51
|
Zhang XM, Tang DX, Li QQ, Wang YB, Xu ZH, Li WJ, Yu H. Complex microbial communities inhabiting natural Cordyceps militaris and the habitat soil and their predicted functions. Antonie van Leeuwenhoek 2021; 114:465-477. [PMID: 33638738 DOI: 10.1007/s10482-021-01534-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/08/2021] [Indexed: 11/30/2022]
Abstract
Cordyceps militaris is a traditional Chinese medicinal food that is challenging to quality maintaining while mass cultivation. Many studies have found that abundant microbes inhabit Ophiocordyceps sinensis and perform important functions for their host. In this study, our objective was to reveal the microbial communities that inhabit C. militaris and analyze their potential functions. High-throughput sequencing of 16S rRNA and ITS genes was used to compare the diversity and composition of the bacterial and fungal communities associated with naturally occurring C. militaris collected from Yunnan Province, southwestern China. The diversity and richness of the microbial communities and the number of function genes of the bacteria were significantly higher in the habitat soil than in the fruiting body. The sclerotia and stromata samples shared the same microbiota and functions. The main bacterial phyla were Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria, and Ascomycota was the main fungal phylum. The growth-promoting bacteria Herbaspirillum and the plant probiotic Phyllobacterium, which may enhance C. militaris quality and facilitate its cultivation, were detected in the fruiting body samples. Genes related to metabolism were more abundant in the soil bacteria, while membrane transport genes were more abundant in the endophytic bacteria of C. militaris. Our study is the first to reveal the unexpectedly high diversity of the microbial communities and the bacterial functions inhabiting the natural C. militaris using high-throughput sequencing, and our results provide insights into mining the functions of microorganisms in the development and quality of C. militaris.
Collapse
Affiliation(s)
- Xiao-Mei Zhang
- Yunnan Herbal Laboratory, Ecology and Environmental Sciences, Yunnan University, No. 2 Cuihu Lake North Road, Kunming, 650091, Yunnan, China.,College of Basic Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, Yunnan, China.,The Research Center of Cordyceps Development and Utilization of Kunming, Yunnan Herbal Biotech Co. Ltd., Kunming, 650106, China
| | - De-Xiang Tang
- Yunnan Herbal Laboratory, Ecology and Environmental Sciences, Yunnan University, No. 2 Cuihu Lake North Road, Kunming, 650091, Yunnan, China.,The Research Center of Cordyceps Development and Utilization of Kunming, Yunnan Herbal Biotech Co. Ltd., Kunming, 650106, China.,The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming, 650091, China
| | - Qing-Qing Li
- Kunming Xianghao Technology Co., Ltd., Kunming, 650204, China
| | - Yuan-Bing Wang
- Yunnan Herbal Laboratory, Ecology and Environmental Sciences, Yunnan University, No. 2 Cuihu Lake North Road, Kunming, 650091, Yunnan, China.,The Research Center of Cordyceps Development and Utilization of Kunming, Yunnan Herbal Biotech Co. Ltd., Kunming, 650106, China.,The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming, 650091, China
| | - Zhi-Hong Xu
- Yunnan Herbal Laboratory, Ecology and Environmental Sciences, Yunnan University, No. 2 Cuihu Lake North Road, Kunming, 650091, Yunnan, China.,The Research Center of Cordyceps Development and Utilization of Kunming, Yunnan Herbal Biotech Co. Ltd., Kunming, 650106, China.,The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming, 650091, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Hong Yu
- Yunnan Herbal Laboratory, Ecology and Environmental Sciences, Yunnan University, No. 2 Cuihu Lake North Road, Kunming, 650091, Yunnan, China. .,The Research Center of Cordyceps Development and Utilization of Kunming, Yunnan Herbal Biotech Co. Ltd., Kunming, 650106, China. .,The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming, 650091, China.
| |
Collapse
|
52
|
Wang Y, Cheng H, Chang F, Zhao L, Wang B, Wan Y, Yue M. Endosphere Microbiome and Metabolic Differences Between the Spots and Green Parts of Tricyrtis macropoda Leaves. Front Microbiol 2021; 11:599829. [PMID: 33505373 PMCID: PMC7829350 DOI: 10.3389/fmicb.2020.599829] [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: 08/28/2020] [Accepted: 11/24/2020] [Indexed: 11/16/2022] Open
Abstract
Background Plant leaves are important organs for photosynthesis and biological energy production. The leaves of Tricyrtis macropoda have an unusual spotted pattern. However, whether the spots of T. macropoda affect the plant microbiome and metabolites is unclear. In this study, we compared differences in the endosphere microbiome and plant metabolites in green parts and spots and the effects of spots on the photosynthesis of leaves. Methods 16S/ITS sequences and metabolite spectra were obtained by high-throughput amplicon sequencing and ultra-high-performance liquid chromatography–high-resolution mass spectrometry, respectively. Changes in the diversity of the endophytic microbial community and metabolites were studied, and the effect of T. macropoda leaf spots on photosynthesis was examined by chlorophyll fluorescence. Results The results showed that the relative abundance of Cercospora fungi in the leaf spots of T. macropoda was significantly higher than that in the green parts (P < 0.05) while Colletotrichum fungi showed low abundance in the spots. Alkaloid and ketone metabolites were decreased in the green parts compared with the spots, and amino acids, organic acids, lipids, and other compounds were increased in the green parts compared with the spots. A combined analysis of microbial communities and metabolites showed a significant correlation between the endophytic fungal communities and metabolite production. The changes in these metabolites may cause changes in local leaf color. In addition, we found that the spot areas of T. macropoda can be photosynthetically normal. Conclusion This research showed the relationship between endophytic microorganisms and metabolites, and the findings advance our understanding of endophyte–plant interactions and provide a new direction for investigating the relationship between endophytes and phenotypes.
