Abstract
Background
This study aimed to examine the effects of intensive cultivation practices on the rhizosphere microecology of Panax notoginseng. Additionally, we sought to compare these practices with an understory cultivation model that was intended to mimic native growth conditions, with the objective of improving the quality of Radix Notoginseng.
Methods
The total saponin and active ingredient content in both cultivation methods were quantified using high-performance liquid chromatography (HPLC). The nutrients of the rhizosphere soils associated with both cultivation methods (understory cultivated P. notoginseng rhizosphere soil [UCPS] and intensive cultivated P. notoginseng rhizosphere soil [ICPS]) were analyzed. The microbial communities present in UCPS and ICPS were characterized using metagenomic sequencing.
Results
The underground biomass accounted for 71.21 % and 74.00 % of the total biomass in understory cultivated P. notoginseng (UCPn) and intensively cultivated P. notoginseng (ICPn), respectively. The total saponin content in the main root of UCPn was found to be 109.24 ± 3.40 mg/g, compared to 91.31 ± 5.82 mg/g in ICPn. The concentration of medicinal ingredients (ginsenoside Rb1 + ginsenoside Rg1 + notoginsenoside R1) in UCPn was 10.83 %, while ICPn exhibited a higher concentration of 13.39 %. Microbial biomarkers identified in UCPS include Bradyrhizobium, Pseudomonas, and Paraburkholderia, which are associated with nitrogen cycling processes. In contrast, Variovorax and Sphingobium were predominant in ICPS, contributing to phosphorus metabolism.
Conclusion
Rhizosphere soil microbial biomarkers influence soil carbon nutrition, which directly impacts the quality of UCPn. The quality of ICPn is primarily determined by phosphorus-related biomarkers, with indirect influences from carbon and nitrogen nutrition.
Keywords: Ginsenosides, Metagenomics, Panax notoginseng, Saponin, Understory cultivation
Graphical abstract
Highlights
-
•
Reintroducing medicinal plants into understory cultivation is an effective strategy for sustainable agriculture.
-
•
Understory cultivated Panax notoginseng is beneficial for the balance of rhizosphere microorganisms.
-
•
Bioorganic carbon is the driving factors for the growth of Panax notoginseng.
-
•
Understory cultivated Panax notoginseng improved the quality of Radix Notoginseng.
1. Introduction
Since the 21st century, approximately 80 % of the 0.70 billion hectares of farmland and permanent crop field worldwide has been dedicated to intensive cultivation of crops [1]. The intensive cultivation benefits to a significant increase in crop yield, but it also results in a high incidence of crop diseases, ultimately accompanying with a decline in crop yield and quality. Meanwhile, it has been believed that intensive cultivation considerably reduces agricultural biodiversity, especially for the microbial diversity of rhizosphere soil [2,3]. This phenomenon is especially obvious in the intensively cultivated fruits, vegetables and medicinal crops, such as Fusarium wilt of banana, cucumber downy mildew disease, watermelons, strawberries, Panax ginseng root rot disease [4], Panax notoginseng round spot disease [5] and Panax quinquefolium root rot [6]. Collectively, intensive cultivation presents serious challenges to global agricultural production. Therefore, reintroducing crops, such as Panax notoginseng, to their native growth environments is becoming a future trend in environmentally friendly agriculture.
Understory cultivated ecosystem could enhance the growth of crop species native to understory habitats [7], and ensure the quality of crop products [8]. As an improvement on the intensive agriculture, understory cultivation might protect the ecological environment [9] and promote sustainable development of arable field [10]. In fact, it has been confirmed that the quality of understory cultivated medicinal plants is nearly as good as or even better than that of wild individuals [11].
Panax notoginseng (Burk.) F.H. Chen, a shade-demanding species, belongs to Panax genus of Araliaceae and is an important medicinal plant in China. The dried root of P. notoginseng is referred to as Radix Notoginseng and shows the ability to enhance blood circulation, dissolve blood stasis, unblock blood vessels, regulate menstruation, and alleviate pain. In latest decades, P. notoginseng has been intensively cultivated in Yunnan and Guangxi Province of China [12]. However, P. notoginseng commonly suffer from serious diseases under artificial intensive cultivation, and thus pesticides is excessively used to control diseases, and consequently Radix Notoginseng show excessive content of pesticide residues and heavy metals [[13], [14], [15]]. These adverse obstacles cannot be still overcome in the intensively cultivated P. notoginseng (ICPn). In recent years, scientists have successfully reintroduced P. notoginseng to under forest land to create a native environment for its growth, and P. notoginseng that grow under the agroforestry eco-system is well known as understory cultivated P. notoginseng (UCPn).
In the Panax genus, several beneficial microorganisms isolated from the understory cultivated P. ginseng rhizosphere suggests that many of them have the potential to improve the quality and production of Radix Ginseng [16]. For the understory cultivated P. quinquefolium, the soil pH and soil organic matter increase, the relative abundances of beneficial bacteria, such as Proteobacteria phyla, Bacteroidota phyla, and Actinobacteria phyla, also increase and consequently the quality of Radix Quinquefolium has been improved [17]. In the P. notoginseng-pine agroforestry eco-system, UCPn entophytes is transferred to pine trees, leading to an enrichment of beneficial microbiomes such as Massilia, Marmoricola and Herbaspirillum in the roots of the pine trees [9,18]. Overall, the diverse assembly mechanisms within the microbiomes associated with UCPn have been found to be essential for the improvement of P. notoginseng quality. In recent years, research on UCPn has primarily focused on the following aspects: the greater root weight of P. notoginseng plants grown under forest conditions compared to those cultivated in the field, and the identification of Candidatus Rokubacteria and Candidatus Nitrostelea as biomarker taxa in the rhizospheres of forest cultivated P. notoginseng [19]. The bacterial Nitrosomonadaceae, Xanthomonadaceae, as well as the genera Mycobacterium and Arthrobacter, which were found to be enriched in soils associated with higher crop yields, exhibited a positive correlation with the yields of P. notoginseng [20]. Additionally, the biomarker of UCPn is predominantly represented by Bradyrhizobium, Streptomyces, and Actinomadura, whereas ICPn is characterized by Sphingomonas, Variovorax, and Novosphingobium; UCPn exhibits a higher abundance of disease-suppressive phyla and plant growth-promoting traits, thereby enhancing the rhizosphere functions of P. notoginseng [21]. Moreover, the genera Pseudomonas, Massilia, Sphingobium, and Phoma exhibit a positive correlation with underground biomass, whereas the genera Staphylotrichum, Chaetosphaeria, and Podospora demonstrate a positive association with the overall saponin content [22].
However, little attention has been given to the differences in rhizosphere soil microbial community, rhizosphere soil nutrients, and phenotypic traits P. notoginseng grown understory and intensive cultivation environments, and to the interaction between microbial community and P. notoginseng. There is also limited information available on the relationship between the quality of P. notoginseng and soil microbial community. Thus, there is a necessity for a comprehensively comparative analysis on the medicinal crop P. notoginseng under intensive cultivation and understory cultivation.
2. Materials and methods
2.1. Plant growth
The seeds used in this experiment are from the conventionally cultivated P. notoginseng (Burk.) F. H. Chen species, provided by Wenshan Miao Xiang San Qi Science and Technology Co., Ltd. The fertilizers used include 6-6-9 (N-P2O5-K2O) organic fertilizer (Yunnan Yunye Chemical Fertilizer Co., Ltd.) and 17-17-17 (N-P2O5-K2O) compound fertilizer (YUNTIANHUA Group Co., Ltd.), along with common pesticides and agricultural tools. According to the experimental requirements, the P. notoginseng seeds were intensively raised in the nursery starting on October 30, 2019. Based on a planting density of approximately 32,000 plants per 667 m2 during the field transplanting period, the total number of seedlings in this experiment was about 57,600,000 plants, with a seedling period of one year. The one-year-growth P. notoginseng seedlings were used for the transplanting experiment involving both UCPn and ICPn. These P. notoginseng plants will be harvested three years after transplantation, and their roots will be used as experimental materials.
