{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001393","ANALYSIS_ID":"AN002327","VERSION":"1","CREATED_ON":"June 4, 2020, 4:06 pm"},

"PROJECT":{"PROJECT_TITLE":"Sea-ice diatom compatible solute shifts","PROJECT_TYPE":"Marine Metabolomics","PROJECT_SUMMARY":"Sea-ice algae provide an important source of primary production in polar regions, yet we have limited understanding of their responses to the seasonal cycling of temperature and salinity. Using a targeted liquid chromatography-mass spectrometry-based metabolomics approach, we found that axenic cultures of the Antarctic sea-ice diatom, Nitzschia lecointei, displayed large differences in their metabolomes when grown in a matrix of conditions that included temperatures of –1 and 4°C, and salinities of 32 and 41, despite relatively small changes in growth rate. Temperature exerted a greater effect than salinity on cellular metabolite pool sizes, though the N- or S-containing compatible solutes, 2,3-dihydroxypropane-1-sulfonate (DHPS), glycine betaine (GBT), dimethylsulfoniopropionate (DMSP), and proline responded strongly to both temperature and salinity, suggesting complexity in their control. We saw the largest (> 4 fold) response to salinity for proline. DHPS, a rarely studied but potential compatible solute, reached the highest intracellular compatible solute concentrations of ~ 85 mM. When comparing the culture findings to natural Arctic sea-ice diatom communities, we found extensive overlap in metabolite profiles, highlighting the relevance of culture-based studies to probe environmental questions. Large changes in sea-ice diatom metabolomes and compatible solutes over a seasonal cycle could be significant components of biogeochemical cycling within sea ice.","INSTITUTE":"University of Washington","DEPARTMENT":"School of Oceanography","LABORATORY":"Ingalls Lab","LAST_NAME":"Dawson","FIRST_NAME":"Hannah","ADDRESS":"1501 NE Boat Street, Marine Science Building, Room G, Seattle, WA 98195","EMAIL":"hmdawson@uw.edu","PHONE":"2062216750","FUNDING_SOURCE":"Booth Foundation, NSF, UW Graduate Top Scholar Award, Gordon and Betty Moore Foundation","PUBLICATIONS":"Dawson et al., Elementa"},

"STUDY":{"STUDY_TITLE":"Sea-ice diatom compatible solute shifts","STUDY_TYPE":"Compatible solutes were quantified in sea-ice diatoms","STUDY_SUMMARY":"Sea-ice algae provide an important source of primary production in polar regions, yet we have limited understanding of their responses to the seasonal cycling of temperature and salinity. Using a targeted liquid chromatography-mass spectrometry-based metabolomics approach, we found that axenic cultures of the Antarctic sea-ice diatom, Nitzschia lecointei, displayed large differences in their metabolomes when grown in a matrix of conditions that included temperatures of –1 and 4°C, and salinities of 32 and 41, despite relatively small changes in growth rate. Temperature exerted a greater effect than salinity on cellular metabolite pool sizes, though the N- or S-containing compatible solutes, 2,3-dihydroxypropane-1-sulfonate (DHPS), glycine betaine (GBT), dimethylsulfoniopropionate (DMSP), and proline responded strongly to both temperature and salinity, suggesting complexity in their control. We saw the largest (> 4 fold) response to salinity for proline. DHPS, a rarely studied but potential compatible solute, reached the highest intracellular compatible solute concentrations of ~ 85 mM. When comparing the culture findings to natural Arctic sea-ice diatom communities, we found extensive overlap in metabolite profiles, highlighting the relevance of culture-based studies to probe environmental questions. Large changes in sea-ice diatom metabolomes and compatible solutes over a seasonal cycle could be significant components of biogeochemical cycling within sea ice.","INSTITUTE":"University of Washington","DEPARTMENT":"School of Oceanography","LABORATORY":"Ingalls Lab","LAST_NAME":"Dawson","FIRST_NAME":"Hannah","ADDRESS":"1501 NE Boat Street, Marine Science Building, Room G, Seattle, WA 98195","EMAIL":"hmdawson@uw.edu","PHONE":"2062216750","PUBLICATIONS":"Dawson et al., Elementa"},

"SUBJECT":{"SUBJECT_TYPE":"Other","SUBJECT_SPECIES":"Nitzschia lecointei","TAXONOMY_ID":"186028","GENDER":"Not applicable"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"32ppt-1C_A",
"Factors":{"Type":"Smp","Salinity":"32","Temp_degC":"-1"},
"Additional sample data":{"Replicate":"A","RFU":"605.6","Vol_L":"0.07","RAW_FILE_NAME":"170410_Smp_32ppt-1C_A;170413_Smp_40ppt4C_C;170410_Smp_32ppt-1C_A"}
},
{
"Subject ID":"-",
"Sample ID":"32ppt-1C_B",
"Factors":{"Type":"Smp","Salinity":"32","Temp_degC":"-1"},
"Additional sample data":{"Replicate":"B","RFU":"551.2","Vol_L":"0.07","RAW_FILE_NAME":"170410_Smp_32ppt-1C_B;170413_Smp_32ppt-1C_B;170410_Smp_32ppt-1C_B"}
},
{
"Subject ID":"-",
"Sample ID":"32ppt-1C_C",
"Factors":{"Type":"Smp","Salinity":"32","Temp_degC":"-1"},
"Additional sample data":{"Replicate":"C","RFU":"550.6","Vol_L":"0.07","RAW_FILE_NAME":"170410_Smp_32ppt-1C_C;170413_Smp_32ppt-1C_C;170410_Smp_32ppt-1C_C"}
},
{
"Subject ID":"-",
"Sample ID":"32ppt4C_A",
"Factors":{"Type":"Smp","Salinity":"32","Temp_degC":"4"},
"Additional sample data":{"Replicate":"A","RFU":"847.1","Vol_L":"0.07","RAW_FILE_NAME":"170410_Smp_32ppt4C_A;170413_Smp_32ppt4C_B;170410_Smp_32ppt4C_A"}
},
{
"Subject ID":"-",
"Sample ID":"32ppt4C_B",
"Factors":{"Type":"Smp","Salinity":"32","Temp_degC":"4"},
"Additional sample data":{"Replicate":"B","RFU":"967.1","Vol_L":"0.07","RAW_FILE_NAME":"170410_Smp_32ppt4C_B;170413_Smp_32ppt4C_A;170410_Smp_32ppt4C_B"}
},
{
"Subject ID":"-",
"Sample ID":"32ppt4C_C",
"Factors":{"Type":"Smp","Salinity":"32","Temp_degC":"4"},
"Additional sample data":{"Replicate":"C","RFU":"918.5","Vol_L":"0.07","RAW_FILE_NAME":"170410_Smp_32ppt4C_C;170413_Smp_32ppt4C_C;170410_Smp_32ppt4C_C"}
},
{
"Subject ID":"-",
"Sample ID":"40ppt-1C_A",
"Factors":{"Type":"Smp","Salinity":"40","Temp_degC":"-1"},
"Additional sample data":{"Replicate":"A","RFU":"860.2","Vol_L":"0.07","RAW_FILE_NAME":"170410_Smp_40ppt-1C_A;170413_Smp_40ppt-1C_A;170410_Smp_40ppt-1C_A"}
},
{
"Subject ID":"-",
"Sample ID":"40ppt-1C_B",
"Factors":{"Type":"Smp","Salinity":"40","Temp_degC":"-1"},
"Additional sample data":{"Replicate":"B","RFU":"681.6","Vol_L":"0.07","RAW_FILE_NAME":"170410_Smp_40ppt-1C_B;170413_Smp_40ppt4C_B;170410_Smp_40ppt-1C_B"}
},
{
"Subject ID":"-",
"Sample ID":"40ppt-1C_C",
"Factors":{"Type":"Smp","Salinity":"40","Temp_degC":"-1"},
