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Comparative Metabolomic Analysis of Dendrobium officinale under Different Cultivation Substrates.

ABSTRACT: Dendrobium officinale, a precious herbal medicine, has been used for a long time in Chinese history. The metabolites of D. officinale, regarded as its effective components to fight diseases, are significantly affected by cultivation substrates. In this study, ultra-performance liquid chromatography mass spectrometry (UPLC-MS/MS) was conducted to analyze D. officinale stems cultured in three different substrates: pine bark (PB), coconut coir (CC), and a pine bark: coconut coir 1:1 mix (PC). A total of 529 metabolites were identified. Multivariate statistical analysis methods were employed to analyze the difference in the content of metabolites extracted from different groups. By the criteria of variable importance in projection (VIP) value ?1 and absolute log2 (fold change) ?1, there were a total of 68, 51, and 57 metabolites, with significant differences in content across groups being filtrated out between PB and PC, PB and CC, and PC and CC, respectively. The comparisons among the three groups revealed that flavonoids were the metabolites that fluctuated most. The results suggested the D. officinale stems from the PB group possessed a higher flavonoid content. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that the significantly regulated metabolites were mainly connected with flavonoid biosynthesis. A comprehensive profile of the metabolic differentiation of D. officinale planted in different substrates was provided, which supports the selection of an optimum cultivation substrate for a higher biomass yield of D. officinale.

SUBMITTER: Zuo SM

PROVIDER: S-EPMC7465462 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Comparative Metabolomic Analysis of Dendrobium officinale under Different Cultivation Substrates.

Zuo Si-Min SM Yu Hai-Dong HD Zhang Weimin W Zhong Qiuping Q Chen Wenxue W Chen Weijun W Yun Yong-Huan YH Chen Haiming H

Metabolites 20200810 8

Dendrobium officinale, a precious herbal medicine, has been used for a long time in Chinese history. The metabolites of D. officinale, regarded as its effective components to fight diseases, are significantly affected by cultivation substrates. In this study, ultra-performance liquid chromatography mass spectrometry (UPLC-MS/MS) was conducted to analyze D. officinale stems cultured in three different substrates: pine bark (PB), coconut coir (CC), and a pine bark: coconut coi ...[more]

PMID: 32785071

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Project description:Dendrobium officinale Kimura et Migo is a famous plant with a high medicinal value which has been recorded in the Chinese Pharmacopoeia (2020 Edition). The medicinal properties of D. officinale are based on its chemical composition. However, there are no reports on how different cultivation methods affect its chemical composition. In order to reveal this issue, samples of the D. officinale were collected in this study through tree epiphytic cultivation, stone epiphytic cultivation, and greenhouse cultivation. Polysaccharides were determined by phenol sulfuric acid method and secondary metabolites were detected by the UPLC-MS technique. In addition, with regards to metabolomics, we used multivariate analyses including principal component analysis (PCA) and orthogonal partial least squares analysis (OPLS-DA) to screen for differential metabolites which met the conditions of variable importance projection values >1, fold change >4, and p < 0.05. The differential metabolites were taken further for metabolic pathway enrichment analysis, which was based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and validated by antioxidant activity. Comparing the three groups of samples according to the standards of the ChP (2020 edition), the results showed that the polysaccharide content of the samples from stony epiphytic cultivation and greenhouse cultivation was significantly higher than that of the samples from live tree epiphytic cultivation. Metabolomic analysis revealed that there were 185 differential metabolites among the 3 cultivation methods, with 99 of the differential metabolites being highest in the stone epiphytic cultivation. The results of the metabolic pathway enrichment analysis showed that the different cultivation strategies mainly effected four carbohydrate metabolic pathways, five secondary metabolite synthesis pathways, six amino acid metabolic pathways, one nucleotide metabolism pathway, three cofactor and vitamin metabolism pathways, and one translation pathway in genetic information processing. Furthermore, D. officinale from stone epiphytic cultivation which had the best antioxidant activity was implicated in differential metabolite production. This study revealed the effects of different cultivation methods on the chemical composition of D. officinale and also provided a reference for establishing the quality control standards to aid its development and utilization.

