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Wang W, Portal-Gonzalez N, Wang X, Li J, Li H, Portieles R, Borras-Hidalgo O, He W, Santos-Bermudez R. Insights into the microbial assembly and metabolites associated with ginger (Zingiber officinale L. Roscoe) microbial niches and agricultural environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174395. [PMID: 38992353 DOI: 10.1016/j.scitotenv.2024.174395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024]
Abstract
Ginger, a vegetable export from China, is well-known for its spicy flavour and use in traditional Chinese medicine. By examining the interactions of ginger plants' microbiome and metabolome, we can gain insights to advance agriculture, the environment, and other fields. Our study used metataxonomic analysis to investigate ginger plants' prokaryotic and fungal microbiomes in open fields and greenhouses. We also conducted untargeted metabolomic analysis to identify specific metabolites closely associated with ginger microbiome assembly under both agricultural conditions. Various bacteria and fungi were classified as generalists or specialists based on their ability to thrive in different environments and microbial niches. Our results indicate that ginger plants grown in greenhouses have a greater prokaryotic diversity, while those grown in open fields exhibit a greater fungal diversity. We have identified specific co-occurring prokaryotic and fungal genera associated with ginger plant agroecosystems that can enhance the health and growth of ginger plants while maintaining a healthy environment. In the open field these genera include Sphingomonas, Methylobacterium-Methylorubrum, Bacillus, Acidovorax, Rhizobium, Microbacterium, unclassified_f_Comamonadaceae, Herbaspirillum, Klebsiella, Enterobacter, Chryseobacterium, Nocardioides, Subgroup_10, Enterococcus, Pseudomonas, Devosia, g_unclassified_f_Chaetomiaceae, Pseudaleuria, Mortierella, Cheilymenia, and Pseudogymnoascus. In the greenhouse, the enriched genera were Rhizobium, Stenotrophomonas, Aureimonas, Bacillus, Nocardioides, Pseudomonas, Enterobacter, Delftia, Trichoderma, Mortierella, Cheilymenia, Schizothecium, and Actinomucor. Our research has identified several previously unknown microbial genera for ginger plant agroecosystems. Furthermore, our study has important implications for understanding the correlation between ginger's microbiome and metabolome profiles in diverse environments and may pave the way for future research. Specific microbial genera in crop production environments are associated with essential metabolites, including Safingol, Docosatrienoic acid, P-acetaminophen, and Hypoglycin B.
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Affiliation(s)
- Wenbo Wang
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
| | - Nayanci Portal-Gonzalez
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China
| | - Xia Wang
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China
| | - Jialin Li
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
| | - Roxana Portieles
- Joint R&D Center of Biotechnology, RETDA, Yota Bio-Engineering Co., Ltd., 99 Shenzhen Road, Rizhao 276826, Shandong, People's Republic of China.
| | - Orlando Borras-Hidalgo
- Joint R&D Center of Biotechnology, RETDA, Yota Bio-Engineering Co., Ltd., 99 Shenzhen Road, Rizhao 276826, Shandong, People's Republic of China.