"Additional sample data":{"Replicate":"C","RFU":"814.3","Vol_L":"0.07","RAW_FILE_NAME":"170410_Smp_40ppt-1C_C;170413_Smp_40ppt-1C_C;170410_Smp_40ppt-1C_C"}
},
{
"Subject ID":"-",
"Sample ID":"40ppt4C_A",
"Factors":{"Type":"Smp","Salinity":"40","Temp_degC":"4"},
"Additional sample data":{"Replicate":"A","RFU":"581.8","Vol_L":"0.07","RAW_FILE_NAME":"170410_Smp_40ppt4C_A;170413_Smp_40ppt4C_A;170410_Smp_40ppt4C_A"}
},
{
"Subject ID":"-",
"Sample ID":"40ppt4C_B",
"Factors":{"Type":"Smp","Salinity":"40","Temp_degC":"4"},
"Additional sample data":{"Replicate":"B","RFU":"681.6","Vol_L":"0.07","RAW_FILE_NAME":"170410_Smp_40ppt4C_B;170413_Smp_40ppt-1C_B;170410_Smp_40ppt4C_B"}
},
{
"Subject ID":"-",
"Sample ID":"40ppt4C_C",
"Factors":{"Type":"Smp","Salinity":"40","Temp_degC":"4"},
"Additional sample data":{"Replicate":"C","RFU":"662","Vol_L":"0.07","RAW_FILE_NAME":"170410_Smp_40ppt4C_C;170413_Smp_32ppt-1C_A;170410_Smp_40ppt4C_C"}
},
{
"Subject ID":"-",
"Sample ID":"ASWFilterBlk_1",
"Factors":{"Type":"Blk","Salinity":"NA","Temp_degC":"NA"},
"Additional sample data":{"Replicate":"1","RFU":"NA","Vol_L":"0.3","RAW_FILE_NAME":"170612_Blk_ASWFilterBlk_1;170615_Blk_ASWFilterBlk_1;170612_Blk_ASWFilterBlk_1"}
},
{
"Subject ID":"-",
"Sample ID":"ASWFilterBlk_2",
"Factors":{"Type":"Blk","Salinity":"NA","Temp_degC":"NA"},
"Additional sample data":{"Replicate":"2","RFU":"NA","Vol_L":"0.3","RAW_FILE_NAME":"170612_Blk_ASWFilterBlk_2;170615_Blk_ASWFilterBlk_2;170612_Blk_ASWFilterBlk_2"}
},
{
"Subject ID":"-",
"Sample ID":"ASWFilterBlk_3",
"Factors":{"Type":"Blk","Salinity":"NA","Temp_degC":"NA"},
"Additional sample data":{"Replicate":"3","RFU":"NA","Vol_L":"0.3","RAW_FILE_NAME":"170612_Blk_ASWFilterBlk_3;170615_Blk_ASWFilterBlk_3;170612_Blk_ASWFilterBlk_3"}
},
{
"Subject ID":"-",
"Sample ID":"MediaBlk_ppt32",
"Factors":{"Type":"Blk","Salinity":"32","Temp_degC":"NA"},
"Additional sample data":{"Replicate":"ppt32","RFU":"1","Vol_L":"0.07","RAW_FILE_NAME":"170410_Blk_MediaBlk_ppt32;170413_Blk_MediaBlk_ppt32;170410_Blk_MediaBlk_ppt32"}
},
{
"Subject ID":"-",
"Sample ID":"MediaBlk_ppt40",
"Factors":{"Type":"Blk","Salinity":"40","Temp_degC":"NA"},
"Additional sample data":{"Replicate":"ppt40","RFU":"1","Vol_L":"0.07","RAW_FILE_NAME":"170410_Blk_MediaBlk_ppt40;170413_Blk_MediaBlk_ppt40;170410_Blk_MediaBlk_ppt40"}
},
{
"Subject ID":"-",
"Sample ID":"S2C_4",
"Factors":{"Type":"Smp","Salinity":"NA","Temp_degC":"NA"},
"Additional sample data":{"Replicate":"4","RFU":"NA","Vol_L":"0.1671","RAW_FILE_NAME":"170612_Smp_S2C_4;170615_Smp_S2C_4;170612_Smp_S2C_4"}
},
{
"Subject ID":"-",
"Sample ID":"S2C_5",
"Factors":{"Type":"Smp","Salinity":"NA","Temp_degC":"NA"},
"Additional sample data":{"Replicate":"5","RFU":"NA","Vol_L":"0.2486","RAW_FILE_NAME":"170612_Smp_S2C_5;170615_Smp_S2C_5;170612_Smp_S2C_5"}
},
{
"Subject ID":"-",
"Sample ID":"S2C_6",
"Factors":{"Type":"Smp","Salinity":"NA","Temp_degC":"NA"},
