{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002282","ANALYSIS_ID":"AN003727","VERSION":"1","CREATED_ON":"09-01-2023"},

"PROJECT":{"PROJECT_TITLE":"Arabdiopsis Root VOCs","PROJECT_SUMMARY":"The rhizosphere is a unique niche surrounding plant roots, where soluble and volatile molecules mediate signaling between plants and the associated microbiota. The preferred lifestyle of soil microbes is in the form of biofilms. However, little is known about whether root VOCs (rVOCs) can influence soil biofilms beyond the 2-10 mm rhizosphere zone influenced by soluble root exudates. Here, we report that rVOCs shift the microbiome composition and growth dynamics of complex soil biofilms. This signaling is evolutionarily conserved from ferns to higher plants, which suggests its coevolution. The defense phytohormone methyl jasmonate (MeJA) is present in rVOCs and drives this bioactivity at nanomolar levels within a few hours.","INSTITUTE":"National University of Singapore","DEPARTMENT":"Biological Sciences","LABORATORY":"AESB Lab","LAST_NAME":"Kulkarni","FIRST_NAME":"Omkar","ADDRESS":"NA","EMAIL":"komkar21@gmail.com","PHONE":"98668733","DOI":"http://dx.doi.org/10.21228/M8R997"},

"STUDY":{"STUDY_TITLE":"Detection of Methyl jasmonate (MeJA) in Plant root VOCs","STUDY_SUMMARY":"Methyl jasmonate (MeJA) is a well-known plant hormone known for plant defense and plant-plant signaling. However, most of the studies are focussed on its aboveground presence and functions. Here we report that MeJA is also released by plant roots in a volatile form. More importantly, it is shown in Arabidopsis growing in natural conditions in soil.","INSTITUTE":"National University of Singapore","LAST_NAME":"Kulkarni","FIRST_NAME":"Omkar","ADDRESS":"Dept of Biological Sciences,Metabolites Biology Lab,, Science drive 4,Block S1A #06-03","EMAIL":"komkar21@gmail.com","PHONE":"98668733","SUBMIT_DATE":"2022-08-25"},

"SUBJECT":{"SUBJECT_TYPE":"Plant","SUBJECT_SPECIES":"Arabidopsis thaliana","TAXONOMY_ID":"3702","AGE_OR_AGE_RANGE":"2 weeks"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"4",
"Sample ID":"tube10_jmt1B",
"Factors":{"Genotype":"jmt"},
"Additional sample data":{"RAW_FILE_NAME":"tube10_jmt1B.D"}
},
{
"Subject ID":"5",
"Sample ID":"tube11_jmt2A",
"Factors":{"Genotype":"jmt"},
"Additional sample data":{"RAW_FILE_NAME":"tube11_jmt2A.D"}
},
{
"Subject ID":"5",
"Sample ID":"tube12_jmt2B",
"Factors":{"Genotype":"jmt"},
"Additional sample data":{"RAW_FILE_NAME":"tube12_jmt2B.D"}
},
{
"Subject ID":"6",
"Sample ID":"tube13_jmt3A",
"Factors":{"Genotype":"jmt"},
"Additional sample data":{"RAW_FILE_NAME":"tube13_jmt3A.D"}
},
{
"Subject ID":"6",
"Sample ID":"tube14_jmt3B",
"Factors":{"Genotype":"jmt"},
"Additional sample data":{"RAW_FILE_NAME":"tube14_jmt3B.D"}
},
{
"Subject ID":"4",
"Sample ID":"tube9_jmt1A",
"Factors":{"Genotype":"jmt"},
"Additional sample data":{"RAW_FILE_NAME":"tube9_jmt1A.D"}
},
{
"Subject ID":"NA",
"Sample ID":"tube1",
"Factors":{"Genotype":"NA"},
"Additional sample data":{"RAW_FILE_NAME":"tube1.D"}
},
{
"Subject ID":"NA",
"Sample ID":"tube2_emptypot",
"Factors":{"Genotype":"NA"},
"Additional sample data":{"RAW_FILE_NAME":"tube2_emptypot.D"}
},
{
"Subject ID":"1",
"Sample ID":"tube3_soil1A",
"Factors":{"Genotype":"NA"},
"Additional sample data":{"RAW_FILE_NAME":"tube3_soil1A.D"}
},
{
"Subject ID":"1",
"Sample ID":"tube4_soil1B",
"Factors":{"Genotype":"NA"},
"Additional sample data":{"RAW_FILE_NAME":"tube4_soil1B.D"}
},
{
"Subject ID":"2",
"Sample ID":"tube5_soil2A",
"Factors":{"Genotype":"NA"},
"Additional sample data":{"RAW_FILE_NAME":"tube5_soil2A.D"}
},
{
"Subject ID":"2",
"Sample ID":"tube6_soil2B",
"Factors":{"Genotype":"NA"},
"Additional sample data":{"RAW_FILE_NAME":"tube6_soil2B.D"}
},
{
"Subject ID":"3",
"Sample ID":"tube7_soil3A",
"Factors":{"Genotype":"NA"},
"Additional sample data":{"RAW_FILE_NAME":"tube7_soil3A.D"}
},
{
"Subject ID":"3",
"Sample ID":"tube8_soil3B",
"Factors":{"Genotype":"NA"},
"Additional sample data":{"RAW_FILE_NAME":"tube8_soil3B.D"}
},
{
"Subject ID":"7",
"Sample ID":"tube15_WT1A",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"tube15_WT1A.D"}
},
{
"Subject ID":"7",
"Sample ID":"tube16_WT1B",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"tube16_WT1B.D"}
},
{
"Subject ID":"8",
"Sample ID":"tube17_WT2A",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"tube17_WT2A.D"}
},
{
"Subject ID":"8",
"Sample ID":"tube18_WT2B",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"tube18_WT2B.D"}
},
{
"Subject ID":"9",
"Sample ID":"tube19_WT3A",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"tube19_WT3A.D"}
},
{
"Subject ID":"9",
"Sample ID":"tube20_WT3B",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"tube20_WT3B.D"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Root VOCs and soil VOCs were trapped as described here (Schulz-Bohm et al., 2018). Briefly, 2 Tenax cartridges were fitted into the side arms of the glass pots in such a way that their opening was exposed toward the plant roots/soil. VOCs were sampled for 40 hours and immediately analyzed by thermal desorption-gas chromatography‒mass spectrometry.","SAMPLE_TYPE":"Plant"},

