Summary of Study ST002537

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 PR001633. The data can be accessed directly via it's Project DOI: 10.21228/M8MM8Q 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 ID	ST002537
Study Title	Osmoprotectants play a major role in the Portulaca oleracea resistance to high levels of salinity stress - Insights from a metabolomics and proteomics integrated approach
Study Summary	Purslane is an invasive plant and is considered the eighth most common weed in the world. Because of that, its outdoor production in extensive areas faces several concerns. Kong & Zheng (2014) evaluated the potential of producing purslane in a hydroponic system, generating approximately 5.75 kg of fresh matter per m2 per month, which might yield 57.5 tons/hectare/year if cultivated in a bimestrial regime. The high productivity of purslane, when grown in controlled-environment agriculture, can open many opportunities for the purslane industry, even in the context of biosaline agriculture. Building up a robust multi-omics database on the response of purslane to salt stress and the subsequent study of it via an MOI analysis can create the basis for a future system biology approach to decode the genetics behind its resistance to salinity stress. The present study is a second step in building a robust database on the morpho-physiological and molecular responses of Portulaca oleracea L. to salinity stress and its subsequent use in attempting to decode the genetics behind its resistance to this abiotic stress. After reporting on the characterization of the morpho-physiological responses of young purslane plants to such stress using a robust salinization protocol, here we report a study on adult purslane plants through the characterization of the untargeted metabolome and proteome profiles on the leaves and roots of this halophyte species submitted to very high salinity stress, and the consequent use of single- and multi-omics analysis strategies to study it.
Institute	Embrapa Agroenergy
Last Name	Souza Júnior
First Name	Manoel Teixeira
Address	Parque Estacao Biologica final Asa Norte Brasília DF 70770-901 BR, PQEB, sn - Asa Norte, DF
Email	manoel.souza@embrapa.br
Phone	+55 (61) 3448-4246
Submit Date	2023-04-03
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2023-06-06
Release Version	1

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Project:

Project ID:	PR001633
Project DOI:	doi: 10.21228/M8MM8Q
Project Title:	Osmoprotectants play a major role in the Portulaca oleracea resistance to high levels of salinity stress - Insights from a metabolomics and proteomics integrated approach
Project Summary:	Purslane is an invasive plant and is considered the eighth most common weed in the world. Because of that, its outdoor production in extensive areas faces several concerns. Kong & Zheng (2014) evaluated the potential of producing purslane in a hydroponic system, generating approximately 5.75 kg of fresh matter per m2 per month, which might yield 57.5 tons/hectare/year if cultivated in a bimestrial regime. The high productivity of purslane, when grown in controlled-environment agriculture, can open many opportunities for the purslane industry, even in the context of biosaline agriculture. Building up a robust multi-omics database on the response of purslane to salt stress and the subsequent study of it via an MOI analysis can create the basis for a future system biology approach to decode the genetics behind its resistance to salinity stress. The present study is a second step in building a robust database on the morpho-physiological and molecular responses of Portulaca oleracea L. to salinity stress and its subsequent use in attempting to decode the genetics behind its resistance to this abiotic stress. After reporting on the characterization of the morpho-physiological responses of young purslane plants to such stress using a robust salinization protocol, here we report a study on adult purslane plants through the characterization of the untargeted metabolome and proteome profiles on the leaves and roots of this halophyte species submitted to very high salinity stress, and the consequent use of single- and multi-omics analysis strategies to study it.
Institute:	Embrapa Agroenergy
Last Name:	Souza Júnior
First Name:	Manoel Teixeira
Address:	Parque Estacao Biologica final Asa Norte Brasília DF 70770-901 BR, PQEB, sn - Asa Norte, DF
Email:	manoel.souza@embrapa.br
Phone:	+55 (61) 3448-4246

Subject:

Subject ID:	SU002637
Subject Type:	Plant
Subject Species:	Portulaca oleracea
Taxonomy ID:	46147

