Summary of Study ST003535

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 PR002175. The data can be accessed directly via it's Project DOI: 10.21228/M8GJ7D This work is supported by NIH grant, U2C- DK119886.

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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.

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Study IDST003535
Study TitleArsenic-induced enhancement of diazotrophic recruitment and nitrogen fixation in Pteris vittata rhizosphere
Study SummaryHeavy metal contamination poses an escalating global challenge to soil ecosystems. Hyperaccumulators play a crucial role in environmental remediation and resource recovery. The enrichment of diazotrophs and resulting nitrogen accumulation promoted hyperaccumulator growth and facilitated phytoremediation. Nonetheless, the regulatory mechanism of hyperaccumulator biological nitrogen fixation has remained elusive. Here, we report the mechanism by which arsenic regulates biological nitrogen fixation in the arsenic-hyperaccumulator Pteris vittata. Field investigations and greenhouse experiments, based on multi-omics approaches, reveal that elevated arsenic stress induces an enrichment of key diazotrophs, enhances plant nitrogen acquisition, and thus improves plant growth. Metabolomic analysis and microfluidic experiments further demonstrate that the upregulation of specific root metabolites plays a crucial role in recruiting key diazotrophic bacteria. These findings highlight the pivotal role of nitrogen-acquisition mechanisms in the arsenic hyperaccumulation of Pteris vittata, and provide valuable insights into the plant stress resistance.
Institute
Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University
Last NameLin
First NameJiahui
Address866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
Emaillinjh.link@zju.edu.cn
Phone18968220088
Submit Date2024-10-24
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2024-11-14
Release Version1
Jiahui Lin Jiahui Lin
https://dx.doi.org/10.21228/M8GJ7D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002175
Project DOI:doi: 10.21228/M8GJ7D
Project Title:Arsenic-induced enhancement of diazotrophic recruitment and nitrogen fixation in Pteris vittata rhizosphere
Project Summary:The enrichment of diazotrophs and resulting nitrogen accumulation promoted hyperaccumulator growth and facilitated phytoremediation. Nonetheless, the regulatory mechanism of hyperaccumulator biological nitrogen fixation has remained elusive. Here, we report the mechanism by which arsenic regulates biological nitrogen fixation in the arsenic-hyperaccumulator Pteris vittata. Field investigations and greenhouse experiments, based on multi-omics approaches, reveal that elevated arsenic stress induces an enrichment of key diazotrophs, enhances plant nitrogen acquisition, and thus improves plant growth. Metabolomic analysis and microfluidic experiments further demonstrate that the upregulation of specific root metabolites plays a crucial role in recruiting key diazotrophic bacteria. These findings highlight the pivotal role of nitrogen-acquisition mechanisms in the arsenic hyperaccumulation of Pteris vittata, and provide valuable insights into the plant stress resistance.
Institute:Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University
Last Name:Lin
First Name:Jiahui
Address:866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
Email:linjh.link@zju.edu.cn
Phone:18968220088

Subject:

Subject ID:SU003664
Subject Type:Plant
Subject Species:Pteris vittata
Taxonomy ID:13821

Factors:

Subject type: Plant; Subject species: Pteris vittata (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Soil condition
SA387460s36Bulk soil Severe arsenic
SA387461s50Bulk soil Severe arsenic
SA387462s49Bulk soil Severe arsenic
SA387463s48Bulk soil Severe arsenic
SA387464s47Bulk soil Severe arsenic
SA387465s46Bulk soil Severe arsenic
SA387466s45Bulk soil Severe arsenic
SA387467s44Bulk soil Severe arsenic
SA387468s43Bulk soil Severe arsenic
SA387469s42Bulk soil Severe arsenic
SA387470s41Bulk soil Severe arsenic
SA387471s40Bulk soil Severe arsenic
SA387472s38Bulk soil Severe arsenic
SA387473s37Bulk soil Severe arsenic
SA387474s39Bulk soil Severe arsenic
SA387475s17Bulk soil Slight arsenic
SA387476s18Bulk soil Slight arsenic
SA387477s19Bulk soil Slight arsenic
SA387478s20Bulk soil Slight arsenic
SA387479s11Bulk soil Slight arsenic
SA387480s12Bulk soil Slight arsenic
SA387481s13Bulk soil Slight arsenic
SA387482s14Bulk soil Slight arsenic
SA387483s15Bulk soil Slight arsenic
SA387484s16Bulk soil Slight arsenic
SA387485s35Rhizosphere Severe arsenic
SA387486s34Rhizosphere Severe arsenic
SA387487s33Rhizosphere Severe arsenic
SA387488s32Rhizosphere Severe arsenic
SA387489s31Rhizosphere Severe arsenic
SA387490s30Rhizosphere Severe arsenic
SA387491s29Rhizosphere Severe arsenic
SA387492s28Rhizosphere Severe arsenic
SA387493s27Rhizosphere Severe arsenic
SA387494s26Rhizosphere Severe arsenic
SA387495s25Rhizosphere Severe arsenic
SA387496s24Rhizosphere Severe arsenic
SA387497s23Rhizosphere Severe arsenic
SA387498s22Rhizosphere Severe arsenic
SA387499s21Rhizosphere Severe arsenic
SA387500s3Rhizosphere Slight arsenic
SA387501s4Rhizosphere Slight arsenic
SA387502s5Rhizosphere Slight arsenic
SA387503s6Rhizosphere Slight arsenic
SA387504s7Rhizosphere Slight arsenic
SA387505s2Rhizosphere Slight arsenic
SA387506s8Rhizosphere Slight arsenic
SA387507s1Rhizosphere Slight arsenic
SA387508s10Rhizosphere Slight arsenic
SA387509s9Rhizosphere Slight arsenic
SA387510rootG5Root Severe arsenic
SA387511rootG15Root Severe arsenic
SA387512rootG14Root Severe arsenic
SA387513rootG13Root Severe arsenic
SA387514rootG12Root Severe arsenic
SA387515rootG11Root Severe arsenic
SA387516rootG10Root Severe arsenic
SA387517rootG9Root Severe arsenic
SA387518rootG8Root Severe arsenic
SA387519rootG7Root Severe arsenic
SA387520rootG6Root Severe arsenic
SA387521rootG3Root Severe arsenic
SA387522rootG4Root Severe arsenic
SA387523rootG2Root Severe arsenic
SA387524rootG1Root Severe arsenic
SA387525root1Root Slight arsenic
SA387526root10Root Slight arsenic
SA387527root9Root Slight arsenic
SA387528root8Root Slight arsenic
SA387529root7Root Slight arsenic
SA387530root6Root Slight arsenic
SA387531root5Root Slight arsenic
SA387532root4Root Slight arsenic
SA387533root3Root Slight arsenic
SA387534root2Root Slight arsenic
Showing results 1 to 75 of 75

Collection:

Collection ID:CO003657
Collection Summary:Wild Pteris vittata plants with intact roots, rhizosphere soils, and adjacent bulk soils (0.3 meters from the root) were collected from low-As (<1000 ppm, n=10) and high-As (>1000 ppm, n=15) sites in Wenshan, Yunnan, China. In the lab, metabolites from the rhizospheric soils, roots, and bulk soils were extracted for metabolomic analyses following the protocol outlined below. To collect rhizosphere metabolites, roots were gently shaken to remove loosely adhering soil, followed by the careful collection of the closely adhering soil. The collected rhizosphere soil was then freeze-dried and pulverized in a grinder with glass beads (55 Hz, 2 min). Subsequently, 5 g of rhizospheric soil was transferred into a sterile centrifuge tube containing 25 mL of a pre-cooled (4 ℃) mixed solution of acetonitrile: methanol: H2O (2:2:1, v/v/v). The mixture underwent two rounds of vortexing for 30 s each on a BE-96 Vortex mixer, coupled with 30-min ultrasonication at 60 Hz on a KW-100TDV ultrasonic cleaner. Following centrifugation at 10,000 × g for 10 min at 4 ℃ using a H1850-R refrigerated centrifuge, the supernatant was filtered through a 0.2-μm sterile membrane filter (Millipore, Bedford, USA) to isolate the rhizosphere metabolites. The metabolites were then concentrated into a 2-mL centrifuge tube, dried into a powder, and stored at -80 ℃. This procedure was also applied for the collection of bulk soil metabolites.
Collection Protocol Filename:P_vittata_Methods.pdf
Sample Type:Root, Rhizosphere, Soil

