Summary of Study ST002282
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 PR001462. The data can be accessed directly via it's Project DOI: 10.21228/M8R997 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 | ST002282 |
| Study Title | Detection of Methyl jasmonate (MeJA) in Plant root VOCs |
| Study Summary | Methyl jasmonate (MeJA) is a well-known plant hormone known for plant defense and plant-plant signaling. However, most of the studies are focussed on its aboveground presence and functions. Here we report that MeJA is also released by plant roots in a volatile form. More importantly, it is shown in Arabidopsis growing in natural conditions in soil. |
| Institute | National University of Singapore |
| Last Name | Kulkarni |
| First Name | Omkar |
| Address | Dept of Biological Sciences,Metabolites Biology Lab,, Science drive 4,Block S1A #06-03 |
| komkar21@gmail.com | |
| Phone | 98668733 |
| Submit Date | 2022-08-25 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-11-25 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001462 |
| Project DOI: | doi: 10.21228/M8R997 |
| Project Title: | Arabdiopsis Root VOCs |
| Project Summary: | The rhizosphere is a unique niche surrounding plant roots, where soluble and volatile molecules mediate signaling between plants and the associated microbiota. The preferred lifestyle of soil microbes is in the form of biofilms. However, little is known about whether root VOCs (rVOCs) can influence soil biofilms beyond the 2-10 mm rhizosphere zone influenced by soluble root exudates. Here, we report that rVOCs shift the microbiome composition and growth dynamics of complex soil biofilms. This signaling is evolutionarily conserved from ferns to higher plants, which suggests its coevolution. The defense phytohormone methyl jasmonate (MeJA) is present in rVOCs and drives this bioactivity at nanomolar levels within a few hours. |
| Institute: | National University of Singapore |
| Department: | Biological Sciences |
| Laboratory: | AESB Lab |
| Last Name: | Kulkarni |
| First Name: | Omkar |
| Address: | NA |
| Email: | komkar21@gmail.com |
| Phone: | 98668733 |
Subject:
| Subject ID: | SU002368 |
| Subject Type: | Plant |
| Subject Species: | Arabidopsis thaliana |
| Taxonomy ID: | 3702 |
| Age Or Age Range: | 2 weeks |
Factors:
Subject type: Plant; Subject species: Arabidopsis thaliana (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA218501 | tube11_jmt2A | jmt |
| SA218502 | tube9_jmt1A | jmt |
| SA218503 | tube10_jmt1B | jmt |
| SA218504 | tube12_jmt2B | jmt |
| SA218505 | tube13_jmt3A | jmt |
| SA218506 | tube14_jmt3B | jmt |
| SA218487 | tube7_soil3A | NA |
| SA218488 | tube1 | NA |
| SA218489 | tube6_soil2B | NA |
| SA218490 | tube8_soil3B | NA |
| SA218491 | tube2_emptypot | NA |
| SA218492 | tube5_soil2A | NA |
| SA218493 | tube3_soil1A | NA |
| SA218494 | tube4_soil1B | NA |
| SA218495 | tube17_WT2A | WT |
| SA218496 | tube15_WT1A | WT |
| SA218497 | tube18_WT2B | WT |
| SA218498 | tube20_WT3B | WT |
| SA218499 | tube16_WT1B | WT |
| SA218500 | tube19_WT3A | WT |
| Showing results 1 to 20 of 20 |
Collection:
| Collection ID: | CO002361 |
| Collection Summary: | Root VOCs and soil VOCs were trapped as described here (Schulz-Bohm et al., 2018). Briefly, 2 Tenax cartridges were fitted into the side arms of the glass pots in such a way that their opening was exposed toward the plant roots/soil. VOCs were sampled for 40 hours and immediately analyzed by thermal desorption-gas chromatography‒mass spectrometry. |
| Sample Type: | Plant |
Treatment:
| Treatment ID: | TR002380 |
| Treatment Summary: | No specific treatment. |
Sample Preparation:
| Sampleprep ID: | SP002374 |
| Sampleprep Summary: | After 40 hours of VOC trapping, Tenax cartridges were immediately subjected to thermal desorption. |
Combined analysis:
| Analysis ID | AN003727 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 7890B |
| Column | Agilent DB-FFAP |
| MS Type | EI |
| MS instrument type | Single quadrupole |
| MS instrument name | Agilent 5977B |
| Ion Mode | UNSPECIFIED |
| Units | ion intensity peak area |
Chromatography:
| Chromatography ID: | CH002760 |
| Chromatography Summary: | Sample preparation and injection were performed using the fully automated Gerstel MPS-2 autosampler and Gerstel MAESTRO software. Volatile compounds were adsorbed on a Tenax TA tube. A thermal desorption unit (TDU) was used to thermally desorb the volatiles in splitless mode at 230°C for 10 min. To ensure that the volatiles released from the TDU were quantitatively trapped, a cooled injection system-programmed temperature vaporizer (CIS-PTV) was used. The CIS was heated from 80°C to 230°C at a rate of 12°C/s with the split valve closed during sample injection into the GC inlet. Analyses of volatile compounds were performed on an Agilent 7890B GC coupled to a 5977B quadruple mass spectrometer. Separation of compounds was performed on a DB-FFAP column (60 m x 250 µm x 0.25 µm, Agilent Technologies, Middleburg, OI, USA). Helium was used as the carrier gas at a flow rate of 1.9 ml/min, and solvent vent mode was used. The inlet temperature was 250°C. The oven program was as follows: initial temperature of 50°C held for 1 min, increased to 230°C at the rate of 10°C/min and held for 20 min. The temperature of the ion source and transfer line was 250°C. |
| Instrument Name: | Agilent 7890B |
| Column Name: | Agilent DB-FFAP |
| Chromatography Type: | GC |
MS:
| MS ID: | MS003475 |
| Analysis ID: | AN003727 |
| Instrument Name: | Agilent 5977B |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| MS Comments: | The mass spectrometer was in electron ionization mode with an ionization energy of 70 eV, scan range of 40-300 m/z and solvent delay of 3.75 minutes. Analysis was performed in single ion monitoring (SIM) mode by monitoring the ions at 83, 151.1, and 224.1 with a dwell time of 150 ms. Mass Hunter Qualitative Analysis was used to extract and integrate peak spectra. The peak area of these ions was considered for the relative quantification of MeJA among different samples. |
| Ion Mode: | UNSPECIFIED |
