VERSION                          	1
CREATED_ON                       	09-01-2023
PR:PROJECT_TITLE                 	Arabdiopsis Root VOCs
PR:PROJECT_SUMMARY               	The rhizosphere is a unique niche surrounding plant roots, where soluble and
PR:PROJECT_SUMMARY               	volatile molecules mediate signaling between plants and the associated
PR:PROJECT_SUMMARY               	microbiota. The preferred lifestyle of soil microbes is in the form of biofilms.
PR:PROJECT_SUMMARY               	However, little is known about whether root VOCs (rVOCs) can influence soil
PR:PROJECT_SUMMARY               	biofilms beyond the 2-10 mm rhizosphere zone influenced by soluble root
PR:PROJECT_SUMMARY               	exudates. Here, we report that rVOCs shift the microbiome composition and growth
PR:PROJECT_SUMMARY               	dynamics of complex soil biofilms. This signaling is evolutionarily conserved
PR:PROJECT_SUMMARY               	from ferns to higher plants, which suggests its coevolution. The defense
PR:PROJECT_SUMMARY               	phytohormone methyl jasmonate (MeJA) is present in rVOCs and drives this
PR:PROJECT_SUMMARY               	bioactivity at nanomolar levels within a few hours.
PR:INSTITUTE                     	National University of Singapore
PR:DEPARTMENT                    	Biological Sciences
PR:LABORATORY                    	AESB Lab
PR:LAST_NAME                     	Kulkarni
PR:FIRST_NAME                    	Omkar
PR:ADDRESS                       	NA
PR:EMAIL                         	komkar21@gmail.com
PR:PHONE                         	98668733
PR:DOI                           	http://dx.doi.org/10.21228/M8R997
ST:STUDY_TITLE                   	Detection of Methyl jasmonate (MeJA) in Plant root VOCs
ST:STUDY_SUMMARY                 	Methyl jasmonate (MeJA) is a well-known plant hormone known for plant defense
ST:STUDY_SUMMARY                 	and plant-plant signaling. However, most of the studies are focussed on its
ST:STUDY_SUMMARY                 	aboveground presence and functions. Here we report that MeJA is also released by
ST:STUDY_SUMMARY                 	plant roots in a volatile form. More importantly, it is shown in Arabidopsis
ST:STUDY_SUMMARY                 	growing in natural conditions in soil.
ST:INSTITUTE                     	National University of Singapore
ST:LAST_NAME                     	Kulkarni
ST:FIRST_NAME                    	Omkar
ST:ADDRESS                       	Dept of Biological Sciences,Metabolites Biology Lab,, Science drive 4,Block S1A
ST:ADDRESS                       	#06-03
ST:EMAIL                         	komkar21@gmail.com
ST:PHONE                         	98668733
ST:SUBMIT_DATE                   	2022-08-25
SU:SUBJECT_TYPE                  	Plant
SU:SUBJECT_SPECIES               	Arabidopsis thaliana
SU:TAXONOMY_ID                   	3702
SU:AGE_OR_AGE_RANGE              	2 weeks
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS           	4	tube10_jmt1B	Genotype:jmt	RAW_FILE_NAME=tube10_jmt1B.D
SUBJECT_SAMPLE_FACTORS           	5	tube11_jmt2A	Genotype:jmt	RAW_FILE_NAME=tube11_jmt2A.D
SUBJECT_SAMPLE_FACTORS           	5	tube12_jmt2B	Genotype:jmt	RAW_FILE_NAME=tube12_jmt2B.D
SUBJECT_SAMPLE_FACTORS           	6	tube13_jmt3A	Genotype:jmt	RAW_FILE_NAME=tube13_jmt3A.D
