Temporal Dynamics of Rhizosphere Communities Across the Life Cycle of Panax notoginseng.
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ABSTRACT:
SUBMITTER: Wei G
PROVIDER: S-EPMC9010977 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Background:Panax notoginseng is a highly valuable medicinal plant. Reduced P. notoginseng yield is a common and serious problem that arises in a continuous cropping system. Variation in the composition and function of soil microbial community is considered the primary cause of yield reduction. Methods:This study used shotgun metagenomic sequencing approaches to describe the taxonomic and functional features of P. notoginseng rhizosphere microbiome and screen microbial taxa and functional traits related to yields. Results:At the family and genus level, a total of 43 families and 45 genera (relative abundance?>?0.1%) were obtained, and the correlation with the yield of P. notoginseng was further analyzed. Nitrosomonadaceae, Xanthomonadaceae, Mycobacterium and Arthrobacter that were enriched in soils with higher yields were positively correlated with P. notoginseng yields, thereby suggesting that they might increase yields. Negative correlation coefficients indicated that Xanthobacteraceae, Caulobacteraceae, Oxalobacteraceae, Chitinophagaceae, Sphingomonas, Hyphomicrobium, Variovorax and Phenylobacterium might be detrimental to P. notoginseng growth. A total of 85 functional traits were significantly (P?<?0.05) correlated with P. notoginseng yields. Functional traits, likely steroid biosynthesis and MAPK signaling pathway were positively correlated with P. notoginseng yields. In contrast, functional traits, such as bacterial secretion system, ABC transporters, metabolism of xenobiotics by cytochrome P450 and drug metabolism-cytochrome P450, were negatively associated with yields. Conclusions:This study describes an overview of the rhizosphere microbiome of P. notoginseng with discrepant yields and identifies the taxa and functional traits related to yields. Our results provide valuable information to guide the isolation and culture of potentially beneficial microorganisms and to utilize the power of the microbiome to increase plant yields in a continuous cropping system.
| S-EPMC7418314 | biostudies-literature
Project description:Panax notoginseng (Burk.) F. H. Chen is a Chinese medicinal plant of the Araliaceae family used for the treatment of cardiovascular and cerebrovascular diseases in Asia. P. notoginseng is vulnerable to root rot disease, which reduces the yield of P. notoginseng. In this study, we analyzed the rhizosphere soil and root endophyte microbial communities of P. notoginseng from different geographical locations using high-throughput sequencing. Our results revealed that the P. notoginseng rhizosphere soil microbial community was more diverse than the root endophyte community. Rhodopseudomonas, Actinoplanes, Burkholderia, and Variovorax paradoxus can help P. notoginseng resist the invasion of root rot disease. Ilyonectria mors-panacis, Pseudomonas fluorescens, and Pseudopyrenochaeta lycopersici are pathogenic bacteria of P. notoginseng. The upregulation of amino acid transport and metabolism in the soil would help to resist pathogens and improve the resistance of P. notoginseng. The ABC transporter and gene modulating resistance genes can improve the disease resistance of P. notoginseng, and the increase in the number of GTs (glycosyltransferases) and GHs (glycoside hydrolases) families may be a molecular manifestation of P. notoginseng root rot. In addition, the complete genomes of two Flavobacteriaceae species and one Bacteroides species were obtained. This study demonstrated the microbial and functional diversity in the rhizosphere and root microbial community of P. notoginseng and provided useful information for a better understanding of the microbial community in P. notoginseng root rot. Our results provide insights into the molecular mechanism underlying P. notoginseng root rot and other plant rhizosphere microbial communities.
| S-EPMC8766989 | biostudies-literature
Project description:BACKGROUND AND AIMS:Sanqi ginseng (Panax notoginseng) growth is often hampered by replant failure. In this study, we aimed to examine the role of autotoxicity in Sanqi replant failures and assess the role of ginsenosides in autotoxicity. METHODS:The autotoxicities were measured using seedling emergence bioassays and root cell vigor staining. The ginsenosides in the roots, soils, and root exudates were identified with HPLC-MS. RESULTS:The seedling emergence and survival rate decreased significantly with the continuous number of planting years from one to three years. The root exudates, root extracts, and extracts from consecutively cultivated soils also showed significant autotoxicity against seedling emergence and growth. Ginsenosides, including R1, Rg1, Re, Rb1, Rb3, Rg2, and Rd, were identified in the roots and consecutively cultivated soil. The ginsenosides, Rg1, Re, Rg2, and Rd, were identified in the root exudates. Furthermore, the ginsenosides, R1, Rg1, Re, Rg2, and Rd, caused autotoxicity against seedling emergence and growth and root cell vigor at a concentration of 1.0 µg/mL. CONCLUSION:Our results demonstrated that autotoxicity results in replant failure of Sanqi ginseng. While Sanqi ginseng consecutively cultivated, some ginsenosides can accumulate in rhizosphere soils through root exudates or root decomposition, which impedes seedling emergence and growth.
