Summary of Study ST004122
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002591. The data can be accessed directly via it's Project DOI: 10.21228/M8QZ83 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST004122 |
| Study Title | Untargeted rhizosphere metabolomics of Artemisia argyi under cadmium stress with synthetic microbial community inoculation |
| Study Type | LC-MS |
| Study Summary | This study investigated rhizosphere metabolic responses of Artemisia argyi to inoculation with a native two-member synthetic microbial community (SynCom) in cadmium-contaminated soils. Pot experiments were conducted using soils from a historically polluted mining area in Hunan Province, China, with SynCom-inoculated and uninoculated plants grown for 60 days under 400 mg/kg Cd stress. Rhizosphere soil metabolites were extracted with methanol containing an internal standard and analyzed by UHPLC-Q Exactive MS in positive and negative ionization modes. Untargeted metabolomics revealed 39% fatty acyls, 14% organooxygen compounds, and 11% carboxylic acids and derivatives as dominant classes. SynCom inoculation significantly upregulated key intermediates in microbial respiration and carbon metabolism (e.g., 6-phosphogluconic acid, succinic acid, fumaric acid) and biomarkers of microbial biomass and root-derived carbon input (lanosterin, β-sitosterol). Enrichment of signaling molecules such as nobiletin suggested enhanced antioxidative capacity and potential chemoattraction of beneficial microbes including Pseudomonas, Rahnella, and functional partners. These results indicate that SynCom inoculation reshapes rhizosphere metabolic networks to promote carbon retention and microbial resilience under heavy metal stress. |
| Institute | Central South University, China |
| Department | School of Metallurgy and Environment |
| Last Name | He |
| First Name | Xiao |
| Address | 932 South Lushan Road |
| hexiao0507@gmail.com | |
| Phone | +86 13805204537 |
| Submit Date | 2025-08-09 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-08-25 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002591 |
| Project DOI: | doi: 10.21228/M8QZ83 |
| Project Title: | Metabolomic responses of Artemisia argyi to synthetic microbial community inoculation under cadmium stress |
| Project Type: | Environmental metabolomics |
| Project Summary: | This project aims to investigate the metabolic responses of Artemisia argyi to inoculation with a native synthetic microbial community (SynCom) in cadmium-contaminated soils. We will perform untargeted rhizosphere metabolomics and targeted leaf volatile metabolomics to assess how SynCom inoculation influences primary and secondary metabolic pathways under heavy metal stress. The study will focus on identifying key metabolites and metabolic pathways related to microbial carbon fixation, soil organic carbon accumulation, stress signaling, and essential oil biosynthesis. The findings are expected to provide insights into the mechanisms by which SynCom enhances phytoremediation efficiency, carbon sequestration, and the economic utilization potential of A. argyi in mining-impacted environments. |
| Institute: | Central South University, China |
| Department: | School of Metallurgy and Environment |
| Last Name: | He |
| First Name: | Xiao |
| Address: | No. 932 Lushan South Road, Changsha 410083, P.R. China |
| Email: | hexiao0507@gmail.com |
| Phone: | +86 13805204537 |
| Contributors: | Rui Xu |
Subject:
| Subject ID: | SU004271 |
| Subject Type: | Plant |
| Subject Species: | Artemisia argyi |
| Taxonomy ID: | 259893 |
| Genotype Strain: | NA |
| Age Or Age Range: | 60 days |
| Gender: | Not applicable |
Factors:
Subject type: Plant; Subject species: Artemisia argyi (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Treatment | IonMode |
|---|---|---|---|---|
| SA476371 | N_1_neg | rhizosphere soil | No SynCom | Negative |
| SA476372 | N_2_neg | rhizosphere soil | No SynCom | Negative |
| SA476373 | N_3_neg | rhizosphere soil | No SynCom | Negative |
| SA476374 | N_1_pos | rhizosphere soil | No SynCom | Positive |
| SA476375 | N_2_pos | rhizosphere soil | No SynCom | Positive |
| SA476376 | N_3_pos | rhizosphere soil | No SynCom | Positive |
| SA476377 | Syn_1_neg | rhizosphere soil | SynCom inoculation | Negative |
| SA476378 | Syn_2_neg | rhizosphere soil | SynCom inoculation | Negative |
| SA476379 | Syn_3_neg | rhizosphere soil | SynCom inoculation | Negative |
| SA476380 | Syn_1_pos | rhizosphere soil | SynCom inoculation | Positive |
| SA476381 | Syn_2_pos | rhizosphere soil | SynCom inoculation | Positive |
| SA476382 | Syn_3_pos | rhizosphere soil | SynCom inoculation | Positive |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO004264 |
| Collection Summary: | Rhizosphere soil was collected from Artemisia argyi plants grown in a greenhouse pot experiment under cadmium stress. Plants received either no inoculum (control) or a native two-member SynCom. At harvest, roots were gently shaken to remove bulk soil; tightly adhered rhizosphere soil was brushed/vortexed from roots into sterile 2 mL tubes, immediately placed on ice, flash-frozen in liquid nitrogen within 30 min, and stored at −80 °C until extraction for LC-MS metabolomics. |
| Collection Protocol Filename: | XH_LC-MS_protocol.pdf |