Treatment:

Treatment ID:TR003673
Treatment Summary:No treatment. Wild Pteris vittata plants with intact roots, rhizosphere soils, and adjacent bulk soils (0.3 meters from the root) were collected from low-As (<1000 ppm, n=10) and high-As (>1000 ppm, n=15) sites in Wenshan, Yunnan, China. In the lab, metabolites from the rhizospheric soils, roots, and bulk soils were extracted for metabolomic analyses without any additional laboratory treatment.

Sample Preparation:

Sampleprep ID:SP003671
Sampleprep Summary:Equal amounts of preprocessed metabolome powder were re-dissolved by the precise addition of 300 μL of an acetonitrile solution containing 4 ppm 2-amino-3-(2-chlorophenyl)-propionic acid, prepared with 0.1% formic acid (1:9, v/v; stored at 4 ℃). The supernatant was then filtered through 0.2-μm membranes (Millipore, Bedford, USA) and transferred into vials for further detection.
Sampleprep Protocol Filename:P_vittata_Methods.pdf

Combined analysis:

Analysis ID AN005806 AN005807
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF-X Orbitrap Thermo Q Exactive HF-X Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH004409
Methods Filename:P_vittata_Methods.pdf
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:40
Flow Gradient:2:98 (A/B, v/v) at 0 min, 2:98 (A/B, v/v) at 1.0 min, 50:50 (A/B, v/v) at 9.0 min, 98:2 (A/B, v/v) at 12.0 min, 98:2 (A/B, v/v) at 13.5 min, 2:98 (A/B, v/v) at 14.0 min, 2:98 (A/B, v/v) at 17.0 min
Flow Rate:0.25 mL/min
Solvent A:100% acetonitrile
Solvent B:100% water; 5 mM ammonium formate
Chromatography Type:Reversed phase
  
Chromatography ID:CH004410
Methods Filename:P_vittata_Methods.pdf
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:40
Flow Gradient:2:98 (A/B, v/v) at 0 min, 2:98 (A/B, v/v) at 1.0 min, 50:50 (A/B, v/v) at 9.0 min, 98:2 (A/B, v/v) at 12.0 min, 98:2 (A/B, v/v) at 13.5 min, 2:98 (A/B, v/v) at 14.0 min, 2:98 (A/B, v/v) at 20.0 min
Flow Rate:0.25 mL/min
Solvent A:100% acetonitrile; 0.1% formic acid
Solvent B:100% water; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS005526
Analysis ID:AN005806
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:In untargeted metabolomics analysis, the raw MS data were converted to mzXML format by MSConvert in ProteoWizard software package (v3.0) and processed by XCMS70 (v3.2) for peak picking and alignment. The XCMS settings were as follows: method = “centWave”, ppm = 15, peakwidth = c(5,30), mzwid = 0.015, mzdiff = 0.01, and bw = 2.
Ion Mode:POSITIVE
Analysis Protocol File:P_vittata_Methods.pdf
  
MS ID:MS005527
Analysis ID:AN005807
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:In untargeted metabolomics analysis, the raw MS data were converted to mzXML format by MSConvert in ProteoWizard software package (v3.0) and processed by XCMS70 (v3.2) for peak picking and alignment. The XCMS settings were as follows: method = “centWave”, ppm = 15, peakwidth = c(5,30), mzwid = 0.015, mzdiff = 0.01, and bw = 2.
Ion Mode:NEGATIVE
Analysis Protocol File:P_vittata_Methods.pdf
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