{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001393","ANALYSIS_ID":"AN002329","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":"NEGATIVE","MS_COMMENTS":"See protocol, data from culture samples"},

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

"Data":[{"Metabolite":"DHPS","32ppt-1C_A":"25874543.94","32ppt-1C_B":"25489446.27","32ppt-1C_C":"26512505.63","32ppt4C_A":"14887867.22","32ppt4C_B":"12509887.49","32ppt4C_C":"15735596.73","40ppt-1C_A":"20589709.18","40ppt-1C_B":"28831546.29","40ppt-1C_C":"24234743.79","40ppt4C_A":"24751035.71","40ppt4C_B":"21576599.44","40ppt4C_C":"20423500.57","MediaBlk_ppt32":"14220","MediaBlk_ppt40":"13070"}],

"Metabolites":[{"Metabolite":"DHPS","quantitated m/z":"155.001422","CHEBI":"CHEBI:60997","KEGGNAME":"(R)-2,3-Dihydroxypropane-1-sulfonate","MS_method":"HILIC_QE_Neg","KEGG ID":"C19675"}]
}

}