Factors:

Subject type: Plant; Subject species: Portulaca oleracea (Factor headings shown in green)

mb_sample_id	local_sample_id	Group
SA255042	Purslane_CP1_Adult_Leaf_Lipidic_Negative	Leaf_Control
SA255043	Purslane_CP3_Adult_Leaf_Lipidic_Positive	Leaf_Control
SA255044	Purslane_CP2_Adult_Leaf_Lipidic_Negative	Leaf_Control
SA255045	Purslane_CP4_Adult_Leaf_Lipidic_Negative	Leaf_Control
SA255046	Purslane_CP1_Adult_Leaf_Polar_Positive	Leaf_Control
SA255047	Purslane_CP2_Adult_Leaf_Lipidic_Positive	Leaf_Control
SA255048	Purslane_CP3_Adult_Leaf_Lipidic_Negative	Leaf_Control
SA255049	Purslane_CP4_Adult_Leaf_Lipidic_Positive	Leaf_Control
SA255050	Purslane_CP4_Adult_Leaf_Polar_Positive	Leaf_Control
SA255051	Purslane_CP1_Adult_Leaf_Lipidic_Positive	Leaf_Control
SA255052	Purslane_CP2_Adult_Leaf_Polar_Positive	Leaf_Control
SA255053	Purslane_CP1_Adult_Leaf_Polar_Negative	Leaf_Control
SA255054	Purslane_CP3_Adult_Leaf_Polar_Positive	Leaf_Control
SA255055	Purslane_CP4_Adult_Leaf_Polar_Negative	Leaf_Control
SA255056	Purslane_CP3_Adult_Leaf_Polar_Negative	Leaf_Control
SA255057	Purslane_CP2_Adult_Leaf_Polar_Negative	Leaf_Control
SA255058	Purslane_SP4_Adult_Leaf_Lipidic_Positive	Leaf_Stressed
SA255059	Purslane_SP3_Adult_Leaf_Lipidic_Positive	Leaf_Stressed
SA255060	Purslane_SP1_Adult_Leaf_Lipidic_Negative	Leaf_Stressed
SA255061	Purslane_SP4_Adult_Leaf_Lipidic_Negative	Leaf_Stressed
SA255062	Purslane_SP2_Adult_Leaf_Lipidic_Positive	Leaf_Stressed
SA255063	Purslane_SP3_Adult_Leaf_Lipidic_Negative	Leaf_Stressed
SA255064	Purslane_SP2_Adult_Leaf_Lipidic_Negative	Leaf_Stressed
SA255065	Purslane_SP4_Adult_Leaf_Polar_Positive	Leaf_Stressed
SA255066	Purslane_SP3_Adult_Leaf_Polar_Positive	Leaf_Stressed
SA255067	Purslane_SP1_Adult_Leaf_Lipidic_Positive	Leaf_Stressed
SA255068	Purslane_SP1_Adult_Leaf_Polar_Positive	Leaf_Stressed
SA255069	Purslane_SP1_Adult_Leaf_Polar_Negative	Leaf_Stressed
SA255070	Purslane_SP2_Adult_Leaf_Polar_Positive	Leaf_Stressed
SA255071	Purslane_SP4_Adult_Leaf_Polar_Negative	Leaf_Stressed
SA255072	Purslane_SP3_Adult_Leaf_Polar_Negative	Leaf_Stressed
