#METABOLOMICS WORKBENCH MicrometaboliteNR_20240105_093107 DATATRACK_ID:4560 STUDY_ID:ST003041 ANALYSIS_ID:AN004988 PROJECT_ID:PR001283 VERSION 1 CREATED_ON January 11, 2024, 8:17 am #PROJECT PR:PROJECT_TITLE MICROMETABOLITE PR:PROJECT_SUMMARY The overall objective of MICROMETABOLITE is to explore interactions between PR:PROJECT_SUMMARY plants and microorganisms involved in the production of secondary metabolites PR:PROJECT_SUMMARY (SM) for introducing novel ingredients in pharmaceutical and cosmeceutical PR:PROJECT_SUMMARY industry. Effects of microorganisms on the plant metabolome and the biosynthesis PR:PROJECT_SUMMARY of bioactive SM will be studied in the Boraginaceae plant family, aimed at PR:PROJECT_SUMMARY optimising plant cultivation and alkannins/shikonins (A/S) production. PR:PROJECT_SUMMARY Microorganisms will be integrated in plant production systems, and protocols PR:PROJECT_SUMMARY needed for efficient implementation in industry will be elaborated. Thereby a PR:PROJECT_SUMMARY platform will be established that will support long-term interactions between PR:PROJECT_SUMMARY academia and industry. PR:INSTITUTE Aristotle University of Thessaloniki PR:DEPARTMENT School of Chemical Engineering PR:LAST_NAME Rodić PR:FIRST_NAME Nebojša PR:ADDRESS Stepe Stepanovića 5, Čonoplja, Vojvodina, Serbia PR:EMAIL nebojsa.rodic@hotmail.com PR:PHONE +381648766400 PR:FUNDING_SOURCE Horizon 2020 PR:PROJECT_COMMENTS This research was supported by the European Union's Horizon 2020 research and PR:PROJECT_COMMENTS innovation programme under the Marie Skłodowska-Curie grant agreement No 721635 #STUDY ST:STUDY_TITLE Soil pH, developmental stages and geographical origin differently influence the ST:STUDY_TITLE root metabolomic diversity and root-related microbial diversity of Echium ST:STUDY_TITLE vulgare from native habitats ST:STUDY_SUMMARY This study examines the impact of different factors (geographic location, soil ST:STUDY_SUMMARY pH, genetic cluster, developmental stage) on the metabolome and microbiome of ST:STUDY_SUMMARY wild Echium vulgare, as well as the microbiome-metabolome correlation contained ST:STUDY_SUMMARY therein. Samples analyzed are wild Echium vulgare plant roots collected at six ST:STUDY_SUMMARY locations in Austria; out of the six locations, four contain plant roots from ST:STUDY_SUMMARY two different developmental stages. Extraction of metabolites and subsequent ST:STUDY_SUMMARY UHPLC-HRMS analysis were performed to obtain data for metabolomics analysis. ST:INSTITUTE Aristotle University of Thessaloniki ST:LAST_NAME Rodić ST:FIRST_NAME Nebojša ST:ADDRESS Stepe Stepanovića 5, Čonoplja, Vojvodina, Serbia ST:EMAIL nebojsa.rodic@hotmail.com ST:PHONE +381648766400 #SUBJECT SU:SUBJECT_TYPE Plant SU:SUBJECT_SPECIES Echium vulgare #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - EV_A1 Location:A | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_A1.raw SUBJECT_SAMPLE_FACTORS - EV_A2 Location:A | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_A2.raw SUBJECT_SAMPLE_FACTORS - EV_A3 Location:A | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_A3.raw SUBJECT_SAMPLE_FACTORS - EV_A4 Location:A | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_A4.raw SUBJECT_SAMPLE_FACTORS - EV_A5 Location:A | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_A5.raw SUBJECT_SAMPLE_FACTORS - EV_AI Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_AI.raw SUBJECT_SAMPLE_FACTORS - EV_AII Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_AII.raw SUBJECT_SAMPLE_FACTORS - EV_AIV Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_AIV.raw SUBJECT_SAMPLE_FACTORS - EV_AV Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_AV.raw SUBJECT_SAMPLE_FACTORS - EV_AVI Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_AVI.raw SUBJECT_SAMPLE_FACTORS - EV_AVII Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_AVII.raw SUBJECT_SAMPLE_FACTORS - EV_AVIII Location:A | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_AVIII.raw SUBJECT_SAMPLE_FACTORS - EV_B1 Location:B | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_B1.raw SUBJECT_SAMPLE_FACTORS - EV_B2 Location:B | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_B2.raw SUBJECT_SAMPLE_FACTORS - EV_B3 Location:B | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_B3.raw SUBJECT_SAMPLE_FACTORS - EV_B4 Location:B | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_B4.raw SUBJECT_SAMPLE_FACTORS - EV_B5 Location:B | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_B5.raw SUBJECT_SAMPLE_FACTORS - EV_B6 Location:B | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_B6.raw SUBJECT_SAMPLE_FACTORS - EV_BI Location:B | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_BI.raw SUBJECT_SAMPLE_FACTORS - EV_BII Location:B | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_BII.raw SUBJECT_SAMPLE_FACTORS - EV_BIII Location:B | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_BIII.raw SUBJECT_SAMPLE_FACTORS - EV_BIV Location:B | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_BIV.raw SUBJECT_SAMPLE_FACTORS - EV_BV Location:B | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_BV.raw SUBJECT_SAMPLE_FACTORS - EV_BVI Location:B | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G1 Sample type=sample; RAW_FILE_NAME=EV_BVI.raw SUBJECT_SAMPLE_FACTORS - EV_C1 Location:C | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_C1.raw SUBJECT_SAMPLE_FACTORS - EV_C2 Location:C | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_C2.raw SUBJECT_SAMPLE_FACTORS - EV_C3 Location:C | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_C3.raw SUBJECT_SAMPLE_FACTORS - EV_C4 Location:C | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_C4.raw SUBJECT_SAMPLE_FACTORS - EV_C5 Location:C | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_C5.raw SUBJECT_SAMPLE_FACTORS - EV_C6 Location:C | Developmental Stage:flowering | Soil pH:neutral | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_C6.raw SUBJECT_SAMPLE_FACTORS - EV_CI Location:C | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_CI.raw SUBJECT_SAMPLE_FACTORS - EV_CII Location:C | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_CII.raw SUBJECT_SAMPLE_FACTORS - EV_CIII Location:C | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_CIII.raw SUBJECT_SAMPLE_FACTORS - EV_CIV Location:C | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_CIV.raw SUBJECT_SAMPLE_FACTORS - EV_CV Location:C | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_CV.raw SUBJECT_SAMPLE_FACTORS - EV_CVI Location:C | Developmental Stage:rosette | Soil pH:neutral | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_CVI.raw SUBJECT_SAMPLE_FACTORS - EV_EI Location:E | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_EI.raw SUBJECT_SAMPLE_FACTORS - EV_EII Location:E | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_EII.raw SUBJECT_SAMPLE_FACTORS - EV_EIII Location:E | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_EIII.raw SUBJECT_SAMPLE_FACTORS - EV_EIV Location:E | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_EIV.raw SUBJECT_SAMPLE_FACTORS - EV_EV Location:E | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_EV.raw SUBJECT_SAMPLE_FACTORS - EV_EVI Location:E | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_EVI.raw SUBJECT_SAMPLE_FACTORS - EV_F1 Location:F | Developmental Stage:flowering | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_F1.raw SUBJECT_SAMPLE_FACTORS - EV_F2 Location:F | Developmental Stage:flowering | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_F2.raw SUBJECT_SAMPLE_FACTORS - EV_F3 Location:F | Developmental Stage:flowering | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_F3.raw SUBJECT_SAMPLE_FACTORS - EV_F4 Location:F | Developmental Stage:flowering | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_F4.raw SUBJECT_SAMPLE_FACTORS - EV_F5 Location:F | Developmental Stage:flowering | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_F5.raw SUBJECT_SAMPLE_FACTORS - EV_F6 Location:F | Developmental Stage:flowering | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_F6.raw SUBJECT_SAMPLE_FACTORS - EV_FI Location:F | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_FI.raw SUBJECT_SAMPLE_FACTORS - EV_FII Location:F | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_FII.raw