"TREATMENT":{"TREATMENT_SUMMARY":"No specific treatment."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"After 40 hours of VOC trapping, Tenax cartridges were immediately subjected to thermal desorption."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Sample preparation and injection were performed using the fully automated Gerstel MPS-2 autosampler and Gerstel MAESTRO software. Volatile compounds were adsorbed on a Tenax TA tube. A thermal desorption unit (TDU) was used to thermally desorb the volatiles in splitless mode at 230°C for 10 min. To ensure that the volatiles released from the TDU were quantitatively trapped, a cooled injection system-programmed temperature vaporizer (CIS-PTV) was used. The CIS was heated from 80°C to 230°C at a rate of 12°C/s with the split valve closed during sample injection into the GC inlet. Analyses of volatile compounds were performed on an Agilent 7890B GC coupled to a 5977B quadruple mass spectrometer. Separation of compounds was performed on a DB-FFAP column (60 m x 250 µm x 0.25 µm, Agilent Technologies, Middleburg, OI, USA). Helium was used as the carrier gas at a flow rate of 1.9 ml/min, and solvent vent mode was used. The inlet temperature was 250°C. The oven program was as follows: initial temperature of 50°C held for 1 min, increased to 230°C at the rate of 10°C/min and held for 20 min. The temperature of the ion source and transfer line was 250°C.","INSTRUMENT_NAME":"Agilent 7890B","COLUMN_NAME":"Agilent DB-FFAP","CHROMATOGRAPHY_TYPE":"GC"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 5977B","INSTRUMENT_TYPE":"Single quadrupole","MS_TYPE":"EI","MS_COMMENTS":"The mass spectrometer was in electron ionization mode with an ionization energy of 70 eV, scan range of 40-300 m/z and solvent delay of 3.75 minutes. Analysis was performed in single ion monitoring (SIM) mode by monitoring the ions at 83, 151.1, and 224.1 with a dwell time of 150 ms. Mass Hunter Qualitative Analysis was used to extract and integrate peak spectra. The peak area of these ions was considered for the relative quantification of MeJA among different samples.","ION_MODE":"UNSPECIFIED"},

"MS_METABOLITE_DATA":{
"Units":"ion intensity peak area",

"Data":[{"Metabolite":"Methyl Jasmonate","tube10_jmt1B":"51380.3500","tube11_jmt2A":"","tube12_jmt2B":"12718.9000","tube13_jmt3A":"15363.3500","tube14_jmt3B":"33962.7200","tube9_jmt1A":"581408.6500","tube1":"2347.0800","tube2_emptypot":"11247.8800","tube3_soil1A":"14200.1900","tube4_soil1B":"","tube5_soil2A":"42016.5100","tube6_soil2B":"20850.5350","tube7_soil3A":"8040.0100","tube8_soil3B":"603018.8700","tube15_WT1A":"117534.9900","tube16_WT1B":"13982.3400","tube17_WT2A":"168327.7200","tube18_WT2B":"6365.8400","tube19_WT3A":"271639.5400","tube20_WT3B":"6804.8800"}],

"Metabolites":[{"Metabolite":"Methyl Jasmonate","pubchem_id":"5281929","inchi_key":"","kegg_id":"C11512","other_id":"","other_id_type":"","ri":"","ri_type":"","moverz_quant":"","":""}]
}

}