Summary of Study ST002021

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 PR001283. The data can be accessed directly via it's Project DOI: 10.21228/M8VX1B 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	ST002021
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
Department	School of Chemical Engineering
Laboratory	Organic Chemistry Laboratory
Last Name	Rodic
First Name	Nebojsa
Address	Stepe Stepanovica 5, Conoplja, Vojvodina, 25210, Yugoslavia
Email	nebojsa.rodic@hotmail.com
Phone	+381648766400
Submit Date	2021-11-28
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2022-01-06
Release Version	1

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Project:

Project ID:	PR001283
Project DOI:	doi: 10.21228/M8VX1B
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
Department:	School of Chemical Engineering
Laboratory:	Organic Chemistry Laboratory
Last Name:	Rodic
First Name:	Nebojsa
Address:	Stepe Stepanovica 5, Conoplja, Vojvodina, 25210, Serbia
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

Subject:

Subject ID:	SU002103
Subject Type:	Plant
Subject Species:	Alkanna tinctoria

Factors:

Subject type: Plant; Subject species: Alkanna tinctoria (Factor headings shown in green)

mb_sample_id	local_sample_id	developmental stage
SA189356	II.15	blooming \| soil type:Austrian
SA189357	II.16	blooming \| soil type:Austrian
SA189358	II.18	blooming \| soil type:Austrian
SA189359	II.13	blooming \| soil type:Austrian
SA189360	II.17	blooming \| soil type:Austrian
SA189361	II.14	blooming \| soil type:Austrian
SA189362	II.5	blooming \| soil type:Greek A
SA189363	II.6	blooming \| soil type:Greek A
SA189364	II.4	blooming \| soil type:Greek A
SA189365	II.3	blooming \| soil type:Greek A
SA189366	II.2	blooming \| soil type:Greek A
SA189367	II.1	blooming \| soil type:Greek A
SA189368	II.11	blooming \| soil type:Greek B
SA189369	II.12	blooming \| soil type:Greek B
SA189370	II.10	blooming \| soil type:Greek B
SA189371	II.9	blooming \| soil type:Greek B
SA189372	II.8	blooming \| soil type:Greek B
SA189373	II.7	blooming \| soil type:Greek B
SA189374	III.14	fruiting \| soil type:Austrian
SA189375	III.13	fruiting \| soil type:Austrian
SA189376	III.15	fruiting \| soil type:Austrian
SA189377	III.16	fruiting \| soil type:Austrian
SA189378	III.17	fruiting \| soil type:Austrian
SA189379	III.18	fruiting \| soil type:Austrian
SA189380	III.5	fruiting \| soil type:Greek A
SA189381	III.6	fruiting \| soil type:Greek A
SA189382	III.3	fruiting \| soil type:Greek A
SA189383	III.4	fruiting \| soil type:Greek A
SA189384	III.2	fruiting \| soil type:Greek A
SA189385	III.1	fruiting \| soil type:Greek A
SA189386	III.10	fruiting \| soil type:Greek B
SA189387	III.11	fruiting \| soil type:Greek B
SA189388	III.12	fruiting \| soil type:Greek B
SA189389	III.9	fruiting \| soil type:Greek B
SA189390	III.8	fruiting \| soil type:Greek B
SA189391	III.7	fruiting \| soil type:Greek B
SA189392	I.18	growth \| soil type:Austrian
SA189393	I.16	growth \| soil type:Austrian
SA189394	I.14	growth \| soil type:Austrian
SA189395	I.15	growth \| soil type:Austrian
SA189396	I.13	growth \| soil type:Austrian
SA189397	I.17	growth \| soil type:Austrian
SA189398	I.1	growth \| soil type:Greek A
SA189399	I.5	growth \| soil type:Greek A
SA189400	I.4	growth \| soil type:Greek A
SA189401	I.3	growth \| soil type:Greek A
SA189402	I.6	growth \| soil type:Greek A
SA189403	I.2	growth \| soil type:Greek A
SA189404	I.9	growth \| soil type:Greek B
SA189405	I.12	growth \| soil type:Greek B
SA189406	I.11	growth \| soil type:Greek B
SA189407	I.10	growth \| soil type:Greek B
SA189408	I.8	growth \| soil type:Greek B
SA189409	I.7	growth \| soil type:Greek B
SA189347	QC_UCL_AT_03	QC \| soil type:NA
SA189348	QC_UCL_AT_02	QC \| soil type:NA
SA189349	QC_UCL_AT_01	QC \| soil type:NA
SA189350	QC_UCL_AT_05	QC \| soil type:NA
SA189351	QC_UCL_AT_04	QC \| soil type:NA
SA189352	QC_UCL_AT_06	QC \| soil type:NA
SA189353	QC_UCL_AT_08	QC \| soil type:NA
SA189354	QC_UCL_AT_09	QC \| soil type:NA
SA189355	QC_UCL_AT_07	QC \| soil type:NA

Showing results 1 to 63 of 63

Showing results 1 to 63 of 63

Collection:

Collection ID:	CO002096
Collection Summary:	Alkanna tinctoria plants were provided as rooted acclimatized individuals, originally collected and identified from natural populations
Sample Type:	Plant

Treatment:

Treatment ID:	TR002115
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.

Treatment ID:

TR002115

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.

Sample Preparation:

Sampleprep ID:	SP002109
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.

Sampleprep ID:

SP002109

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.

Combined analysis:

Analysis ID	AN003291
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Thermo Accela 1250
Column	Waters Acquity UPLC HSS C18 SB (100 x 2.1mm, 1.8um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo LTQ Discovery Orbitrap
Ion Mode	POSITIVE
Units	intensity units

Chromatography:

Chromatography ID:	CH002431
Instrument Name:	Thermo Accela 1250
Column Name:	Waters Acquity UPLC HSS C18 SB (100 x 2.1mm, 1.8um)
Column Temperature:	50
Flow Rate:	0.3mL/min
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003062
Analysis ID:	AN003291
Instrument Name:	Thermo LTQ Discovery Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
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.
Ion Mode:	POSITIVE