Summary of Study ST002995
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 PR001865. The data can be accessed directly via it's Project DOI: 10.21228/M8NF08 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 | ST002995 |
| Study Title | Untargeted metabolomics of Quercus ilex seedlings under drought and Phytophthora cinnamomi inoculation stresses |
| Study Type | Untargeted MS-based metabolomics |
| Study Summary | Holm oak (Quercus ilex) is considered one of the major structural elements of the Mediterranean forests and the agrosilvopastoral Spanish “dehesa”, representing an outstanding example of ecological and socio-economic sustainability of forest ecosystems. The exotic pathogen Phytophthora cinnamomi is one of the most aggressive of woody species, and together drought is considered one of the main drivers of holm oak decline. The effect and responses of P. cinnamomi inoculation has been studied on the offspring of mother trees growing in declined and non-declined areas of two Andalusian populations (Cordoba and Huelva). Damage symptoms, mortality, and chlorophyll fluorescence have been evaluated in seedlings inoculated under humid and drought conditions. The effect and responses depended on the population, being more accused in Huelva than in Cordoba population. An integrative proteomic and metabolomic analysis revealed the involvement of different metabolic pathways in response to the pathogen in both populations, such as amino acid metabolism pathways in Huelva, and terpenoids and flavonoids biosynthesis in Cordoba. However, a differential response was not observed between seedlings inoculated under humid and drought conditions. A protective mechanism of the photosynthetic apparatus is launched in response to defective photosynthetic activity in inoculated plants, which seems to be more efficient in the Cordoba population. In addition, enzymes and metabolites of the phenylpropanoid and flavonoid biosynthesis pathways may confer higher resistance to Cordoba population. Some of these enzymes are proposed as markers of resilience, among which glyoxalase I, glutathione reductase, thioredoxin reductase, and cinnamyl alcohol dehydrogenase are candidates. |
| Institute | University of Cordoba |
| Department | Department of Biochemistry and Molecular Biology |
| Laboratory | Agroforestry and Plant Biochemistry, Proteomics and Systems Biology |
| Last Name | Tienda Parrilla |
| First Name | Marta |
| Address | Campus de Rabanales, Córdoba, Córdoba, 14014, Spain |
| b72tipam@uco.es | |
| Phone | 634925272 |
| Submit Date | 2023-11-28 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | Other |
| Release Date | 2023-12-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001865 |
| Project DOI: | doi: 10.21228/M8NF08 |
| Project Title: | Metabolomic study of the Quercus ilex response to Phytophthora cinnamomi, the main causal agent of the decline syndrome, and the identification of putative markers of resistance |
| Project Type: | LC-MS analysis |
| Project Summary: | Holm oak (Quercus ilex) is considered one of the major structural elements of the Mediterranean forests and the agrosilvopastoral Spanish “dehesa”, representing an outstanding example of ecological and socio-economic sustainability of forest ecosystems. The exotic pathogen Phytophthora cinnamomi is one of the most aggressive of woody species, and together drought is considered one of the main drivers of holm oak decline. The effect and responses of P. cinnamomi inoculation has been studied on the offspring of mother trees growing in declined and non-declined areas of two Andalusian populations (Cordoba and Huelva). Damage symptoms, mortality, and chlorophyll fluorescence have been evaluated in seedlings inoculated under humid and drought conditions. The effect and responses depended on the population, being more accused in Huelva than in Cordoba population. An integrative proteomic and metabolomic analysis revealed the involvement of different metabolic pathways in response to the pathogen in both populations, such as amino acid metabolism pathways in Huelva, and terpenoids and flavonoids biosynthesis in Cordoba. However, a differential response was not observed between seedlings inoculated under humid and drought conditions. A protective mechanism of the photosynthetic apparatus is launched in response to defective photosynthetic activity in inoculated plants, which seems to be more efficient in the Cordoba population. In addition, enzymes and metabolites of the phenylpropanoid and flavonoid biosynthesis pathways may confer higher resistance to Cordoba population. Some of these enzymes are proposed as markers of resilience, among which glyoxalase I, glutathione reductase, thioredoxin reductase, and cinnamyl alcohol dehydrogenase are candidates. |
| Institute: | University of Cordoba |
| Department: | Department of Biochemistry and Molecular Biology |
| Laboratory: | Agroforestry and Plant Biochemistry, Proteomics and Systems Biology |
| Last Name: | Tienda Parrilla |
| First Name: | Marta |
| Address: | Campus de Rabanales, Córdoba, Córdoba, 14014, Spain |
| Email: | b72tipam@uco.es |
| Phone: | 634925272 |
| Funding Source: | This research was funded by the Spanish Ministry of Economy and Competitiveness in the framework of Projects PID2019-109038RB-I00 and PID2022-141599OB-I00, and PROYEXCEL_00881 grants from the Junta de Andalucía |
Subject:
| Subject ID: | SU003108 |
| Subject Type: | Plant |
| Subject Species: | Quercus ilex |
| Taxonomy ID: | 1753 |
| Age Or Age Range: | Six-month-old seedlings |
Factors:
Subject type: Plant; Subject species: Quercus ilex (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor |
|---|---|---|
| SA326153 | CO_Combined_2_neg | CO_Combined |
| SA326154 | CO_Combined_1_neg | CO_Combined |
| SA326155 | CO_Combined_3_pos | CO_Combined |
| SA326156 | CO_Combined_2_pos | CO_Combined |
| SA326157 | CO_Combined_1_pos | CO_Combined |
| SA326158 | CO_Combined_3_neg | CO_Combined |
| SA326159 | CO_Control_2_neg | CO_Control |
| SA326160 | CO_Control_3_neg | CO_Control |
| SA326161 | CO_Control_1_pos | CO_Control |
| SA326162 | CO_Control_1_neg | CO_Control |
| SA326163 | CO_Control_2_pos | CO_Control |
| SA326164 | CO_Control_3_pos | CO_Control |
| SA326165 | HU_Combined_1_pos | HU_Combined |
| SA326166 | HU_Combined_1_neg | HU_Combined |
| SA326167 | HU_Combined_3_pos | HU_Combined |
| SA326168 | HU_Combined_2_neg | HU_Combined |
| SA326169 | HU_Combined_2_pos | HU_Combined |
| SA326170 | HU_Combined_3_neg | HU_Combined |
| SA326171 | HU_Control_3_neg | HU_Control |
| SA326172 | HU_Control_1_neg | HU_Control |
| SA326173 | HU_Control_3_pos | HU_Control |
| SA326174 | HU_Control_2_pos | HU_Control |
| SA326175 | HU_Control_1_pos | HU_Control |
| SA326176 | HU_Control_2_neg | HU_Control |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO003101 |
| Collection Summary: | Metabolomics analyses were performed when leaf chlorophyll fluorescence decreased 35% (day 12 of the experiment) on plant subjected to combined stresses, relative to the control plants. For that, all healthy leaves from three biological replicates per treatment (control and combined stresses) and population (Córdoba and Huelva) of seedlings from the non-infected adult trees were collected, washed with distilled water, dried with paper, frozen in liquid nitrogen and stored in the dark and cold (-80 ºC) until use. Six-month-old seedlings were subjected to two different treatments: (1) control (irrigation to field capacity, non-inoculated with P. cinnamomi) and (2) combined stress (inoculated with P. cinnamomi and non-irrigated) |
| Sample Type: | Plant |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003117 |
| Treatment Summary: | The treatments were performed as described by Ruiz-Gómez et al. 2018 and San-Eufrasio et al. 2021. Briefly, inoculation with P. cinnamomi was performed by root immersion during 10 min in Carrot-Agar (CA) liquid medium at a concentration of 43 chlamydospores/μl. Roots of control seedlings were also immersed in CA liquid without P. cinnamomi. After inoculation, seedlings were transplanted into pots with fresh perlite and flooded for 48 h. Then, excess water was removed before drought treatment. Drought was imposed by withholding water for 28 days [36]. The presence of P. cinnamomi in the inoculated plants was confirmed on day 12 of the experiment by using fine roots (<2 mm thick, ~1 cm long) placed in Petri dishes of selective medium (PARPBH) |
| Treatment: | Abiotic (drought) and biotic (inoculation with P. cinnamomi) stresses |
| Plant Growth Location: | Córdoba, Andalucía |
| Plant Plot Design: | Randomized design |
| Plant Growth Stage: | Six-month-old seedlings |
| Plant Metab Quench Method: | Liquid N2 |
| Plant Storage: | Fresh |
Sample Preparation:
| Sampleprep ID: | SP003114 |
| Sampleprep Summary: | Metabolites were extracted from freeze-dried leaf powder. Briefly, a buffer containing 1200 μL of cold ethanol: water (80:20) was added to 30 mg of leaf powder, tissue disruption was driven by maceration with pistil, vortexed (10 s) and sonicated (ultrasonic bath, 40 kHZ for 10 min). After centrifugation (16,000×g, 4°C, 6 min) the supernatant was vacuum dried at 30 °C (Speedvac, Eppendorf Vacuum Concentrator Plus/5301, Eppendorf, Leicestershire, UK). |
| Processing Method: | Ethanol:Water |
| Processing Storage Conditions: | On ice |
| Extraction Method: | Ethanol:Water |
| Extract Cleanup: | Centrifugation |
| Extract Storage: | -80℃ |
| Sample Resuspension: | Methanol |
| Sample Derivatization: | NO |
| Sample Spiking: | NO |
Combined analysis:
| Analysis ID | AN004919 | AN004920 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Waters Acquity | Waters Acquity |
| Column | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTRAP | QTRAP |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak Area | Peak Area |
Chromatography:
| Chromatography ID: | CH003714 |
| Chromatography Summary: | Chromatographic separations were performed using an Acquity UPLC BEH C18 column (2.1 x 100 mm, 1.7 µm) (Waters). The column was maintained at 40 °C and eluted under the following conditions: 5% B for 1 min, linear gradient from 5% to 100% in solvent B for 9 min, isocratic at 100% B for 2 min, and return to initial conditions, 5% B for 3 min. A flow rate of 0.5 mL/min was used. Eluent A was 0.1% formic acid in water and eluent B was 0.1% formic acid in methanol. Injection volume was 5 µl. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 40 °C |
| Flow Gradient: | 5% B for 1 min, linear gradient from 5% to 100% in solvent B for 9 min, isocratic at 100% B for 2 min, and return to initial conditions, 5% B for 3 min |
| Flow Rate: | 0.5 mL/min |
| Solvent A: | 0.1% formic acid in water |
| Solvent B: | 0.1% formic acid in methanol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004662 |
| Analysis ID: | AN004919 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | QTRAP |
| MS Type: | ESI |
| MS Comments: | POS |
| Ion Mode: | POSITIVE |
| MS ID: | MS004663 |
| Analysis ID: | AN004920 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | QTRAP |
| MS Type: | ESI |
| MS Comments: | NEG |
| Ion Mode: | NEGATIVE |
