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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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Tong M, Ding Y, Yu H, Zhang W, Wu D. Integrated non-targeted metabolomics and transcriptomics reveals the browning mechanism of scraped ginger (Zingiber officinale Rosc.). J Food Sci 2024; 89:3260-3275. [PMID: 38685879 DOI: 10.1111/1750-3841.17084] [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: 10/28/2023] [Revised: 03/27/2024] [Accepted: 04/06/2024] [Indexed: 05/02/2024]
Abstract
Ginger (Zingiber officinale Rosc.) possesses a rich nutritional profile, making it a valuable ingredient for a wide range of culinary applications. After removing its outer skin, ginger can be effectively utilized in the production of pickles and other processed food products. However, following scraping, ginger undergoes a series of physiological and biochemical changes during storage, which can impact its subsequent development and utilization in food. Thus, the current study aimed to investigate the browning mechanism of scraped ginger using non-targeted metabolomics and transcriptomics. The findings revealed 149 shared differential metabolites and 639 shared differential genes among freshly scraped ginger, ginger browned for 5 days, and ginger browned for 15 days. These metabolites and genes are primarily enriched in stilbenes, diarylheptane, and gingerol biosynthesis, phenylpropanoid biosynthesis, and tyrosine metabolism. Through the combined regulation of these pathways, the levels of phenolic components (such as chlorogenic acid and ferulic acid) and the ginger indicator component (6-gingerol) decreased, whereas promoting an increase in the content of coniferaldehyde and curcumin. Additionally, the activities of polyphenol oxidase (PPO) and peroxidase (POD) were significantly increased (p-adjust <0.05). This study hypothesized that chlorogenic and ferulic acid undergo polymerization under the catalysis of PPO and POD, thereby exacerbating the lignification of scraped ginger. These findings offer a theoretical foundation for understanding the browning mechanism of ginger after scraping. PRACTICAL APPLICATION: Ginger's quality and nutrition can change when its skin is removed. This happens due to physical and biochemical reactions during scraping. The browning that occurs affects both the taste and health benefits of ginger, we can better understand how to prevent browning and maintain ginger's quality. This research sheds light on improving ginger processing techniques for better products.
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Affiliation(s)
- Moru Tong
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Anhui Province Key Laboratory of Traditional Chinese Medicine Decoction Pieces of New Manufacturing Technology, Hefei, China
- Traditional Chinese Medicine Concoction Heritage Base of the State Administration of Traditional Chinese Medicine, Hefei, China
- Anhui Collaborative Innovation Centre for Quality Enhancement of Taoist Chinese Medicinal Materials established by the Ministry of Commerce of Anhui Province, Hefei, China
| | - Yangfei Ding
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Anhui Province Key Laboratory of Traditional Chinese Medicine Decoction Pieces of New Manufacturing Technology, Hefei, China
- Traditional Chinese Medicine Concoction Heritage Base of the State Administration of Traditional Chinese Medicine, Hefei, China
- Anhui Collaborative Innovation Centre for Quality Enhancement of Taoist Chinese Medicinal Materials established by the Ministry of Commerce of Anhui Province, Hefei, China
| | - Hao Yu
- Bozhou University, Bozhou, China
| | - Wei Zhang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Anhui Province Key Laboratory of Traditional Chinese Medicine Decoction Pieces of New Manufacturing Technology, Hefei, China
- Traditional Chinese Medicine Concoction Heritage Base of the State Administration of Traditional Chinese Medicine, Hefei, China
- Anhui Collaborative Innovation Centre for Quality Enhancement of Taoist Chinese Medicinal Materials established by the Ministry of Commerce of Anhui Province, Hefei, China
| | - Deling Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Anhui Province Key Laboratory of Traditional Chinese Medicine Decoction Pieces of New Manufacturing Technology, Hefei, China
- Traditional Chinese Medicine Concoction Heritage Base of the State Administration of Traditional Chinese Medicine, Hefei, China
- Anhui Collaborative Innovation Centre for Quality Enhancement of Taoist Chinese Medicinal Materials established by the Ministry of Commerce of Anhui Province, Hefei, China
