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Gao Y, Xu Y, Dong Z, Guo Y, Luo J, Wang F, Yan L, Zou X. Endophytic Fungal Diversity and Its Interaction Mechanism with Medicinal Plants. Molecules 2025; 30:1028. [PMID: 40076252 PMCID: PMC11902086 DOI: 10.3390/molecules30051028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2025] [Revised: 02/20/2025] [Accepted: 02/21/2025] [Indexed: 03/14/2025] Open
Abstract
This paper reviewed the diversity of endophytic fungi and their interactions with medicinal plants, along with the research methodologies utilized to investigate these interactions. It mainly includes the diversity of endophytic fungi, as well as distribution diversity, species diversity, and the diversity of their metabolites and functions, including antibacterial, anti-inflammatory, anti-tumor, insecticidal, antioxidant capabilities, and so on. The research methodologies employed to investigate the interactions between endophytic fungi and medicinal plants are categorized into metagenomics, transcriptomics, metatranscriptomics, proteomics, and metabolomics. Furthermore, this study anticipates the potential applications of secondary metabolites derived from endophytic fungi in both medicine and agriculture.
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Affiliation(s)
- Yuan Gao
- School of Pharmacy, Harbin University of Commerce, Harbin 150076, China; (Y.X.); (Z.D.); (Y.G.); (J.L.); (F.W.); (L.Y.)
| | - Yan Xu
- School of Pharmacy, Harbin University of Commerce, Harbin 150076, China; (Y.X.); (Z.D.); (Y.G.); (J.L.); (F.W.); (L.Y.)
| | - Zhijia Dong
- School of Pharmacy, Harbin University of Commerce, Harbin 150076, China; (Y.X.); (Z.D.); (Y.G.); (J.L.); (F.W.); (L.Y.)
| | - Yuyang Guo
- School of Pharmacy, Harbin University of Commerce, Harbin 150076, China; (Y.X.); (Z.D.); (Y.G.); (J.L.); (F.W.); (L.Y.)
| | - Jianghan Luo
- School of Pharmacy, Harbin University of Commerce, Harbin 150076, China; (Y.X.); (Z.D.); (Y.G.); (J.L.); (F.W.); (L.Y.)
| | - Fuling Wang
- School of Pharmacy, Harbin University of Commerce, Harbin 150076, China; (Y.X.); (Z.D.); (Y.G.); (J.L.); (F.W.); (L.Y.)
| | - Lijun Yan
- School of Pharmacy, Harbin University of Commerce, Harbin 150076, China; (Y.X.); (Z.D.); (Y.G.); (J.L.); (F.W.); (L.Y.)
| | - Xiang Zou
- Engineering Research Center of Natural Antineoplastic Drugs, Ministry of Education, Harbin University of Commerce, Harbin 150076, China
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Verma V, Srivastava A, Garg SK, Singh VP, Arora PK. Incorporating omics-based tools into endophytic fungal research. BIOTECHNOLOGY NOTES (AMSTERDAM, NETHERLANDS) 2023; 5:1-7. [PMID: 39416692 PMCID: PMC11446381 DOI: 10.1016/j.biotno.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 10/19/2024]
Abstract
Fungal endophytes are valuable sources of bioactive compounds with diverse applications. The exploration of these compounds not only contributes to our understanding of ecological interactions but also holds promise for the development of novel products with agricultural, medicinal, and industrial significance. Continued exploration of fungal endophyte diversity and understanding the ecological roles of bioactive compounds present opportunities for new discoveries and applications. Omics techniques, which include genomics, transcriptomics, proteomics, and metabolomics, contribute to the discovery of novel bioactive compounds produced by fungal endophytes with their potential applications. The omics techniques play a critical role in unraveling the complex interactions between fungal endophytes and their host plants, providing valuable insights into the molecular mechanisms and potential applications of these relationships. This review provides an overview of how omics techniques contribute to the study of fungal endophytes.
