Summary of Study ST002779

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 PR001734. The data can be accessed directly via it's Project DOI: 10.21228/M8K72B 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.

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Study IDST002779
Study TitleContribution of sugar transporters to spatial microbiota colonization along the longitudinal root axis of Arabidopsis
Study SummaryLongitudinal gut-axes of animals show spatial heterogeneity of microbiota related to physiological differentiation. Plant roots show functional heterogeneity in cellular architecture, transcriptome, metabolic states, and immunity. We hypothesized that axial differentiation impacts spatial colonization by rhizobiota along the root axis. We developed two growth systems, ArtSoil and CD-Rhizotrons, to dissect Arabidopsis thaliana roots into three segments. We identified distinct rhizobiota communities in the segments, supporting spatial microbiota differentiation along the axis. Root metabolite profiling revealed differential enrichment and specificity. Correlation analyses point to strong reliance of rhizobiota on carbohydrate supply from the host. Bioinformatic analyses and GUS histochemistry indicate sugar and/or microbe-induced accumulation of SWEET2, 4, and 12 sugar uniporters. Profiling of root-segments in sweet mutants showed impaired spatial rhizobiota arrangement. Correlation analysis revealed complex interconnected metabolite-rhizobiota networks. This work uncovers interdependency between root physiology and microbiota colonization and a contribution of SWEETs to shaping local adaptation of root microbiota.
Institute
Heinrich Heine University Düsseldorf
Last NameWesthoff
First NamePhilipp
AddressUniversitätsstr. 1 40225 Düsseldorf
Emailphilipp.westhoff@hhu.de
Phone+49 211-8110926
Submit Date2023-06-26
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2024-02-08
Release Version1
Philipp Westhoff Philipp Westhoff
https://dx.doi.org/10.21228/M8K72B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001734
Project DOI:doi: 10.21228/M8K72B
Project Title:20-0029 - Role of spatial differentiation of metabolism in local colonization of microbiota along the root axis
Project Summary:Longitudinal gut-axes of animals show spatial heterogeneity of microbiota related to physiological differentiation. Plant roots show functional heterogeneity in cellular architecture, transcriptome, metabolic states, and immunity. We hypothesized that axial differentiation impacts spatial colonization by rhizobiota along the root axis. We developed two growth systems, ArtSoil and CD-Rhizotrons, to dissect Arabidopsis thaliana roots into three segments. We identified distinct rhizobiota communities in the segments, supporting spatial microbiota differentiation along the axis. Root metabolite profiling revealed differential enrichment and specificity. Correlation analyses point to strong reliance of rhizobiota on carbohydrate supply from the host. Bioinformatic analyses and GUS histochemistry indicate sugar and/or microbe-induced accumulation of SWEET2, 4, and 12 sugar uniporters. Profiling of root-segments in sweet mutants showed impaired spatial rhizobiota arrangement. Correlation analysis revealed complex interconnected metabolite-rhizobiota networks. This work uncovers interdependency between root physiology and microbiota colonization and a contribution of SWEETs to shaping local adaptation of root microbiota.
Institute:Heinrich Heine University Düsseldorf
Laboratory:Plant Metabolism and Metabolomics Laboratory
Last Name:Westhoff
First Name:Philipp
Address:Universitätsstr. 1 40225 Düsseldorf
Email:philipp.westhoff@hhu.de
Phone:+49 211-8110926

Subject:

Subject ID:SU002886
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 region genotype
SA29746920-0029_1772cm sweet11;12
SA29747020-0029_1902cm sweet11;12
SA29747120-0029_2062cm sweet11;12
SA29747220-0029_1702cm sweet11;12
SA29747320-0029_1942cm sweet2
SA29747420-0029_1582cm sweet2
SA29747520-0029_1802cm sweet2
SA29747620-0029_1502cm sweet2
SA29747720-0029_1672cm sweet4
SA29747820-0029_1612cm sweet4
SA29747920-0029_1992cm sweet4
SA29748020-0029_1852cm sweet4
SA29746620-0029_1302cm WT
SA29746720-0029_1232cm WT
SA29746820-0029_1202cm WT
SA29748520-0029_2074cm sweet11;12
SA29748620-0029_1784cm sweet11;12
SA29748720-0029_1914cm sweet11;12
SA29748820-0029_1734cm sweet11;12
SA29748920-0029_1714cm sweet11;12
SA29749020-0029_1554cm sweet2
SA29749120-0029_1814cm sweet2
SA29749220-0029_1954cm sweet2
SA29749320-0029_1514cm sweet2
SA29749420-0029_1594cm sweet2
SA29749520-0029_2014cm sweet4
SA29749620-0029_2004cm sweet4
SA29749720-0029_1864cm sweet4
SA29749820-0029_1624cm sweet4
SA29749920-0029_1684cm sweet4
SA29748120-0029_1214cm WT
SA29748220-0029_1314cm WT
SA29748320-0029_1254cm WT
SA29748420-0029_1244cm WT
SA29750420-0029_1746cm sweet11;12
SA29750520-0029_1726cm sweet11;12
SA29750620-0029_2086cm sweet11;12
SA29750720-0029_1926cm sweet11;12
SA29750820-0029_1796cm sweet11;12
SA29750920-0029_1546cm sweet2
SA29751020-0029_1826cm sweet2
SA29751120-0029_1526cm sweet2
SA29751220-0029_1606cm sweet2
SA29751320-0029_1966cm sweet2
SA29751420-0029_1696cm sweet4
SA29751520-0029_2026cm sweet4
SA29751620-0029_2036cm sweet4
SA29751720-0029_1636cm sweet4
SA29751820-0029_1876cm sweet4
SA29750020-0029_1326cm WT
SA29750120-0029_1276cm WT
SA29750220-0029_1266cm WT
SA29750320-0029_1226cm WT
SA29752420-0029_175whole sweet11;12
SA29752520-0029_176whole sweet11;12
SA29752620-0029_210whole sweet11;12
SA29752720-0029_193whole sweet11;12
SA29752820-0029_209whole sweet11;12
SA29752920-0029_153whole sweet2
SA29753020-0029_198whole sweet2
SA29753120-0029_157whole sweet2
SA29753220-0029_197whole sweet2
SA29753320-0029_184whole sweet2
SA29753420-0029_156whole sweet2
SA29753520-0029_183whole sweet2
SA29753620-0029_188whole sweet4
SA29753720-0029_189whole sweet4
SA29753820-0029_164whole sweet4
SA29753920-0029_205whole sweet4
SA29754020-0029_204whole sweet4
SA29754120-0029_165whole sweet4
SA29754220-0029_166whole sweet4
SA29751920-0029_133whole WT
SA29752020-0029_145whole WT
SA29752120-0029_129whole WT
SA29752220-0029_128whole WT
SA29752320-0029_146whole WT
Showing results 1 to 77 of 77