On October 30, 2020, the understory cultivated P. notoginseng (UCPn)) were planted at five experimental sites in the Lancang and Xundian regions of Yunnan Province, which provided suitable climate, soil, and ecological conditions for the growth of P. notoginseng. These cultivation sites are characterized by a subtropical humid climate, with an average annual temperature of 18 °C, altitudes ranging from 1598.3 to 2182.6 m, and an average annual precipitation of 1733.5 mm. The areas are predominantly covered by Pinus yunnanensis Franch and consist of brown soil. The total area designated for UCPn spans 60 ha, with each of the five experimental sections (I, II, III, IV, and V) allocated 15 ha. The UCPn was maintained for three years without the application of pesticides, fertilizers, or growth regulators. In contrast, intensively cultivated P. notoginseng (ICPn) was also initiated on October 30, 2020, in the Wenshan and Shilin districts, which experience a subtropical low latitude plateau mountain monsoon climate. These ICPn sites, characterized by red soil, have altitudes between 1437.6 m and 2082.5 m, an average annual temperature of 16.3 °C, and an average precipitation of 939.5 mm. Similar to UCPn, the ICPn areas cover 60 ha, with 15 ha allocated for each experimental section. Over the three-year growth cycle of ICPn, various fertilizers and pesticides were utilized in accordance with the growth trends of P. notoginseng (Figs. S1–S2).
2.2. Agronomic traits analysis
In November 2022, the three-years cultivation P. notoginseng roots samples of UCPn and ICPn were collected, with the rhizosphere soil and pine needles being removed immediately after extraction from the P. notoginseng cultivation site. The main roots, rhizomes, branch roots, leaves, and stems of P. notoginseng underwent thorough washing with ultrapure water. Subsequently, these plant parts were separated and placed on individual drying plates in a constant-temperature oven set at 50 °C for 120–144 h, until the moisture content was reduced to below 13 %. They were then cooled to room temperature and stored for later tests. Various agronomic traits were assessed, including the root-to-shoot ratio, root-to-mass ratio, leaf-to-mass ratio, stem-to-mass ratio, and the distribution ratio of aboveground to underground parts, alongside yield calculations. To evaluate the safety of UCPn and ICPn, pesticide residues were analyzed following the “National Food Safety Standard for the Determination of 208 Pesticides and Metabolites Residues in Foods of Plant Origin—Gas Chromatography-Tandem Mass Spectrometry Method, GB23200.113–2018.” [23]. Based on the pesticides and metabolites detection results, P. notoginseng and rhizosphere soil samples from the Xiaolishi experimental section in Lancang County (UCPn) and the Xijiekou experimental section in Shilin County (ICPn) were selected for further experimental research. Additionally, the medicinal ingredient content of UCPn and ICPn was analyzed.
2.3. Preparation of P. notoginseng rhizosphere soil
In November 2022, soil nutrient and microbial diversity samples were collected from the rhizosphere of Panax notoginseng, specifically from intensive cultivation rhizosphere soil (ICPS) and understory cultivated rhizosphere soil (UCPS). Following the excavation of the plants, both soil types were promptly removed. To account for soil processes, nutrient cycling, microbial activity, and plant-root interactions, twenty-five samples were randomly collected from a depth of 0–40 cm, mixed to represent the rooting zone of each cultivation section. Each sample was placed in a sterile bag, immersed in liquid nitrogen, stored in a dry refrigerator, and subsequently sent to the laboratory for preservation at −80 °C.
2.4. Saponin detection of understory and intensive cultivated P. notoginseng
The medicinal ingredients, ginsenosides Rb1, Rg1, and notoginsenoside R1, were analyzed by HPLC (Agilent 1260 Infinity, USA) following the protocol described in our previous report. Briefly, separation was performed on a Poroshell EC-C18 column (4.6 × 150 mm, 4 μm; Agilent). The mobile phase consisted of ultrapure water (A) and acetonitrile (B) with a gradient elution as follows: 20 % B (0–20 min), 20–36 % B (20–55 min), 36–45 % B (55–70 min), 45–60 % B (70–79 min), 80 % B (79–81 min), then returning to 20 % B (81.5–83 min). The flow rate was 0.5 mL/min, injection volume 10 μL, column temperature 30 °C, and detection wavelength 203 nm [24]. The contents of total saponins were detected by UV–Vis spectrophotometry based on colorimetric 5 % vanillin-perchloric acid-77 % sulfuric acid aqueous solution reaction at 548 nm [25]. Three replicates of each sample were extracted, and each extract was analyzed twice. Chromatographic grade acetonitrile, methanol, and formic acid (99.99 % purity) for HPLC analysis were purchased from MREDA., Ltd (Darmstadt, USA). The deionized water was prepared using an ultrapure water on-line resistivity monitor (Shanghai, China). he reference components ginsenoside Rb1 (HPLC Purity ≥98 %), notoginsenoside R1 (HPLC Purity ≥98 %) and ginsenoside Rg1 (HPLC Purity ≥99.44 %) were purchased from Lemeitian Co., Ltd (Chengdu, China).
2.5. Determination of rhizosphere soil nutrient
The analysis of UCPS and ICPS samples included physical, chemical, biological, and biochemical properties. The carbon nutrients analyzed were total carbon (TC), total organic carbon (TOC), particulate organic carbon (POC), readily oxidizable carbon (ROC), dissolved organic carbon (DOC), light fraction organic carbon (LFOC), heavy organic carbon (HOC), total carbon in humic substances (TCCH), humic acid plus fulvic acid (HA + FA), humin (Hu), and microbial biomass carbon (MBC). The nitrogen nutrients included total nitrogen (TN), alkali-hydrolyzable nitrogen (AHN), available nitrogen (AN), nitrate nitrogen (NO3−-N), nitrite nitrogen (NO2−-N), total soluble nitrogen (TSN), organic nitrogen (ON), and microbial biomass nitrogen (MBN). The phosphorus nutrients comprised total phosphorus (TP), available acid phosphorus (AAP), organic phosphorus (OP), inorganic phosphorus (IP), and microbial biomass phosphorus (MBP). Potassium nutrients included total potassium (TK), fixed available potassium (FAK), and available potassium (AK). Additionally, twelve biogenic metallic elements, lead (Pb), zinc (Zn), vanadium (V), arsenic (As), molybdenum (Mo), antimony (Sb), cobalt (Co), copper (Cu), chromium (Cr), nickel (Ni), cadmium (Cd), and manganese (Mn), were analyzed in both rhizosphere soil samples. The methods used for analyzing soil properties and the abbreviations of parameters are detailed in Table S3. Five replicates of each sample were extracted, and each extraction was analyzed twice.
2.6. Rhizosphere soil microbial community
DNA was extracted from the UCPS and ICPS samples using the hexadecyltrimethylammonium bromide (CTAB) method [26]. The degree of DNA degradation, potential contamination, and DNA concentration were measured using the Agilent 5400 system (USA).