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Affiliation(s)
- Vinita Verma
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India
| | - Alok Srivastava
- Department of Plant Science, MJP Rohilkhand University, Bareilly, India
| | - Sanjay Kumar Garg
- Department of Plant Science, MJP Rohilkhand University, Bareilly, India
| | - Vijay Pal Singh
- Department of Plant Science, MJP Rohilkhand University, Bareilly, India
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Liu X, Cui JL, Zhou ZY, Zhang ZB, Cui XG, Han B, Wang JH, Wang ML, Li YM. "Mini-community" simulation revealed the differences of endophytic fungal communities between the above- and below-ground tissues of Ephedra sinica Stapf. Fungal Biol 2023; 127:1276-1283. [PMID: 37821149 DOI: 10.1016/j.funbio.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 10/13/2023]
Abstract
The microecology of endophytic fungi in special habitats, such as the interior of different tissues from a medicinal plant, and its effects on the formation of metabolites with different biological activities are of great importance. However, the factors affecting fungal community formation are unclear. This study is the first to utilize "mini-community" remodeling to understand the above phenomena. First, high-throughput sequencing technology was applied to explore the community composition and diversity of endophytic fungi in the above-ground tissues (Ea) and below-ground tissues (Eb) of Ephedra sinica. Second, fungi were obtained through culture-dependent technology and used for "mini-community" remodeling in vitro. Then, the effects of environmental factors, partner fungi, and plant tissue fluid (internal environment) on endophytic fungal community formation were discussed. Results showed that environmental factors played a decisive role in the selection of endophytic fungi, that is, in Ea and Eb, 93.8% and 25.3% of endophytic fungi were halophilic, respectively, and 10.6% and 60.2% fungi were sensitive to high temperature (33 °C), respectively. Meanwhile, pH had little effect on fungal communities. The internal environment of the plant host further promoted the formation of endophytic fungal communities.
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Affiliation(s)
- Xi Liu
- Institute of Applied Chemistry, Shanxi University, Taiyuan, Shanxi, 030006, People's Republic of China; Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, Shanxi, 030006, People's Republic of China
| | - Jin-Long Cui
- Institute of Applied Chemistry, Shanxi University, Taiyuan, Shanxi, 030006, People's Republic of China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijng, 100700, People's Republic of China.
| | - Zhong-Ya Zhou
- Institute of Applied Chemistry, Shanxi University, Taiyuan, Shanxi, 030006, People's Republic of China; Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, Shanxi, 030006, People's Republic of China
| | - Zong-Bao Zhang
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, Shanxi, 030006, People's Republic of China
| | - Xuan-Ge Cui
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, Shanxi, 030006, People's Republic of China
| | - Bo Han
- Institute of Applied Chemistry, Shanxi University, Taiyuan, Shanxi, 030006, People's Republic of China; Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, Shanxi, 030006, People's Republic of China
| | - Jun-Hong Wang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, Shanxi, 030006, People's Republic of China
| | - Meng-Liang Wang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, Shanxi, 030006, People's Republic of China
| | - Yi-Min Li
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, 712046, People's Republic of China.
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Zhang H, Xia Y, Cui JL, Ji X, Miao SM, Zhang G, Li YM. The composition characteristics of endophytic communities and their relationship with metabolites profile in Ephedra sinica under wild and cultivated conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:95648-95659. [PMID: 37556062 DOI: 10.1007/s11356-023-29145-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/31/2023] [Indexed: 08/10/2023]
Abstract
Ephedra sinica is one of the most famous Chinese medicinal plants. The insufficient supply of wild resources has led to the increased use of cultivated products. However, the related medicinal quality differs significantly. Although the influence of external environment on the quality of E. sinica has been studied, the impact of endophytic microbes on it remains vague. This study characterized differential metabolites and microbial community compositions in wild and cultivated E. sinica by combining metabolomics with microbiomics, and explored the effect of endophytes on the formation of differential metabolites further. The results showed that the difference in quality between wild and cultivated E. sinica was mainly in the productions of alkaloids, flavonoids, and terpenoids. The associated endophytes had special compositional characteristics. For instance, the distribution and abundance of dominant endophytes varied between wild and cultivated E. sinica. Several endophytes had significant or highly significant correlations with the formations of ephedrine, pseudoephedrine, D-cathinone, methcathinone, coumarin, kaempferol, rhamnetin, or phenylacetic acid. This study will deepen our understanding of the plant-endophyte interactions and provide a strategy for the quality control of E. sinica products.
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Affiliation(s)
- Hui Zhang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, Shanxi, China
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Ye Xia
- Department of Food Science and Technology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Jin-Long Cui
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, Shanxi, China.