SUBJECT_SAMPLE_FACTORS           	6	tube14_jmt3B	Genotype:jmt	RAW_FILE_NAME=tube14_jmt3B.D
SUBJECT_SAMPLE_FACTORS           	4	tube9_jmt1A	Genotype:jmt	RAW_FILE_NAME=tube9_jmt1A.D
SUBJECT_SAMPLE_FACTORS           	NA	tube1	Genotype:NA	RAW_FILE_NAME=tube1.D
SUBJECT_SAMPLE_FACTORS           	NA	tube2_emptypot	Genotype:NA	RAW_FILE_NAME=tube2_emptypot.D
SUBJECT_SAMPLE_FACTORS           	1	tube3_soil1A	Genotype:NA	RAW_FILE_NAME=tube3_soil1A.D
SUBJECT_SAMPLE_FACTORS           	1	tube4_soil1B	Genotype:NA	RAW_FILE_NAME=tube4_soil1B.D
SUBJECT_SAMPLE_FACTORS           	2	tube5_soil2A	Genotype:NA	RAW_FILE_NAME=tube5_soil2A.D
SUBJECT_SAMPLE_FACTORS           	2	tube6_soil2B	Genotype:NA	RAW_FILE_NAME=tube6_soil2B.D
SUBJECT_SAMPLE_FACTORS           	3	tube7_soil3A	Genotype:NA	RAW_FILE_NAME=tube7_soil3A.D
SUBJECT_SAMPLE_FACTORS           	3	tube8_soil3B	Genotype:NA	RAW_FILE_NAME=tube8_soil3B.D
SUBJECT_SAMPLE_FACTORS           	7	tube15_WT1A	Genotype:WT	RAW_FILE_NAME=tube15_WT1A.D
SUBJECT_SAMPLE_FACTORS           	7	tube16_WT1B	Genotype:WT	RAW_FILE_NAME=tube16_WT1B.D
SUBJECT_SAMPLE_FACTORS           	8	tube17_WT2A	Genotype:WT	RAW_FILE_NAME=tube17_WT2A.D
SUBJECT_SAMPLE_FACTORS           	8	tube18_WT2B	Genotype:WT	RAW_FILE_NAME=tube18_WT2B.D
SUBJECT_SAMPLE_FACTORS           	9	tube19_WT3A	Genotype:WT	RAW_FILE_NAME=tube19_WT3A.D
SUBJECT_SAMPLE_FACTORS           	9	tube20_WT3B	Genotype:WT	RAW_FILE_NAME=tube20_WT3B.D
CO:COLLECTION_SUMMARY            	Root VOCs and soil VOCs were trapped as described here (Schulz-Bohm et al.,
CO:COLLECTION_SUMMARY            	2018). Briefly, 2 Tenax cartridges were fitted into the side arms of the glass
CO:COLLECTION_SUMMARY            	pots in such a way that their opening was exposed toward the plant roots/soil.
CO:COLLECTION_SUMMARY            	VOCs were sampled for 40 hours and immediately analyzed by thermal
CO:COLLECTION_SUMMARY            	desorption-gas chromatography‒mass spectrometry.
CO:SAMPLE_TYPE                   	Plant
TR:TREATMENT_SUMMARY             	No specific treatment.
SP:SAMPLEPREP_SUMMARY            	After 40 hours of VOC trapping, Tenax cartridges were immediately subjected to
SP:SAMPLEPREP_SUMMARY            	thermal desorption.
CH:CHROMATOGRAPHY_SUMMARY        	Sample preparation and injection were performed using the fully automated
CH:CHROMATOGRAPHY_SUMMARY        	Gerstel MPS-2 autosampler and Gerstel MAESTRO software. Volatile compounds were
CH:CHROMATOGRAPHY_SUMMARY        	adsorbed on a Tenax TA tube. A thermal desorption unit (TDU) was used to
CH:CHROMATOGRAPHY_SUMMARY        	thermally desorb the volatiles in splitless mode at 230°C for 10 min. To ensure
CH:CHROMATOGRAPHY_SUMMARY        	that the volatiles released from the TDU were quantitatively trapped, a cooled
CH:CHROMATOGRAPHY_SUMMARY        	injection system-programmed temperature vaporizer (CIS-PTV) was used. The CIS
CH:CHROMATOGRAPHY_SUMMARY        	was heated from 80°C to 230°C at a rate of 12°C/s with the split valve closed
CH:CHROMATOGRAPHY_SUMMARY        	during sample injection into the GC inlet. Analyses of volatile compounds were
CH:CHROMATOGRAPHY_SUMMARY        	performed on an Agilent 7890B GC coupled to a 5977B quadruple mass spectrometer.