The KneadData software was used to perform quality control on the raw data (using Trimmatic) and remove the host (using Bowtie2) [27,28]. Using Kraken2 and https://www.bioincloud.tech to compare the microbial nucleic acid database. This involved screening sequences attributed to bacteria, fungi, archaea, and viruses both the NCBI NT nucleic acid database the RefSeq whole genome database to determine the quantity of sequences per species in the sample. Subsequently, Bracken was employed to assess the true abundance of species present in the sample. Commencing with quality procedures and the elimination of host gene reads, the reads from each sample were subjected to comparison with UniRef90 database using the HUMAnN3 software, which is based on DIAMOND. Subsequently, annotation details and relative abundance tables for each functional database were acquired by leveraging the corresponding relationship between UniRef90 ID and the respective database.
2.7. Data analysis
The experiment data was statistically analyzed using the Statistical Package for the Social Sciences (SPSS) version 26.0 (SPSS Inc., Chicago, IL, USA). The results were analyzed and plotted using GraphPad Prism 8.3.0 and expressed as the mean ± standard deviation (). Metagenomic data of P. notoginseng rhizosphere soil microorganisms were analyzed on https://www.bioincloud.tech. The correlation heatmap depicting the relationship between nutrient and microbial interactions was generated using the Chiplot platform (https://www.chiplot.online). The structural equation modeling was analyzed using SmartPLS 3.2.9 software (SmartPLS® GmbH, Germany). A significance level of P < 0.05 was considered, and P < 0.01 was considered to be highly significant statistically. Five replicates were established for the experiment.
3. Results and analysis
3.1. Agronomic traits and Radix Notoginseng quality of UCPn and UCPn
3.1.1. Agronomic traits
In the UCPn, the distribution proportions of stem, leaf and root were 11.52 % ± 1.92 %, 17.27 % ± 1.88 %, and 71.21 % ± 2.93 %, respectively. In the ICPn, the proportions of stem, leaf and root were 10.76 % ± 2.07 %, 15.23 % ± 2.62 % and 74.00 % ± 3.46 %, respectively. Significant differences were observed in the distribution proportions of UCPn and ICPn in the same part under forest and intensive cultivation eco-environments (P < 0.05) (Fig. 1A). Specifically, the root-shoot ratio of ICPn was 2.61 ± 0.44, which was significantly higher than that of UCPn, with a root-shoot ratio of 2.20 ± 0.36 (Fig. 1B). As a medicinal plant with the main medicinal properties concentrated in the root, the root-total biomass ratio of P. notoginseng is an important indicator for assessing its yield. In this experiment, the root-total biomass ratio of ICPn was 0.72 ± 0.03, which was not significantly different from the contribution value of UCPn, with a root-total biomass ratio of 0.73 ± 0.03 (Fig. 1C). Here, we used leaf-mass ratio to illustrate the synergistic growth relationship between the underground and aboveground parts of P. notoginseng. In UCPn, the leaf-mass ratio was 0.08 ± 0.02, which was significantly lower than the value of UCPn at 0.16 ± 0.03 (Fig. 1D). For the stem-biomass ratio, the UCPn was 0.20 ± 0.02, while the ICPn showed a value of 0.12 ± 0.02 (Fig. 1E). Finally, we predicted the yield of UCPn and ICPn based on the above analysis. The main root yield of UCPn was 2038.50 ± 675.06 kg/hm2-DW, while ICPn yielded 5961.20 ± 1486.00 kg/hm2-DW of Radix Notoginseng (Fig. 1F). There was a significant difference of P. notoginseng yield between the two cultivation environments (P < 0.05).
Fig. 1.
Agronomic traits of understory cultivated P. notoginseng (UCPn) (ⅰ) and intensively cultivated P. notoginseng (ICPn) (ⅱ). (A) The distribution percentage of each part of UCPn and ICPn. (B) The root-shoot ratio of UCPn and ICPn. (C) The root-mass ratio of UCPn and ICPn. (D) The leaf-mass ratio of UCPn and ICPn. (E) The stem-mass ratio of UCPn and ICPn. (F) The yield of UCPn and ICPn. ∗ Indicated the result is significant difference at P < 0.05.
3.1.2. Total saponin and medicinal ingredients content of UCPn and ICPn
In this experiment, the total saponin content in the main roots of UCPn was 109.24 ± 3.40 mg/g, which was significantly higher than the content of 91.31 ± 5.82 mg/g in the main roots of ICPn (P < 0.05) (Fig. 2A). A total saponin content of 180.25 ± 8.06 mg/g was detected in the rhizome of UCPn, while the total saponin content in the rhizome of ICPn was 158.12 ± 7.20 mg/g (P < 0.05) (Fig. 2B). Corresponding to the total saponin content in the main root and rhizome, the total saponin content in the branch roots of P. notoginseng from UCPn and ICPn were 100.10 ± 10.29 mg/g and 74.90 ± 3.32 mg/g, respectively (P < 0.05) (Fig. 2C). Further, this experiment determined the levels of Rb1 + Rg1 + R1 in the main roots of UCPn and ICPn. In the UCPn main root, the combined content of Rb1 + Rg1 + R1 was 108.34 ± 0.63 mg/g (10.83 %), which was significantly lower than the content of ICPn main root at 133.85 ± 3.37 mg/g (13.39 %) (P < 0.05). The content of major active ingredients in both P. notoginseng main root samples met the requirements of the Chinese Pharmacopoeia (Fig. 2D). In another aspect, the content of Rb1 + Rg1 + R1 in the rhizomes of UCPn and ICPn were 165.68 ± 0.15 mg/g and 191.65 ± 1.71 mg/g, respectively (P < 0.05) (Fig. 2E). As a food or traditional Chinese medicine supplement, the content of Rb1 + Rg1 + R1 were 94.94 ± 13.10 mg/g and 88.94 ± 0.47 mg/g in branch roots of UCPn and ICPn (P < 0.05) (Fig. 2F). Here, our aim was to analyze the driving factors that affect the agronomic traits, total saponin content, and major active ingredients of UCPn and ICPn by studying the differences between both cultivation environments.
Fig. 2.
Total saponin and major active ingredients (ginsenoside Rb1 + ginsenoside Rg1 + notoginsenoside R1) contents of understory cultivated P. notoginseng (UCPn) (ⅰ) and intensively cultivated P. notoginseng (ICPn) (ⅱ). The total saponin content of the main root, rhizome and branch root of UCPn and ICPn are represented by A, B, and C, respectively. The contents of Rb1, Rg1 and R1 in the main root, rhizome and branch root of UCPn and ICPn are represented by D, E and F, respectively. ∗ Indicated the result is significant difference at P < 0.05.
3.2. Nutrient of UCPS and ICPS
In this experiment, we analyzed the content of 12 carbon nutrients, 8 nitrogen nutrients, 5 phosphorus nutrients, 3 potassium nutrients, and 12 mineral ions in UCPS and ICPS, including pH values (Table 1). The pH of UCPS was 6.20, which was significantly higher than the pH of 5.89 of ICPS, indicating the rhizosphere soil of forest cultivated environment is closer to neutrality. In terms of the content of carbon nutrients, twelve constituents including TC, TOC, POC, ROC, DOC, LFOC, HOC, TCCH, (HA + FA), Hu and MBC were significantly higher in UCPS than in ICPS (P < 0.05). For the nitrogen nutrients, most of the markers in the UCPS were significantly higher than those in the ICPS, except for the MBN at the content of 48.06 ± 39.75 mg/kg in ICPS. However, the MBP content in the ICPS was significantly higher than that in the UCPS. For the potassium nutrients, UCPS showed higher levels of fast-acting potassium (FAK) and available potassium (AK), while ICPS had higher content of total potassium (TK) compared to UCPS (P < 0.05). In ICPS, more than half of the elemental content was higher than that in the UCPS, including Pb, Zn, As, Mo, Sb, Cu, Cr, Ni and Cd (Table 1).