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing, 100700, China.
| | - Xin Ji
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, Shanxi, China
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Shuang-Man Miao
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, Shanxi, China
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Gang Zhang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, 712046, China
| | - Yi-Min Li
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, 712046, China
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Li R, Duan W, Ran Z, Chen X, Yu H, Fang L, Guo L, Zhou J. Diversity and correlation analysis of endophytes and metabolites of Panax quinquefolius L. in various tissues. BMC PLANT BIOLOGY 2023; 23:275. [PMID: 37226095 DOI: 10.1186/s12870-023-04282-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 05/13/2023] [Indexed: 05/26/2023]
Abstract
BACKGROUND Panax quinquefolius L. (American ginseng) is widely used in medicine due to its wealth of diverse pharmacological effects. Endophytes colonize within P. quinquefolius in multiple tissue types. However, the relationship between endophytes and the production of their active ingredients in different parts of the plant is not clear. RESULTS In this study, the relationship of endophytic diversity and the metabolites produced in different plant tissues of P. quinquefolius were analyzed using metagenomic and metabolomic approaches. The results showed relatively similar endophyte composition in roots and fibrils, but obvious differences between endophyte populations in stems and leaves. Species abundance analysis showed that at the phylum level, the dominant bacterial phylum was Cyanobacteria for roots, fibrils, stems and leaves, Ascomycota forroots and fibrils roots, and Basidiomycota for stems and leaves. LC-MS/MS technology was used to quantitatively analyze the metabolites in different tissues of P. quinquefolius. A total of 398 metabolites and 294 differential metaboliteswere identified, mainly organic acids, sugars, amino acids, polyphenols, and saponins. Most of the differential metabolites were enriched in metabolic pathways such as phenylpropane biosynthesis, flavonoid biosynthesis, citric acid cycle, and amino acid biosynthesis. Correlation analysis showed a positive and negative correlation between the endophytes and the differential metabolites. Conexibacter significantly enriched in root and fibril was significantly positively correlated with saponin differential metabolites, while cyberlindnera significantly enriched in stem and leaf was significantly negatively correlated with differential metabolites (p < 0.05). CONCLUSION The endophytic communities diversity were relatively similar in the roots and fibrils of P. quinquefolius, while there were greater differences between the stems and leaves. There was significant difference in metabolite content between different tissues of P. quinquefolius. Correlation analysis methods demonstrated a correlation between endophytes and differential metabolism.
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Affiliation(s)
- Rui Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, PR China
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, PR China
| | - Wanying Duan
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, PR China
| | - Zhifang Ran
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, PR China
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, PR China
| | - Xiaoli Chen
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, PR China
| | - Hongxia Yu
- Weihai Wendeng District Dao-di Ginseng Industry Development Co. LTD, Weihai, 264407, PR China
| | - Lei Fang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, PR China.
| | - Lanping Guo
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China.
| | - Jie Zhou
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, PR China.
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Guo ZX, Li XK, Cui JL, Miao SM, Wang ML, Wang JH, Danial M. Transcriptional Regulatory Mechanism of Differential Metabolite Formation in Root and Stem of Ephedra sinica. Appl Biochem Biotechnol 2022; 194:5506-5521. [DOI: 10.1007/s12010-022-04039-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2022] [Indexed: 11/27/2022]
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Sagita R, Quax WJ, Haslinger K. Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts. Front Bioeng Biotechnol 2021; 9:649906. [PMID: 33791289 PMCID: PMC8005728 DOI: 10.3389/fbioe.2021.649906] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022] Open
Abstract
The bioprospecting of secondary metabolites from endophytic fungi received great attention in the 1990s and 2000s, when the controversy around taxol production from Taxus spp. endophytes was at its height. Since then, hundreds of reports have described the isolation and characterization of putative secondary metabolites from endophytic fungi. However, only very few studies also report the genetic basis for these phenotypic observations. With low sequencing cost and fast sample turnaround, genetics- and genomics-based approaches have risen to become comprehensive approaches to study natural products from a wide-range of organisms, especially to elucidate underlying biosynthetic pathways. However, in the field of fungal endophyte biology, elucidation of biosynthetic pathways is still a major challenge. As a relatively poorly investigated group of microorganisms, even in the light of recent efforts to sequence more fungal genomes, such as the 1000 Fungal Genomes Project at the Joint Genome Institute (JGI), the basis for bioprospecting of enzymes and pathways from endophytic fungi is still rather slim. In this review we want to discuss the current approaches and tools used to associate phenotype and genotype to elucidate biosynthetic pathways of secondary metabolites in endophytic fungi through the lens of bioprospecting. This review will point out the reported successes and shortcomings, and discuss future directions in sampling, and genetics and genomics of endophytic fungi. Identifying responsible biosynthetic genes for the numerous secondary metabolites isolated from endophytic fungi opens the opportunity to explore the genetic potential of producer strains to discover novel secondary metabolites and enhance secondary metabolite production by metabolic engineering resulting in novel and more affordable medicines and food additives.
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Affiliation(s)
| | | | - Kristina Haslinger
- Groningen Institute of Pharmacy, Chemical and Pharmaceutical Biology, University of Groningen, Groningen, Netherlands
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