Collapse
Affiliation(s)
- Yan Wang
- Microbiology Institute of Shaanxi, Xi'an, China
| | - Huyin Cheng
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Fan Chang
- Microbiology Institute of Shaanxi, Xi'an, China
| | - Le Zhao
- School of Biological Sciences and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Bin Wang
- College of Chemistry, Biology and Materials Science, East China University of Technology, Nanchang, China
| | - Yi Wan
- Microbiology Institute of Shaanxi, Xi'an, China
| | - Ming Yue
- School of Life Sciences, Northwest University, Xi'an, China
| |
Collapse
|
53
|
Liu JM, Wang SS, Zheng X, Jin N, Lu J, Huang YT, Fan B, Wang FZ. Antimicrobial Activity Against Phytopathogens and Inhibitory Activity on Solanine in Potatoes of the Endophytic Bacteria Isolated From Potato Tubers. Front Microbiol 2020; 11:570926. [PMID: 33281766 PMCID: PMC7705204 DOI: 10.3389/fmicb.2020.570926] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/28/2020] [Indexed: 11/29/2022] Open
Abstract
As an important global crop, the potato (Solanum tuberosum L.) contains the endotoxin solanine that leads to human poisoning and major economic losses. Poisoning symptoms and even acute poisoning may occur when the content of solanine in potatoes exceeds 200 mg/kg. In addition, potatoes are susceptible to some pathogenic bacteria, including Streptomyces scabies and Erwinia carotovora subsp. atroseptica (Van Hall) dye, which can cause potato scab and potato blackleg disease, respectively. In this study, 37 culturable endophytic bacteria strains were obtained from potato tubers based on the culture-dependent method. Results indicated that nine strains showed antimicrobial activity against at least one pathogen by antimicrobial activity screening and 23 strains showed inhibitory activity on solanine in potato tubers. Among them, strain P-NA2-14 (Bacillus megaterium NBRC 15308T, 99.31%) showed not only better antimicrobial activity against both the two indicator pathogens, but also the best inhibitory activity on solanine, which was proved to be a potential biocontrol bacterium. Meanwhile, the relationship between the distribution of the endophytic bacterial community and the content of solanine in potato tubers was studied by Illumina-based analysis, indicating that the distribution of the endophytic bacterial community was obviously influenced by the content of solanine. The results showed a new insight into the relationship between plant secondary metabolites and endophytic bacteria in potato tubers and provided potential new technical support for the biological control of potato storage.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Bei Fan
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feng-Zhong Wang
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
54
|
Dickey JR, Fordyce JA, Lebeis SL. Bacterial communities of the Salvia lyrata rhizosphere explained by spatial structure and sampling grain. MICROBIAL ECOLOGY 2020; 80:846-858. [PMID: 32888042 DOI: 10.1007/s00248-020-01594-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Advancements in molecular technology have reduced the constraints that the grain of observation, or the spatial resolution and volume of the sampling unit, has on the characterization of plant-associated microbiomes. With discrete ecological sampling and massive parallel sequencing, we can more precisely portray microbiome community assembly and microbial recruitment to host tissue over space and time. Here, we differentiate rarefied community richness and relative abundance in bacterial microbiomes of Salvia lyrata dependent on three spatial depths, which are discrete physical distances from the soil surface within the rhizosphere microhabitat as a proxy for the root system zones. To assess the impact of sampling grain on rarefied community richness and relative abundance, we evaluated the variation of these metrics between samples pooled prior to DNA extraction and samples pooled after sequencing. A distance-based redundancy analysis with the quantitative Jaccard distance revealed that rhizosphere microbiomes vary in richness between rhizosphere soil depths. At all orders of diversity, rarefied microbial richness was consistently lowest at the deepest samples taken (approximately 4 cm from soil surface) in comparison with other rhizosphere soil depths. We additionally show that finer grain sampling (i.e., three samples of equal volume pooled after sequencing) recovers greater microbial richness when using 16S rRNA gene sequencing to describe microbial communities found within the rhizosphere system. In summary, to further elucidate the extent host-specific microbiomes assemble within the rhizosphere, the grain at which bacterial communities are sampled should reflect and encompass fine-scale heterogeneity of the system.
Collapse
Affiliation(s)
- Jonathan R Dickey
- Department of Ecology and Evolutionary Biology, The University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996, USA.
| | - James A Fordyce
- Department of Ecology and Evolutionary Biology, The University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996, USA
| | - Sarah L Lebeis
- Department of Microbiology, The University of Tennessee, 307 Ken and Blaire Mossman Bldg., Knoxville, TN, 37996, USA
| |
Collapse
|
55
|
Liu Y, Li Y, Luo W, Liu S, Chen W, Chen C, Jiao S, Wei G. Soil potassium is correlated with root secondary metabolites and root-associated core bacteria in licorice of different ages. PLANT AND SOIL 2020; 456:61-79. [PMID: 32895581 PMCID: PMC7468178 DOI: 10.1007/s11104-020-04692-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 08/24/2020] [Indexed: 05/09/2023]
Abstract
AIMS Licorice (Glycyrrhiza uralensis Fisch.) is a crucial medicinal herb as it accumulates glycyrrhizin and liquiritin in roots. Licorice root-associated bacterial communities shaped by soil characteristics are supposed to regulate the accumulation of root secondary metabolites. METHODS The soil characteristics, root secondary metabolites, and root-associated bacterial communities were analyzed in licorice plants of different ages to explore their temporal dynamics and interaction mechanisms. RESULTS Temporal variation in soil characteristics and root secondary metabolites was distinct. The alpha-diversity of root-associated bacterial communities decreased with root proximity, and the community composition was clustered in the rhizosphere. Different taxa that were core-enriched from the dominant taxa in the bulk soil, rhizosphere soil, and root endosphere displayed varied time-decay relationships. Soil total potassium (TK) as a key factor regulated the temporal variation in some individual taxa in the bulk and rhizosphere soils; these taxa were associated with the adjustment of root secondary metabolites across different TK levels. CONCLUSIONS Licorice specifically selects root-associated core bacteria over the course of plant development, and TK is correlated with root secondary metabolites and individual core-enriched taxa in the bulk and rhizosphere soils, which may have implications for practical licorice cultivation.