Table 1.
The physicochemical properties of UCPS and ICPS. ∗ Indicated the result is significant difference at P < 0.05, ∗∗ Indicated the result is significant difference at P < 0.01, ns (not significant) indicates that there was no statistically significant difference.
| Class | Physicochemical properties | Understory cultivated Panax notoginseng rhizosphere soil (UCPS) | Intensively cultivated Panax notoginseng rhizosphere soil (ICPS) | Significant |
|---|---|---|---|---|
| Soil physical properties | pH | 6.20 | 5.89 | ∗ |
| DHR | 74.40 % ± 2.22 % | 74.72 % ± 2.00 % | ns | |
| Soil chemical properties | ||||
| C | TC (g/kg) | 27.4 ± 6.1 | 16.2 ± 8.6 | ∗∗ |
| TOC (g/kg) | 39.5 ± 9.52 | 20.5 ± 12.57 | ∗∗ | |
| POC (g/kg) | 2.9 ± 0.25 | 1.5 ± 0.17 | ∗ | |
| ROC (%) | 1.59 % ± 0.27 % | 0.89 % ± 0.47 % | ∗ | |
| DOC (g/kg) | 186.38 ± 58.05 | 151.00 ± 48.86 | ∗ | |
| LFOC (g/kg) | 153.61 ± 127.98 | 69.66 ± 37.46 | ∗∗ | |
| HOC (g/kg) | 18.5 ± 2.1 | 10.6 ± 6.6 | ∗ | |
| TCCH (g/kg) | 21.23 ± 4.35 | 12.00 ± 6.95 | ∗∗ | |
| HA + FA (g/kg) | 7.2 ± 1.8 | 5.2 ± 2.8 | ∗ | |
| Hu (g/kg) | 14.0 ± 2.9 | 6.8 ± 6.2 | ∗ | |
| MBC (mg/kg) | 974.17 ± 226.35 | 902.06 ± 378.80 | ∗ | |
| N | TN (g/kg) | 1.49 ± 0.23 | 1.29 ± 0.33 | ∗ |
| AHN (mg/kg) | 147.10 ± 28.21 | 123.74 ± 39.63 | ∗ | |
| AN (mg/kg) | 36.65 ± 5.68 | 17.41 ± 9.59 | ∗∗ | |
| NO3−-N (mg/kg) | 6.92 ± 9.39 | 3.61 ± 2.95 | ∗∗ | |
| NO2−-N (mg/kg) | 0.12 ± 0.05 | 0.11 ± 0.03 | ns | |
| TSN (mg/kg) | 89.69 ± 22.51 | 53.72 ± 15.08 | ∗ | |
| MBN (mg/kg) | 39.06 ± 16.97 | 48.06 ± 39.75 | ∗ | |
| SON (mg/kg) | 43.87 ± 18.67 | 31.46 ± 6.80 | ∗ | |
| P | TP (g/kg) | 1.72 ± 0.49 | 1.03 ± 0.48 | ∗ |
| AAP (mg/kg) | 37.64 ± 33.17 | 30.23 ± 40.33 | ∗ | |
| OP (mg/kg) | 917.55 ± 386.97 | 515.77 ± 266.69 | ∗∗ | |
| IP (mg/kg) | 689.75 ± 89.81 | 466.79 ± 192.03 | ∗∗ | |
| MBP (mg/kg) | 16.88 ± 8.11 | 24.70 ± 13.01 | ∗ | |
| K | TK (g/kg) | 14.19 ± 3.38 | 21.14 ± 11.09 | ∗ |
| FAK (mg/kg) | 353.41 ± 52.38 | 221.75 ± 57.85 | ∗∗ | |
| AK (mg/kg) | 367.19 ± 57.80 | 234.71 ± 56.78 | ∗∗ | |
| 12 biogenic metallic elements (mg/kg) | Pb | 5.93 ± 2.19 | 87.38 ± 93.16 | ∗∗∗ |
| Zn | 50.79 ± 17.50 | 78.15 ± 45.43 | ∗ | |
| V | 97.66 ± 18.80 | 88.06 ± 31.27 | ∗ | |
| As | 3.60 ± 0.98 | 32.86 ± 18.55 | ∗∗∗ | |
| Mo | 0.75 ± 0.13 | 1.13 ± 0.35 | ∗∗ | |
| Sb | 0.55 ± 0.36 | 16.50 ± 13.74 | ∗∗∗ | |
| Co | 13.01 ± 7.44 | 9.11 ± 1.90 | ∗ | |
| Cu | 21.30 ± 14.31 | 32.76 ± 10.37 | ∗ | |
| Cr | 32.13 ± 13.37 | 47.63 ± 7.11 | ∗ | |
| Ni | 12.99 ± 4.36 | 29.13 ± 9.07 | ∗∗ | |
| Cd | 0.13 ± 0.07 | 0.16 ± 0.06 | ∗ | |
| Mn | 0.58 ± 0.23 | 0.44 ± 0.13 | ∗ | |
3.3. Microbial community of UCPS and ICPS
In this experiment, five samples of UCPS yielded a total of 130,721,746 high-quality reads, averaging 26,144,349.2 reads per sample. Additionally, five samples of ICPS yielded 121,709,920 high-quality reads, averaging 24,341,984 reads per sample. The thresholds for sequence similarity were set at 98.89 % and 98.9 %. For rhizosphere soil microorganisms, a total of 3196 bacterial and 322 fungal operational taxonomic units (OTUs) were identified through the calculation (Tables S4–S5). The Chao1 and ace indexes in the ICPS were higher than that in UCPS, suggesting that ICPS samples have a greater total number of microbial species and diversities, while the Shannon and Simpson indexes indicate that the microbial community diversity in ICPS samples was not significantly difference from UCPS. The Kruskal-Wallis's test was conducted on the Shannon indexes of both groups, showing that the F-value and P-values were 6.818 and 0.009, respectively (Fig. S3A–D). These results indicated that there was a significant difference in the diversity of rhizosphere soil microorganisms and microbial community structure between the UCPS and ICPS. The microbial community structures of the UCPS and ICPS were significantly different and clearly divided into two distinct classes, yielding an F-value of 21.609 and a P-value of 0.014 (Fig. S3E). These results indicated that both the UCPS and ICPS had significant effects on the P. notoginseng rhizosphere microbial structure, and the influence of the ICPS eco-environment on beta diversity was greater than that of the UCPS.
From phylum level, we analyzed microbial communities that showed significant differences at 95 % confidence intervals, the relative abundance of Pseudomonadota, Acidobacteriota, Ascomycota, Nitrososphaerota, Chloroflexota and Basidiomycota in UCPS were significantly higher than ICPS, while Nitrospirota, Gemmatimonadota, Bacillota, Thermoproteota, Actinomycetota showed higher relative abundance in ICPS (Fig. S3G). Bradyrhizobium, Paraburkholderia, and Mycobacterium showed significantly higher relative abundance in UCPS at 95 % confidence intervals. On the other hand, Mesorhizobium, Sphingobium, Streptomyces and Variovorax in ICPS was significantly higher than that in UCPS (Fig. 3A, Fig. S3H–I).
Fig. 3.
The biomarkers in understory cultivated P. notoginseng rhizosphere soil (UCPS) and intensive cultivated P. notoginseng rhizosphere soil (ICPS) were analyzed at the species level using Linear Discriminant Analysis (LDA) with a threshold of >4 (A). The biomarkers of UCPS were Bradyrhizobium sp., B. lablabi, Pseudomonas qingdaonensis etc.; The biomarkers of ICPS were Variovorax sp. WDL1, V. boronicumulans and Sphingobium sp. TKS (B).