Project description:Dendrobium officinale is a rare and traditional medicinal plant with high pharmacological and nutritional value. The self-incompatibility mechanism of D. officinale reproductive isolation was formed in the long-term evolution process, but intraspecific hybridization of different germplasm resources leads to a large gap in the yield, quality, and medicinal value of D. officinale. To investigate the biological mechanism of self-incompatibility in D. officinale, cytological observation and the transcriptome analysis was carried out on the samples of self-pollination and cross-pollination in D. officinale. Results for self-pollination showed that the pollen tubes could grow in the style at 2 h, but most of pollen tubes stopped growing at 4 h, while a large number of cross-pollinated pollen tubes grew along the placental space to the base of ovary, indicating that the self-incompatibility of D. officinale may be gametophyte self-incompatibility. A total of 63.41 G basesum of D. officinale style samples from non-pollinated, self-pollination, and cross-pollination by RNA-seq were obtained, and a total of 1944, 1758, and 475 differentially expressed genes (DEGs) in the comparison of CK (non-pollinated) vs. HF (cross-pollination sample), CK vs. SF (self-pollination sample) and SF vs. HF were identified, respectively. Forty-one candidate genes related to self-incompatibility were found by function annotation of DEGs, including 6 Ca2+ signal genes, 4 armed repeat containing (ARC) related genes, 11 S-locus receptor kinase (SRK) related genes, 2 Exo70 family genes, 9 ubiquitin related genes, 1 fatty acid related gene, 6 amino acid-related genes, 1 pollen-specific leucine-rich repeat extensin-like protein (LRX) related gene and 1 lectin receptor-like kinases (RLKs) related gene, showed that self-incompatibility mechanism of D. officinale involves the interaction of multiple genes and pathways. The results can provide a basis for the study of the self-incompatibility mechanism of D. officinale, and provide ideas for the preservation and utilization of high-quality resources of D. officinale.

Project description:Application of plant artificial cultivation substrates lead to alteration of rhizosphere environment. Whether this alteration could lead to root microbiome variation was limitedly investigated. This work aims to determine the diversity shifts in the root microbiome of cucumber under different plant cultivation substrates and predict corresponding function of these different root bacterial microbiota. Cucumber root samples cultivated with two artificial cultivation substrates and greenhouse soils were prepared. Subsequently, high throughput sequencing and bioinformatics analysis were applicated to compare the root bacterial diversity of cucumber cultivated in different substrates and their corresponding function. In total, 311,039 sequences were obtained, and they were annotated to 42 operational taxonomic units (OTUs), belonging to 28 genera, 18 families, 12 orders, four classes, and three phyla. The α and β diversity of samples from the two cultivation substrates and greenhouse soils were significantly different. Only 2-3 bacterial species were found to be discrepancy between cucumber root samples from artificial cultivation substrates and from greenhouse soils. The relative abundance of genus Asticcacaulis, Methylophilus, Massilia, Dyella, and Devosia in samples of artificial cultivation substrates was significantly higher than that of soils, while the relative abundance of genus Phenylobacterium, Noviherbaspirillum, and Arenimonas was significantly lower than that of soils. Besides, compared to cucumber root bacterial community cultivated in soils, the abundance of synthetic pathways for flavonoids and flavonols, bile acids, indole alkaloids, lactose, and neolactose increased by 41.6-, 28.7-, 5.9-, and 5.5-fold, respectively, in the bacterial community of the substrate 1-cultivated roots, and the abundance of clavulanic acid, receptor interaction, sesquiterpenoid, bile acid, flavonoid and flavonol, indole alkaloid, lactose, and neolactose synthetic pathways increased by 42.3-, 32.4-, 32.4-, 13.9-, 10.3-, 6.3-, and 5.2-fold, respectively, in the bacterial community of the substrate two-cultivated roots. This paper verified the diversity shifts in the root microbiome of cucumber under different plant cultivation substrates. Besides, the corresponding function difference of these different root bacterial microbiota was predicted. This work would provide theoretical support for discovering microbial resources and building artificial microbial flora.

Dataset Information

Comparative Metabolomic Analysis of Dendrobium officinale under Different Cultivation Substrates.

Publications

Comparative Metabolomic Analysis of <i>Dendrobium officinale</i> under Different Cultivation Substrates.

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