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Eshawu AB, Ghalsasi VV. Metabolomics of natural samples: A tutorial review on the latest technologies. J Sep Sci 2024; 47:e2300588. [PMID: 37942863 DOI: 10.1002/jssc.202300588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/29/2023] [Accepted: 11/06/2023] [Indexed: 11/10/2023]
Abstract
Metabolomics is the study of metabolites present in a living system. It is a rapidly growing field aimed at discovering novel compounds, studying biological processes, diagnosing diseases, and ensuring the quality of food products. Recently, the analysis of natural samples has become important to explore novel bioactive compounds and to study how environment and genetics affect living systems. Various metabolomics techniques, databases, and data analysis tools are available for natural sample metabolomics. However, choosing the right method can be a daunting exercise because natural samples are heterogeneous and require untargeted approaches. This tutorial review aims to compile the latest technologies to guide an early-career scientist on natural sample metabolomics. First, different extraction methods and their pros and cons are reviewed. Second, currently available metabolomics databases and data analysis tools are summarized. Next, recent research on metabolomics of milk, honey, and microbial samples is reviewed. Finally, after reviewing the latest trends in technologies, a checklist is presented to guide an early-career researcher on how to design a metabolomics project. In conclusion, this review is a comprehensive resource for a researcher planning to conduct their first metabolomics analysis. It is also useful for experienced researchers to update themselves on the latest trends in metabolomics.
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Affiliation(s)
- Ali Baba Eshawu
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Vihang Vivek Ghalsasi
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India
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Ren Y, Li WB, Li ZX, Zhang WL, Jue DW, Xing HT, Li HL, Li Q. Dynamic transcriptome profiling provides insights into rhizome enlargement in ginger (Zingiber officinale Rosc.). PLoS One 2023; 18:e0287969. [PMID: 37450442 PMCID: PMC10348538 DOI: 10.1371/journal.pone.0287969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 06/17/2023] [Indexed: 07/18/2023] Open
Abstract
The rhizome is an economically important part of ginger (Zingiber officinale Rosc.). However, the mechanism of ginger rhizome enlargement remains unclear. In this study, we performed an integrated analysis of the hormone content and transcriptome of ginger at three rhizome enlargement stages: initial enlargement (S1), middle enlargement (S2), and peak enlargement (S3). With rhizome enlargement, the levels of the hormones zeatin (ZT), gibberellic acid (GA), indole acetic acid (IAA), and jasmonic acid (JA) were significantly increased, and this increase was positively correlated with rhizome diameter. Transcriptomic analysis identified a large number of differentially expressed genes (DEGs); the number of DEGs were 2,206 in the transition from S1 to S2, and 1,151 in the transition from S2 to S3. The expression of several genes related to hormone biosynthesis and signalling and cell division or expansion, and transcription factors was significantly altered, which suggests that these genes play essential roles in rhizome enlargement. The results of correlation analysis suggested that the process of ginger rhizome enlargement may be primarily related to the regulation of endogenous cytokinin, GA3, auxin, and JA biosynthesis pathways and signal transduction; GRAS, HB, MYB, MYB122, bZIP60, ARF1, ARF2, E2FB1, and E2FB2, which may regulate the expression of rhizome formation-related genes; and CYC2, CDKB1, CDKB2, EXPA1, and XTH7, which may mediate cell division and expansion. These results provide gene resources and information that will be useful for the molecular breeding in ginger.
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Affiliation(s)
- Yun Ren
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Wen Bo Li
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Fuling, Chongqing, China
| | - Zhe Xin Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Wen Lin Zhang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Deng Wei Jue
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Hai Tao Xing
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Hong Lei Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Qiang Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
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Health benefits of bioactive components in pungent spices mediated via the involvement of TRPV1 channel. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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