SA255073	Purslane_SP2_Adult_Leaf_Polar_Negative	Leaf_Stressed
SA255074	Purslane_CP4_Adult_Root_Polar_Negative	Root_Control
SA255075	Purslane_CP3_Adult_Root_Polar_Negative	Root_Control
SA255076	Purslane_CP1_Adult_Root_Polar_Positive	Root_Control
SA255077	Purslane_CP4_Adult_Root_Polar_Positive	Root_Control
SA255078	Purslane_CP2_Adult_Root_Polar_Negative	Root_Control
SA255079	Purslane_CP3_Adult_Root_Polar_Positive	Root_Control
SA255080	Purslane_CP2_Adult_Root_Polar_Positive	Root_Control
SA255081	Purslane_CP1_Adult_Root_Lipidic_Negative	Root_Control
SA255082	Purslane_CP4_Adult_Root_Lipidic_Negative	Root_Control
SA255083	Purslane_CP3_Adult_Root_Lipidic_Negative	Root_Control
SA255084	Purslane_CP1_Adult_Root_Polar_Negative	Root_Control
SA255085	Purslane_CP1_Adult_Root_Lipidic_Positive	Root_Control
SA255086	Purslane_CP2_Adult_Root_Lipidic_Negative	Root_Control
SA255087	Purslane_CP4_Adult_Root_Lipidic_Positive	Root_Control
SA255088	Purslane_CP3_Adult_Root_Lipidic_Positive	Root_Control
SA255089	Purslane_CP2_Adult_Root_Lipidic_Positive	Root_Control
SA255090	Purslane_SP1_Adult_Root_Polar_Positive	Root_Stressed
SA255091	Purslane_SP3_Adult_Root_Polar_Negative	Root_Stressed
SA255092	Purslane_SP4_Adult_Root_Polar_Negative	Root_Stressed
SA255093	Purslane_SP3_Adult_Root_Polar_Positive	Root_Stressed
SA255094	Purslane_SP2_Adult_Root_Polar_Negative	Root_Stressed
SA255095	Purslane_SP4_Adult_Root_Polar_Positive	Root_Stressed
SA255096	Purslane_SP2_Adult_Root_Polar_Positive	Root_Stressed
SA255097	Purslane_SP1_Adult_Root_Lipidic_Positive	Root_Stressed
SA255098	Purslane_SP3_Adult_Root_Lipidic_Negative	Root_Stressed
SA255099	Purslane_SP2_Adult_Root_Lipidic_Negative	Root_Stressed
SA255100	Purslane_SP1_Adult_Root_Lipidic_Negative	Root_Stressed
SA255101	Purslane_SP4_Adult_Root_Lipidic_Negative	Root_Stressed
SA255102	Purslane_SP2_Adult_Root_Lipidic_Positive	Root_Stressed
SA255103	Purslane_SP4_Adult_Root_Lipidic_Positive	Root_Stressed
SA255104	Purslane_SP3_Adult_Root_Lipidic_Positive	Root_Stressed
SA255105	Purslane_SP1_Adult_Root_Polar_Negative	Root_Stressed

