#METABOLOMICS WORKBENCH omkar123_20230420_161302 DATATRACK_ID:3875 STUDY_ID:ST002867 ANALYSIS_ID:AN004700 PROJECT_ID:PR001462
VERSION             	1
CREATED_ON             	September 19, 2023, 11:06 am
#PROJECT
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:LAST_NAME                     	Kulkarni
PR:FIRST_NAME                    	Omkar
PR:ADDRESS                       	Dept of Biological Sciences,Metabolites Biology Lab,, Science drive 4,Block S1A
PR:ADDRESS                       	#06-03
PR:EMAIL                         	omkar@u.nus.edu
PR:PHONE                         	98668733
#STUDY
ST:STUDY_TITLE                   	Root VOCs of Arabidopsis thaliana and its mutants
ST:STUDY_SUMMARY                 	This study provides a comprehensive list of root VOCs detected from the
ST:STUDY_SUMMARY                 	rhizosphere of Arabidopsis thaliana and the mutants belonging to their
ST:STUDY_SUMMARY                 	biosynthetic pathways.
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                         	omkar@u.nus.edu
ST:PHONE                         	98668733
#SUBJECT
SU:SUBJECT_TYPE                  	Plant
SU:SUBJECT_SPECIES               	Arabidopsis thaliana
SU:TAXONOMY_ID                   	3702
#FACTORS
#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           	-	cyp83b1_1	Genotype:cyp83b1	RAW_FILE_NAME=cyp83b1_1.D
SUBJECT_SAMPLE_FACTORS           	-	cyp83b1_2	Genotype:cyp83b1	RAW_FILE_NAME=cyp83b1_2.D
SUBJECT_SAMPLE_FACTORS           	-	cyp83b1_3	Genotype:cyp83b1	RAW_FILE_NAME=cyp83b1_3.D
SUBJECT_SAMPLE_FACTORS           	-	fps1_1	Genotype:fps1	RAW_FILE_NAME=fps1_1.D
SUBJECT_SAMPLE_FACTORS           	-	fps1_2	Genotype:fps1	RAW_FILE_NAME=fps1_2.D
SUBJECT_SAMPLE_FACTORS           	-	fps1_3	Genotype:fps1	RAW_FILE_NAME=fps1_3.D
SUBJECT_SAMPLE_FACTORS           	-	fps2_1	Genotype:fps2	RAW_FILE_NAME=fps2_1.D
SUBJECT_SAMPLE_FACTORS           	-	fps2_2	Genotype:fps2	RAW_FILE_NAME=fps2_2.D
SUBJECT_SAMPLE_FACTORS           	-	fps2_3	Genotype:fps2	RAW_FILE_NAME=fps2_3.D
SUBJECT_SAMPLE_FACTORS           	-	ggpps_1	Genotype:ggpps	RAW_FILE_NAME=ggpps_1.D
SUBJECT_SAMPLE_FACTORS           	-	ggpps_2	Genotype:ggpps	RAW_FILE_NAME=ggpps_2.D
SUBJECT_SAMPLE_FACTORS           	-	ggpps_3	Genotype:ggpps	RAW_FILE_NAME=ggpps_3.D
SUBJECT_SAMPLE_FACTORS           	-	gpps_1	Genotype:gpps	RAW_FILE_NAME=gpps_1.D
SUBJECT_SAMPLE_FACTORS           	-	gpps_2	Genotype:gpps	RAW_FILE_NAME=gpps_2.D
SUBJECT_SAMPLE_FACTORS           	-	gpps_3	Genotype:gpps	RAW_FILE_NAME=gpps_3.D
SUBJECT_SAMPLE_FACTORS           	-	hpl_1	Genotype:hpl	RAW_FILE_NAME=hpl_1.D
SUBJECT_SAMPLE_FACTORS           	-	hpl_2	Genotype:hpl	RAW_FILE_NAME=hpl_2.D
SUBJECT_SAMPLE_FACTORS           	-	hpl_3	Genotype:hpl	RAW_FILE_NAME=hpl_3.D
SUBJECT_SAMPLE_FACTORS           	-	lox1_1	Genotype:lox1	RAW_FILE_NAME=lox1_1.D
SUBJECT_SAMPLE_FACTORS           	-	lox1_2	Genotype:lox1	RAW_FILE_NAME=lox1_2.D
SUBJECT_SAMPLE_FACTORS           	-	lox1_3	Genotype:lox1	RAW_FILE_NAME=lox1_3.D
SUBJECT_SAMPLE_FACTORS           	-	pal1_1	Genotype:pal1	RAW_FILE_NAME=pal1_1.D
