandez-Cortes A, Cuezva S, Saiz-Jimenez C, Sanchez-Moral S. Diversity of Microfungi in a High Radon Cave Ecosystem. Front Microbiol 2022; 13:869661. [PMID: 35572646 PMCID: PMC9093739 DOI: 10.3389/fmicb.2022.869661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Castañar Cave is a clear example of an oligotrophic ecosystem with high hygrothermal stability both seasonal and interannual and the particularity of registering extraordinary levels of environmental radiation. These environmental conditions make the cave an ideal laboratory to evaluate both the responses of the subterranean environment to sudden changes in the matter and energy fluxes with the exterior and also any impact derived from its use as a tourist resource under a very restrictive access regime. In 2008, a fungal outbreak provoked by a vomit contaminated the sediments which were removed and subsequently treated with hydrogen peroxide. Fungal surveys were carried out in 2008 and 2009. The visits were resumed in 2014. Here, 12 years after the outbreak, we present an exhaustive study on the cave sediments in order to know the distribution of the different fungal taxa, as well as the prevalence and spatio-temporal evolution of the fungi caused by the vomit over the years under the conditions of relative isolation and high radiation that characterize this cave.
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Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), Madrid, Spain
| | - Alena Nováková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, Prague, Czechia
| | - Valme Jurado
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), Seville, Spain
| | | | - Soledad Cuezva
- Department of Geology, Geography and Environment, University of Alcala, Alcala de Henares, Spain
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), Seville, Spain
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), Madrid, Spain
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Microbial Community Changes in the Rhizosphere Soil of Healthy and Rusty Panax ginseng and Discovery of Pivotal Fungal Genera Associated with Rusty Roots. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8018525. [PMID: 32016120 PMCID: PMC6985933 DOI: 10.1155/2020/8018525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/18/2019] [Accepted: 12/26/2019] [Indexed: 12/14/2022]
Abstract
Panax ginseng Meyer, a valuable medicinal plant, is severely threatened by rusty root, a condition that greatly affects its yield and quality. Studies investigating the relationship between soil microbial community composition and rusty roots are vital for the production of high-quality ginseng. Here, high-throughput sequencing was employed to systematically characterize changes in the soil microbial community associated with rusty roots. Fungal diversity was lower in the soils of rusty root-affected P. ginseng than in those of healthy plants. Importantly, principal coordinate analysis separated the fungal communities in the rhizosphere soils of rusty root-affected ginseng from those of healthy plants. The dominant bacterial and fungal genera differed significantly between rhizosphere soils of healthy and rusty root-affected P. ginseng, and linear discriminant analysis effect size (LEfSe) further indicated a strong imbalance in the soil microbial community of diseased plants. Significantly enriched bacterial genera (including Rhodomicrobium, Knoellia, Nakamurella, Asticcacaulis, and Actinomadura) were mainly detected in the soil of rusty root-affected P. ginseng, whereas significantly enriched fungal genera (including Xenopolyscytalum, Arthrobotrys, Chalara, Cryptococcus, and Scutellinia) were primarily detected in the soil of healthy plants. Importantly, five fungal genera (Cylindrocarpon, Acrophialophora, Alternaria, Doratomyces, and Fusarium) were significantly enriched in the soil of rusty root-affected plants compared with that of healthy plants, suggesting that an increase in the relative abundance of these pathogenic fungi (Cylindrocarpon, Alternaria, and Fusarium) may be associated with ginseng rusty roots. Additionally, this study is the first to report that an increase in the relative abundances of Acrophialophora and Doratomyces in the rhizosphere of P. ginseng may be associated with the onset of rusty root symptoms in this plant. Our findings provide potentially useful information for developing biological control strategies against rusty root, as well as scope for future screening of fungal pathogens in rusty roots of P. ginseng.
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Zhang J, Fan S, Qin J, Dai J, Zhao F, Gao L, Lian X, Shang W, Xu X, Hu X. Changes in the Microbiome in the Soil of an American Ginseng Continuous Plantation. FRONTIERS IN PLANT SCIENCE 2020; 11:572199. [PMID: 33365038 PMCID: PMC7750500 DOI: 10.3389/fpls.2020.572199] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 10/30/2020] [Indexed: 05/22/2023]
Abstract
American ginseng is an important herbal medicinal crop in China. In recent years, there has been an increasing market demand for ginseng, but the production area has been shrinking due to problems associated with continuous monocropping. We analyzed the microbiome in bulk soils to assess whether and, if so, what changes in the bulk soil microbiome are associated with continuous American ginseng cropping. The alpha diversity of fungi and bacteria was significantly lower in the soils planted with American ginseng than the virgin (non-planted) land. The relative abundance of Fusarium spp. and Ilyonectria spp., known plant root pathogens, was much higher in the soils cropped with American ginseng than the non-planted. On the other hand, a number of bacteria with biodegradation function, such as Methylibium spp., Sphingomonas spp., Variovorax spp., and Rubrivivax spp., had lower abundance in the soils cropped with American ginseng than the non-cropped. In addition, soil pH was lower in the field planted with American ginseng than the non-planted. Accumulation of fungal root pathogens and reduction of soil pH may, therefore, have contributed to the problems associated with continuous monocropping of American ginseng.