The linear discriminant analysis effect size (LEfSe) technique was used to identify the biomarkers for each group. As a result, the beneficial microbiomes Bradyrhizobium arachidis, B. diazoefficiens, B. erythrophlei, B. lablabi, B. sp. SEMIA, Pseudomonas qingdaonensis and Paraburkholderia phytofirmans etc., were identified as the biomarkers of the UCPS. Additionally, Variovorax sp. WDL1, V. boronicumulans and Sphingobium sp. TKS etc., were the identifying biomarkers of the ICPS (Fig. 3 B).
3.4. Interaction of biomarkers and the physicochemical of UCPS and ICPS
In the UCPS, the Pearson correlation coefficient indicated that TOC has a highly significant positive correlation with TCH, TN and Cu. TCH has a highly significant positive correlation with HOC. AN have a highly significant positive correlation with TCH (P < 0.01, Pearson r > 0.6). Additionally, Mantel test analysis revealed a significant positive correlation between core microorganism Pseudomonas qingdaonensis with TOC and Mn (P < 0.01, r ≥ 0.5), and a significant positive correlation with NO3−-N (P < 0.05, 0.5 > r > 0.25). Furthermore, a significant positive correlation was shown between Bradyrhizobium diazoeficiens and AHN (P < 0.05, r > 0.5). Bradyrhizobium arachidis also exhibited a significant positive correlation with DOC, LFOC and Cu (P < 0.05, r > 0.5 or 0.5 > r > 0.25) (Fig. 4A).
Fig. 4.
The association between rhizosphere soil biomarkers (LEfSe OTUs at species level) and rhizosphere soil physicochemical properties of understory cultivated P. notoginseng (UCPn) and intensively cultivated P. notoginseng (ICPn) were demonstrated by partial Mantel tests. (A) The association of rhizosphere soil physicochemical properties and biomarkers of UCPS. (B) The association of rhizosphere soil physicochemical properties and biomarkers in ICPS. Note: Pairwise comparisons of soil variables are depicted using a color gradient to represent Pearson's correlation coefficients. The width of each edge matches Mantel's r statistic for the corresponding distance correlations. The solid line represents a positive correlation, while the dashed line represents a negative correlation. Note. ∗ Indicated the result is significant difference at P < 0.05, ∗∗ Indicated the result is significant difference at P < 0.01, Indicated the result is significant difference at P < 0.001.
In the ICPS, the Pearson correlation coefficient indicated a highly significant positive correlation between physicochemical components and biomarkers UCPn rhizosphere soil. TOC was significantly positively correlated with HOC and TCCH. Specifically, AK was highly significantly positively correlated with FAK. There was a highly significant positive correlation between Hu, AN and NO3−-N. And zinc (Zn) was significantly positively correlated with lead (Pb), Antimony (Sb) was significantly positively correlated with arsenic (As) and nickel (Ni) (r > 0.6). The Mantel test analysis revealed a significant positive correlation between the core microbial Variovorax boronicumulans and MBC (0.01 < P < 0.05, R ≥ 0.5) (Fig. 4B). This finding indicated that biogenic metallic elements were prevalent in the ICPS. Meanwhile, the medium metallic element V. boronicumulans mitigated the accumulation of excessive biogenic metallic elements (such as Pb, As, etc.) in the main root and rhizomes of P. notoginseng by positively regulating the content of MBC.
3.5. Association of rhizosphere soil microbial community, soil parameters and P. notoginseng plant parameters
In the C nutrition metabolic cycle, we have identified a total of 26 metabolic pathways in UCPS and ICPS. The main metabolic pathways involved CBB cycle (PrkB), rTCA cycle (AclAB, CcsAB, ccl), Wood-Ljungdahl pathway (AcsABCDE), 3-Hydroxypropionate Bicycle, Glycolysis (glk, pfk, pyk), Entner-Doudoroff pathway, glucose 6P to glyceraldehyde-3P+ pyruvate and Gluconeogenesis (fbp, pck) (Fig. S4A). For N nutrition metabolic cycle, A total of 11 metabolic pathways have been identified, including dissimilatory nitrate reduction, nitrate to ammonia (NirBD, NrfAH, NifDKH and VnfDKGH), nitrogen fixation, nitrification, ammonia to hydroxylamine (AmoABC), nitration and hydroxylamine oxidoreductase to nitrate (hao) pathways (Fig. S4B). The main pathways of sulfur cycles included the conversion of assimilatory sulfate reduction to sulfite (CysJI or sir), dissimilatory sulfate redacted to sulfite (Sat and AprAB), thiosulfate oxidation (sox, DoxAD, TsdA) and sulfite oxidation (SorB, SuoX, SoeABC) (Fig. S4D). DMSP undergoes demethylation through the DmdA enzyme pathway to produce MMPA. It could also generate DMS through the DddS and AlmA1 pathway, which then oxidizes to form DMSO through the tmm and DdhA pathway. In this pathway, the metabolic capacity of rhizosphere soil microorganisms in ICPS was significantly higher than that of rhizosphere soil microorganisms in UCPS. Conversely, microorganisms in the UCPS have a significantly greater capacity to convert DMSO into DMS through demethylation pathways compared to those in the ICPS (Fig. S4C).
3.6. P. notoginseng-rhizosphere soil system: In relation to soil nutrients and biomarkers
In the UCPS cultivation environment, the quality of P. notoginseng was significantly influenced by various environmental factors, as indicated by the high R-squared value of 0.669. Specifically, the Partial least squares structural equation modeling (PLS-SEM) indicated that rhizosphere soil microorganisms were an indirect driving factor for the quality of P. notoginseng in UCPn (path coefficient: 0.00025). Rhizosphere soil biomarkers had a direct effect on the soil microbial organic carbon (TCCH, HA + FA, Hu and MBC) and non-microbial organic carbon (TOC, POC, ROC and DOC), which in turn directly showed impact on the quality of UCPn (path coefficients: 0.263, R2 = 0.006). Additionally, the organic nitrogen (TSN, MBN and SON) and inorganic nitrogen (AHN, AN, NO3−-N and NO2−-N) showed a direct negative effect on UCPn (path coefficients: 0.936, R2 = 0.910). Conversely, soil inorganic phosphorus (AAP & IP) and organic phosphorus (OP & MBP) negatively impacted the quality of UCPn (path coefficients: 0.464, R2 = 0.016) (Fig. 5A). In the ICPn, the quality of P. notoginseng is primarily influenced by biomarkers and phosphorus nutrition (R2 = 0.546). The effects of carbon nutrition (path coefficient: 0.305, R2 = 0.164) and nitrogen nutrition (path coefficient: 0.096, R2 = 0.778) on the quality of P. notoginseng was indirect. However, the influence of biomarkers on C, N and P is direct, and P nutrients showed positive effect on the quality of ICPn (with path coefficients of 0.287 and R2 = 0.698) (Fig. 5B).
Fig. 5.
Partial least squares structural equation modeling (PLS-SEM) were used to analyze data from the multivariate experimental indicators. Note: Circles represent different latent variables, while boxes represent the observed variables corresponding to each latent variable. The numbers in the top right corner of each of the soil or microbial parameter boxes is the squared-multiple correlation (R2). A red solid line indicates a positive correlation between two latent variables, while a black dashed line indicates a negative correlation between two latent variables. The number on each line between two latent variable is the path coefficient (a path coefficient of −1 indicates a completely negative correlation, while a path coefficient of 1 indicates a completely positive correlation).