SUBJECT_SAMPLE_FACTORS           	-	pal1_2	Genotype:pal1	RAW_FILE_NAME=pal1_2.D
SUBJECT_SAMPLE_FACTORS           	-	pal1_3	Genotype:pal1	RAW_FILE_NAME=pal1_3.D
SUBJECT_SAMPLE_FACTORS           	-	soil_1	Genotype:soil	RAW_FILE_NAME=soil_1.D
SUBJECT_SAMPLE_FACTORS           	-	soil_2	Genotype:soil	RAW_FILE_NAME=soil_2.D
SUBJECT_SAMPLE_FACTORS           	-	tgg1_1	Genotype:tgg1	RAW_FILE_NAME=tgg1_1.D
SUBJECT_SAMPLE_FACTORS           	-	tgg1_2	Genotype:tgg1	RAW_FILE_NAME=tgg1_2.D
SUBJECT_SAMPLE_FACTORS           	-	tgg1_3	Genotype:tgg1	RAW_FILE_NAME=tgg1_3.D
SUBJECT_SAMPLE_FACTORS           	-	tgg2_1	Genotype:tgg2	RAW_FILE_NAME=tgg2_1.D
SUBJECT_SAMPLE_FACTORS           	-	tgg2_2	Genotype:tgg2	RAW_FILE_NAME=tgg2_2.D
SUBJECT_SAMPLE_FACTORS           	-	tgg2_3	Genotype:tgg2	RAW_FILE_NAME=tgg2_3.D
SUBJECT_SAMPLE_FACTORS           	-	Wt_1	Genotype:Wt	RAW_FILE_NAME=Wt_1.D
SUBJECT_SAMPLE_FACTORS           	-	Wt_2	Genotype:Wt	RAW_FILE_NAME=Wt_2.D
SUBJECT_SAMPLE_FACTORS           	-	Wt_3	Genotype:Wt	RAW_FILE_NAME=Wt_3.D
#COLLECTION
CO:COLLECTION_SUMMARY            	Root VOCs and soil VOCs were trapped as described here (Schulz-Bohm, et al,
CO:COLLECTION_SUMMARY            	2018, "Calling from distance: attraction of soil bacteria by plant root
CO:COLLECTION_SUMMARY            	volatiles", The ISME Journal, 12(5), pp.1252-1262.). Briefly, 1 Tenax cartridge
CO:COLLECTION_SUMMARY            	was fitted into the side arms of the glass pots in such a way that their opening
CO:COLLECTION_SUMMARY            	was exposed toward the plant roots/soil. The other arm received a constant
CO:COLLECTION_SUMMARY            	airflow from an aerator. VOCs were sampled for 40 hours and immediately analyzed
CO:COLLECTION_SUMMARY            	by thermal desorption-gas chromatography‒mass spectrometry.
CO:SAMPLE_TYPE                   	Plant
#TREATMENT
TR:TREATMENT_SUMMARY             	No specific treatment.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	After 40 hours of VOC trapping, Tenax cartridges were immediately subjected to
SP:SAMPLEPREP_SUMMARY            	thermal desorption.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Chromatography GC column used was DB-FFAP, 60m length, 250um inner diameter,
CH:CHROMATOGRAPHY_SUMMARY        	0.25um film thickness)
CH:CHROMATOGRAPHY_TYPE           	GC
CH:INSTRUMENT_NAME               	Agilent 7890B
CH:COLUMN_NAME                   	Agilent DB-FFAP (60m x 250um, 0.25um)
CH:SOLVENT_A                     	NA
CH:SOLVENT_B                     	NA
CH:FLOW_GRADIENT                 	NA
CH:FLOW_RATE                     	NA
CH:COLUMN_TEMPERATURE            	NA
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Agilent 5977B
MS:INSTRUMENT_TYPE               	QTOF
MS:MS_TYPE                       	EI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	Analysis was performed using MassHunter Qualified software to extract and
MS:MS_COMMENTS                   	integrate peat spectra to profile the root volatiles from WT and mutant lines.