Showing results 1 to 64 of 64

Showing results 1 to 64 of 64

Collection:

Collection ID:	CO002630
Collection Summary:	Leaves and roots from both treatments - five replicates per treatment - were collected for biomass and mineral analysis. Fifteen samples of substrate were collected for mineral analysis, five before salinization, and ten at the end of the experiment - five from control and five from stressed plants. Leaves and roots from both treatments - five replicates per treatment - were collected and immediately immersed in liquid nitrogen and then stored at -80 °C until extraction of metabolites or proteins.
Sample Type:	Plant

Treatment:

Treatment ID:	TR002649
Treatment Summary:	The B1 accession of purslane (Portulaca oleracea L.) used in this study belongs to the Purslane Collection at Embrapa Agroenergia. Seeds underwent disinfection following the same procedure described in Belo Silva et al. (2022), which consisted of soaking in 2% sodium hypochlorite and Tween® 20 for five minutes, under slow agitation, and then washing with sterile water and drying on sterilized filter paper. After being seeded on a culture medium (MS 1/2 strength, Phytagel 0.2%, and pH 5.8) (Murashige and Skoog, 1962), it was kept for germination in a Growth chamber Conviron mod. Adaptis 1000TC (Controlled Environments Ltd, Winnipeg, Canada) at 150 μmol/m2/s of light and 30°C. After 13 days, seedlings were individually transferred to 200 ml plastic cups containing 100 g of sterilized substrate - clay soil, vermiculite, and a commercial substrate (Bioplant®), 2:1:1 (v:v:v) ratio – and transferred to another Conviron® growth chamber mod. PGW40 at 25±2°C, 500±20 μmol/m2/s of light, 65±5% air relative humidity, and photoperiod of 16/8 h (light/dark), and kept there until the end of the experiments. The plants were allowed to acclimatize for three days, and the salinity stress started three weeks after the end of the acclimatization period. The salinization experiment consisted of two salinity levels (0.0 and 2.0 g of NaCl / 100 g of the substrate), with 16 replicates (plants) in a completely randomized design, and the stress lasted 12 days. During the entire experiment, plants were at field capacity. To avoid the loss of Na+ or Cl-, no leakage of the saline solution was allowed to get out of the plastic cup, as described previously in Belo Silva et al. (2022). The water lost due to evapotranspiration was replaced with deionized water daily, and the electric conductivity at field capacity (ECfc) and water potential in the substrate solution was measured once - on the 8th day of stress - for all replicates.

Treatment ID:

TR002649

Treatment Summary:

The B1 accession of purslane (Portulaca oleracea L.) used in this study belongs to the Purslane Collection at Embrapa Agroenergia. Seeds underwent disinfection following the same procedure described in Belo Silva et al. (2022), which consisted of soaking in 2% sodium hypochlorite and Tween® 20 for five minutes, under slow agitation, and then washing with sterile water and drying on sterilized filter paper. After being seeded on a culture medium (MS 1/2 strength, Phytagel 0.2%, and pH 5.8) (Murashige and Skoog, 1962), it was kept for germination in a Growth chamber Conviron mod. Adaptis 1000TC (Controlled Environments Ltd, Winnipeg, Canada) at 150 μmol/m2/s of light and 30°C. After 13 days, seedlings were individually transferred to 200 ml plastic cups containing 100 g of sterilized substrate - clay soil, vermiculite, and a commercial substrate (Bioplant®), 2:1:1 (v:v:v) ratio – and transferred to another Conviron® growth chamber mod. PGW40 at 25±2°C, 500±20 μmol/m2/s of light, 65±5% air relative humidity, and photoperiod of 16/8 h (light/dark), and kept there until the end of the experiments. The plants were allowed to acclimatize for three days, and the salinity stress started three weeks after the end of the acclimatization period. The salinization experiment consisted of two salinity levels (0.0 and 2.0 g of NaCl / 100 g of the substrate), with 16 replicates (plants) in a completely randomized design, and the stress lasted 12 days. During the entire experiment, plants were at field capacity. To avoid the loss of Na+ or Cl-, no leakage of the saline solution was allowed to get out of the plastic cup, as described previously in Belo Silva et al. (2022). The water lost due to evapotranspiration was replaced with deionized water daily, and the electric conductivity at field capacity (ECfc) and water potential in the substrate solution was measured once - on the 8th day of stress - for all replicates.

Sample Preparation:

Sampleprep ID:	SP002643
Sampleprep Summary:	For the metabolomics study, the following substances were acquired from Sigma Aldrich (Merck, USA): methanol UHPLC grade, acetonitrile LC-MS grade, methyl-tert-butyl-ether, formic acid LC-MS grade, and sodium hydroxide ACS grade. Water was obtained using a Milli-Q system (Millipore, USA). Metabolites were extracted using a well-established protocol, which provides polar and lipidic fractions from the same samples. In this protocol, we first ground the plant material (roots or leaves) in a ball mill (Biospec Products, USA), then added to a microtube containing 1 mL from a solution (1:3) of methanol and methyl-tert-butyl-ether at -20°C. Samples were incubated for 10 min at 4.0 °C, then ultrasonicated for another 10 min in an ice bath. A solution (1:3) of methanol and water was added to each microtube and then submitted to centrifugation (12,000 rpm at 4.0°C for 5 min). The polar (upper) and non-polar (lower) fractions were collected and vacuum-dried in a speed vac system overnight (Centrivap, Labconco, Kansas City, MO, USA). Four microliters of the extract were resuspended in 850 μL of the methanol and water (1:3) solvent mixture and then analyzed by UHPLC-MS.

