{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002807","ANALYSIS_ID":"AN004564","VERSION":"1","CREATED_ON":"August 4, 2023, 1:45 am"},

"PROJECT":{"PROJECT_TITLE":"Metabolomic response of river biofilm to cobalt","PROJECT_SUMMARY":"The metabolomic fingerprints of mature biofilms maintained in aquatic microcosms.","INSTITUTE":"Muséum Nationale d'Histoire Naturelle","LAST_NAME":"Marie","FIRST_NAME":"Benjamin","ADDRESS":"12 rue Buffon 75005 Paris","EMAIL":"bmarie@mnhn.fr","PHONE":"+33140793212"},

"STUDY":{"STUDY_TITLE":"Metabolomic response of river biofilm to cobalt","STUDY_SUMMARY":"Metabolites are low molecular-weight molecules produced during cellular metabolism. The global expression of the (meta-)metabolome could thus potentially be used to characterize the exposure of an organism or a community to a specific stressor. Here, the meta-metabolomic fingerprints of mature biofilms were examined after 1, 3 and 7 days of exposure to five concentrations of cobalt (0, 10-7, 10-6, 5 x 10-6 and 10-5 M) in aquatic microcosms. The global changes in meta-metabolomic fingerprints were in plain agreement with those of the other biological parameters studied (cobalt bioaccumulation, biomass, chlorophyll). To better understand the dose-responses of the biofilm meta-metabolome, the untargeted LC-HRMS metabolomic data were further processed using DRomics to build dose-response model curves and to calculate benchmark doses to be aggregated into an empirical cumulative density function. A trend analysis of the dose-response curves suggests the presence of homeostasis (0 - 4.7 x 10-7 M), defense (4.7 x 10-7 – 2.7 x 10-6 M) and damage (higher than 2.7 x 10-6 M) response ranges in biofilms exposed to various cobalt concentrations. The present study demonstrates that the use of untargerted meta-metabolomics represents a promising approach for environmental risk assessment of metals by relating molecular defense and damage mechanisms to contaminant concentration.","INSTITUTE":"Muséum Nationale d'Histoire Naturelle","LAST_NAME":"Marie","FIRST_NAME":"Benjamin","ADDRESS":"12 rue Buffon 75005 Paris","EMAIL":"bmarie@mnhn.fr","PHONE":"+33140793212"},