| Sample Type: | rhizosphere soil |
| Collection Method: | Roots excised; bulk soil removed by gentle shaking. Remaining root-adhered soil brushed/vortexed into sterile 2 mL polypropylene tubes using sterile spatulas; tubes kept on wet ice; samples flash-frozen in liquid N₂ within 30 min. |
| Collection Location: | Central South University, Changsha, Hunan, China |
| Collection Frequency: | Once at harvest (day 60 after transplanting) |
| Collection Duration: | 5 min per plant (from uprooting to freezing) |
| Volumeoramount Collected: | 0.20 g rhizosphere soil per sample (fresh weight) |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR004280 |
| Treatment Summary: | Artemisia argyi plants were grown in pots containing cadmium-contaminated mining soil with or without inoculation of a native synthetic microbial community. |
| Treatment: | Biological treatment |
| Treatment Compound: | native synthetic microbial community |
| Treatment Route: | Soil application |
| Treatment Dose: | SynCom inoculation: 50 mL suspension (OD600=0.8) per pot |
| Plant Growth Location: | Central South University, Changsha, China |
| Plant Light Period: | 16 h light / 8 h dark photoperiod |
| Plant Humidity: | 60 ± 5% RH |
| Plant Temp: | 25 ± 2 °C |
| Plant Watering Regime: | Watered with deionized water every 3 days to maintain ~60% field capacity |
| Plant Nutritional Regime: | No additional fertilizer applied |
| Plant Estab Date: | 2024-04-15 |
| Plant Harvest Date: | 2024-06-15 |
Sample Preparation:
| Sampleprep ID: | SP004277 |
| Sampleprep Summary: | Fresh rhizosphere soil samples of Artemisia argyi were collected in the field, immediately frozen in liquid nitrogen, and stored at –80 °C until extraction. For LC-MS analysis, 100 mg of freeze-dried and homogenized soil was extracted with 1 mL of 70% methanol (v/v) containing an internal standard. The mixture was vortexed for 3 min and sonicated in an ice-water bath for 10 min, followed by incubation at –20 °C for 1 h. Samples were centrifuged at 12,000 rpm for 10 min at 4 °C, and the supernatant was filtered through a 0.22 μm PTFE membrane and stored at –80 °C prior to LC-MS analysis. For GC-MS analysis, 100 mg of homogenized soil was extracted with 1 mL of methanol:chloroform:water (2.5:1:1, v/v/v), vortexed, sonicated, and centrifuged as above. The polar phase was transferred to a fresh vial, dried under vacuum, derivatized with 20 mg/mL methoxyamine hydrochloride in pyridine at 37 °C for 90 min, followed by silylation with MSTFA at 37 °C for 30 min, and stored at –80 °C until injection. |
| Sampleprep Protocol Filename: | XH_LC-MS_protocol.pdf |
| Processing Method: | Sample homogenization, solvent extraction, centrifugation, filtration |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | Methanol-based extraction for LC-MS; Methanol:chloroform:water extraction for GC-MS |
| Extract Enrichment: | Not applicable |
| Extract Cleanup: | 0.22 μm PTFE membrane filtration (LC-MS extracts only) |
| Extract Storage: | -80℃ |
Chromatography:
| Chromatography ID: | CH005190 |
| Chromatography Summary: | Positive mode: Reversed-phase UHPLC separation of rhizosphere metabolite extracts was performed on a Thermo Vanquish system equipped with a Waters ACQUITY UPLC HSS T3 column (100 × 2.1 mm, 1.8 μm). The mobile phases consisted of Solvent A2 (0.1% formic acid in water) and Solvent B2 (0.1% formic acid in acetonitrile). A gradient elution was applied (0–1 min, 8% B2; 1–8 min, 8–98% B2; 8–10 min, 98% B2; 10–10.1 min, 98–8% B2; 10.1–12 min, 8% B2). The flow rate was 0.30 mL/min with a column temperature maintained at 40 °C. |
| Methods Filename: | XH_LC-MS_protocol.pdf |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 40 °C |
| Flow Gradient: | 0–1 min, 8% B; 1–8 min, 8–98% B; 8–10 min, 98% B; 10–10.1 min, 98–8% B; 10.1–12 min, 8% B |
| Flow Rate: | 0.30 mL/min |
| Solvent A: | 100% Water; 0.1% formic acid |
| Solvent B: | 100% Acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH005191 |
| Chromatography Summary: | Negative mode: Reversed-phase UHPLC separation of rhizosphere metabolite extracts was performed on a Thermo Vanquish system using the same Waters ACQUITY UPLC HSS T3 column (100 × 2.1 mm, 1.8 μm). The mobile phases consisted of Solvent A3 (5 mM ammonium formate in water) and Solvent B3 (acetonitrile). A gradient elution was applied (0–1 min, 8% B3; 1–8 min, 8–98% B3; 8–10 min, 98% B3; 10–10.1 min, 98–8% B3; 10.1–12 min, 8% B3). The flow rate was 0.30 mL/min with a column temperature maintained at 40 °C. |
| Methods Filename: | XH_LC-MS_protocol.pdf |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 40 °C |
| Flow Gradient: | 0–1 min, 8% B；1–8 min, 8–98% B；8–10 min, 98% B；10–10.1 min, 98–8% B；10.1–12 min, 8% B |
| Flow Rate: | 0.30 mL/min |
| Solvent A: | 100% water; 5 mM Ammonium formate |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006834 |
| Analysis Type: | MS |
| Analysis Protocol File: | XH_LC-MS_protocol.pdf |
| Chromatography ID: | CH005190 |
| Num Factors: | 4 |
| Num Metabolites: | 137 |
| Units: | peak area |
| Analysis ID: | AN006835 |
| Analysis Type: | MS |
| Analysis Protocol File: | XH_LC-MS_protocol.pdf |
| Chromatography ID: | CH005191 |
| Num Factors: | 4 |
| Num Metabolites: | 48 |
| Units: | peak area |
