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Wang B, Geng Y, Lin Y, Xia Q, Wei F, Yang S, Huang X, Zhang J, Cai Z, Zhao J. Root rot destabilizes the Sanqi rhizosphere core fungal microbiome by reducing the negative connectivity of beneficial microbes. Appl Environ Microbiol 2024; 90:e0223723. [PMID: 38315008 PMCID: PMC10952445 DOI: 10.1128/aem.02237-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
The stability of microbial communities, especially among core taxa, is essential for supporting plant health. However, the impacts of disease infection on the stability of rhizosphere fungal core microbiome remain largely unexplored. In this study, we delved into the effects of root rot infestation on the community structure, function, network complexity, and stability of Sanqi fungal core microbiomes, employing amplicon sequencing combined with co-occurrence network and cohesion analyses. Our investigation revealed that root rot disease led to a decrease in the α-diversity but an increase in the β-diversity of the Sanqi fungal core microbiomes in the rhizosphere. Notably, Ilyonectria, Plectosphaerella, and Fusarium emerged as indicator species in the rhizosphere core microbiome of root rot-infected Sanqi plants, while Mortierella predominated as the dominant biomarker taxa in healthy soils. Additionally, root rot diminished the complexity and modularity of the rhizosphere networks by reducing the metrics associated with nodes, edges, degrees, and modularity. Furthermore, root rot resulted in a reduction in the proportion of negative connections in the network and the negative/positive cohesion of the entire core fungal microbiome. Particularly noteworthy was the observation that root rot infection destabilized the rhizosphere core fungal microbiome by weakening the negative connectivity associated with beneficial agents. Collectively, these results highlight the significance of the negative connectivity of beneficial agents in ensuring the stability of core microbial community.IMPORTANCERoot rot disease has been reported as the most devastating disease in the production process of artificial cultivated Sanqi ginseng, which seriously threatens the Sanqi industry. This study provides valuable insights into how root rot influences microbial relationships within the community. These findings open up opportunities for disease prevention and the promotion of plant health by regulating microbial interactions. In summary, the research sheds light on the ecological consequences of root rot on rhizosphere fungal microbiomes and offers potential strategies for managing soil-borne diseases and enhancing plant health.
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Affiliation(s)
- Baoying Wang
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Yuhang Geng
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Yulan Lin
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Qing Xia
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Fugang Wei
- Miaoxiang Sanqi Technology Co., Ltd., Wenshan, China
| | - Shaozhou Yang
- Miaoxiang Sanqi Technology Co., Ltd., Wenshan, China
| | - Xinqi Huang
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing, China
- Key Laboratory of Virtual Geographical Environment (Nanjing Normal University), Ministry of Education, Nanjing, China
| | - Zucong Cai
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
- Key Laboratory of Virtual Geographical Environment (Nanjing Normal University), Ministry of Education, Nanjing, China
| | - Jun Zhao
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
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Liu B, Lin W, Chen S, Xiang T, Yang Y, Yin Y, Xu G, Liu Z, Liu L, Pan J, Xie L. Gut Microbiota as an Objective Measurement for Auxiliary Diagnosis of Insomnia Disorder. Front Microbiol 2019; 10:1770. [PMID: 31456757 PMCID: PMC6701205 DOI: 10.3389/fmicb.2019.01770] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/17/2019] [Indexed: 12/27/2022] Open
Abstract
Insomnia is a type of sleep disorder which is associated with various diseases’ development and progression, such as obesity, type II diabetes and cardiovascular diseases. Recent investigation of the gut-brain axis enhances our understanding of the role of the gut microbiota in brain-related diseases. However, whether the gut microbiota is associated with insomnia remains unknown. In the present investigation, leveraging the 16S rDNA amplicon sequencing of V3-V4 region and the novel bioinformatic analysis, it was demonstrated that between insomnia and healthy populations, the composition, diversity and metabolic function of the gut microbiota are significantly changed. Other than these, redundancy analysis, co-occurrence analysis and PICRUSt underpin the gut taxa composition, signaling pathways, and metabolic functions perturbed by insomnia disorder. Moreover, random forest together with cross-validation identified two signature bacteria, which could be used to distinguish the insomnia patients from the healthy population. Furthermore, based on the relative abundance and clinical sleep parameter, we constructed a prediction model utilizing artificial neural network (ANN) for auxiliary diagnosis of insomnia disorder. Overall, the aforementioned study provides a comprehensive understanding of the link between the gut microbiota and insomnia disorder.
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Affiliation(s)
- Bingdong Liu
- Department of Psychiatry, The First Affiliated Hospital of Jinan University, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Weifeng Lin
- Department of Psychiatry, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Shujie Chen
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ting Xiang
- Department of Psychiatry, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yifan Yang
- Department of Psychiatry, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yulong Yin
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Guohuan Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhihong Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Li Liu
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiyang Pan
- Department of Psychiatry, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Liwei Xie
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,Zhujiang Hospital, Southern Medical University, Guangzhou, China
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