"Additional sample data":{"Replicate":"6","RFU":"NA","Vol_L":"0.2049","RAW_FILE_NAME":"170612_Smp_S2C_6;170615_Smp_S2C_6;170612_Smp_S2C_6"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cultured diatom cells at different salinities and temperatures grown to exponential phase were filtered onto 0.2-micron filters and extracted for metabolites as described in methods. Three dedicated ice cores were sampled from the Chukchi Sea near Utqiaġvik, AK. The bottom 5-cm sections were placed in polycarbonate tubs, allowed to melt at 4°C in artificial seawater, and filtered onto 0.2-micron filters. Filters were extracted for metabolites as described in methods. All filters were frozen in liquid nitrogen immediately after filtration and stored in a -80 C freezer until extraction.","SAMPLE_TYPE":"Diatom cells/Particulate matter from sea ice cores","STORAGE_CONDITIONS":"Described in summary"},

"TREATMENT":{"TREATMENT_SUMMARY":"Diatom cells were cultured in a matrix of two temperatures (–1°C and 4°C) and two salinities (32 and 40) in triplicate. There was no treatment for the sea ice cores – this was a study of how the cultured diatoms compare to the diatom-dominated Arctic sea-ice communities."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Each sample was extracted using a modified Bligh-Dyer extraction. Briefly, filters were cut up and put into 15 mL teflon centrifuge tubes containing a mixture of 100 µm and 400 µm silica beads. Heavy isotope-labeled internal standards were added along with ~2 mL of cold aqueous solvent (50:50 methanol:water) and ~3 mL of cold organic solvent (dichloromethane). The samples were shaken on a FastPrep-24 Homogenizer for 30 seconds and chilled in a -20 °C freezer repeatedly for three cycles of bead-beating and a total of 30 minutes of chilling. The organic and aqueous layers were separated by spinning samples in a centrifuge at 4,300 rpm for 2 minutes at 4 °C. The aqueous layer was removed to a new glass centrifuge tube. The remaining organic fraction was rinsed three more times with additions of 1 to 2 mL of 50:50 methanol:water. All aqueous rinses were combined for each sample and dried down under N2 gas. The remaining organic layer was transferred into a clean glass centrifuge tube and the remaining bead beating tube was rinsed two more times with cold organic solvent. The combined organic rinses were centrifuged, transferred to a new tube, and dried under N2 gas. Dried aqueous fractions were re-dissolved in 380 µL of water. Dried organic fractions were re-dissolved in 380 µL of 1:1 water:acetonitrile. 20 µL of isotope-labeled injection standards in water were added to both fractions. Blank filters were extracted alongside samples as methodological blanks.","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACTION_METHOD":"Bligh-Dyer","EXTRACT_STORAGE":"-80℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"See attached summary","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Waters Acquity I-Class","COLUMN_NAME":"SeQuant ZIC- pHILIC (150 x 2.1mm, 5um)"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF hybrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"See protocol, data from culture samples"},

"MS_METABOLITE_DATA":{
"Units":"Normalized Peak Area Per RFU",