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Affiliation(s)
- Jiguang Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Sanhong Fan
- College of Life Science, Northwest A&F University, Yangling, China
| | - Jun Qin
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jichen Dai
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Fangjie Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Liqiang Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Xihong Lian
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Wenjing Shang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Xiangming Xu
- NIAB East Malling Research (EMR), Kent, United Kingdom
| | - Xiaoping Hu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
- *Correspondence: Xiaoping Hu
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Liu D, Sun H, Ma H. Deciphering Microbiome Related to Rusty Roots of Panax ginseng and Evaluation of Antagonists Against Pathogenic Ilyonectria. Front Microbiol 2019; 10:1350. [PMID: 31275274 PMCID: PMC6591430 DOI: 10.3389/fmicb.2019.01350] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/31/2019] [Indexed: 11/17/2022] Open
Abstract
Plant roots host diverse microbes that are closely associated with root fitness. Currently, the relationship between microbes and rusty roots of Panax ginseng remains unclear. Here, we described the root-associated microbiome in rusty and healthy ginseng by metagenomic sequencing of 16S rRNA and ITS regions. Being enriched in Diseased-roots (Dr) of ginseng and their rhizosphere soil, the fungus of Ilyonectria, was identified as the most probable cause of the disease after ITS analysis. Meanwhile, an increase of Mortierella was observed in Healthy-roots (Hr). Surprisingly, an enriched Fusarium was found in both Hr and their rhizosphere soil. Besides, in comparison with Hr, decreased relative abundance of Actinomycetales and increased relative abundance of Pseudomonadales was observed in Dr after 16S rRNA analysis. What's more, we isolated several microorganisms as antagonists that showed strong inhibiting effects on Ilyonectria in plate assays. In field trials, inoculation of Bacillus sp. S-11 displayed apparent suppression effect against Ilyonectria and shifted microbial communities in rhizosphere soil. Our research identified key microbiota involved in rusty roots of P. ginseng and offered potential biocontrol solutions to rusty disease.
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Affiliation(s)
- Defei Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huanjun Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hongwu Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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Lu XH, Zhang XM, Jiao XL, Hao JJ, Zhang XS, Luo Y, Gao WW. Taxonomy of fungal complex causing red-skin root of Panax ginseng in China. J Ginseng Res 2019; 44:506-518. [PMID: 32372873 PMCID: PMC7195572 DOI: 10.1016/j.jgr.2019.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/17/2018] [Accepted: 01/21/2019] [Indexed: 11/24/2022] Open
Abstract
Background Red-skin root of Asian ginseng (Panax ginseng) significantly reduces the quality and limits the production of ginseng in China. The disease has long been thought to be a noninfectious physiological disease, except one report that proved it was an infectious disease. However, the causal agents have not been successfully determined. In the present study, we were to reveal the pathogens that cause red-skin disease. Methods Ginseng roots with red-skin root symptoms were collected from commercial fields in Northeast China. Fungi were isolated from the lesion and identified based on morphological characters along with multilocus sequence analyses on internal transcription spacer, β-tubulin (tub2), histone H3 (his3), and translation elongation factor 1α (tef-1α). Pathogens were confirmed by inoculating the isolates in ginseng roots. Results A total of 230 isolates were obtained from 209 disease samples. These isolates were classified into 12 species, including Dactylonectria sp., D. hordeicola, Fusariumacuminatum, F. avenaceum, F. solani, F. torulosum, Ilyonectria mors-panacis, I. robusta, Rhexocercosporidium panacis, and three novel species I. changbaiensis, I. communis, and I. qitaiheensis. Among them, I. communis, I. robusta, and F. solani had the highest isolation frequencies, being 36.1%, 20.9%, and 23.9%, respectively. All these species isolated were pathogenic to ginseng roots and caused red-skin root disease under appropriate condition. Conclusion Fungal complex is the causal agent of red-skin root in P. ginseng.
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Affiliation(s)
- Xiao H Lu
- Biotechnology Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Biological Control, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xi M Zhang
- Biotechnology Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao L Jiao
- Biotechnology Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianjun J Hao
- Department of Plant Science, School of Food and Agriculture, The University of Maine, Maine, USA
| | - Xue S Zhang
- Biotechnology Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi Luo
- Biotechnology Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei W Gao
- Biotechnology Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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