| | - Wenxing He
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
| | - Ramon Santos-Bermudez
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
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Liu S, Hou Y, Zheng K, Ma Q, Wen M, Shao S, Wu S. Exploring the diversity, bioactivity of endophytes, and metabolome in Synsepalum dulcificum. Front Microbiol 2024; 15:1258208. [PMID: 38476934 PMCID: PMC10929569 DOI: 10.3389/fmicb.2024.1258208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Synsepalum dulcificum exhibits high edible and medicinal value; however, there have been no reports on the exploration of its endophyte resources. Here, we conducted analyses encompassing plant metabolomics, microbial diversity, and the biological activities of endophytic metabolites in S. dulcificum. High-throughput sequencing identified 4,913 endophytic fungal amplicon sequence variants (ASVs) and 1,703 endophytic bacterial ASVs from the roots, stems, leaves, flowers, and fruits of S. dulcificum. Fungi were classified into 5 phyla, 24 classes, 75 orders, 170 families, and 313 genera, while bacteria belonged to 21 phyla, 47 classes, 93 orders, 145 families, and 232 genera. Furthermore, there were significant differences in the composition and content of metabolites in different tissues of S. dulcificum. Spearman's correlation analysis of the differential metabolites and endophytes revealed that the community composition of the endophytes correlated with plant-rich metabolites. The internal transcribed spacer sequences of 105 isolates were determined, and phylogenetic analyses revealed that these fungi were distributed into three phyla (Ascomycota, Basidiomycota, and Mucoromycota) and 20 genera. Moreover, 16S rDNA sequencing of 46 bacteria revealed they were distributed in 16 genera in three phyla: Actinobacteria, Proteobacteria, and Firmicutes. The antimicrobial activities (filter paper method) and antioxidant activity (DPPH and ABTS assays) of crude extracts obtained from 68 fungal and 20 bacterial strains cultured in different media were evaluated. Additionally, the α-glucosidase inhibitory activity of the fungal extracts was examined. The results showed that 88.6% of the strains exhibited antimicrobial activity, 55.7% exhibited antioxidant activity, and 85% of the fungi exhibited α-glucosidase inhibitory activity. The research suggested that the endophytes of S. dulcificum are highly diverse and have the potential to produce bioactive metabolites, providing abundant species resources for developing antibiotics, antioxidants and hypoglycemic drugs.
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Affiliation(s)
- Sisi Liu
- Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
| | - Yage Hou
- Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
| | - Kaixuan Zheng
- Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
| | - Qian Ma
- Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
| | - Meng Wen
- Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
| | - Shicheng Shao
- Department of Gardening and Horticulture, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla County, Yunnan, China
| | - Shaohua Wu
- Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
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Wu X, Yang Y, Zhang H. Microbial fortification of pharmacological metabolites in medicinal plants. Comput Struct Biotechnol J 2023; 21:5066-5072. [PMID: 37867972 PMCID: PMC10589376 DOI: 10.1016/j.csbj.2023.10.024] [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: 07/08/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/24/2023] Open
Abstract
Medicinal plants are rich in secondary metabolites with beneficial pharmacological effects. The production of plant secondary metabolites is subjected to the influences by environmental factors including the plant-associated microbiome, which is crucial to the host's fitness and survival. As a result, research interests are increasing in exploiting microbial capacities for enhancing plant production of pharmacological metabolites. A growing body of recent research provides accumulating evidence in support of developing microbe-based tools for achieving this objective. This mini review presents brief summaries of recent studies on medicinal plants that demonstrate microbe-augmented production of pharmacological terpenoids, polyphenols, and alkaloids, followed by discussions on some key questions beyond the promising observations. Explicit molecular insights into the underlying mechanisms will enhance microbial applications for metabolic fortification in medicinal plants.
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Affiliation(s)
- Xiaoxuan Wu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Yang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- Nanchang Institute of Industrial Innovation, Chinese Academy of Sciences, Nanchang 330224, China
- Jiangxi Center for Innovation and Incubation of Industrial Technologies, Chinese Academy of Sciences, Nanchang 330200, China
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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Zhang M, Miao Y, Zhang X, Sun X, Li M, Huang L. Revealing ecotype influences on Cistanche sinensis: from the perspective of endophytes to metabolites characteristics. Front Microbiol 2023; 14:1154688. [PMID: 37538848 PMCID: PMC10394521 DOI: 10.3389/fmicb.2023.1154688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/17/2023] [Indexed: 08/05/2023] Open
Abstract