Collapse
Affiliation(s)
- Yang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100 People’s Republic of China
| | - Yanmei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100 People’s Republic of China
| | - Wen Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100 People’s Republic of China
| | - Shuang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100 People’s Republic of China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100 People’s Republic of China
| | - Chun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100 People’s Republic of China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100 People’s Republic of China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100 People’s Republic of China
| |
Collapse
|
56
|
Pang Z, Xu P, Yu D. Environmental adaptation of the root microbiome in two rice ecotypes. Microbiol Res 2020; 241:126588. [PMID: 32892063 DOI: 10.1016/j.micres.2020.126588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/11/2020] [Accepted: 08/21/2020] [Indexed: 01/28/2023]
Abstract
The root microbiome plays a key role that can influence host plant growth and abiotic stress. While there has been extensive characterization of community structure, spatial compartmentalization, and the impact of drought stresses on the root microbiome in rice and other plants, there is relatively little known about the differences in root microbiome among rice ecotypes in natural upland and lowland fields. Herein, we used two rice ecotypes, upland and irrigated ecotype rice (two Indica and two Japonica genotypes), as a model to explore the responses of the root microbiome under different environmental conditions. We aimed to identify environment-induced adaptation in the root bacterial and fungal composition of rice ecotypes by high-throughput sequencing. Rice from lowland field or upland had significantly altered overall bacterial and fungal community compositions of the two ecotypes, with diversity of both ecotypes greatly decreased from lowland field to upland. The overall response of the root microbiome to upland conditions was taxonomically driven by the enrichment of family Enterobacteriaceae and genera Serratia, and phylum Ascomycota. Interestingly, rice ecotypes specifically enriched root microbes when they were transferred from their original environment, such as the enrichment of class Thermoleophilia and phylum Actinobacteria when the irrigated ecotype rice was moved from lowland to upland field. These results revealed that different environmental conditions and rice ecotypes resulted in a restructuring of root microbiome communities, and suggested the possibility that components responsible for the beneficial attributes in the altered root microbiome might contribute to the adaptation of different ecotypes in natural fields.
Collapse
Affiliation(s)
- Zhiqiang Pang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China.
| | - Diqiu Yu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091 China.
| |
Collapse
|
57
|
Luo L, Dong L, Huang Q, Ma S, Fantke P, Li J, Jiang J, Fitzgerald M, Yang J, Jia Z, Zhang J, Wang H, Dai Y, Zhu G, Xing Z, Liang Y, Li M, Wei G, Song J, Wei J, Peng C, Zhang H, Zhang W, Wang S, Mizuno K, Marco AAG, Wu L, Xu J, Xiong C, Chen S. Detection and risk assessments of multi-pesticides in 1771 cultivated herbal medicines by LC/MS-MS and GC/MS-MS. CHEMOSPHERE 2020; 262:127477. [PMID: 32799136 DOI: 10.1016/j.chemosphere.2020.127477] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/20/2020] [Accepted: 06/20/2020] [Indexed: 02/05/2023]
Abstract
Focus on the safety of herbal medicines has mainly been directed towards the presence of intrinsic toxicity, as found in the cases of renal and hepatic dysfunction caused by aristolochic acids. However, contamination from extrinsic hazards may impart an even greater reduction in their safety and efficacy. This study reveals that pesticides were present in the majority (88%) of a comprehensive cross-section (n = 1771) of herbal medicine samples. Alarmingly, more than half (59%) contained pesticides over the European Pharmacopoeia (EP) limit, and 43% of them contained 35 varieties of banned, extremely toxic pesticides, eight of which were detected at levels over 500 times higher than the default Maximum Residue Limit (MRL). DDTs, carbofuran, and mevinphos were confirmed as being among the most risk-inducing pesticides by three different risk assessment methods, reported to produce carcinogenic, genotoxic, reproductive, and developmental effects, in addition to carrying nephrotoxicity and hepatotoxicity. In light of these findings, and withstanding that extrinsic hazards can be controlled unlike intrinsic toxicity, the authors here strongly recommend the application of herbal medicine quality-control measures and solutions to safeguard against a neglected but certainly potentially serious health risk posed to the majority of the global population that consumes herbal medicines.
Collapse
Affiliation(s)
- Lu Luo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Linlin Dong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Qin Huang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Shuangcheng Ma
- National Institutes for Food and Drug Control, Beijing, 100050, PR China
| | - Peter Fantke
- Quantitative Sustainability Assessment, Department of Technology, Management and Economics, Technical University of Denmark, Produktionstorvet 424, 2800 Kgs, Lyngby, Denmark
| | - Jianhui Li
- Waters Technologies Shanghai Limited, Block 13, City of Elite, 1000 Jinhai Road, Pu Dong New District, Shanghai, 201206, PR China
| | - Jingwen Jiang
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Martin Fitzgerald
- Department of Life Sciences, University of Westminster, 115 New Cavendish Street, W1W 6UW, London, UK
| | - Jane Yang
- Waters Technologies Shanghai Limited, Block 13, City of Elite, 1000 Jinhai Road, Pu Dong New District, Shanghai, 201206, PR China
| | - Zhengwei Jia
- Waters Technologies Shanghai Limited, Block 13, City of Elite, 1000 Jinhai Road, Pu Dong New District, Shanghai, 201206, PR China
| | - Jiqing Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Haifeng Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Yuntao Dai
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Guangwei Zhu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Zhihan Xing
- College of Science and Mathematics, University of Massachusetts Boston, 100 William T. Morrissey Blvd, Boston, MA, 02125-3393, USA
| | - Yichuan Liang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Mengzhi Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Guangfei Wei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, PR China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, PR China
| | - Cheng Peng
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, PR China
| | - Han Zhang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, PR China
| | - Wei Zhang
- Pharmacogenetics Research Institute, Institute of Clinical Pharmacology, Central South University, Changsha, 410008, Hunan, PR China
| | - Shumei Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Kaito Mizuno
- Suzuka University of Medical Science, 1001-1, Kishioka, Suzuka, 510-0293, Japan
| | - Alarcon Arauco Gian Marco
- Intelligence of Science and Technology, School of Automation and Electrical Engineering, University of Science and Technology, Beijing, 100083, PR China
| | - Lan Wu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Chao Xiong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China.