4. Discussion
4.1. The rich nutrients in UCPS improve the aboveground growth of UCPn
Researchers have confirmed that roots play an important role in absorbing nutrients such as soil TOC and facilitating N cycling from the soil to the root sheath during plant growth [29]. When the root system's absorption capacity exceeds the consumption capacity of the aboveground part, plants will prioritize the growth of the aboveground part, such as stem and leaves [30]. As the mineral elements are in short supply, plants frequently allocate a larger percentage of their biomass into their roots [31]. This result confirms that the various forms of carbon nutrition (TOC, LFOC, TCCH or MBC), N nutrition (AN, NO3−-N, MBN), phosphorus nutrition (AAP, OP, IP), and potassium nutrition (FAK, AK) in the UCPS are significantly higher than those in the ICPS, possibly leading to a higher ratio of aboveground stems and leaves, and the root-shoot ratio and root-mass ratio of ICPn is significantly higher than that of UCPn (Fig. 1, Table 1). This result confirms that artificial supplementation of the macronutrients nitrogen, phosphorus, potassium, and magnesium lead to an accumulation of carbohydrates in the roots, which improves the underground parts ratio of ICPn. In contrast, the abundant organic carbon and nitrogen nutrients in the forest land contribute to the luxuriant foliage of UCPn. Overall, the root-shoot ratio and root-mass ratio of ICPn is significantly higher than those of UCPn, while the leaf-mass ratio and stem-mass ratio of UCPn is significantly higher than that of ICPn.
4.2. The total saponin content is significantly higher in UCPn than in ICPn
The overall saponin levels are a key factor in assessing the medicinal properties of Panax genus plants. In this experiment, the total saponin content in the main roots, rhizome, and branch roots of UCPn are significant than that of ICPn (Fig. 2). As indicated in the previous report, the total saponin content of P. notoginseng ranges from 11.03 % to 12.61 % [10,32], consistent with the UCPn main roots in this experiment. Normally, at high planting densities, the strong intraspecific competition of P. notoginseng resulted in stress, as well as the accumulation of phytohormones such as jasmonic acid and salicylic acid, antioxidants including gentiobiose, oxalic acid, dehydroascorbic acid, and other stress resistance-related metabolites, which led to high ginsenoside accumulation [33]. However, at low densities and complex biodiversity conditions, P. notoginseng disrupts normal carbohydrate metabolism by upregulating galactose metabolism, resulting in significantly lower biomass of underground parts and ginsenoside content [33].
According to the 2020 edition of the Pharmacopoeia of the People's Republic of China, the major active ingredients in Radix Notoginseng are ginsenoside Rb1, ginsenoside Rg1 and notoginsenoside R1, which should collectively constitute at least 5 %. In this study, the content of Rg1 + Re + Rb1 in each part of UCPn and ICPn was significantly higher than requirements of the Pharmacopoeia of the People's Republic of China. The researchers have detected that the content of Rb1 + Rg1 + R1 in P. notoginseng rhizome ranges from 78.82 to 129.29 mg/g, a slightly differences from the results of this study [34]. If determining the origin and cultivation conditions for the differences of P. notoginseng, essential characteristic markers such as linoleic acid, palmitic acid, malic acid, sucrose, fructose, Rg1, Rf, Rb1, R1, malonyl-Rb1, malonyl-Rg1, malonyl-Rf, Rd and Re may serve as comparison conditions [35]. Overall, our results suggest that the total saponin content of UCPn is higher than that of ICPn, while the medicinal ingredients Rb1 + Rg1 + R1 exhibit greater levels in ICPn compared to UCPn.
4.3. The improvement of medicinal ingredients of UCPn is facilitated by higher organic nutrient levels and balanced microbial communities
In this experiment, fourteen rhizosphere biomarkers were found in the UCPS, including Bradyrhizobium arachidis, B. diazoefficiens, B. sp. SEMIA, B. erythrophlei, B. lablabi, Pseudomonas qingdaonensis and Paraburkholderia phytofirmans (Fig. 3B & Fig. S3). Bradyrhizobium is a broad category of bacteria with various lifestyles, which is best known for their nitrogen fixation in nodules in symbiosis with legumes [36]. Most species of Bradyrhizobium are capable of photosynthesis and play a role in promoting plant growth and development [37]. Herein, Braziliensis arachidis forms symbiotic relationships with medicinal plants such as Sophora flavescens and is involved in nitrogen fixation, which enhances the content of matrine in legumes [38].Several genes of B. diazoefficiens involved in central carbon metabolism positively and directly regulate the conversion of glucose-6-phosphate to glyceraldehyde-3-phosphate and pyruvate, as well as gluconeogenesis (Fbp, Pck) [39], resulting in a significant increase in HOC (18.5 ± 2.1 g/kg) in UCPS (Fig. S4A, Table 1). It is important to note that B. diazoefficiens uses thiosulfate as an electron donor for respiration and participates in the Calvin-Benson-Bassham (CBB) cycle metabolic pathway (Fig. S4A) [40], specifically through the PrkB pathway in sulfur metabolism in UCPS. It has been confirmed that the species P. qingdaonensis exhibits resistance to heavy metals, degrades hydrocarbons, and promotes plant growth [41]. Paraburkholderia, a bacterium known to have beneficial effects on plant growth and health, has the ability to enhance plant resistance to both biotic and abiotic stresses [42]. Herein, P. phytofirmans may play a positive role in regulating UCPn growth and resisting biotic and abiotic stresses, which is beneficial for improving the quality of UCPn.
Besides, twenty rhizosphere biomarkers were found in the ICPS, such as Variovorax sp. WDL1, V. boronicumulans and Sphingobium sp. TKS (Fig. 3B, Fig. S3 & Table 1). Variovorax increased the rate of As oxidation in soil [43], nitrogen fixation [44] and degradation of pesticide residues [45]. Variovorax sp. WDL1 acts as a biodegradation species, mediating the degradation of the phenylurea herbicide linuron by expressing a novel linuron-hydrolyzing enzyme (HylA). It also dissolves natural organic matter to serve as a supplementary carbon source [46,47]. V. boronicumulans mediates two consecutive methylation steps in the biosynthesis of the Brevianamide-type bishomosesquiterpene chlororaphen, potentially providing a foundational pathway for the biosynthesis of triterpenoid saponins in ICPn [48]. This pathway may provide a source of raw materials for the biosynthesis of ICPn triterpenoid saponin, such as ginsenosideRb1, Rg1 or notoginsenoside R1. Sphingobium sp. TKS mediates the degradation of γ-hexachlorocyclohexane [49], providing insights into the decomposition of pesticide residues in ICPS. This discovery indicates that most species of Variovorax have a positive effect on promoting the degradation of excessive heavy metals in ICPS.
5. Conclusion
In the understory cultivation of P. notoginseng, a balanced microbial community significantly enhances rhizosphere soil nutrients, positively impacting the yield and quality of Radix Notoginseng. These microbial biomarkers facilitate organic matter metabolism, promote the accumulation of medicinal compounds, and increase total saponin content in UCPn. Conversely, intensively cultivated P. notoginseng exhibits nutrient deficiencies, including microbial and non-microbial organic carbon, organic nitrogen, and inorganic nitrogen, which impede its capacity to accumulate medicinal ingredients and result in lower total saponin levels in ICPn. Thus, reintroducing shade-demanding medicinal crops in understory cultivation presents a viable solution to address farmland scarcity, particularly in China.
CrediT author statement
Zheng-Wei Liang: Methodology, writing–original draft. Yan-Hui Guan: Data curation. Zheng Lv: Formal analysis. Sheng-Chao Yang: Project administration. Ming Zhao: Validation, writing–review & editing. Jun-Wen Chen: Conceptualization, funding acquisition, writing–review & editing.