Introduction Plant microorganism is critical to plant health, adaptability, and productive forces. Intriguingly, the metabolites and microorganisms can act upon each other in a plant. The union of metabolomics and microbiome may uncover the crucial connections of the plant to its microbiome. It has important benefits for the agricultural industry and human being health, particularly for Chinese medical science investigation. Methods In this last 2 years study, on the strength of the UPLC-MS/MS detection platform, we accurately qualitatively, and quantitatively measured the Cistanche sinensis fleshy stems of two ecotypes. Thereafter, through high-throughput amplicon sequencing 16S/ITS sequences were procured. Results PhGs metabolites including echinacoside, isoacteoside, and cistanoside A were significantly downregulated at two ecotypes of C. sinensis. Add up to 876 metabolites were monitored and 231 differential metabolites were analyzed. Further analysis of 34 core differential metabolites showed that 15 compounds with up-regulated belonged to phenolic acids, flavonoids, and organic acids, while 19 compounds with down-regulated belonged to phenolic acids, flavonoids, alkaloids, amino acids, lipids, and nucleotides. There was no noteworthy discrepancy in the endophytic bacteria's α and β diversity between sandy and loam ecotypes. By comparison, the α and β diversity of endophytic fungi was notably distinct. The fungal community of the loam ecotype is more abundant than the sandy ecotype. However, there were few such differences in bacteria. Most abundant genera included typical endophytes such as Phyllobacterium, Mycobacterium, Cistanche, Geosmithia, and Fusarium. LEfSe results revealed there were 11 and 20 biomarkers of endophytic bacteria and fungi in C. sinensis at two ecotypes, respectively. The combination parsing of microflora and metabolites indicated noteworthy relativity between the endophytic fungal communities and metabolite output. Key correlation results that Anseongella was positive relation with Syringin, Arsenicitalea is negative relation with 7-methylxanthine and Pseudogymnoascus is completely positively correlated with nepetin-7-O-alloside. Discussion The aim of this research is: (1) to explore firstly the influence of ecotype on C. sinensis from the perspective of endophytes and metabolites; (2) to investigate the relationship between endophytes and metabolites. This discovery advances our understanding of the interaction between endophytes and plants and provides a theoretical basis for cultivation of C. sinensis in future.
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Affiliation(s)
- Min Zhang
- Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization, College of Pharmacy, Baotou Medical College, Baotou, China
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Inner Mongolia Hospital of Traditional Chinese Medicine, Hohhot, China
- Inner Mongolia Traditional Chinese and Mongolian Medical Research Institute, Hohhot, China
| | - Yujing Miao
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinke Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao Sun
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Minhui Li
- Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization, College of Pharmacy, Baotou Medical College, Baotou, China
- Inner Mongolia Hospital of Traditional Chinese Medicine, Hohhot, China
- Inner Mongolia Traditional Chinese and Mongolian Medical Research Institute, Hohhot, China
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Bao Y, Zhang R, Jiang X, Liu F, He Y, Hu H, Hou X, Hao L, Pei X. Detoxification mechanisms of ginseng to aconite: A review. JOURNAL OF ETHNOPHARMACOLOGY 2023; 304:116009. [PMID: 36516908 DOI: 10.1016/j.jep.2022.116009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Aconite (Fuzi, FZ), the processed root tuber of Aconitum carmichaelii Debx., is utilized as a classic medicine to treat diseases of the cardiovascular system and immune system. Resulting from the narrow margin of safety between a therapeutic dose and a toxic dose, FZ often causes cardiotoxicity including hypotension, palpitation, and bradycardia. Contributing to the detoxification effects of the other famous herbal medicine ginseng (Renshen, RS), which is the dried root and rhizome of Panax ginseng C. A. Meyer, people broadly combine FZ and RS as compatibility more than 1800 years to attenuate the toxicity of FZ. However, the systematic detoxification mechanisms of RS to FZ have not been fully revealed. AIM OF THE REVIEW Aiming to provide a comprehensive interpretation of the attenuation processes of FZ via RS, this review summarizes the up-to-date information about regulatory mechanisms of RS to FZ to shed the light on the essence of detoxification. MATERIALS AND METHODS Literature was searched in electronic databases, including PubMed, Web of Science ScienceDirect, Google Scholar, CNKI and WanFang Data. Relevant studies on detoxification mechanisms were included while irrelevant and duplicate studies were excluded. According to the study design, subject, intervention regime, outcome, first author and year of publication of included data, detoxification mechanisms of RS to FZ were summarized and visualized. RESULTS A total of 144 studies were identified through databases from their inception up to Oct. 2022. Included information indicated that diester-diterpenoid alkaloids (DDAs) were the main toxic substances of FZ. The main mechanisms that RS attenuates the toxicity of FZ were transforming toxic compounds of FZ, affecting the absorption and metabolism of FZ as well as the FZ-induced cell toxicity alleviation. CONCLUSION FZ, as a famous traditional Chinese medicine, has good prospects for utilization. The narrow margin of safety between a therapeutic dose and a toxic dose of FZ limits its clinical effect and safety while RS is always combined with FZ to alleviate its toxicity. However, mechanisms responsible for the detoxification process have not been well identified. Therefore, detoxification mechanisms of RS to FZ are reviewed to ensure the safety and effectiveness of FZ.
