Summary of Study ST002867
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 | ST002867 |
| Study Title | Root VOCs of Arabidopsis thaliana and its mutants |
| Study Summary | This study provides a comprehensive list of root VOCs detected from the rhizosphere of Arabidopsis thaliana and the mutants belonging to their biosynthetic pathways. |
| 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 |
| omkar@u.nus.edu | |
| Phone | 98668733 |
| Submit Date | 2023-04-20 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | GC-MS |
| Release Date | 2023-09-21 |
| 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: | SU002979 |
| Subject Type: | Plant |
| Subject Species: | Arabidopsis thaliana |
| Taxonomy ID: | 3702 |
Factors:
Subject type: Plant; Subject species: Arabidopsis thaliana (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA313008 | cyp83b1_2 | cyp83b1 |
| SA313009 | cyp83b1_1 | cyp83b1 |
| SA313010 | cyp83b1_3 | cyp83b1 |
| SA313011 | fps1_2 | fps1 |
| SA313012 | fps1_1 | fps1 |
| SA313013 | fps1_3 | fps1 |
| SA313014 | fps2_1 | fps2 |
| SA313015 | fps2_2 | fps2 |
| SA313016 | fps2_3 | fps2 |
| SA313017 | ggpps_1 | ggpps |
| SA313018 | ggpps_2 | ggpps |
| SA313019 | ggpps_3 | ggpps |
| SA313020 | gpps_1 | gpps |
| SA313021 | gpps_2 | gpps |
| SA313022 | gpps_3 | gpps |
| SA313023 | hpl_3 | hpl |
| SA313024 | hpl_2 | hpl |
| SA313025 | hpl_1 | hpl |
| SA313026 | lox1_2 | lox1 |
| SA313027 | lox1_3 | lox1 |
| SA313028 | lox1_1 | lox1 |
| SA313029 | pal1_3 | pal1 |
| SA313030 | pal1_1 | pal1 |
| SA313031 | pal1_2 | pal1 |
| SA313032 | soil_1 | soil |
| SA313033 | soil_2 | soil |
| SA313034 | tgg1_2 | tgg1 |
| SA313035 | tgg1_1 | tgg1 |
| SA313036 | tgg1_3 | tgg1 |
| SA313037 | tgg2_1 | tgg2 |
| SA313038 | tgg2_2 | tgg2 |
| SA313039 | tgg2_3 | tgg2 |
| SA313005 | Wt_2 | Wt |
| SA313006 | Wt_3 | Wt |
| SA313007 | Wt_1 | Wt |
| Showing results 1 to 35 of 35 |
Collection:
| Collection ID: | CO002972 |
| Collection Summary: | Root VOCs and soil VOCs were trapped as described here (Schulz-Bohm, et al, 2018, "Calling from distance: attraction of soil bacteria by plant root volatiles", The ISME Journal, 12(5), pp.1252-1262.). Briefly, 1 Tenax cartridge was fitted into the side arms of the glass pots in such a way that their opening was exposed toward the plant roots/soil. The other arm received a constant airflow from an aerator. VOCs were sampled for 40 hours and immediately analyzed by thermal desorption-gas chromatography‒mass spectrometry. |
| Sample Type: | Plant |
Treatment:
| Treatment ID: | TR002988 |
| Treatment Summary: | No specific treatment. |
Sample Preparation:
| Sampleprep ID: | SP002985 |
| Sampleprep Summary: | After 40 hours of VOC trapping, Tenax cartridges were immediately subjected to thermal desorption. |
Combined analysis:
| Analysis ID | AN004700 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 7890B |
| Column | Agilent DB-FFAP (60m x 250um, 0.25um) |
| MS Type | EI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 5977B |
| Ion Mode | POSITIVE |
| Units | % relative peak abundance |
Chromatography:
| Chromatography ID: | CH003540 |
| Chromatography Summary: | Chromatography GC column used was DB-FFAP, 60m length, 250um inner diameter, 0.25um film thickness) |
| Instrument Name: | Agilent 7890B |
| Column Name: | Agilent DB-FFAP (60m x 250um, 0.25um) |
| Column Temperature: | NA |
| Flow Gradient: | NA |
| Flow Rate: | NA |
| Solvent A: | NA |
| Solvent B: | NA |
| Chromatography Type: | GC |
MS:
| MS ID: | MS004447 |
| Analysis ID: | AN004700 |
| Instrument Name: | Agilent 5977B |
| Instrument Type: | QTOF |
| MS Type: | EI |
| MS Comments: | Analysis was performed using MassHunter Qualified software to extract and integrate peat spectra to profile the root volatiles from WT and mutant lines. The data from only soil was considered as the blank and was subtracted from the rVOCs data. Compounds were identified by using the library NIST 2020 (Agilent Technologies, Palo Alto, CA, USA) with minimum hit count of 65. The compounds that were found to be present in at least two biological replicates out of three were taken into consideration for further analysis. |
| Ion Mode: | POSITIVE |