| |
Collapse
|
58
|
Microbiome technology empowers the development of traditional Chinese medicine. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1759-1761. [PMID: 32789726 DOI: 10.1007/s11427-020-1778-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/11/2020] [Indexed: 02/07/2023]
|
59
|
Structure and Function of Bacterial Microbiota in Eucommia ulmoides Bark. Curr Microbiol 2020; 77:3623-3632. [DOI: 10.1007/s00284-020-02157-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022]
|
60
|
Henkhaus N, Bartlett M, Gang D, Grumet R, Jordon‐Thaden I, Lorence A, Lyons E, Miller S, Murray S, Nelson A, Specht C, Tyler B, Wentworth T, Ackerly D, Baltensperger D, Benfey P, Birchler J, Chellamma S, Crowder R, Donoghue M, Dundore‐Arias JP, Fletcher J, Fraser V, Gillespie K, Guralnick L, Haswell E, Hunter M, Kaeppler S, Kepinski S, Li F, Mackenzie S, McDade L, Min Y, Nemhauser J, Pearson B, Petracek P, Rogers K, Sakai A, Sickler D, Taylor C, Wayne L, Wendroth O, Zapata F, Stern D. Plant science decadal vision 2020-2030: Reimagining the potential of plants for a healthy and sustainable future. PLANT DIRECT 2020; 4:e00252. [PMID: 32904806 PMCID: PMC7459197 DOI: 10.1002/pld3.252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/15/2020] [Indexed: 05/17/2023]
Abstract
Plants, and the biological systems around them, are key to the future health of the planet and its inhabitants. The Plant Science Decadal Vision 2020-2030 frames our ability to perform vital and far-reaching research in plant systems sciences, essential to how we value participants and apply emerging technologies. We outline a comprehensive vision for addressing some of our most pressing global problems through discovery, practical applications, and education. The Decadal Vision was developed by the participants at the Plant Summit 2019, a community event organized by the Plant Science Research Network. The Decadal Vision describes a holistic vision for the next decade of plant science that blends recommendations for research, people, and technology. Going beyond discoveries and applications, we, the plant science community, must implement bold, innovative changes to research cultures and training paradigms in this era of automation, virtualization, and the looming shadow of climate change. Our vision and hopes for the next decade are encapsulated in the phrase reimagining the potential of plants for a healthy and sustainable future. The Decadal Vision recognizes the vital intersection of human and scientific elements and demands an integrated implementation of strategies for research (Goals 1-4), people (Goals 5 and 6), and technology (Goals 7 and 8). This report is intended to help inspire and guide the research community, scientific societies, federal funding agencies, private philanthropies, corporations, educators, entrepreneurs, and early career researchers over the next 10 years. The research encompass experimental and computational approaches to understanding and predicting ecosystem behavior; novel production systems for food, feed, and fiber with greater crop diversity, efficiency, productivity, and resilience that improve ecosystem health; approaches to realize the potential for advances in nutrition, discovery and engineering of plant-based medicines, and "green infrastructure." Launching the Transparent Plant will use experimental and computational approaches to break down the phytobiome into a "parts store" that supports tinkering and supports query, prediction, and rapid-response problem solving. Equity, diversity, and inclusion are indispensable cornerstones of realizing our vision. We make recommendations around funding and systems that support customized professional development. Plant systems are frequently taken for granted therefore we make recommendations to improve plant awareness and community science programs to increase understanding of scientific research. We prioritize emerging technologies, focusing on non-invasive imaging, sensors, and plug-and-play portable lab technologies, coupled with enabling computational advances. Plant systems science will benefit from data management and future advances in automation, machine learning, natural language processing, and artificial intelligence-assisted data integration, pattern identification, and decision making. Implementation of this vision will transform plant systems science and ripple outwards through society and across the globe. Beyond deepening our biological understanding, we envision entirely new applications. We further anticipate a wave of diversification of plant systems practitioners while stimulating community engagement, underpinning increasing entrepreneurship. This surge of engagement and knowledge will help satisfy and stoke people's natural curiosity about the future, and their desire to prepare for it, as they seek fuller information about food, health, climate and ecological systems.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Andrew Nelson
- Boyce Thompson Institute for Plant ResearchIthacaNYUSA
| | | | - Brett Tyler
- Center for Genome Research and Biocomputing, and Department of Botany and Plant PathologyOregon State UniversityCorvallisArmenia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Fay‐Wei Li
- Boyce Thompson Institute, and Plant Biology SectionCornell UniversityIthacaNYUSA
| | | | | | - Ya Min
- Harvard UniversitySeattleWAUSA
| | | | | | | | - Katie Rogers
- American Society of Plant BiologistsRockvilleMDUSA
| | | | | | | | | | | | | | - David Stern
- Boyce Thompson Institute for Plant ResearchIthacaNYUSA
| |
Collapse
|
61
|
Mapook A, Hyde KD, McKenzie EHC, Jones EBG, Bhat DJ, Jeewon R, Stadler M, Samarakoon MC, Malaithong M, Tanunchai B, Buscot F, Wubet T, Purahong W. Taxonomic and phylogenetic contributions to fungi associated with the invasive weed Chromolaena odorata (Siam weed). FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00444-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
62
|
Gong X, Li X, Bo A, Shi RY, Li QY, Lei LJ, Zhang L, Li MH. The interactions between gut microbiota and bioactive ingredients of traditional Chinese medicines: A review. Pharmacol Res 2020; 157:104824. [PMID: 32344049 DOI: 10.1016/j.phrs.2020.104824] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/09/2020] [Accepted: 04/06/2020] [Indexed: 02/06/2023]
Abstract
In recent years, the interaction between the bioactive ingredients of traditional Chinese medicine (TCM) and gut microbiota has been a focus of many studies. When TCM enters the digestive tract, some bioactive ingredients are not absorbed into the gut well thus leading to low bioavailability. Ingredients of TCM are metabolised, or biotransformed by gut microbiota, thereby producing new bioactive molecules, and promote medicine absorption into the circulation. At the same time, the ingredients of TCM effect the composition and structure of gut microbiota, thereby influencing the remote function of diseased organs / tissues through the systemic action of the gut microbiota. In this review, we summarise the gut microbiota-mediated metabolism of flavonoids, alkaloids, terpenoids, saponins, polysaccharides, phenylpropanoids, and organic acids, along with a discussion on the metabolites formed and the biotransformation pathways involving various enzymes. We also highlight the importance of bioactive ingredients of TCM in regulating gut microbiota.