MS:MS_COMMENTS                   	The data from only soil was considered as the blank and was subtracted from the
MS:MS_COMMENTS                   	rVOCs data. Compounds were identified by using the library NIST 2020 (Agilent
MS:MS_COMMENTS                   	Technologies, Palo Alto, CA, USA) with minimum hit count of 65. The compounds
MS:MS_COMMENTS                   	that were found to be present in at least two biological replicates out of three
MS:MS_COMMENTS                   	were taken into consideration for further analysis.
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	% relative peak abundance
MS_METABOLITE_DATA_START
Samples	Wt_1	Wt_2	Wt_3	tgg1_1	tgg1_2	tgg1_3	tgg2_1	tgg2_2	tgg2_3	pal1_1	pal1_2	pal1_3	lox1_1	lox1_2	lox1_3	hpl_1	hpl_2	hpl_3	gpps_1	gpps_2	gpps_3	ggpps_1	ggpps_2	ggpps_3	fps1_1	fps1_2	fps1_3	fps2_1	fps2_2	fps2_3	cyp83b1_1	cyp83b1_2	cyp83b1_3	soil_1	soil_2
Factors	Genotype:Wt	Genotype:Wt	Genotype:Wt	Genotype:tgg1	Genotype:tgg1	Genotype:tgg1	Genotype:tgg2	Genotype:tgg2	Genotype:tgg2	Genotype:pal1	Genotype:pal1	Genotype:pal1	Genotype:lox1	Genotype:lox1	Genotype:lox1	Genotype:hpl	Genotype:hpl	Genotype:hpl	Genotype:gpps	Genotype:gpps	Genotype:gpps	Genotype:ggpps	Genotype:ggpps	Genotype:ggpps	Genotype:fps1	Genotype:fps1	Genotype:fps1	Genotype:fps2	Genotype:fps2	Genotype:fps2	Genotype:cyp83b1	Genotype:cyp83b1	Genotype:cyp83b1	Genotype:soil	Genotype:soil
(4Z)-5-Methyl-4-undecene	0.028026025	0.022987098	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
(E)-3-pentacosene	0.100914478	0.053482838	0	0.464664385	0	0.313033615	0	0	0	0	0	0	0	0	0	0.148317806	0.188856322	0	0	0	0	0.041152901	0.193389865	0	0	0	0	0	4.636990806	0.093530869	0.117037267	0.079466595	0.734307455	0	0
1-Octanol	0.059227441	0.092808179	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
6-oxabicyclo[3.1.0]hexane-2,4-diol	0.050403509	0.041579433	0.115199497	0	0	0	0	0	0	0	0	0	0	0	0	0.327915362	0.292637882	0	0	0	0	0	0.34941768	0.125385386	0.126436452	0	0.157032626	0	0	0	0	0	0	0	0
2-Nonen-1-ol, (Z)-	0.029154099	0	0.516859213	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
1-Nonanol	0.059227441	0	0.101670318	0	0	0	0.111793552	0.059694601	0.294335109	0.116798981	1.553570475	0.216591396	0.299417296	0.136834554	0.068811757	0	0.282292865	0.045976289	1.416119057	0.701106396	0.379857398	0	0.859566496	0.236273274	0.090993613	0.906096292	0.177973465	0.672883216	0.368320856	0.118587883	0.345880774	0.136010363	0.489448518	0	0
Nonanoic acid	0.076609246	0.106034569	0	0.249904226	0.580368938	1.073023606	0	0	0	0	0	0	0.277121046	0.152920267	0.525911192	0.344480253	0.423645231	0.130749629	0	0	0	0.064491915	0.413916816	0.120665656	0	0	0	0	0	0	0	0	0	0	0
Propanoic acid	0	0.120832339	0.369385874	0.875081299	0.120118739	0	0	0	0	0	0	0	0.488087313	0.275633649	0.304375787	0	0.506773495	0.183190512	0	0	0	0	0.096095406	0.240749684	0	0	0	0	0	0	0	0	0	0	0
2-(2,2-dimethoxypropyl)-3-(methoxymethyl)oxepin-4,5-dicarboxylic acid dimethyl ester	0.12271267	0.05155766	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Dibutyl phthalate	0.138993221	0	1.301560845	0	0	0	24.45754653	71.54554551	0.190361908	0	0	0	52.80465616	73.02316777	52.0500236	0	0	0	0	0	0	0	27.93196883	68.90017662	62.71059899	0	34.14943656	0	0	0	0	0	0	0	0