| S-EPMC4335038 | biostudies-literature
Project description:Panax notoginseng (Araliaceae) is an important ginseng herb with various health benefits and a history of cultivation in southwestern China over 400 years. In recent years P. notoginseng has faced serious continuous-cropping obstacles due to its large-scale cultivation. In this study, we aim to explore the allelochemicals of P. notoginseng and their interactions with various plants and rhizosphere microorganisms. The chemical constituents of the soil cultivated with 3-year-old P. notoginseng were studied by column chromatography, spectroscopic and GC-MS analyses. We identified 13 volatile components and isolated six triterpenes (1-4, 6-7) and one anthraquinone (5). Compounds 1-7 were tested for their effects on seed germination and root elongation in P. notoginseng, corn, wheat, turnip, water spinach and Arabidopsis thaliana. We also examined the effect of compounds 1-7 on the growth of ten rhizosphere microorganisms of P. notoginseng. At a concentration of 1.0 μg mL-1, compounds 3 and 5-7 caused the death of P. notoginseng root cells and compounds 2, 6 and 7 induced the death of root cells of A. thaliana. Compounds 1-5 and 7 inhibited elongation of A. thaliana root tip cells at a concentration of 10.0 μg mL-1. Moreover, at a concentration of 0.1 mg mL-1, compounds 3, 4, 6 and 7 inhibited the growth of probiotics and promoted the growth of pathogens of P. notoginseng. These results suggest that these isolated ursane-type triterpenoid acids and anthraquinone are potential allelochemicals that contribute to continuous-cropping obstacles of P. notoginseng.
| S-EPMC7584786 | biostudies-literature
Project description:Panax notoginseng, an important Chinese medicinal herb, can be mainly cultivated in two planting patterns, cropland planting (DT) and understory planting (LX). We speculate that the rhizosphere microbiome may vary in DT and LX and may play an important role in promoting the growth and health of P. notoginseng. In the present study, culture-independent Illumina HiSeq was employed to investigate the rhizosphere bacteria and fungi under DT and LX planting patterns. Predominant phyla include Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Ascomycota in the two planting patterns. DT has higher alpha diversity index than LX. The predominant LX-core genera include Bradyrhizobium, Streptomyces, and Actinomadura, and the predominant DT-core genera include Sphingomonas, Variovorax, and Novosphingobium. Total relative abundance of the disease-suppression phylum (Proteobacteria, Firmicutes, and Actinobacteria) and the potential plant growth-promoting rhizobacteria (PGPR) were both significantly higher in LX than in DT. We also identified over-presented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition, and plant growth promotion in P. notoginseng rhizosphere. Our findings provide a valuable reference for studying beneficial microbes and pathogens of P. notoginseng planted in DT and LX.
| S-EPMC8219928 | biostudies-literature
Project description:Recent results demonstrated that either non-coding or coding genes generate phased secondary small interfering RNAs (phasiRNAs) guided by specific miRNAs. Till now, there is no studies for phasiRNAs in Panax notoginseng (Burk.) F.H. Chen (P. notoginseng), an important traditional Chinese herbal medicinal plant species. Here we performed a genome-wide discovery of phasiRNAs and its host PHAS loci in P. notoginseng by analyzing small RNA sequencing profiles. Degradome sequencing profile was used to identify the trigger miRNAs of these phasiRNAs and potential targets of phasiRNAs. We also used RLM 5'-RACE to validate some of the identified phasiRNA targets. After analyzing 24 small RNA sequencing profiles of P. notoginseng, 204 and 90 PHAS loci that encoded 21 and 24 nucleotide (nt) phasiRNAs were identified. Furthermore, we found that phasiRNAs produced from some pentatricopeptide repeat-contain (PPR) genes target another layer of PPR genes as validated by both the degradome sequencing profile and RLM 5'-RACE analysis. We also find that miR171 with 21 nt triggers the 21 nt phasiRNAs from its conserved targets. We validated that some phasiRNAs generated from PPRs are functional by targeting other PPRs in trans. These results provide the first set of PHAS loci and phasiRNAs in P. notoginseng, and enhance our understanding of PHAS in plants.
2018-02-14 | GSE98118 | GEO
Project description:Five new 12-membered resorcylic acid lactone derivatives, penicimenolides A-E (1-5), one new ring-opened resorcylic acid lactone derivative penicimenolide F (6), and six known biogenetically related derivatives (7-12) were isolated from the culture broth of a strain of Penicillium sp. (NO. SYP-F-7919), a fungus obtained from the rhizosphere soil of Panax notoginseng collected from the Yunnan province of China. Their structures were elucidated by extensive NMR analyses, a modified Mosher's method, chemical derivatization and single crystal X-ray diffraction analysis. Compounds 2-4 exhibited potent cytotoxicity against the U937 and MCF-7 tumour cell lines and showed moderate cytotoxic activity against the SH-SY5Y and SW480 tumour cell lines. The substitution of an acetyloxy or 2-hydroxypropionyloxy group at C-7 significantly increased the cytotoxic activity of the resorcylic acid lactone derivatives. Subsequently, the possible mechanism of compound 2 against MCF-7 cells was preliminarily investigated by in silico analysis and experimental validation, indicating compound 2 may act as a potential MEK/ERK inhibitor. Moreover, proteomics analysis was performed to explore compound 2-regulated concrete mechanism underlying MEK/ERK pathway, which is still need further study in the future. In addition, compounds 2-4 and 7 exhibited a significant inhibitory effect on NO production induced by LPS.