Collapse
Affiliation(s)
- Xue Gong
- Baotou Medical College, Baotou, Inner Mongolia, China
| | - Xue Li
- Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Agula Bo
- Baotou Medical College, Baotou, Inner Mongolia, China
| | - Ru-Yu Shi
- Baotou Medical College, Baotou, Inner Mongolia, China
| | - Qin-Yu Li
- Baotou Medical College, Baotou, Inner Mongolia, China
| | - Lu-Jing Lei
- Inner Mongolia Institute of Traditional Chinese Medicine, Hohhot, Inner Mongolia, China
| | - Lei Zhang
- Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Min-Hui Li
- Baotou Medical College, Baotou, Inner Mongolia, China; Inner Mongolia Medical University, Hohhot, Inner Mongolia, China; Inner Mongolia Institute of Traditional Chinese Medicine, Hohhot, Inner Mongolia, China; Qiqihar Medical University, Qiqihar, Heilongjiang, China; Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources and Utilization, Baotou Medical College, Baotou, Inner Mongolia, China.
| |
Collapse
|
63
|
Comeau D, Novinscak A, Joly DL, Filion M. Spatio-Temporal and Cultivar-Dependent Variations in the Cannabis Microbiome. Front Microbiol 2020; 11:491. [PMID: 32265895 PMCID: PMC7105690 DOI: 10.3389/fmicb.2020.00491] [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: 12/16/2019] [Accepted: 03/06/2020] [Indexed: 11/13/2022] Open
Abstract
The incipient legalization and commercialization of Cannabis sativa in Canada have promulgated research into characterizing the plant’s microbiome as it promotes many facets of plant growth and health. The emblematic production of commercially important secondary metabolites, namely tetrahydrocannabinol (THC), cannabidiol (CBD) and terpenes, has warranted investigating the modulating capacity of these molecules on the plant microbiome. C. sativa cultivars can be classified into chemotypes depending on the relative levels of THC and CBD they produce; their biosynthesis also varies spatially and temporally during the life cycle of the plant. To study the differential microbiome structure and diversity between cultivars in a spatio-temporal manner, we extracted microbial DNA from the rhizosphere, endorhizosphere, and phyllosphere during the entire life cycle of three different chemotypes; CBD Yummy (<1% THC/13% CBD), CBD shark (6% THC/10% CBD) and Hash (14% THC/ < 1% CBD). Illumina marker gene sequencing of bacterial (16S) and fungal (ITS) communities were coupled to the QIIME2, PICRUSt, and LEfSe pipelines for analysis. Our study describes spatio-temporal and cultivar-dependent variations in the fungal and bacterial microbiome of C. sativa, and details strong cultivar-dependent variance in the belowground microbiome. Furthermore, the predicted pathway abundance of the bacterial microbiome is concomitantly subject to spatio-temporal variations; pathways related to lipid, amino acid, glucose and pentose metabolism were noteworthy. These results describe, for the first time, spatio-temporal and cultivar-dependent variations in the microbiome of C. sativa produced under strict commercial settings. Describing the microbiome is the first step in discoveries that could help in engineering a plant growth and health promoting microbiome in future works.
Collapse
Affiliation(s)
- Dominique Comeau
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | - Amy Novinscak
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | - David L Joly
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | - Martin Filion
- Department of Biology, University of Moncton, Moncton, NB, Canada
| |
Collapse
|
64
|
Research Advances of Beneficial Microbiota Associated with Crop Plants. Int J Mol Sci 2020; 21:ijms21051792. [PMID: 32150945 PMCID: PMC7084388 DOI: 10.3390/ijms21051792] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/14/2022] Open
Abstract
Plants are associated with hundreds of thousands of microbes that are present outside on the surfaces or colonizing inside plant organs, such as leaves and roots. Plant-associated microbiota plays a vital role in regulating various biological processes and affects a wide range of traits involved in plant growth and development, as well as plant responses to adverse environmental conditions. An increasing number of studies have illustrated the important role of microbiota in crop plant growth and environmental stress resistance, which overall assists agricultural sustainability. Beneficial bacteria and fungi have been isolated and applied, which show potential applications in the improvement of agricultural technologies, as well as plant growth promotion and stress resistance, which all lead to enhanced crop yields. The symbioses of arbuscular mycorrhizal fungi, rhizobia and Frankia species with their host plants have been intensively studied to provide mechanistic insights into the mutual beneficial relationship of plant–microbe interactions. With the advances in second generation sequencing and omic technologies, a number of important mechanisms underlying plant–microbe interactions have been unraveled. However, the associations of microbes with their host plants are more complicated than expected, and many questions remain without proper answers. These include the influence of microbiota on the allelochemical effect caused by one plant upon another via the production of chemical compounds, or how the monoculture of crops influences their rhizosphere microbial community and diversity, which in turn affects the crop growth and responses to environmental stresses. In this review, first, we systematically illustrate the impacts of beneficial microbiota, particularly beneficial bacteria and fungi on crop plant growth and development and, then, discuss the correlations between the beneficial microbiota and their host plants. Finally, we provide some perspectives for future studies on plant–microbe interactions.