Sampleprep ID:

SP002643

Sampleprep Summary:

For the metabolomics study, the following substances were acquired from Sigma Aldrich (Merck, USA): methanol UHPLC grade, acetonitrile LC-MS grade, methyl-tert-butyl-ether, formic acid LC-MS grade, and sodium hydroxide ACS grade. Water was obtained using a Milli-Q system (Millipore, USA). Metabolites were extracted using a well-established protocol, which provides polar and lipidic fractions from the same samples. In this protocol, we first ground the plant material (roots or leaves) in a ball mill (Biospec Products, USA), then added to a microtube containing 1 mL from a solution (1:3) of methanol and methyl-tert-butyl-ether at -20°C. Samples were incubated for 10 min at 4.0 °C, then ultrasonicated for another 10 min in an ice bath. A solution (1:3) of methanol and water was added to each microtube and then submitted to centrifugation (12,000 rpm at 4.0°C for 5 min). The polar (upper) and non-polar (lower) fractions were collected and vacuum-dried in a speed vac system overnight (Centrivap, Labconco, Kansas City, MO, USA). Four microliters of the extract were resuspended in 850 μL of the methanol and water (1:3) solvent mixture and then analyzed by UHPLC-MS.

Combined analysis:

Analysis ID	AN004175	AN004176
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Shimadzu Nexera X2	Shimadzu Nexera X2
Column	Waters ACQUITY UPLC BEH C8 (150 x 2.1mm,1.7um)	Waters ACQUITY UPLC BEH C8 (150 x 2.1mm,1.7um)
MS Type	ESI	ESI
MS instrument type	QTOF	QTOF
MS instrument name	Bruker maXis Impact qTOF	Bruker maXis Impact qTOF
Ion Mode	POSITIVE	NEGATIVE
Units	m/z	m/z

Chromatography:

Chromatography ID:	CH003093
Instrument Name:	Shimadzu Nexera X2
Column Name:	Waters ACQUITY UPLC BEH C8 (150 x 2.1mm,1.7um)
Column Temperature:	40 °C
Flow Gradient:	isocratic at the start (0 - 0.5 min) with 4% of B solvent, then at linear gradient (0.5 – 10 min) with 34% B and (10 – 15 min) with 100% B, and finally isocratic (15 – 18 min) with 100% B
Flow Rate:	400 μL min−1
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile; 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003922
Analysis ID:	AN004175
Instrument Name:	Bruker maXis Impact qTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	For external calibration, we used a sodium formate solution (10 mM NaOH solution in 50/50 v/v isopropanol/water containing 0.2% formic acid) directly injected through a 6-port valve at the beginning of each chromatographic run. UHPLC-MS data was acquired by the HyStar Application version 3.2 (Bruker Daltonics, Germany). Data pre-processing was performed using the software DataAnalysis version 4.4 (Bruker Daltonics, Germany), where raw data from the UHPLC-MS analysis were exported as .mzXML files.
Ion Mode:	POSITIVE

MS ID:	MS003923
Analysis ID:	AN004176
Instrument Name:	Bruker maXis Impact qTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	For external calibration, we used a sodium formate solution (10 mM NaOH solution in 50/50 v/v isopropanol/water containing 0.2% formic acid) directly injected through a 6-port valve at the beginning of each chromatographic run. UHPLC-MS data was acquired by the HyStar Application version 3.2 (Bruker Daltonics, Germany). Data pre-processing was performed using the software DataAnalysis version 4.4 (Bruker Daltonics, Germany), where raw data from the UHPLC-MS analysis were exported as .mzXML files.
Ion Mode:	NEGATIVE