#METABOLOMICS WORKBENCH TruxalCarlson_20200324_121313 DATATRACK_ID:1951 STUDY_ID:ST001393 ANALYSIS_ID:AN002328 PROJECT_ID:PR000956 VERSION 1 CREATED_ON June 4, 2020, 4:06 pm #PROJECT PR:PROJECT_TITLE Sea-ice diatom compatible solute shifts PR:PROJECT_TYPE Marine Metabolomics PR:PROJECT_SUMMARY Sea-ice algae provide an important source of primary production in polar PR:PROJECT_SUMMARY regions, yet we have limited understanding of their responses to the seasonal PR:PROJECT_SUMMARY cycling of temperature and salinity. Using a targeted liquid chromatography-mass PR:PROJECT_SUMMARY spectrometry-based metabolomics approach, we found that axenic cultures of the PR:PROJECT_SUMMARY Antarctic sea-ice diatom, Nitzschia lecointei, displayed large differences in PR:PROJECT_SUMMARY their metabolomes when grown in a matrix of conditions that included PR:PROJECT_SUMMARY temperatures of –1 and 4°C, and salinities of 32 and 41, despite relatively PR:PROJECT_SUMMARY small changes in growth rate. Temperature exerted a greater effect than salinity PR:PROJECT_SUMMARY on cellular metabolite pool sizes, though the N- or S-containing compatible PR:PROJECT_SUMMARY solutes, 2,3-dihydroxypropane-1-sulfonate (DHPS), glycine betaine (GBT), PR:PROJECT_SUMMARY dimethylsulfoniopropionate (DMSP), and proline responded strongly to both PR:PROJECT_SUMMARY temperature and salinity, suggesting complexity in their control. We saw the PR:PROJECT_SUMMARY largest (> 4 fold) response to salinity for proline. DHPS, a rarely studied but PR:PROJECT_SUMMARY potential compatible solute, reached the highest intracellular compatible solute PR:PROJECT_SUMMARY concentrations of ~ 85 mM. When comparing the culture findings to natural Arctic PR:PROJECT_SUMMARY sea-ice diatom communities, we found extensive overlap in metabolite profiles, PR:PROJECT_SUMMARY highlighting the relevance of culture-based studies to probe environmental PR:PROJECT_SUMMARY questions. Large changes in sea-ice diatom metabolomes and compatible solutes PR:PROJECT_SUMMARY over a seasonal cycle could be significant components of biogeochemical cycling PR:PROJECT_SUMMARY within sea ice. PR:INSTITUTE University of Washington PR:DEPARTMENT School of Oceanography PR:LABORATORY Ingalls Lab PR:LAST_NAME Dawson PR:FIRST_NAME Hannah PR:ADDRESS 1501 NE Boat Street, Marine Science Building, Room G, Seattle, WA 98195 PR:EMAIL hmdawson@uw.edu PR:PHONE 2062216750 PR:FUNDING_SOURCE Booth Foundation, NSF, UW Graduate Top Scholar Award, Gordon and Betty Moore PR:FUNDING_SOURCE Foundation PR:PUBLICATIONS Dawson et al., Elementa #STUDY ST:STUDY_TITLE Sea-ice diatom compatible solute shifts ST:STUDY_TYPE Compatible solutes were quantified in sea-ice diatoms ST:STUDY_SUMMARY Sea-ice algae provide an important source of primary production in polar ST:STUDY_SUMMARY regions, yet we have limited understanding of their responses to the seasonal ST:STUDY_SUMMARY cycling of temperature and salinity. Using a targeted liquid chromatography-mass ST:STUDY_SUMMARY spectrometry-based metabolomics approach, we found that axenic cultures of the ST:STUDY_SUMMARY Antarctic sea-ice diatom, Nitzschia lecointei, displayed large differences in ST:STUDY_SUMMARY their metabolomes when grown in a matrix of conditions that included ST:STUDY_SUMMARY temperatures of –1 and 4°C, and salinities of 32 and 41, despite relatively ST:STUDY_SUMMARY small changes in growth rate. Temperature exerted a greater effect than