Collapse
|
65
|
Maggini V, Mengoni A, Bogani P, Firenzuoli F, Fani R. Promoting Model Systems of Microbiota-Medicinal Plant Interactions. TRENDS IN PLANT SCIENCE 2020; 25:223-225. [PMID: 31948792 DOI: 10.1016/j.tplants.2019.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/27/2019] [Accepted: 12/10/2019] [Indexed: 05/24/2023]
Abstract
The role of the interaction(s) between medicinal plants (MPs) and their endophytes (bacterial microbiome) in the production of bioactive compounds (BCs) with therapeutic properties is emerging. Here, we propose Echinacea purpurea (L.) Moench as a new model to reveal the intimate crosstalk between MPs and bacterial endophytes, aiming to discover (new) BCs.
Collapse
Affiliation(s)
- Valentina Maggini
- Research and Innovation Center in Phytotherapy and Integrated Medicine, Careggi, University Hospital, Florence, Italy; Department of Biology, University of Florence, Florence, Italy.
| | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
| | - Patrizia Bogani
- Department of Biology, University of Florence, Florence, Italy
| | - Fabio Firenzuoli
- Research and Innovation Center in Phytotherapy and Integrated Medicine, Careggi, University Hospital, Florence, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Florence, Italy.
| |
Collapse
|
66
|
Kim CH, Sung KK, Kim DH, Chu H, Kang GH, Moon YJ, Shin HR, Lee S. Development of Integrative Medicine Therapy for Gastrointestinal Autoimmune Diseases: A study protocol for a registry study. Integr Med Res 2020; 9:65-71. [PMID: 32090019 PMCID: PMC7025267 DOI: 10.1016/j.imr.2020.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 11/30/2022] Open
Abstract
Background Although the incidence of AD, including gastrointestinal AD, increases every year, there is no effective therapy for it yet. This causes high medical costs to be spent on the management of autoimmune patients every year. The aim of this study is to identify the characteristics related to the causes and symptoms of gastrointestinal autoimmune disease (AD) by collecting patients’ information and to further contribute to the development of an integrative medicine therapy for gastrointestinal AD. Methods/design This study is a registry study of patients diagnosed with gastrointestinal AD. Subjects who voluntarily sign a written consent form after receiving a sufficient explanation will be assessed for compliance with the inclusion and exclusion criteria through a screening process on their first visit. A total of 35 subjects will be recruited; 15 will be assigned to the patient group, 10 to the control group, 8 to the caregiver group, and 2 to the medical staff group. The clinical information of the subjects will be evaluated through statistical analyses. As this study is a registry study, it will not test specific hypotheses. Discussion If this study identifies the significant characteristics of gastrointestinal AD patients, the results will be useful for the development of integrative medicine methods for the treatment of gastrointestinal AD. Study registration This study was registered with the Clinical Research Information Service (CRIS) of the Korea National Institute of Health (NIH), Republic of Korea (KCT0003976, date of registration: May 23, 2019).
Collapse
Affiliation(s)
- Cheol-Hyun Kim
- Department of Internal Medicine and Neuroscience, College of Korean Medicine, Wonkwang University, Iksan, Republic of Korea
| | - Kang-Keyng Sung
- Department of Internal Medicine and Neuroscience, College of Korean Medicine, Wonkwang University, Iksan, Republic of Korea.,Internal Medicine and Neuroscience, Jangheung Integrative Medical Hospital, Wonkwang University, Jangheung, Republic of Korea
| | - Do-Hyeon Kim
- Department of Digestive Internal Medicine, St. Carollo General Hospital, Suncheon, Republic of Korea
| | - Hongmin Chu
- Department of Internal Medicine and Neuroscience, College of Korean Medicine, Wonkwang University, Iksan, Republic of Korea
| | - Geon-Hui Kang
- Clinical Trial Center, Wonkwang University Gwangju Hospital, Gwangju, Republic of Korea
| | - Yeon-Ju Moon
- Department of Internal Medicine and Neuroscience, College of Korean Medicine, Wonkwang University, Iksan, Republic of Korea
| | - Hye-Ryung Shin
- Department of Internal Medicine and Neuroscience, College of Korean Medicine, Wonkwang University, Iksan, Republic of Korea
| | - Sangkwan Lee
- Department of Internal Medicine and Neuroscience, College of Korean Medicine, Wonkwang University, Iksan, Republic of Korea.,Clinical Trial Center, Wonkwang University Gwangju Hospital, Gwangju, Republic of Korea.,Hanbang Cardio-Renal Syndrome Research Center, College of Oriental Medicine, Wonkwang University, Iksan, Republic of Korea
| |
Collapse
|
67
|
Wang Y, Wang H, Cheng H, Chang F, Wan Y, She X. Niche differentiation in the rhizosphere and endosphere fungal microbiome of wild Paris polyphylla Sm. PeerJ 2020; 8:e8510. [PMID: 32071817 PMCID: PMC7007733 DOI: 10.7717/peerj.8510] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/03/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The plant microbiome is one of the key determinants of plant health and metabolite production. The plant microbiome affects the plant's absorption of nutrient elements, improves plant tolerance to negative environmental factors, increases the accumulation of active components, and alters tissue texture. The microbial community is also important for the accumulation of secondary metabolites by plants. However, there are few studies on the niche differentiation of endophytic microorganisms of plants, especially at different elevations. METHODS We investigated the effects of altitude on the community composition of endophytic fungal communities and the differentiation of endophytic microorganisms among different niches in Paris polyphylla Sm. The rhizosphere soil, roots, rhizomes and leaves of wild-type P. polyphylla Sm. at different altitudes were sampled, and the fungal communities of all samples were analyzed by internal transcribed spacer one amplification sequencing. RESULTS The results showed that in rhizosphere soil, the number of operational taxonomic units (OTUs) that could be classified or identified decreased significantly with increasing altitude, whereas in the endosphere of plants, the total number of OTUs was higher at intermediate altitudes than other altitudes. Furthermore, the structural variability in the rhizosphere fungal community was significantly lower than that in the endophytic communities. In addition, our results confirmed the presence of niche differentiation among members of the endophytic microbial community. Finally, we also determined that the predominant genus of mycobiota in the rhizome was Cadophora. This study provides insight into the relationships between the endosphere microbiome and plants and can guide the artificial cultivation of this plant.