Collection:

Collection ID:CO002879
Collection Summary:Approximately 25-35 sterilized A. thaliana seeds were sown in a row on ArtSoil and grown for 3 weeks. After 3 weeks, the roots were measured (2, 4, and 6 cm from the root tip) and harvested by slicing with a scalpel. The roots were rinsed in distilled water, and blotted dry on Whatman filter papers before they were weighed and kept in 1.5 ml microcentrifuge tubes containing 2 metal beads each. The samples were flash frozen in liquid nitrogen and stored in -80°C until the extraction process.
Sample Type:Arabidopsis thaliana

Treatment:

Treatment ID:TR002895
Treatment Summary:no treatment

Sample Preparation:

Sampleprep ID:SP002892
Sampleprep Summary:For metabolite extraction, 0.5 mL of chilled extraction buffer (2:5:2 ratio of ddH2O: methanol: chloroform containing 5µM ribitol as internal standard) was added into each root sample and vortex for 20 secs. Metal beads in the tubes were removed. Sample tubes were shaken on a rotary shaker for 30 mins at 4°C. The samples were then centrifuged at 20, 000g for 5 mins at 4°C. After centrifugation, 0.5 ml of supernatant was carefully aspirated and transferred to a clean 1.5 ml microcentrifuge tube. Samples were stored at-80°C. For GC-MS analysis 30µl of sample were dried by vacuum centrifugation in glass inlet tubes. Dried samples were derivatized according to (Gu et al. 2012 DOI:10.1039/c2ib00109h) and measured as described (Shim et al. 2019 DOI:10.3389/fpls.2019.01726)

Combined analysis:

Analysis ID AN004525 AN004526
Analysis type MS MS
Chromatography type GC GC
Chromatography system Agilent 7890B Agilent 7890B
Column Agilent HP5-MS (30m x 0.25mm, 0.25um) Agilent HP5-MS (30m x 0.25mm, 0.25um)
MS Type EI EI
MS instrument type QTOF Single quadrupole
MS instrument name Agilent 7200 QTOF Agilent 5977B
Ion Mode POSITIVE POSITIVE
Units Relative intensity Relative intensity

Chromatography:

Chromatography ID:CH003399
Chromatography Summary:Dried samples were derivatized according to (Gu et al. 2012 DOI:10.1039/c2ib00109h) and measured as described (Shim et al. 2019 DOI:10.3389/fpls.2019.01726)
Instrument Name:Agilent 7890B
Column Name:Agilent HP5-MS (30m x 0.25mm, 0.25um)
Column Temperature:350
Flow Gradient:N/A for GC
Flow Rate:N/A for GC
Solvent A:N/A for GC
Solvent B:N/A for GC
Chromatography Type:GC
Solvent C:N/A for GC

MS:

MS ID:MS004272
Analysis ID:AN004525
Instrument Name:Agilent 7200 QTOF
Instrument Type:QTOF
MS Type:EI
MS Comments:Metabolites were ionized with an electron impact source at 70V and 200 °C source temperature and recorded in a mass range of m/z 60 to m/z 800 at 20 scans per second
Ion Mode:POSITIVE
  
MS ID:MS004273
Analysis ID:AN004526
Instrument Name:Agilent 5977B
Instrument Type:Single quadrupole
MS Type:EI
MS Comments:Metabolites were ionized with an electron impact source at 70V and 200 °C source temperature and recorded in a mass range of m/z 60 to m/z 800 at 20 scans per second
Ion Mode:POSITIVE
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