"SUBJECT":{"SUBJECT_TYPE":"Other organism","SUBJECT_SPECIES":"Biofilm microbial community"},
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"Sample ID":"20220202_B11_7j_M1_87_1_682",
"Factors":{"Sampling day":"7","Experimental group":"m","Cobalt concentration":"5 x 10-6"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B11_7j_M1_87_1_682"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B11_7j_M2_88_1_683",
"Factors":{"Sampling day":"7","Experimental group":"m","Cobalt concentration":"5 x 10-6"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B11_7j_M2_88_1_683"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B12_7j_M1_89_1_684",
"Factors":{"Sampling day":"7","Experimental group":"m","Cobalt concentration":"5 x 10-6"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B12_7j_M1_89_1_684"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B12_7j_M2_90_1_685",
"Factors":{"Sampling day":"7","Experimental group":"m","Cobalt concentration":"5 x 10-6"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B12_7j_M2_90_1_685"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B13_1j_M1_31_1_617",
"Factors":{"Sampling day":"1","Experimental group":"n","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B13_1j_M1_31_1_617"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B13_1j_M2_32_1_618",
"Factors":{"Sampling day":"1","Experimental group":"n","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B13_1j_M2_32_1_618"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B14_1j_M1_33_1_619",
"Factors":{"Sampling day":"1","Experimental group":"n","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B14_1j_M1_33_1_619"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B14_1j_M2_34_1_620",
"Factors":{"Sampling day":"1","Experimental group":"n","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B14_1j_M2_34_1_620"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B15_1j_M1_35_1_621",
"Factors":{"Sampling day":"1","Experimental group":"n","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B15_1j_M1_35_1_621"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B15_1j_M2_36_1_622",
"Factors":{"Sampling day":"1","Experimental group":"n","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B15_1j_M2_36_1_622"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B13_3j_M1_61_1_652",
"Factors":{"Sampling day":"3","Experimental group":"o","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B13_3j_M1_61_1_652"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B13_3j_M2_62_1_653",
"Factors":{"Sampling day":"3","Experimental group":"o","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B13_3j_M2_62_1_653"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B14_3j_M1_63_1_654",
"Factors":{"Sampling day":"3","Experimental group":"o","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B14_3j_M1_63_1_654"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B14_3j_M2_64_1_655",
"Factors":{"Sampling day":"3","Experimental group":"o","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B14_3j_M2_64_1_655"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B15_3j_M1_65_1_656",
"Factors":{"Sampling day":"3","Experimental group":"o","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B15_3j_M1_65_1_656"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B15_3j_M2_66_1_657",
"Factors":{"Sampling day":"3","Experimental group":"o","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B15_3j_M2_66_1_657"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B13_7j_M1_91_1_687",
"Factors":{"Sampling day":"7","Experimental group":"p","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B13_7j_M1_91_1_687"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B13_7j_M2_92_1_688",
"Factors":{"Sampling day":"7","Experimental group":"p","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B13_7j_M2_92_1_688"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B14_7j_M1_93_1_689",
"Factors":{"Sampling day":"7","Experimental group":"p","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B14_7j_M1_93_1_689"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B14_7j_M2_94_1_690",
"Factors":{"Sampling day":"7","Experimental group":"p","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B14_7j_M2_94_1_690"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B15_7j_M1_95_1_691",
"Factors":{"Sampling day":"7","Experimental group":"p","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B15_7j_M1_95_1_691"}
},
{
"Subject ID":"-",
"Sample ID":"20220202_B15_7j_M2_96_1_692",
"Factors":{"Sampling day":"7","Experimental group":"p","Cobalt concentration":"1 x 10-5"},
"Additional sample data":{"RAW_FILE_NAME":"Conversion MZXML20220202_B15_7j_M2_96_1_692"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Four weeks before the start of the experiment, the mature biofilms were collected by natural colonisation of glass slides (5 x 10 cm).","SAMPLE_TYPE":"Microbial biofilm"},

"TREATMENT":{"TREATMENT_SUMMARY":"A total of 15 microcosms were filled with 15 L of the Gave de Pau water; three for each of the five exposure conditions: 2 x 10-9 M (background concentration used as control), 1 x 10-7, 1 x 10-6, 5 x 10-6 and 1 x10-5 M Co. Cobalt (Cobalt Standard for ICP, 1000 mg·L-1, Supelco, Germany) was added in each microcosm and let equilibrating for 24 h (D-1). The microcosms were placed in one of the artificial streams of the facility in order to maintain the water temperature at 13.5 ± 1.0°C (Table S2). After one, three and seven days of exposure (D1, D3 and D7), slides were collected from each microcosm for metabolomics."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Briefly, freeze-dried biofilms (1 mg) were diluted in 10 µL of cold 75% methanol acidified with 0.1% formic acid and sonicated on ice during 30 s, at 80 % of the maximum intensity (SONICS Vibra Cell, Newton, CT, USA; 130 Watts, 20 kHz). The homogenates were then centrifuged at 4°C (12,000 g: 10 min). The supernatants were then collected and stored in the dark at -20°C.","PROCESSING_STORAGE_CONDITIONS":"-20℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Thermo Acclaim Polar Advantage II (150 x 3mm,3um)","SOLVENT_A":"Water","SOLVENT_B":"ACN","FLOW_GRADIENT":"5-90%","FLOW_RATE":"300 microliter per minute","COLUMN_TEMPERATURE":"40"},

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

"MS":{"INSTRUMENT_NAME":"Bruker maXis Impact qTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Metabolites were subsequently ionised and analysed using an electrospray ionization hybrid quadrupole time-of-flight high-resolution mass spectrometer (ESI-Qq-TOF Compact, Bruker) at 2 Hz speed on the 50–1500 m/z range on positive autoMS/MS mode between 2 and 8 Hz speed on the 50–1500 m/z range with information-dependent acquisition (IDA).","MS_RESULTS_FILE":"ST002807_AN004564_Results.txt UNITS:Dalton Has m/z:Neutral masses Has RT:Yes RT units:Seconds"}

}