Declaration of competing interest
The authors declare that there are no conflicts of interest.
Acknowledgements
This work was supported by National Key Research and Development Plan of China (2021YFD1601003), Major Special Science and Technology Project of Yunnan Province (202502AU100003); Yunnan Characteristic Plant Extraction Laboratory Co., Ltd. (2022YKZY001).
Footnotes
Supplementary data to this article can be found online at https://doi.org/10.1016/j.jgr.2025.11.006.
Contributor Information
Sheng-Chao Yang, Email: shengchaoyang@163.com.
Ming Zhao, Email: zhaoming02292002@aliyun.com.
Jun-Wen Chen, Email: cjw31412@hotmail.com.
Appendix A. Supplementary data
The following are the Supplementary data to this article.
References
- 1.Food and Agriculture Organization of the United Nations . 2023. FAOSTAT: land use 2000-2023. [Google Scholar]
- 2.Gupta A., Singh U.B., Sahu P.K., Paul S., Kumar A., Malviya D., et al. Linking soil microbial diversity to modern agriculture practices: a review. Int J Environ Res Public Health. 2022;19(5):3141. doi: 10.3390/ijerph19053141. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Huang S., Yu J., Hou D., Yue H., Zhang D., Li Y., et al. Response of soil microbial community diversity to continuous cucumber cropping in facilities along the Yellow River irrigation area. PLoS One. 2023;18(8) doi: 10.1371/journal.pone.0289772. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Cho G., Kim D.R., Kwak Y.S. Transition from Ginseng Root Rot disease-conducive soil to -Suppressive soil mediated by Pseudomonadaceae. Microbiol Spectr. 2023;11(4) doi: 10.1128/spectrum.01150-23. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Yang K., Wang H.L., Ye C., Wang Z.H., Ye K.H., Zhang S., et al. Infection characteristics and physical prevention strategy of Panax notoginseng round spot disease caused by Mycocentrospora acerina. Plant Dis. 2022;106(10):2607–2617. doi: 10.1094/PDIS-01-22-0087-RE. [DOI] [PubMed] [Google Scholar]
- 6.Fan S., Zhao F., Zhang J., Shang W., Hu X. American Ginseng root rot caused by Fusarium redolens in China. Plant Dis. 2021;105(9):2734. [Google Scholar]
- 7.Ma R., Sun L., Chen X., Mei B., Chang G., Wang M., et al. Proteomic analyses provide novel insights into plant growth and ginsenoside biosynthesis in forest cultivated Panax ginseng (F. Ginseng) Front Plant Sci. 2016;7:1. doi: 10.3389/fpls.2016.00001. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Chen W., Balan P., Popovich D.G. Ginsenosides analysis of New Zealand-grown forest Panax ginseng by LC-QTOF-MS/MS. J Ginseng Res. 2020;44(4):552–562. doi: 10.1016/j.jgr.2019.04.007. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Jia W., Wang S., He X., Zhao X. Different factors drive the assembly of pine and Panax notoginseng-associated microbiomes in Panax notoginseng-pine agroforestry systems. Front Microbiol. 2022;13 doi: 10.3389/fmicb.2022.1018989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Yang K., Wang H., Luo L., Zhu S., Huang H., Wei Z., et al. Effects of different soil moisture on the growth, quality, and root rot disease of organic Panax notoginseng cultivated under pine forests. J Environ Manage. 2023;329 doi: 10.1016/j.jenvman.2022.117069. [DOI] [PubMed] [Google Scholar]
- 11.Ramawat K.G., Arora J. In: Medicinal plants: domestication, biotechnology and regional importance. Ekiert H.M., Ramawat K.G., Arora J., editors. Springer International Publishing; Cham: 2021. Medicinal plants domestication, cultivation, improvement, and alternative technologies for the production of high value therapeutics: an overview; pp. 1–29. [Google Scholar]
- 12.Wang J., Liu X. Yunnan Wei Heng Foundation industry Technology Co., Ltd; Kunming: 2020. Panax notoginseng industry data analysis report in 2020, China; pp. 1–33. [Google Scholar]
- 13.Fu Y., Dou X., Lu Q., Qin J., Luo J., Yang M. Comprehensive assessment for the residual characteristics and degradation kinetics of pesticides in Panax notoginseng and planting soil. Sci Total Environ. 2020;714(C) doi: 10.1016/j.scitotenv.2020.136718. [DOI] [PubMed] [Google Scholar]
- 14.Yang Y., Zheng K., Guo L.P., Wang C.X., Zhong D.B., Shang L., et al. Rapid determination and dietary intake risk assessment of 249 pesticide residues in Panax notoginseng. Ecotoxicol Environ Saf. 2022;233 doi: 10.1016/j.ecoenv.2022.113348. [DOI] [PubMed] [Google Scholar]
- 15.Zhao L., Li Y., Ren W., Huang Y., Wang X., Fu Z., et al. Pesticide residues in soils planted with Panax notoginseng in south China, and their relationships in Panax notoginseng and soil. Ecotoxicol Environ Saf. 2020;201 doi: 10.1016/j.ecoenv.2020.110783. [DOI] [PubMed] [Google Scholar]
- 16.Goodwin P.H. The rhizosphere microbiome of ginseng. Microorganisms. 2022;10(6):1152. doi: 10.3390/microorganisms10061152. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.Chen X., Ran Z., Li R., Duan W., Song Z., Fang L., et al. Biochar reduces the cadmium content of Panax quinquefolium L. by improving rhizosphere microecology. Sci Total Environ. 2024;915 doi: 10.1016/j.scitotenv.2024.170005. [DOI] [PubMed] [Google Scholar]
- 18.Deng L., Luo L., Li Y., Wang L., Zhang J., Zi B., et al. Autotoxic ginsenoside stress induces changes in root exudates to recruit the beneficial burkholderia strain B36 as revealed by transcriptomic and metabolomic approaches. J Agric Food Chem. 2023;71(11):4536–4549. doi: 10.1021/acs.jafc.3c00311. [DOI] [PubMed] [Google Scholar]
- 19.Shi R., Gu H., He S., Xiong B., Huang Y., Horowitz A.R., et al. Comparative metagenomic and metabolomic profiling of rhizospheres of Panax notoginseng grown under forest and field conditions. Agronomy. 2021;11(12):2488. 2488. [Google Scholar]
- 20.Li M., Chen Z., Qian J., Wei F., Zhang G., Wang Y., et al. Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields. Chin Med. 2020;15(1):85. doi: 10.1186/s13020-020-00364-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 21.Kui L., Chen B., Chen J., Sharifi R., Dong Y., Zhang Z., et al. A comparative analysis on the structure and function of the Panax notoginseng rhizosphere microbiome. Front Microbiol. 2021;12 doi: 10.3389/fmicb.2021.673512. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 22.Wei G., Li M., Zhang G., Chen Z., Wei F., Jiao S., et al. Rhizosphere microbiome is associated with yield and medical value of the perennial Panax notoginseng. Research Square. 2020 PPR188287. [Google Scholar]
- 23.National Health Commission of the People's Republic of China . 2018. National food safety standard determination of 208 pesticides and metabolites residues in foods of plant origin-gas chromatography-tandem mass spectrometry method; pp. 1–46. GB23200.113-2018. Beijing. [Google Scholar]
- 24.Liang Z., Guan Y., Li R., Xu S., Yang S., Jiang W., et al. Bioactive components in Panax notoginseng and Panax quinquefolium leaves and their antioxidant, antihypertensive and anti-inflammatory capacities. Ind Crops Prod. 2024;210 [Google Scholar]
