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.

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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 IDST002995
Study TitleUntargeted metabolomics of Quercus ilex seedlings under drought and Phytophthora cinnamomi inoculation stresses
Study TypeUntargeted MS-based metabolomics
Study SummaryHolm 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
DepartmentDepartment of Biochemistry and Molecular Biology
LaboratoryAgroforestry and Plant Biochemistry, Proteomics and Systems Biology
Last NameTienda Parrilla
First NameMarta
AddressCampus de Rabanales, Córdoba, Córdoba, 14014, Spain
Emailb72tipam@uco.es
Phone634925272
Submit Date2023-11-28
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailOther
Release Date2023-12-20
Release Version1
Marta Tienda Parrilla Marta Tienda Parrilla
https://dx.doi.org/10.21228/M8NF08
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA326153CO_Combined_2_negCO_Combined
SA326154CO_Combined_1_negCO_Combined
SA326155CO_Combined_3_posCO_Combined
SA326156CO_Combined_2_posCO_Combined
SA326157CO_Combined_1_posCO_Combined
SA326158CO_Combined_3_negCO_Combined
SA326159CO_Control_2_negCO_Control
SA326160CO_Control_3_negCO_Control
SA326161CO_Control_1_posCO_Control
SA326162CO_Control_1_negCO_Control
SA326163CO_Control_2_posCO_Control
SA326164CO_Control_3_posCO_Control
SA326165HU_Combined_1_posHU_Combined
SA326166HU_Combined_1_negHU_Combined
SA326167HU_Combined_3_posHU_Combined
SA326168HU_Combined_2_negHU_Combined
SA326169HU_Combined_2_posHU_Combined
SA326170HU_Combined_3_negHU_Combined
SA326171HU_Control_3_negHU_Control
SA326172HU_Control_1_negHU_Control
SA326173HU_Control_3_posHU_Control
SA326174HU_Control_2_posHU_Control
SA326175HU_Control_1_posHU_Control
SA326176HU_Control_2_negHU_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
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