salinity ST:STUDY_SUMMARY on cellular metabolite pool sizes, though the N- or S-containing compatible ST:STUDY_SUMMARY solutes, 2,3-dihydroxypropane-1-sulfonate (DHPS), glycine betaine (GBT), ST:STUDY_SUMMARY dimethylsulfoniopropionate (DMSP), and proline responded strongly to both ST:STUDY_SUMMARY temperature and salinity, suggesting complexity in their control. We saw the ST:STUDY_SUMMARY largest (> 4 fold) response to salinity for proline. DHPS, a rarely studied but ST:STUDY_SUMMARY potential compatible solute, reached the highest intracellular compatible solute ST:STUDY_SUMMARY concentrations of ~ 85 mM. When comparing the culture findings to natural Arctic ST:STUDY_SUMMARY sea-ice diatom communities, we found extensive overlap in metabolite profiles, ST:STUDY_SUMMARY highlighting the relevance of culture-based studies to probe environmental ST:STUDY_SUMMARY questions. Large changes in sea-ice diatom metabolomes and compatible solutes ST:STUDY_SUMMARY over a seasonal cycle could be significant components of biogeochemical cycling ST:STUDY_SUMMARY within sea ice. ST:INSTITUTE University of Washington ST:DEPARTMENT School of Oceanography ST:LABORATORY Ingalls Lab ST:LAST_NAME Dawson ST:FIRST_NAME Hannah ST:ADDRESS 1501 NE Boat Street, Marine Science Building, Room G, Seattle, WA 98195 ST:EMAIL hmdawson@uw.edu ST:PHONE 2062216750 ST:PUBLICATIONS Dawson et al., Elementa #SUBJECT SU:SUBJECT_TYPE Other SU:SUBJECT_SPECIES Nitzschia lecointei SU:TAXONOMY_ID 186028 SU:GENDER Not applicable #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 - 32ppt-1C_A Type:Smp | Salinity:32 | Temp_degC:-1 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_SAMPLE_FACTORS - 32ppt-1C_B Type:Smp | Salinity:32 | Temp_degC:-1 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_SAMPLE_FACTORS - 32ppt-1C_C Type:Smp | Salinity:32 | Temp_degC:-1 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_SAMPLE_FACTORS - 32ppt4C_A Type:Smp | Salinity:32 | Temp_degC:4 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_SAMPLE_FACTORS - 32ppt4C_B Type:Smp | Salinity:32 | Temp_degC:4 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_SAMPLE_FACTORS - 32ppt4C_C Type:Smp | Salinity:32 | Temp_degC:4 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_SAMPLE_FACTORS - 40ppt-1C_A Type:Smp | Salinity:40 | Temp_degC:-1 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_SAMPLE_FACTORS - 40ppt-1C_B Type:Smp | Salinity:40 | Temp_degC:-1 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_SAMPLE_FACTORS - 40ppt-1C_C Type:Smp | Salinity:40 | Temp_degC:-1 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_SAMPLE_FACTORS - 40ppt4C_A Type:Smp | Salinity:40 | Temp_degC:4 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_SAMPLE_FACTORS - 40ppt4C_B Type:Smp | Salinity:40 | Temp_degC:4 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_SAMPLE_FACTORS - 40ppt4C_C Type:Smp | Salinity:40 | Temp_degC:4 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_SAMPLE_FACTORS - ASWFilterBlk_1 Type:Blk | Salinity:NA | Temp_degC:NA Replicate=1; RFU=NA; Vol_L=0.3; RAW_FILE_NAME=170612_Blk_ASWFilterBlk_1;170615_Blk_ASWFilterBlk_1;170612_Blk_ASWFilterBlk_1 SUBJECT_SAMPLE_FACTORS - ASWFilterBlk_2 Type:Blk | Salinity:NA | Temp_degC:NA Replicate=2; RFU=NA; Vol_L=0.3; RAW_FILE_NAME=170612_Blk_ASWFilterBlk_2;170615_Blk_ASWFilterBlk_2;170612_Blk_ASWFilterBlk_2 SUBJECT_SAMPLE_FACTORS - ASWFilterBlk_3 Type:Blk | Salinity:NA | Temp_degC:NA