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Affiliation(s)
- Yiwen Bao
- Pharmacy College of Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, 611137, PR China
| | - Ruiyuan Zhang
- Pharmacy College of Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, 611137, PR China
| | - Xinyi Jiang
- Pharmacy College of Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, 611137, PR China
| | - Fang Liu
- Pharmacy College of Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, 611137, PR China.
| | - Yao He
- Pharmacy College of Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, 611137, PR China.
| | - Huiling Hu
- Pharmacy College of Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, 611137, PR China
| | - Xinlian Hou
- Huarun Sanjiu (Ya'an) Pharmaceutical Group Co., LTD, Ya'an, 625000, PR China
| | - Li Hao
- Huarun Sanjiu (Ya'an) Pharmaceutical Group Co., LTD, Ya'an, 625000, PR China
| | - Xu Pei
- Pharmacy College of Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, 611137, PR China
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Mishra AK, Sudalaimuthuasari N, Hazzouri KM, Saeed EE, Shah I, Amiri KMA. Tapping into Plant-Microbiome Interactions through the Lens of Multi-Omics Techniques. Cells 2022; 11:3254. [PMID: 36291121 PMCID: PMC9600287 DOI: 10.3390/cells11203254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 10/21/2023] Open
Abstract
This review highlights the pivotal role of root exudates in the rhizosphere, especially the interactions between plants and microbes and between plants and plants. Root exudates determine soil nutrient mobilization, plant nutritional status, and the communication of plant roots with microbes. Root exudates contain diverse specialized signaling metabolites (primary and secondary). The spatial behavior of these metabolites around the root zone strongly influences rhizosphere microorganisms through an intimate compatible interaction, thereby regulating complex biological and ecological mechanisms. In this context, we reviewed the current understanding of the biological phenomenon of allelopathy, which is mediated by phytotoxic compounds (called allelochemicals) released by plants into the soil that affect the growth, survival, development, ecological infestation, and intensification of other plant species and microbes in natural communities or agricultural systems. Advances in next-generation sequencing (NGS), such as metagenomics and metatranscriptomics, have opened the possibility of better understanding the effects of secreted metabolites on the composition and activity of root-associated microbial communities. Nevertheless, understanding the role of secretory metabolites in microbiome manipulation can assist in designing next-generation microbial inoculants for targeted disease mitigation and improved plant growth using the synthetic microbial communities (SynComs) tool. Besides a discussion on different approaches, we highlighted the advantages of conjugation of metabolomic approaches with genetic design (metabolite-based genome-wide association studies) in dissecting metabolome diversity and understanding the genetic components of metabolite accumulation. Recent advances in the field of metabolomics have expedited comprehensive and rapid profiling and discovery of novel bioactive compounds in root exudates. In this context, we discussed the expanding array of metabolomics platforms for metabolome profiling and their integration with multivariate data analysis, which is crucial to explore the biosynthesis pathway, as well as the regulation of associated pathways at the gene, transcript, and protein levels, and finally their role in determining and shaping the rhizomicrobiome.
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Affiliation(s)
- Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. Hazzouri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Esam Eldin Saeed
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Iltaf Shah
- Department of Chemistry (Biochemistry), College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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