"Data":[{"Metabolite":"Arginine","32ppt-1C_A":"3001743.408","32ppt-1C_B":"3353997.62","32ppt-1C_C":"3473641.388","32ppt4C_A":"2047106.722","32ppt4C_B":"1698512.647","32ppt4C_C":"2573092.073","40ppt-1C_A":"2335450.843","40ppt-1C_B":"3500449.538","40ppt-1C_C":"3087854.396","40ppt4C_A":"2421586.241","40ppt4C_B":"2355497.196","40ppt4C_C":"2250111.394","MediaBlk_ppt32":"1879293","MediaBlk_ppt40":"1509344"},{"Metabolite":"Betaine","32ppt-1C_A":"56366274.51","32ppt-1C_B":"57471124.47","32ppt-1C_C":"62389815.5","32ppt4C_A":"52668001.74","32ppt4C_B":"42033883.89","32ppt4C_C":"46236727.8","40ppt-1C_A":"58787152.39","40ppt-1C_B":"81983985.9","40ppt-1C_C":"69842894.74","40ppt4C_A":"106876016.9","40ppt4C_B":"88522521.17","40ppt4C_C":"85193418.45","MediaBlk_ppt32":"290210241.2","MediaBlk_ppt40":"405191332.6"},{"Metabolite":"DMSP","32ppt-1C_A":"84298805.04","32ppt-1C_B":"88753782.64","32ppt-1C_C":"91901779.29","32ppt4C_A":"53419515.17","32ppt4C_B":"43157476.06","32ppt4C_C":"50160089.24","40ppt-1C_A":"77844264.95","40ppt-1C_B":"107686663","40ppt-1C_C":"94006701.58","40ppt4C_A":"106265384.7","40ppt4C_B":"85811727","40ppt4C_C":"85883007","MediaBlk_ppt32":"0","MediaBlk_ppt40":"0"},{"Metabolite":"Glutamic acid","32ppt-1C_A":"1437396.143","32ppt-1C_B":"1426585.312","32ppt-1C_C":"1581338.874","32ppt4C_A":"631602.5971","32ppt4C_B":"635460.1096","32ppt4C_C":"804831.9477","40ppt-1C_A":"929326.352","40ppt-1C_B":"1223627.23","40ppt-1C_C":"988213.4447","40ppt4C_A":"790644.5926","40ppt4C_B":"687145.0704","40ppt4C_C":"644907.4562","MediaBlk_ppt32":"11948","MediaBlk_ppt40":"22690"},{"Metabolite":"Glutamine","32ppt-1C_A":"1012372.1","32ppt-1C_B":"962250.7983","32ppt-1C_C":"1112967.323","32ppt4C_A":"983365.3264","32ppt4C_B":"929346.839","32ppt4C_C":"891417.8508","40ppt-1C_A":"891061.3904","40ppt-1C_B":"1022730.047","40ppt-1C_C":"987494.6924","40ppt4C_A":"1173204.373","40ppt4C_B":"1061338.592","40ppt4C_C":"972871.6375","MediaBlk_ppt32":"81580","MediaBlk_ppt40":"99379"},{"Metabolite":"Proline","32ppt-1C_A":"6544300.099","32ppt-1C_B":"7656239.487","32ppt-1C_C":"7636082.312","32ppt4C_A":"3694745.551","32ppt4C_B":"3403697.603","32ppt4C_C":"4411326.56","40ppt-1C_A":"14468261.5","40ppt-1C_B":"18856393.64","40ppt-1C_C":"15358434.32","40ppt4C_A":"12977585.27","40ppt4C_B":"9521670.421","40ppt4C_C":"9583883.542","MediaBlk_ppt32":"1317050.067","MediaBlk_ppt40":"1547480.596"}],

"Metabolites":[{"Metabolite":"Arginine","quantitated m/z":"175.119501","KEGGNAME":"L-Arginine; (S)-2-Amino-5-guanidinovaleric acid; L-Arg","CHEBI":"CHEBI:16467","MS_method":"HILIC_QE_Pos","KEGG ID":"C00062"},{"Metabolite":"Betaine","quantitated m/z":"118.086804","KEGGNAME":"Betaine; Trimethylaminoacetate; Glycine betaine; N,N,N-Trimethylglycine; Trimethylammonioacetate","CHEBI":"CHEBI:17750","MS_method":"HILIC_QE_Pos","KEGG ID":"C00719"},{"Metabolite":"DMSP","quantitated m/z":"135.047977","KEGGNAME":"S,S-Dimethyl-beta-propiothetin; S-Dimethylsulfonium propionic acid; Dimethylpropiothetin; DMPT; DMSP","CHEBI":"CHEBI:16457","MS_method":"HILIC_QE_Pos","KEGG ID":"C04022"},{"Metabolite":"Glutamic acid","quantitated m/z":"148.060984","KEGGNAME":"L-Glutamate; L-Glutamic acid; L-Glutaminic acid; Glutamate","CHEBI":"CHEBI:16015","MS_method":"HILIC_QE_Pos","KEGG ID":"C00025"},{"Metabolite":"Glutamine","quantitated m/z":"147.076968","KEGGNAME":"L-Glutamine; L-2-Aminoglutaramic acid","CHEBI":"CHEBI:18050","MS_method":"HILIC_QE_Pos","KEGG ID":"C00064"},{"Metabolite":"Proline","quantitated m/z":"116.071154","KEGGNAME":"L-Proline; 2-Pyrrolidinecarboxylic acid","CHEBI":"CHEBI:17203","MS_method":"HILIC_QE_Pos","KEGG ID":"C00148"}]
}

}