- 25.Zhang Q., Huang Q. Revised method for determining Ganoderma lingzhi terpenoids by UV-Vis spectrophotometry based on colorimetric vanillin perchloric acid reaction. Mycosystema. 2018;37(12):1792–1801. [Google Scholar]
- 26.Tringe S.G., von Mering C., Kobayashi A., Salamov A.A., Chen K., Chang H.W., et al. Comparative metagenomics of microbial communities. Science. 2005;308(5721):554–557. doi: 10.1126/science.1107851. [DOI] [PubMed] [Google Scholar]
- 27.Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics. 2014;30(15):2114–2120. doi: 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 28.Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359. doi: 10.1038/nmeth.1923. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 29.Li Q., Fu Q., Li T., Liu D., Hou R., Li M., et al. Biochar impacts on the soil environment of soybean root systems. Sci Total Environ. 2022;821 doi: 10.1016/j.scitotenv.2022.153421. [DOI] [PubMed] [Google Scholar]
- 30.Novoplansky A. What plant roots know? Semin Cell Dev Biol. 2019;92:126–133. doi: 10.1016/j.semcdb.2019.03.009. [DOI] [PubMed] [Google Scholar]
- 31.Hermans C., Hammond J.P., White P.J., Verbruggen N. How do plants respond to nutrient shortage by biomass allocation? Trends Plant Sci. 2006;11(12):610–617. doi: 10.1016/j.tplants.2006.10.007. [DOI] [PubMed] [Google Scholar]
- 32.Li N., Gao X., Wang Z., Gong Y., Liu J., Yang Z., et al. Establishment of HPLC fingerprints of Panax notoginseng and determination of five constituents. Chin Tradit Pat Med. 2020;42(5):1232–1237. [Google Scholar]
- 33.Liu H., Gu H., Ye C., Guo C., Zhu Y., Huang H., et al. Planting density affects Panax notoginseng growth and ginsenoside accumulation by balancing primary and secondary metabolism. Front Plant Sci. 2021;12 doi: 10.3389/fpls.2021.628294. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 34.Wang J.R., Yau L.F., Gao W.N., Liu Y., Yick P.W., Liu L., et al. Quantitative comparison and metabolite profiling of saponins in different parts of the root of Panax notoginseng. J Agric Food Chem. 2014;62(36):9024–9034. doi: 10.1021/jf502214x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 35.Zhang X., Chen Z.Y., Qiu Z.D., Liu M., Xu J., Lai C.J., et al. Molecular differentiation of Panax notoginseng grown under different conditions by internal extractive electrospray ionization mass spectrometry and multivariate analysis. Phytochemistry. 2022;194 doi: 10.1016/j.phytochem.2021.113030. [DOI] [PubMed] [Google Scholar]
- 36.Avontuur J.R., Palmer M., Beukes C.W., Chan W.Y., Coetzee M., Blom J., et al. Genome-informed Bradyrhizobium taxonomy: where to from here? Syst Appl Microbiol. 2019;42(4):427–439. doi: 10.1016/j.syapm.2019.03.006. [DOI] [PubMed] [Google Scholar]
- 37.Avontuur J.R., Wilken P.M., Palmer M., Coetzee M.P.A., Stepkowski T., Venter S.N., et al. Complex evolutionary history of photosynthesis in Bradyrhizobium. Microb Genom. 2023;9(9) doi: 10.1099/mgen.0.001105. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 38.Wu Z.Y., Meng X.F., Jiao Y.S., Guo B.L., Sui X.H., Ma S.J., et al. Bradyrhizobium arachidis mediated enhancement of (oxy)matrine content in the medicinal legume Sophora flavescens. Lett Appl Microbiol. 2021;72(5):570–577. doi: 10.1111/lam.13453. [DOI] [PubMed] [Google Scholar]
- 39.Nishihata S., Kondo T., Tanaka K., Ishikawa S., Takenaka S., Kang C., et al. Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation. BMC Microbiol. 2018;18(1):156. doi: 10.1186/s12866-018-1317-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 40.Masuda S., Hennecke H., Fischer H. Requirements for efficient thiosulfate oxidation in Bradyrhizobium diazoefficiens. Genes. 2017;8(12):390. doi: 10.3390/genes8120390. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 41.Chlebek D., Plociniczak T., Gobetti S., Kumor A., Hupert-Kocurek K., Pacwa-Plociniczak M. Analysis of the genome of the heavy metal resistant and hydrocarbon-degrading rhizospheric Pseudomonas qingdaonensis ZCR6 strain and assessment of its plant-growth-promoting traits. Int J Mol Sci. 2021;23(1):214. doi: 10.3390/ijms23010214. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 42.Esmaeel Q., Miotto L., Rondeau M., Leclere V., Clement C., Jacquard C., et al. Paraburkholderia phytofirmans PsJN-Plants interaction: from perception to the induced mechanisms. Front Microbiol. 2018;9:2093. doi: 10.3389/fmicb.2018.02093. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 43.Majumder A., Bhattacharyya K., Bhattacharyya S., Kole S.C. Arsenic-tolerant, arsenite-oxidising bacterial strains in the contaminated soils of West Bengal, India. Sci Total Environ. 2013;463–464:1006–1014. doi: 10.1016/j.scitotenv.2013.06.068. [DOI] [PubMed] [Google Scholar]
- 44.Bizjak T., Sellstedt A., Gratz R., Nordin A. Presence and activity of nitrogen-fixing bacteria in Scots pine needles in a boreal forest: a nitrogen-addition experiment. Tree Physiol. 2023;43(8):1354–1364. doi: 10.1093/treephys/tpad048. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 45.Volova T., Zhila N., Vinogradova O., Shumilova A., Prudnikova S., Shishatskaya E. Characterization of biodegradable poly-3-hydroxybutyrate films and pellets loaded with the fungicide tebuconazole. Environ Sci Pollut Res Int. 2016;23(6):5243–5254. doi: 10.1007/s11356-015-5739-1. [DOI] [PubMed] [Google Scholar]
- 46.Bers K., Batisson I., Proost P., Wattiez R., De Mot R., Springael D. HylA, an alternative hydrolase for initiation of catabolism of the phenylurea herbicide linuron in Variovorax sp. strains Appl Environ Microbiol. 2013;79(17):5258–5263. doi: 10.1128/AEM.01478-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 47.Horemans B., Vandermaesen J., Vanhaecke L., Smolders E., Springael D. Variovorax sp.-mediated biodegradation of the phenyl urea herbicide linuron at micropollutant concentrations and effects of natural dissolved organic matter as supplementary carbon source. Appl Microbiol Biotechnol. 2013;97(22):9837–9846. doi: 10.1007/s00253-013-4690-7. [DOI] [PubMed] [Google Scholar]
- 48.Magnus N., von Reuss S.H., Braack F., Zhang C., Baer K., Koch A., et al. Non-canonical biosynthesis of the Brexane-Type bishomosesquiterpene chlororaphen through two consecutive methylation steps in Pseudomonas chlororaphis O6 and Variovorax boronicumulans PHE5-4. Angew Chem Int Ed Engl. 2023;62(29) doi: 10.1002/anie.202303692. [DOI] [PubMed] [Google Scholar]
- 49.Tabata M., Ohhata S., Kawasumi T., Nikawadori Y., Kishida K., Sato T., et al. Complete genome sequence of a gamma-Hexachlorocyclohexane degrader, Sphingobium sp. Strain TKS, isolated from a gamma-hexachlorocyclohexane-degrading microbial community. Genome Announc. 2016;4(2) doi: 10.1128/genomeA.00247-16. 16. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.