Collapse
Affiliation(s)
- Yan Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- Shaanxi Microbiology Institute, Xi’an, China
- Shaanxi Academy of Sciences, Engineering Center of QinLing Mountains Natural Products, Xi’an, Shaanxi, China
| | - Hanping Wang
- College of Medical, Xi’an International University, Xi’an, China
| | - HuYin Cheng
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xi’an, Shaanxi, China
| | - Fan Chang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- Shaanxi Microbiology Institute, Xi’an, China
| | - Yi Wan
- Shaanxi Microbiology Institute, Xi’an, China
- Shaanxi Academy of Sciences, Engineering Center of QinLing Mountains Natural Products, Xi’an, Shaanxi, China
| | - Xiaoping She
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| |
Collapse
|
68
|
Huang W, Sun D, Fu J, Zhao H, Wang R, An Y. Effects of Continuous Sugar Beet Cropping on Rhizospheric Microbial Communities. Genes (Basel) 2019; 11:E13. [PMID: 31877827 PMCID: PMC7017100 DOI: 10.3390/genes11010013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 11/16/2022] Open
Abstract
The continuous cropping of sugar beet can result in soil degradation and a decrease in the sugar beet yield and quality. However, the role of continuous sugar beet (Beta vulgaris L. var. saccharifera) cropping in shaping the structure and function of the rhizosphere microbial community remains poorly investigated. In this study, we comparatively investigated the impact of different numbers of years of continuous sugar beet cropping on structural and functional changes in the microbial community of the rhizosphere using high-throughput sequencing and bioinformatics analysis. We collected rhizosphere soils from fields continuously cropped for one-year (T1), five-year (T5), and thirty-year (T30) periods, as well as one bulk soil (T0), in the Xinjiang Uygur Autonomous Region. The results demonstrated that continuous sugar beet cropping resulted in a significant decline in the community diversity of soil bacterial and fungal populations from T1 to T5. With continuous change in the structure of the microbial community, the Shannon diversity and observed species were increased in T30. With an abundance of pathogenic microbes, including Acidobacteria, Alternaria, and Fusarium, that were highly enriched in T30, soil-borne diseases could be accelerated, deduced by functional predictions based on 16S rRNA genes. Continuous sugar beet cropping also led to significant declines in beneficial bacteria, including Actinobacteria, Pseudomonas spp., and Bacillus spp. In addition, we profiled and analyzed predictive metabolic characteristics (metabolism and detoxification). The abundance of phenolic acid decarboxylase involved in the phenolic acid degradation pathway was significantly lower in groups T5 and T30 than that in T0 and T1, which could result in the phenolic compounds becoming excessive in long-term continuous cropping soil. Our results provide a deeper understanding of the rhizosphere soil microbial community's response to continuous sugar beet cropping, which is important in evaluating the sustainability of this agricultural practice.
Collapse
Affiliation(s)
- Weijuan Huang
- Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Province Pesticide-fertilizer Technology Research Center, Guangzhou 510316, China; (W.H.)
| | - Donglei Sun
- Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Province Pesticide-fertilizer Technology Research Center, Guangzhou 510316, China; (W.H.)
| | - Jiantao Fu
- Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Province Pesticide-fertilizer Technology Research Center, Guangzhou 510316, China; (W.H.)
| | - Huanhuan Zhao
- Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Province Pesticide-fertilizer Technology Research Center, Guangzhou 510316, China; (W.H.)
| | - Ronghua Wang
- Shihezi Academy of Agricultural Sciences, Xinjiang Uygur Autonomous Region, Shihezi 832000, China
| | - Yuxing An
- Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Province Pesticide-fertilizer Technology Research Center, Guangzhou 510316, China; (W.H.)