Glycerol tricaprylate	0.059796329	0	0.088567492	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.147799531	0.223366652	0.087127797	0	0	0	0	0
Propionic acid, 2-mercapto-, isopropyl ester, benzoate	0.03597711	0.077578736	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
1-(Benzyloxy)-2-fluoro-2-phenyl-3-(p-toluenesulsulfonyloxy)propane	0.730439909	0	51.51165575	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
2-Methyl-1-phenyl-1-propenylisocyanide	0.058494472	0	0.432482979	0.332300972	0.738250239	0	0.140379592	0.026837715	0	0	0	0	0.186284944	0	0.392248906	0.305665298	0.105915779	0	0	0.841507851	0.563704215	0	0	0	0.091534392	0	0.308113713	0.488548669	0.392868751	0.093437676	0	0.189043515	0.19304035	0	0
Hexadecane, 2,6,10,14-tetramethyl-	1.068746441	0.031713047	2.853119875	0	0	0	0	0	0	0	0	0	0	0	0	0.148907052	1.426694495	0	0	0	0	0.19748647	0.133055213	0	0.268348719	2.912126927	0.081361239	5.062555602	4.636990806	0	0.117037267	0	6.118109794	0	0
1-Ethylundecylbenzene	0.021565924	0.018010124	0	0	0.038589413	0.053291702	0	0	0	0	0	0	0.055687623	0.037270745	0	0	0.078605178	0.021916972	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
1-methoxy-4-(1-methoxypropyl)benzene	0	0.015963485	0.055263107	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
3-(4-methoxyphenyl)-4,4-dimethyl-3-hepta-1,6-dienol	0	0.222438796	0.07602477	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
4-(methoxymethoxy)-1-pentyne	0.101247165	0.073432389	0	0	0	0	0.164160679	0	0.191556708	0	0.642465832	0.158024486	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Quinuclidinium-methanesulfonate	2.13489855	0	0.183977377	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
2-Hydroxy-1-[(2-hydroxy)phenyl]-1-propanone	0	0.007379757	0.017874377	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.011413232	0.046882262	0	0	0	0	0	0	0	0	0
Acetophenone	0.036462676	0	0.75079666	1.538127267	0	0.145090537	0	0	0	0	0	0	0.687312536	0.470065523	0	1.639509891	1.495625594	0.395430104	3.3685256	1.670092142	1.855073234	0	1.606076865	0.473853189	0.55731402	2.025998568	0	1.674330996	1.823409001	1.224616378	0	0	0	0	0
Methyl 2-O-Tosyl-.alpha.-D-xylopyranoside	0	0.045357715	0.076239713	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	PubChem ID
(4Z)-5-Methyl-4-undecene	5364593
(E)-3-pentacosene	NA
1-Octanol	957
6-oxabicyclo[3.1.0]hexane-2,4-diol	18506421
2-Nonen-1-ol, (Z)-	5365027
1-Nonanol	8914
Nonanoic acid	8158
Propanoic acid	1032
2-(2,2-dimethoxypropyl)-3-(methoxymethyl)oxepin-4,5-dicarboxylic acid dimethyl ester	NA
Dibutyl phthalate	3026
Glycerol tricaprylate	10850
Propionic acid, 2-mercapto-, isopropyl ester, benzoate	NA
1-(Benzyloxy)-2-fluoro-2-phenyl-3-(p-toluenesulsulfonyloxy)propane	NA
2-Methyl-1-phenyl-1-propenylisocyanide	85638800
Hexadecane, 2,6,10,14-tetramethyl-	73437587
1-Ethylundecylbenzene	NA
1-methoxy-4-(1-methoxypropyl)benzene	4605200
3-(4-methoxyphenyl)-4,4-dimethyl-3-hepta-1,6-dienol	NA
4-(methoxymethoxy)-1-pentyne	NA
Quinuclidinium-methanesulfonate	NA
2-Hydroxy-1-[(2-hydroxy)phenyl]-1-propanone	NA
Acetophenone	7410
Methyl 2-O-Tosyl-.alpha.-D-xylopyranoside	NA
METABOLITES_END
#END