Summary of Study ST003943
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 PR002471. The data can be accessed directly via it's Project DOI: 10.21228/M87K19 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST003943 |
| Study Title | Fluctuations in the metabolome of Haloxylon salicornicum under environmental, seasonal, and diurnal variations in a desert environment |
| Study Summary | Haloxylon salicornicum is a xero-halophyte desert species that is a benchmark species for investigating the mechanisms of drought tolerance. Herein, we aimed to unravel the metabolic mechanisms involved in Haloxylon salicornicum's natural adaptations to drought and soil chemical properties, as well as to identify key metabolites that are regulated in a rhythmic and seasonal manner in response to these conditions. To that end, two soil types (clay and sandy), two seasons (winter and summer), and two two-time points (dawn and midday) were selected. The plant’s hydric status was evaluated, along with primary metabolites, using untargeted metabolomic analysis. The soil variations had no significant effect on the plants’ physiological and metabolic behavior. However, across seasons, H. salicornicum showed high metabolic activities during dawn compared to midday, underscoring its metabolic plasticity to mitigate the effects of high temperatures and sunlight. During winter, the plant’s hydraulic status was relatively high (-1 MPa), facilitating the activation of anabolic pathways, such as carbon fixation and assimilation, as well as the biosynthesis of amino acids and carbohydrates to support growth and prepare carbon reserves. However, in response to the combined drought and heat stresses of summer, the plants exhibited low water potential values, reaching -5 MPa. This resulted in an arrest of anabolic processes and stimulation of catabolic pathways, particularly starch breakdown, to sustain carbon metabolism and maintain energy production. Additionally, efficient antioxidant molecules (e.g., ascorbic acid and caffeic acid) were synthesized to detoxify harmful radicals and protect cellular structures. These results provide valuable insights into the metabolic adaptations of H. salicornicum to its natural environment, offering a foundation for further studies of its genetic regulatory mechanisms. |
| Institute | King Abdullah University of Science and Technology |
| Department | Biological and Environmental Science and Engineering Division |
| Laboratory | Biological and Environmental Science and Engineering Division |
| Last Name | Sioud |
| First Name | Salim |
| Address | 4700 KAUST |
| salim.sioud@kaust.edu.sa | |
| Phone | 0544700623 |
| Submit Date | 2025-06-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | GC-MS |
| Release Date | 2025-06-24 |
| Release Version | 1 |
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Project:
| Project ID: | PR002471 |
| Project DOI: | doi: 10.21228/M87K19 |
| Project Title: | Project Al-Ula Saudi Arabia: Enabling Ecophysiological Research on Haloxylon salicornicum in the Sharaan Nature Reserve |
| Project Summary: | We attempted to elucidate the metabolic mechanisms involved in Haloxylon salicornicum's natural adaptations to drought and soil properties, as well as to identify key metabolites that are regulated in a rhythmic and seasonal manner in response to these environmental conditions. To this end, plants were studied across two soil types (clay and sandy), two seasons (winter and summer), and two time points (dawn and midday). Hydric status and primary metabolites were evaluated using untargeted metabolomics. Soil type had minimal impact on physiological and metabolic responses. However, H. salicornicum exhibited marked diel and seasonal variations in metabolism. During winter, higher water potential (–1 MPa) supported anabolic pathways such as carbon assimilation and the biosynthesis of amino acids and carbohydrates. In contrast, summer drought conditions (–5 MPa) led to the suppression of anabolic activities and the activation of catabolic pathways, including starch degradation, to sustain energy metabolism. The synthesis of antioxidants such as ascorbic and caffeic acids further contributed to cellular protection under stress. These results highlight the metabolic plasticity of H. salicornicum and offer valuable insights into its adaptive strategies, laying the groundwork for future studies on the genetic regulation of drought tolerance in desert ecosystems. |
| Institute: | KAUST |
| Department: | Biological and Environmental Science and Engineering Division |
| Laboratory: | Biological and Environmental Science and Engineering Division |
| Last Name: | Sioud |
| First Name: | Salim |
| Address: | 4700 KAUST, Thuwal, Mecca, 23955-6900, Saudi Arabia |
| Email: | salim.sioud@kaust.edu.sa |