CH:CHROMATOGRAPHY_SUMMARY        	Separation of compounds was performed on a DB-FFAP column (60 m x 250 µm x 0.25
CH:CHROMATOGRAPHY_SUMMARY        	µm, Agilent Technologies, Middleburg, OI, USA). Helium was used as the carrier
CH:CHROMATOGRAPHY_SUMMARY        	gas at a flow rate of 1.9 ml/min, and solvent vent mode was used. The inlet
CH:CHROMATOGRAPHY_SUMMARY        	temperature was 250°C. The oven program was as follows: initial temperature of
CH:CHROMATOGRAPHY_SUMMARY        	50°C held for 1 min, increased to 230°C at the rate of 10°C/min and held for
CH:CHROMATOGRAPHY_SUMMARY        	20 min. The temperature of the ion source and transfer line was 250°C.
CH:INSTRUMENT_NAME               	Agilent 7890B
CH:COLUMN_NAME                   	Agilent DB-FFAP
AN:ANALYSIS_TYPE                 	MS
MS:INSTRUMENT_NAME               	Agilent 5977B
MS:INSTRUMENT_TYPE               	Single quadrupole
MS:MS_TYPE                       	EI
MS:MS_COMMENTS                   	The mass spectrometer was in electron ionization mode with an ionization energy
MS:MS_COMMENTS                   	of 70 eV, scan range of 40-300 m/z and solvent delay of 3.75 minutes. Analysis
MS:MS_COMMENTS                   	was performed in single ion monitoring (SIM) mode by monitoring the ions at 83,
MS:MS_COMMENTS                   	151.1, and 224.1 with a dwell time of 150 ms. Mass Hunter Qualitative Analysis
MS:MS_COMMENTS                   	was used to extract and integrate peak spectra. The peak area of these ions was
MS:MS_COMMENTS                   	considered for the relative quantification of MeJA among different samples.
MS:ION_MODE                      	UNSPECIFIED
MS_METABOLITE_DATA:UNITS         	ion intensity peak area
Samples	tube10_jmt1B	tube11_jmt2A	tube12_jmt2B	tube13_jmt3A	tube14_jmt3B	tube9_jmt1A	tube1	tube2_emptypot	tube3_soil1A	tube4_soil1B	tube5_soil2A	tube6_soil2B	tube7_soil3A	tube8_soil3B	tube15_WT1A	tube16_WT1B	tube17_WT2A	tube18_WT2B	tube19_WT3A	tube20_WT3B
Factors	Genotype:jmt	Genotype:jmt	Genotype:jmt	Genotype:jmt	Genotype:jmt	Genotype:jmt	Genotype:NA	Genotype:NA	Genotype:NA	Genotype:NA	Genotype:NA	Genotype:NA	Genotype:NA	Genotype:NA	Genotype:WT	Genotype:WT	Genotype:WT	Genotype:WT	Genotype:WT	Genotype:WT	
Methyl Jasmonate	51380.3500		12718.9000	15363.3500	33962.7200	581408.6500	2347.0800	11247.8800	14200.1900		42016.5100	20850.5350	8040.0100	603018.8700	117534.9900	13982.3400	168327.7200	6365.8400	271639.5400	6804.8800
metabolite_name	pubchem_id	inchi_key	kegg_id	other_id	other_id_type	ri	ri_type	moverz_quant	
Methyl Jasmonate	5281929		C11512