{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002021","ANALYSIS_ID":"AN003291","VERSION":"1","CREATED_ON":"November 29, 2021, 7:54 am"},

"PROJECT":{"PROJECT_TITLE":"MICROMETABOLITE","PROJECT_SUMMARY":"The overall objective of MICROMETABOLITE is to explore interactions between plants and microorganisms involved in the production of secondary metabolites (SM) for introducing novel ingredients in pharmaceutical and cosmeceutical industry. Effects of microorganisms on the plant metabolome and the biosynthesis of bioactive SM will be studied in the Boraginaceae plant family, aimed at optimising plant cultivation and alkannins/shikonins (A/S) production. Microorganisms will be integrated in plant production systems, and protocols needed for efficient implementation in industry will be elaborated. Thereby a platform will be established that will support long-term interactions between academia and industry.","INSTITUTE":"Aristotle University of Thessaloniki, MICROMETABOLITE project","DEPARTMENT":"School of Chemical Engineering","LAST_NAME":"Rodic","FIRST_NAME":"Nebojsa","ADDRESS":"Stepe Stepanovica 5, Conoplja, Vojvodina, 25210, Yugoslavia","EMAIL":"nebojsa.rodic@hotmail.com","PHONE":"+381648766400","FUNDING_SOURCE":"This research was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 721635"},

"STUDY":{"STUDY_TITLE":"An integrated-omics approach reveals specific bacterial and fungal taxa associated with roots of Alkanna tinctoria L. Tausch correlating with medicinally relevant alkannin derivatives and other secondary metabolites","STUDY_SUMMARY":"Plants are naturally associated with diverse microbial communities, which play significant roles in plant performance, such as growth promotion or fending off pathogens. The roots of Alkanna tinctoria L. are rich in naphthoquinones, particularly the medicinally used chiral compounds alkannin, shikonin and their derivatives. Former studies already have shown that microorganisms may modulate plant metabolism. To further investigate the potential interaction between A. tinctoria and associated microorganisms we performed a greenhouse experiment, in which A. tinctoria plants were grown in the presence of three distinct soil microbiomes. At four defined plant developmental stages we made an in-depth assessment of bacterial and fungal root-associated microbiomes as well as all primary and secondary metabolites. Our results showed that the plant developmental stage was the most important driver influencing the plant metabolite content, revealing peak contents of alkannin/shikonin at the fruiting stage. In contrast, the soil microbiome had the biggest impact on the plant root microbiome. Correlation analyses performed on the measured metabolite content and the abundance of individual bacterial and fungal taxa suggested a dynamic, at times positive or negative relationship between root-associated microorganisms and root metabolism. In particular, the bacterial Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group and the fungal species Penicillium jensenii were found to be positively correlated with higher content of alkannins.","INSTITUTE":"Aristotle University of Thessaloniki, MICROMETABOLITE project","DEPARTMENT":"School of Chemical Engineering","LAST_NAME":"Rodic","FIRST_NAME":"Nebojsa","ADDRESS":"Stepe Stepanovica 5, Conoplja, Vojvodina, 25210, Yugoslavia","EMAIL":"nebojsa.rodic@hotmail.com","PHONE":"+381648766400"},