SUBJECT_SAMPLE_FACTORS - EV_FIII Location:F | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_FIII.raw SUBJECT_SAMPLE_FACTORS - EV_FIV Location:F | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_FIV.raw SUBJECT_SAMPLE_FACTORS - EV_FV Location:F | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_FV.raw SUBJECT_SAMPLE_FACTORS - EV_FVI Location:F | Developmental Stage:rosette | Soil pH:slightly alkaline | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_FVI.raw SUBJECT_SAMPLE_FACTORS - EV_GI Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_GI.raw SUBJECT_SAMPLE_FACTORS - EV_GII Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_GII.raw SUBJECT_SAMPLE_FACTORS - EV_GIII Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_GIII.raw SUBJECT_SAMPLE_FACTORS - EV_GIV Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_GIV.raw SUBJECT_SAMPLE_FACTORS - EV_GV Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_GV.raw SUBJECT_SAMPLE_FACTORS - EV_GVI Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_GVI.raw SUBJECT_SAMPLE_FACTORS - EV_GVII Location:G | Developmental Stage:rosette | Soil pH:moderately acidic | Genetic cluster:G2 Sample type=sample; RAW_FILE_NAME=EV_GVII.raw SUBJECT_SAMPLE_FACTORS - QC_EV_02 Location:NA | Developmental Stage:NA | Soil pH:NA | Genetic cluster:NA Sample type=QC; RAW_FILE_NAME=QC_EV_02.raw SUBJECT_SAMPLE_FACTORS - QC_EV_03 Location:NA | Developmental Stage:NA | Soil pH:NA | Genetic cluster:NA Sample type=QC; RAW_FILE_NAME=QC_EV_03.raw SUBJECT_SAMPLE_FACTORS - QC_EV Location:NA | Developmental Stage:NA | Soil pH:NA | Genetic cluster:NA Sample type=QC; RAW_FILE_NAME=QC_EV.raw #COLLECTION CO:COLLECTION_SUMMARY Echium vulgare plants were collected in six locations in Austria. Four of the CO:COLLECTION_SUMMARY locations contained both rosette-stage and flowering plants, while two of the CO:COLLECTION_SUMMARY remaining locations contained only rosette-stage plants. Roots of the plants CO:COLLECTION_SUMMARY were collected and subsequently analyzed. CO:SAMPLE_TYPE Plant roots CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY After the collection, no additional treatment except for the cutting of roots TR:TREATMENT_SUMMARY was performed. The roots were split into parts for various microbiological TR:TREATMENT_SUMMARY analyses and parts for metabolomics analysis. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Plant roots were ground to a fine powder using a ball mill (Fritsch Pulverisette SP:SAMPLEPREP_SUMMARY 0, Germany). Each powdered sample was weighed (70 mg) into microcentrifuge SP:SAMPLEPREP_SUMMARY tubes, followed by extraction with 3 mL of methanol by ultrasound at 10% power SP:SAMPLEPREP_SUMMARY for 3 h (Bandelin Sonorex Digital 10P, Berlin, Germany) and centrifugation for SP:SAMPLEPREP_SUMMARY 10 minutes at 12.500 rpm (Hermle Z 216 MK, Wehingen, Germany). The supernatants SP:SAMPLEPREP_SUMMARY were collected and subjected to UHPLC-HRMS analysis after filtering with 0.22 SP:SAMPLEPREP_SUMMARY μm syringe filters. SP:PROCESSING_STORAGE_CONDITIONS -80℃ SP:EXTRACT_STORAGE Room temperature #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Accela AS CH:COLUMN_NAME Waters ACQUITY UPLC HSS C18 (100 x 2.1mm,1.8um) CH:SOLVENT_A Ultrapure water (0.1% formic acid) CH:SOLVENT_B LCMS-grade methanol (0.1% formic acid) CH:FLOW_GRADIENT 0 min 95A/5B, 1 min 50A/50B, 8 min 0A/100B, 13 min 0A/100B, 13.01 min 95A/5B, 16 CH:FLOW_GRADIENT min 95A/5B CH:FLOW_RATE 0.3 mL/min CH:COLUMN_TEMPERATURE 50 #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo LTQ Discovery Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS The MS/MS data were obtained for the six most intense m/z peaks in each full MS:MS_COMMENTS scan, with the normalized collision energy set to 35 eV. The acquisition and MS:MS_COMMENTS initial processing of the data were by means of XcaliburTM (Thermo Scientific, MS:MS_COMMENTS USA) software, while data alignment and feature extraction were performed MS:MS_COMMENTS utilizing the XCMS Online platform (The Scripps Research Institute, USA). MS:MS_RESULTS_FILE ST003041_AN004988_Results.txt UNITS:Intensity Has m/z:Yes Has RT:Yes RT units:Minutes #END