| |
Collapse
|
69
|
Dey P. Gut microbiota in phytopharmacology: A comprehensive overview of concepts, reciprocal interactions, biotransformations and mode of actions. Pharmacol Res 2019; 147:104367. [PMID: 31344423 DOI: 10.1016/j.phrs.2019.104367] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/11/2019] [Accepted: 07/19/2019] [Indexed: 02/07/2023]
Abstract
The dynamic and delicate interactions amongst intestinal microbiota, metabolome and metabolism dictates human health and disease. In recent years, our understanding of gut microbial regulation of intestinal immunometabolic and redox homeostasis have evolved mainly out of in vivo studies associated with high-fat feeding induced metabolic diseases. Techniques utilizing fecal transplantation and germ-free mice have been instrumental in reproducibly demonstrating how the gut microbiota affects disease pathogenesis. However, the pillars of modern drug discovery i.e. evidence-based pharmacological studies critically lack focus on intestinal microflora. This is primarily due to targeted in vitro molecular-approaches at cellular-level that largely overlook the etiology of disease pathogenesis from the physiological perspective. Thus, this review aims to provide a comprehensive understanding of the key notions of intestinal microbiota and dysbiosis, and highlight the microbiota-phytochemical bidirectional interactions that affects bioavailability and bioactivity of parent phytochemicals and their metabolites. Potentially by focusing on the three major aspects of gut microbiota i.e. microbial abundance, diversity, and functions, I will discuss phytochemical-microbiota reciprocal interactions, biotransformation of phytochemicals and plant-derived drugs, and pre-clinical and clinical efficacies of herbal medicine on dysbiosis. Additionally, in relation to phytochemical pharmacology, I will briefly discuss the role of dietary-patterns associated with changes in microbial profiles and review pharmacological study models considering possible microbial effects. This review therefore, emphasize on the timely and critically needed evidence-based phytochemical studies focusing on gut microbiota and will provide newer insights for future pre-clinical and clinical phytopharmacological interventions.
Collapse
Affiliation(s)
- Priyankar Dey
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, Ohio, USA.
| |
Collapse
|
70
|
Wang SS, Liu JM, Sun J, Sun YF, Liu JN, Jia N, Fan B, Dai XF. Diversity of culture-independent bacteria and antimicrobial activity of culturable endophytic bacteria isolated from different Dendrobium stems. Sci Rep 2019; 9:10389. [PMID: 31316117 PMCID: PMC6637234 DOI: 10.1038/s41598-019-46863-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/27/2019] [Indexed: 11/23/2022] Open
Abstract
Dendrobium is known for its pharmacological actions including anti-cancer effect, anti-fatigue effect, gastric ulcer protective effect, and so on. At present, only studies on endophytic fungi of Dendrobium affecting the metabolites of host plants have been reported, very little research has been done on endophytic bacteria. In this study, we have demonstrated the great diversity of endophytic bacteria in 6 Dendrobium samples from different origins and cultivars. According to the results of the culture-independent method, the endophytic bacterial community in Dendrobium stems showed obvious different in the 6 samples and was influenced by origin and cultivar. Some bacteria including Ralstonia, Comamonas and Lelliottia were first detected in Dendrobium in this study. Based on the culture-dependent method, a total of 165 cultivable endophytic bacteria isolates were isolated from the sterilized Dendrobium stems, and were classified into 43 species according to the 16S rRNA gene sequence analysis. Moreover, 14 of the 43 strains showed antimicrobial activity against phytopathogen using the Kirby-Bauer method. Strain NA-HTong-7 (Bacillus megaterium, 99.12%) showed the highest antimicrobial activity. This study was the first comprehensive study on endophytic bacteria of Dendrobium from different origins and cultivars, which provides new insights into the endophytic bacteria from Dendrobium.
Collapse
Affiliation(s)
- Shan-Shan Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jia-Meng Liu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China. .,Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing, China.
| | - Jing Sun
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yu-Feng Sun
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jia-Ni Liu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Ning Jia
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Bei Fan
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China. .,Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing, China.
| | - Xiao-Feng Dai
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China. .,Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing, China.
| |
Collapse
|
71
|
Yuan J, Zhang W, Sun K, Tang MJ, Chen PX, Li X, Dai CC. Comparative Transcriptomics and Proteomics of Atractylodes lancea in Response to Endophytic Fungus Gilmaniella sp. AL12 Reveals Regulation in Plant Metabolism. Front Microbiol 2019; 10:1208. [PMID: 31191508 PMCID: PMC6546907 DOI: 10.3389/fmicb.2019.01208] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/13/2019] [Indexed: 12/16/2022] Open
Abstract
The fungal endophyte Gilmaniella sp. AL12 can establish a beneficial association with the medicinal herb Atractylodes lancea, and improve plant growth and sesquiterpenoids accumulation, which is termed “double promotion.” Our previous studies have uncovered the underling primary mechanism based on some physiological evidences. However, a global understanding of gene or protein expression regulation in primary and secondary metabolism and related regulatory processes is still lacking. In this study, we employed transcriptomics and proteomics of Gilmaniella sp. AL12-inoculated and Gilmaniella sp. AL12-free plants to study the impact of endophyte inoculation at the transcriptional and translational levels. The results showed that plant genes involved in plant immunity and signaling were suppressed, similar to the plant response caused by some endophytic fungi and biotroph pathogen. The downregulated plant immunity may contribute to plant-endophyte beneficial interaction. Additionally, genes and proteins related to primary metabolism (carbon fixation, carbohydrate metabolism, and energy metabolism) tended to be upregulated after Gilmaniella sp. AL12 inoculation, which was consistent with our previous physiological evidences. And, Gilmaniella sp. AL12 upregulated genes involved in terpene skeleton biosynthesis, and upregulated genes annotated as β-farnesene synthase and β-caryophyllene synthase. Based on the above results, we proposed that endophyte-plant associations may improve production (biomass and sesquiterpenoids accumulation) by increasing the source (photosynthesis), expanding the sink (glycolysis and tricarboxylic acid cycle), and enhancing the metabolic flux (sesquiterpenoids biosynthesis pathway) in A. lancea. And, this study will help to further clarify plant-endophyte interactions.
Collapse
Affiliation(s)
- Jie Yuan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Meng-Jun Tang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Piao-Xue Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xia Li
- Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of Chinese National Center Rice Improvement, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| |
Collapse
|