| Phone: | +966128082959 |
Subject:
| Subject ID: | SU004080 |
| Subject Type: | Plant |
| Subject Species: | Haloxylon salicornicum |
| Taxonomy ID: | 454511 |
| Gender: | Not applicable |
Factors:
Subject type: Plant; Subject species: Haloxylon salicornicum (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Location | Season | Time of Day |
|---|---|---|---|---|---|
| SA450624 | EBAD_06 | green shoot samples | Evaporation Basin | August | Dawn |
| SA450625 | EBAD_02 | green shoot samples | Evaporation Basin | August | Dawn |
| SA450626 | EBAD_01 | green shoot samples | Evaporation Basin | August | Dawn |
| SA450627 | EBAD_05 | green shoot samples | Evaporation Basin | August | Dawn |
| SA450628 | EBAD_03 | green shoot samples | Evaporation Basin | August | Dawn |
| SA450629 | EBAD_04 | green shoot samples | Evaporation Basin | August | Dawn |
| SA450630 | EBAM_02 | green shoot samples | Evaporation Basin | August | Midday |
| SA450631 | EBAM_04 | green shoot samples | Evaporation Basin | August | Midday |
| SA450632 | EBAM_05 | green shoot samples | Evaporation Basin | August | Midday |
| SA450633 | EBAM_06 | green shoot samples | Evaporation Basin | August | Midday |
| SA450634 | EBAM_01 | green shoot samples | Evaporation Basin | August | Midday |
| SA450635 | EBAM_03 | green shoot samples | Evaporation Basin | August | Midday |
| SA450636 | EBFD_05 | green shoot samples | Evaporation Basin | February | Dawn |
| SA450637 | EBFD_06 | green shoot samples | Evaporation Basin | February | Dawn |
| SA450638 | EBFD_03 | green shoot samples | Evaporation Basin | February | Dawn |
| SA450639 | EBFD_02 | green shoot samples | Evaporation Basin | February | Dawn |
| SA450640 | EBFD_01 | green shoot samples | Evaporation Basin | February | Dawn |
| SA450641 | EBFD_04 | green shoot samples | Evaporation Basin | February | Dawn |
| SA450642 | EBFM_01 | green shoot samples | Evaporation Basin | February | Midday |
| SA450643 | EBFM_02 | green shoot samples | Evaporation Basin | February | Midday |
| SA450644 | EBFM_03 | green shoot samples | Evaporation Basin | February | Midday |
| SA450645 | EBFM_04 | green shoot samples | Evaporation Basin | February | Midday |
| SA450646 | EBFM_05 | green shoot samples | Evaporation Basin | February | Midday |
| SA450647 | EBFM_06 | green shoot samples | Evaporation Basin | February | Midday |
| SA450648 | SSAD_05 | green shoot samples | Sandy Dune | August | Dawn |
| SA450649 | SSAD_06 | green shoot samples | Sandy Dune | August | Dawn |
| SA450650 | SSAD_03 | green shoot samples | Sandy Dune | August | Dawn |
| SA450651 | SSAD_04 | green shoot samples | Sandy Dune | August | Dawn |
| SA450652 | SSAD_02 | green shoot samples | Sandy Dune | August | Dawn |
| SA450653 | SSAD_01 | green shoot samples | Sandy Dune | August | Dawn |
| SA450654 | SSAM_02 | green shoot samples | Sandy Dune | August | Midday |
| SA450655 | SSAM_01 | green shoot samples | Sandy Dune | August | Midday |
| SA450656 | SSAM_04 | green shoot samples | Sandy Dune | August | Midday |
| SA450657 | SSAM_05 | green shoot samples | Sandy Dune | August | Midday |
| SA450658 | SSAM_06 | green shoot samples | Sandy Dune | August | Midday |
| SA450659 | SSAM_03 | green shoot samples | Sandy Dune | August | Midday |
| SA450660 | SSFD_06 | green shoot samples | Sandy Dune | February | Dawn |
| SA450661 | SSFD_05 | green shoot samples | Sandy Dune | February | Dawn |
| SA450662 | SSFD_04 | green shoot samples | Sandy Dune | February | Dawn |
| SA450663 | SSFD_02 | green shoot samples | Sandy Dune | February | Dawn |
| SA450664 | SSFD_01 | green shoot samples | Sandy Dune | February | Dawn |
| SA450665 | SSFD_03 | green shoot samples | Sandy Dune | February | Dawn |
| SA450666 | SSFM_01 | green shoot samples | Sandy Dune | February | Midday |
| SA450667 | SSFM_02 | green shoot samples | Sandy Dune | February | Midday |
| SA450668 | SSFM_03 | green shoot samples | Sandy Dune | February | Midday |
| SA450669 | SSFM_04 | green shoot samples | Sandy Dune | February | Midday |
| SA450670 | SSFM_05 | green shoot samples | Sandy Dune | February | Midday |
| SA450671 | SSFM_06 | green shoot samples | Sandy Dune | February | Midday |
| Showing results 1 to 48 of 48 |
Collection:
| Collection ID: | CO004073 |
| Collection Summary: | Six uniform, exposed, green shoot samples were collected, corresponding to both DWP and MWP measurements. The samples were placed on dry ice during sampling and subsequently stored at -80 °C until analysis |
| Sample Type: | Plant |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR004089 |
| Treatment Summary: | No treatment, this is an observational study. Before extraction, the samples were lyophilized in the VirTis Freezemobile 25XL Lyophilizer (SP Scientific Inc, USA) to remove water and preserve plant extract quality. The lyophilizates were then finely ground in a SPEX Geno Grinder 2010 (SPEX SamplePre, USA) using Geno grinder Grinder 2251PC polycarbonate vials with 11 mm grinding balls. The grinding was performed at 1000 rpm for 4 min. |