| S-EPMC4897632 | biostudies-literature
Project description:Root-knot nematodes (RKNs) are soil-borne pathogens that severely affect Panax notoginseng growth and productivity. Thus, there is an urgent need for biological control agents or green nematicides to control root-knot nematodes. Rhizosphere bacteria can effectively control RKNs through different mechanisms. In this study, the three rhizosphere Bacillus strains, isolated from the root of P. notoginseng, were evaluated for the nematicidal activity and biological control efficacy against root-knot nematodes. In addition, we also evaluated the colonization ability of the two bacterial strains with significant biocontrol effect and dynamic regulation of genes related to systemic resistance in P. notoginseng. The rhizosphere Bacillus velezensis GJ-7 and Bacillus cereus NS-2 showed high nematicidal activity against Meloidogyne hapla in vitro and significantly reduced the number of root galls in three different control experiments. The results of colonization experiments showed that the strains GJ-7 and NS-2 colonized P. notoginseng root rapidly and stably. Additionally, the colonization of the strains NS-2 and GJ-7 activated the defense-responsive genes in P. notoginseng. These results indicated that the B. cereus strain NS-2 and B. velezensis strain GJ-7 have the potential for successful ecological niche occupation and enhance plant resistance and therefore could be considered as potential biocontrol agents against root-knot nematodes.
| S-EPMC9096944 | biostudies-literature
Project description:Bioorganic fertilizers can alleviate (a) biotic stresses and sustainably increase crop yields. The effect of bioorganic fertilizers on the rhizosphere bacterial community of Panax notoginseng and soil metabolism remains unknown. Here, we tracked the changes in the soil physicochemical properties, bacterial microbiota responses, and soil metabolic functions after the addition of a bioorganic fertilizer in a P. notoginseng field. The application of a bioorganic fertilizer reduced the soil acidification, improved the organic matter, and increased the contents of the total/available soil nutrients. Soil amendment with a bioorganic fertilizer significantly affected the structure of the rhizosphere bacterial community, leading to the enrichment of specific bacterial consortia such as Rhodanobacter, Arthrobacter, Sphingomonas, Devosia, Pseudolabrys, Luteimonas, Lysobacter, Nitrosospira, and Nakamurella. Previously, many of these genera have been associated with nutrient cycling, plant productivity, and disease suppression. Metabolome analysis further highlighted that the bioorganic fertilizer treatment significantly reduced phenolic acids and flavonoids and enhanced organic acids, saccharides and alcohols, and amino acids. This result indicates a high survival of bacterial microbiota in the rhizosphere and an availability of nutrients for P. notoginseng growth. This work showed that the application of bioorganic fertilizers significantly improves soil health status, alters soil metabolic functions, and stimulates a specific subset of rhizosphere microbiota for nutrient cycling and disease protection in P. notoginseng.
| S-EPMC8879206 | biostudies-literature
Project description:Endophytes may participate in the conversion of metabolites within medicinal plants, influencing the efficacy of host. However, the distribution of endophytes within medicinal plants P. notoginseng and how it contributes to the conversion of saponins are not well understood. Here, we determined the distribution of saponins and endophytes within P. notoginseng compartments and further confirm the saponin conversion by endophytes. We found metabolites showed compartment specificity within P. notoginseng. Potential saponin biomarkers, such as Rb1, Rg1, Re, Rc and Rd, were obtained. Endophytic diversity, composition and co-occurrence networks also showed compartment specificity, and bacterial alpha diversity values were highest in root compartment, consistently decreased in the stem and leaf compartments, whereas those of fungi showed the opposite trend. Potential bacterial biomarkers, such as Rhizobium, Bacillus, Pseudomonas, Enterobacter, Klebsiella, Pantoea and fungal biomarkers Phoma, Epicoccum, Xylariales, were also obtained. Endophytes related to saponin contents were found by Spearman correlation analysis, and further verification experiments showed that Enterobacter chengduensis could convert ginsenoside Rg1 to F1 at a rate of 13.24%; Trichoderma koningii could convert ginsenoside Rb1 to Rd at a rate of 40.00% and to Rg3 at a rate of 32.31%; Penicillium chermesinum could convert ginsenoside Rb1 to Rd at a rate of 74.24%.
| S-EPMC8313278 | biostudies-literature