"SUBJECT":{"SUBJECT_TYPE":"Plant","SUBJECT_SPECIES":"Alkanna tinctoria"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"I.1",
"Factors":{"developmental stage":"growth","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.2",
"Factors":{"developmental stage":"growth","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.3",
"Factors":{"developmental stage":"growth","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.4",
"Factors":{"developmental stage":"growth","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.5",
"Factors":{"developmental stage":"growth","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.6",
"Factors":{"developmental stage":"growth","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_6.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.7",
"Factors":{"developmental stage":"growth","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_7.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.8",
"Factors":{"developmental stage":"growth","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_8.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.9",
"Factors":{"developmental stage":"growth","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_9.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.10",
"Factors":{"developmental stage":"growth","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_10.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.11",
"Factors":{"developmental stage":"growth","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_11.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.12",
"Factors":{"developmental stage":"growth","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_12.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.13",
"Factors":{"developmental stage":"growth","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_13.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.14",
"Factors":{"developmental stage":"growth","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_14.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.15",
"Factors":{"developmental stage":"growth","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_15.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.16",
"Factors":{"developmental stage":"growth","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_16.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.17",
"Factors":{"developmental stage":"growth","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_17.raw"}
},
{
"Subject ID":"-",
"Sample ID":"I.18",
"Factors":{"developmental stage":"growth","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"1-3_RA_18.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.1",
"Factors":{"developmental stage":"blooming","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.2",
"Factors":{"developmental stage":"blooming","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.3",
"Factors":{"developmental stage":"blooming","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.4",
"Factors":{"developmental stage":"blooming","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.5",
"Factors":{"developmental stage":"blooming","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.6",
"Factors":{"developmental stage":"blooming","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_6.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.7",
"Factors":{"developmental stage":"blooming","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_7.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.8",
"Factors":{"developmental stage":"blooming","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_8.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.9",
"Factors":{"developmental stage":"blooming","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_9.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.10",
"Factors":{"developmental stage":"blooming","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_10.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.11",
"Factors":{"developmental stage":"blooming","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_11.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.12",
"Factors":{"developmental stage":"blooming","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_12.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.13",
"Factors":{"developmental stage":"blooming","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_13.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.14",
"Factors":{"developmental stage":"blooming","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_14.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.15",
"Factors":{"developmental stage":"blooming","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_15.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.16",
"Factors":{"developmental stage":"blooming","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_16.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.17",
"Factors":{"developmental stage":"blooming","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_17.raw"}
},
{
"Subject ID":"-",
"Sample ID":"II.18",
"Factors":{"developmental stage":"blooming","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"15-3_RA_18.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.1",
"Factors":{"developmental stage":"fruiting","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"12-4_RA_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.2",
"Factors":{"developmental stage":"fruiting","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"12-4_RA_2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.3",
"Factors":{"developmental stage":"fruiting","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"12-4_RA_3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.4",
"Factors":{"developmental stage":"fruiting","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"3","RAW_FILE_NAME":"12-4_RA_4D.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.5",
"Factors":{"developmental stage":"fruiting","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"12-4_RA_5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.6",
"Factors":{"developmental stage":"fruiting","soil type":"Greek A"},
"Additional sample data":{"dilution factor":"3","RAW_FILE_NAME":"12-4_RA_6D.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.7",
"Factors":{"developmental stage":"fruiting","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"12-4_RA_7.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.8",
"Factors":{"developmental stage":"fruiting","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"3","RAW_FILE_NAME":"12-4_RA_8D.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.9",
"Factors":{"developmental stage":"fruiting","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"3","RAW_FILE_NAME":"12-4_RA_9D.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.10",
"Factors":{"developmental stage":"fruiting","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"12-4_RA_10.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.11",
"Factors":{"developmental stage":"fruiting","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"12-4_RA_11.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.12",
"Factors":{"developmental stage":"fruiting","soil type":"Greek B"},
"Additional sample data":{"dilution factor":"3","RAW_FILE_NAME":"12-4_RA_12D.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.13",
"Factors":{"developmental stage":"fruiting","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"12-4_RA_13.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.14",
"Factors":{"developmental stage":"fruiting","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"12-4_RA_14.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.15",
"Factors":{"developmental stage":"fruiting","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"3","RAW_FILE_NAME":"12-4_RA_15D.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.16",
"Factors":{"developmental stage":"fruiting","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"3","RAW_FILE_NAME":"12-4_RA_16D.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.17",
"Factors":{"developmental stage":"fruiting","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"12-4_RA_17.raw"}
},
{
"Subject ID":"-",
"Sample ID":"III.18",
"Factors":{"developmental stage":"fruiting","soil type":"Austrian"},
"Additional sample data":{"dilution factor":"3","RAW_FILE_NAME":"12-4_RA_18D.raw"}
},
{
"Subject ID":"-",
"Sample ID":"QC_UCL_AT_01",
"Factors":{"developmental stage":"QC","soil type":"NA"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"QC_UCL_AT.raw"}
},
{
"Subject ID":"-",
"Sample ID":"QC_UCL_AT_02",
"Factors":{"developmental stage":"QC","soil type":"NA"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"QC_UCL_AT_180730210457.raw"}
},
{
"Subject ID":"-",
"Sample ID":"QC_UCL_AT_03",
"Factors":{"developmental stage":"QC","soil type":"NA"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"QC_UCL_AT_180731013653.raw"}
},
{
"Subject ID":"-",
"Sample ID":"QC_UCL_AT_04",
"Factors":{"developmental stage":"QC","soil type":"NA"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"QC_UCL_AT_04.raw"}
},
{
"Subject ID":"-",
"Sample ID":"QC_UCL_AT_05",
"Factors":{"developmental stage":"QC","soil type":"NA"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"QC_UCL_AT_05.raw"}
},
{
"Subject ID":"-",
"Sample ID":"QC_UCL_AT_06",
"Factors":{"developmental stage":"QC","soil type":"NA"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"QC_UCL_AT_06.raw"}
},
{
"Subject ID":"-",
"Sample ID":"QC_UCL_AT_07",
"Factors":{"developmental stage":"QC","soil type":"NA"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"QC_UCL_AT_07.raw"}
},
{
"Subject ID":"-",
"Sample ID":"QC_UCL_AT_08",
"Factors":{"developmental stage":"QC","soil type":"NA"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"QC_UCL_AT_08.raw"}
},
{
"Subject ID":"-",
"Sample ID":"QC_UCL_AT_09",
"Factors":{"developmental stage":"QC","soil type":"NA"},
"Additional sample data":{"dilution factor":"1","RAW_FILE_NAME":"QC_UCL_AT_09.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Alkanna tinctoria plants were provided as rooted acclimatized individuals, originally collected and identified from natural populations","SAMPLE_TYPE":"Plant"},