Sample Preparation:
| Sampleprep ID: | SP004086 |
| Sampleprep Summary: | Primary metabolite extraction was performed according to Salem et al. (2016). Thirty 30 mg of the powder was homogenized with 1 mL of methyl-tert-butyl ether/methanol (HPLC grade; 3:1, v/v) in 2 mL Eppendorf tubes. A few 0.5 mm glass beads were added to the mixture, The samples were then placed in the Bead Blaster 24R (Benchmark Scientific) and subjected to 3 cycles of shaking at 4 °C, for 1.5 minutes. and shaken seven times at 426 rpm for 1.30 min at 4 °C, followed by immediate sonication at 0 °C for 20 min. The homogenate was mixed with 650 µL of a phase separation solution comprising methanol and miliQ water (1:3, v/v), vortexed for 1 min, and then centrifuged at 20,000 rpm for 2 min. Meanwhile, a method blank (0 mg of plant tissue) was prepared as a control for monitoring background effect, as well as a mixture of amino acids, organic acids, and sugars was used as a standard. Simultaneously, a quality control (QC), consisting of an addition of small aliquots from all the studied samples, was prepared and used for further data processing. A 200 µL aliquot of the middle phase (polar phase) of all samples including the blank, standard, and QC were transferred into glass vials and evaporated using the Acid-Resistant CentriVap Vacuum Concentrator (Labconco, USA). Derivatization The dried extract was re-suspended in 30 µL of methoxyamine hydrochloride prepared in pyridine, and the mixture was incubated for 90 min. at 36 °C with an agitation at 600 rpm. The derivatization process was finalized by adding 50 µL of N,O-Bis(trimethylsilyl)trifluoroacetamide) containing 1% trimethylchlorosilane (BSTFA), and spiked with C7-C40 saturated alkanes standard 1000 µg/mL. The homogenate was incubated at 36 °C for 30 min with a shaking at 600 rpm. |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | 4℃ |
| Sample Derivatization: | MSTFA/BSTFA |
Combined analysis:
| Analysis ID | AN006482 |
|---|---|
| Chromatography ID | CH004924 |
| MS ID | MS006181 |
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Thermo Scientific TRACE 1310 GC |
| Column | Thermo Scientific Trace GOLD TG-5SilMS (30m × 0.25mm, 0.25um) |
| MS Type | EI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Scientific Orbitrap Exploris GC 240 |
| Ion Mode | POSITIVE |
| Units | intensity |
Chromatography:
| Chromatography ID: | CH004924 |
| Chromatography Summary: | splitless_Full scan OT 36 min metabolomics |
| Instrument Name: | Thermo Scientific TRACE 1310 GC |
| Column Name: | Thermo Scientific Trace GOLD TG-5SilMS (30m × 0.25mm, 0.25um) |
| Column Temperature: | 280 |
| Flow Gradient: | - |
| Flow Rate: | 1ml/min Helium gas |
| Solvent A: | - |
| Solvent B: | - |
| Chromatography Type: | GC |
MS:
| MS ID: | MS006181 |
| Analysis ID: | AN006482 |
| Instrument Name: | Thermo Scientific Orbitrap Exploris GC 240 |
| Instrument Type: | Orbitrap |
| MS Type: | EI |
| MS Comments: | A Thermo Scientific Orbitrap Exploris GC 240, which has a maximum resolving power of 240,000 (at m/z 200 FWHM), was used for the analysis of the primary metabolites. Sample introduction was performed using a Thermo Scientific™ TriPlus™ RSH auto-sampler, and chromatographic separation of the gas-phase chemical components was achieved using a Thermo Scientific™ TRACE™ 1310 Gas Chromatograph equipped with Thermo Scientific™ Trace GOLD™ TG-5SilMS 30 m × 0.25 mm i.d. × 0.25 μm column. The Orbitrap Exploris GC was tuned and calibrated using PFTBA to achieve mass accuracy of <1.0 ppm. The Orbitrap Exploris 240 mass spectrometer operated in electron ionization (EI) which was set at 300 ˚C, and the electron energy was set to 70eV with an emission current of 50µA. The acquisition mode was set to full scan with a scan range of 35-700 Da and an orbitrap resolution of 60000 (FWHM, measured at m/z 200). The AGC target was set to standard and the maximum injection time was set to auto mode. The data acquisition was lock-mass corrected using GC column bleed siloxane masse of m/z 207. The Trace 1310 GC operated with an injection volume of 1 µl of sample that was injected using a 10 µL syringe into a single gooseneck with glass wool Thermo Scientific™ Liner GOLD. The inlet mode was set to Split mode with a split flow of 40ml/min and a purge flow of 5 ml/min. The helium carrier rate was set to 1.2 ml/min. The oven temperature was maintained initially at 70°C for 2 min and increased to 220 °C at a rate of 8°C/min, then increased to 325 °C at a rate of 16°C/min and was held for 10 min. |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 300 |