Replicate=3; RFU=NA; Vol_L=0.3; RAW_FILE_NAME=170612_Blk_ASWFilterBlk_3;170615_Blk_ASWFilterBlk_3;170612_Blk_ASWFilterBlk_3 SUBJECT_SAMPLE_FACTORS - MediaBlk_ppt32 Type:Blk | Salinity:32 | Temp_degC:NA Replicate=ppt32; RFU=1; Vol_L=0.07; RAW_FILE_NAME=170410_Blk_MediaBlk_ppt32;170413_Blk_MediaBlk_ppt32;170410_Blk_MediaBlk_ppt32 SUBJECT_SAMPLE_FACTORS - MediaBlk_ppt40 Type:Blk | Salinity:40 | Temp_degC:NA Replicate=ppt40; RFU=1; Vol_L=0.07; RAW_FILE_NAME=170410_Blk_MediaBlk_ppt40;170413_Blk_MediaBlk_ppt40;170410_Blk_MediaBlk_ppt40 SUBJECT_SAMPLE_FACTORS - S2C_4 Type:Smp | Salinity:NA | Temp_degC:NA Replicate=4; RFU=NA; Vol_L=0.1671; RAW_FILE_NAME=170612_Smp_S2C_4;170615_Smp_S2C_4;170612_Smp_S2C_4 SUBJECT_SAMPLE_FACTORS - S2C_5 Type:Smp | Salinity:NA | Temp_degC:NA Replicate=5; RFU=NA; Vol_L=0.2486; RAW_FILE_NAME=170612_Smp_S2C_5;170615_Smp_S2C_5;170612_Smp_S2C_5 SUBJECT_SAMPLE_FACTORS - S2C_6 Type:Smp | Salinity:NA | Temp_degC:NA Replicate=6; RFU=NA; Vol_L=0.2049; RAW_FILE_NAME=170612_Smp_S2C_6;170615_Smp_S2C_6;170612_Smp_S2C_6 #COLLECTION CO:COLLECTION_SUMMARY Cultured diatom cells at different salinities and temperatures grown to CO:COLLECTION_SUMMARY exponential phase were filtered onto 0.2-micron filters and extracted for CO:COLLECTION_SUMMARY metabolites as described in methods. Three dedicated ice cores were sampled from CO:COLLECTION_SUMMARY the Chukchi Sea near Utqiaġvik, AK. The bottom 5-cm sections were placed in CO:COLLECTION_SUMMARY polycarbonate tubs, allowed to melt at 4°C in artificial seawater, and filtered CO:COLLECTION_SUMMARY onto 0.2-micron filters. Filters were extracted for metabolites as described in CO:COLLECTION_SUMMARY methods. All filters were frozen in liquid nitrogen immediately after filtration CO:COLLECTION_SUMMARY and stored in a -80 C freezer until extraction. CO:SAMPLE_TYPE Diatom cells/Particulate matter from sea ice cores CO:STORAGE_CONDITIONS Described in summary #TREATMENT TR:TREATMENT_SUMMARY Diatom cells were cultured in a matrix of two temperatures (–1°C and 4°C) TR:TREATMENT_SUMMARY and two salinities (32 and 40) in triplicate. There was no treatment for the sea TR:TREATMENT_SUMMARY ice cores – this was a study of how the cultured diatoms compare to the TR:TREATMENT_SUMMARY diatom-dominated Arctic sea-ice communities. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Each sample was extracted using a modified Bligh-Dyer extraction. Briefly, SP:SAMPLEPREP_SUMMARY filters were cut up and put into 15 mL teflon centrifuge tubes containing a SP:SAMPLEPREP_SUMMARY mixture of 100 µm and 400 µm silica beads. Heavy isotope-labeled internal SP:SAMPLEPREP_SUMMARY standards were added along with ~2 mL of cold aqueous solvent (50:50 SP:SAMPLEPREP_SUMMARY methanol:water) and ~3 mL of cold organic solvent (dichloromethane). The samples SP:SAMPLEPREP_SUMMARY were shaken on a FastPrep-24 Homogenizer for 30 seconds and chilled in a -20 °C SP:SAMPLEPREP_SUMMARY freezer repeatedly for three cycles of bead-beating and a total of 30 minutes of SP:SAMPLEPREP_SUMMARY chilling. The organic and aqueous layers were separated by spinning samples in a SP:SAMPLEPREP_SUMMARY centrifuge at 4,300 rpm for 2 minutes at 4 °C. The aqueous layer was removed to SP:SAMPLEPREP_SUMMARY a new glass centrifuge tube. The remaining organic fraction was rinsed three SP:SAMPLEPREP_SUMMARY more times with additions of 1 to 2 mL of 50:50 methanol:water. All aqueous SP:SAMPLEPREP_SUMMARY rinses