"TREATMENT":{"TREATMENT_SUMMARY":"Plants were produced by micropropagation from several mother plants by the Hellenic Agricultural Organization (HAO, Thessaloniki, Greece). The plants were transferred to 5 L pots containing 4.5 L of sterilized (121° C for 15 min) peat moss and perlite (volume ratio 2:1), mixed with 200 g field soil collected either in Austria or in Greece. Thus, all plants were grown in a substrate with highly similar chemical and physical characteristics, but hosting those microbial communities prevailing in these three distinct soils. Plants were grown in the greenhouse at 16 h light / 8 h dark photoperiod, 25°C with 50% relative humidity (RH) and a photosynthetic photon flux density (PPFD) of 96 μmolm^-2 s^-1. Plants were watered twice per week with deionized water and moved randomly once per week. Plants were harvested at four different defined developmental stages, the first stage (“vegetative growth”) was defined when more than 50% of the individuals started to produce new leaves, “blooming” was the stage when more than 50% of the individuals had flowers, “fruiting” when more than 50% of the individual plants began to produce fruits."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Plant roots were ground to a fine powder using a ball mill (Fritsch Pulverisette 0, Germany). Each powdered sample was weighed (70 mg) into microcentrifuge tubes, followed by extraction with 3 mL of methanol by ultrasound at 10% power for 3 h (Bandelin Sonorex Digital 10P, Berlin, Germany) and centrifugation for 10 minutes at 12.500 rpm (Hermle Z 216 MK, Wehingen, Germany). The supernatants were collected and subjected to UHPLC-HRMS analysis after filtering with 0.22 μm syringe filters."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Accela AS","COLUMN_NAME":"Waters Acquity UPLC HSS C18 SB 1.8 μm 2.1 x 100 mm","FLOW_RATE":"0.3mL/min","COLUMN_TEMPERATURE":"50"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo LTQ Discovery Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"The MS/MS data were obtained for the six most intense m/z peaks in each full scan, with the normalized collision energy set to 35 eV. The acquisition and initial processing of the data were by means of XcaliburTM (Thermo Scientific, USA) software, while data alignment and feature extraction were performed utilizing the XCMS Online platform (The Scripps Research Institute, USA). The batch error correction was done with the help of MetaboAnalyst 5.0.","MS_RESULTS_FILE":"ST002021_AN003291_Results.txt UNITS:intensity units Has m/z:Yes Has RT:Yes RT units:Minutes"}

}