were combined for each sample and dried down under N2 gas. The remaining SP:SAMPLEPREP_SUMMARY organic layer was transferred into a clean glass centrifuge tube and the SP:SAMPLEPREP_SUMMARY remaining bead beating tube was rinsed two more times with cold organic solvent. SP:SAMPLEPREP_SUMMARY The combined organic rinses were centrifuged, transferred to a new tube, and SP:SAMPLEPREP_SUMMARY dried under N2 gas. Dried aqueous fractions were re-dissolved in 380 µL of SP:SAMPLEPREP_SUMMARY water. Dried organic fractions were re-dissolved in 380 µL of 1:1 SP:SAMPLEPREP_SUMMARY water:acetonitrile. 20 µL of isotope-labeled injection standards in water were SP:SAMPLEPREP_SUMMARY added to both fractions. Blank filters were extracted alongside samples as SP:SAMPLEPREP_SUMMARY methodological blanks. SP:PROCESSING_STORAGE_CONDITIONS On ice SP:EXTRACTION_METHOD Bligh-Dyer SP:EXTRACT_STORAGE -80℃ #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY See attached summary CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Waters Acquity I-Class CH:COLUMN_NAME SeQuant ZIC- pHILIC (150 x 2.1mm, 5um) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive HF hybrid Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS See protocol, data from field samples #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS Normalized Peak Area Per L Seawater MS_METABOLITE_DATA_START Samples ASWFilterBlk_1 ASWFilterBlk_2 ASWFilterBlk_3 S2C_4 S2C_5 S2C_6 Factors Type:Blk | Salinity:NA | Temp_degC:NA Type:Blk | Salinity:NA | Temp_degC:NA Type:Blk | Salinity:NA | Temp_degC:NA Type:Smp | Salinity:NA | Temp_degC:NA Type:Smp | Salinity:NA | Temp_degC:NA Type:Smp | Salinity:NA | Temp_degC:NA Arginine 998724860.7 38410690.43 131997020.2 4492823624 1205929204 1278397996 Betaine 173309192.1 94642799.03 108412027.2 2.17E+11 1.43E+11 1.74E+11 Choline 20519953.33 18795610 15920710 42893718588 14485766144 18472019200 DMSP 10188189.9 15233703.3 5995739.59 1.00E+11 86889304436 71480039050 Glutamic acid 16885660 15016280 15317213.33 4304664094 1910550400 2349847840 Glutamine 1124896.667 888733.3333 1291036.667 7023024941 3318025984 4148853120 Homarine 1750053.333 3889353.333 1204423.333 38830278776 16179766272 21784542720 Proline 501806.605 1712098.354 1097333.543 16562807576 5600457952 7864240295 Stachydrine hydrochloride 3408733.333 2874736.667 2229900 39700844424 17094471680 23501409280 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name quantitated m/z KEGGNAME CHEBI MS_method KEGG ID Arginine 175.119501 L-Arginine; (S)-2-Amino-5-guanidinovaleric acid; L-Arg CHEBI:16467 HILIC_QE_Pos C00062 Betaine 118.086804 Betaine; Trimethylaminoacetate; Glycine betaine; N,N,N-Trimethylglycine; Trimethylammonioacetate CHEBI:17750 HILIC_QE_Pos C00719 Choline 104.107539 Choline; Bilineurine CHEBI:15354 HILIC_QE_Pos C00114 DMSP 135.047977 S,S-Dimethyl-beta-propiothetin; S-Dimethylsulfonium propionic acid; Dimethylpropiothetin; DMPT; DMSP CHEBI:16457 HILIC_QE_Pos C04022 Glutamic acid 148.060984 L-Glutamate; L-Glutamic acid; L-Glutaminic acid; Glutamate CHEBI:16015 HILIC_QE_Pos C00025 Glutamine 147.076968 L-Glutamine; L-2-Aminoglutaramic acid CHEBI:18050 HILIC_QE_Pos C00064 Homarine 138.055503 CHEBI:69061 HILIC_QE_Pos Proline 116.071154 L-Proline; 2-Pyrrolidinecarboxylic acid CHEBI:17203 HILIC_QE_Pos C00148 Stachydrine hydrochloride 144.102454 Stachydrine; Proline betaine; L-Proline betaine CHEBI:35280 HILIC_QE_Pos C10172 METABOLITES_END #END