Summary of Study ST001393
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000956. The data can be accessed directly via it's Project DOI: 10.21228/M84386 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001393 |
| 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 |
| hmdawson@uw.edu | |
| Phone | 2062216750 |
| Submit Date | 2020-03-24 |
| Publications | Dawson et al., Elementa |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-09-29 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000956 |
| Project DOI: | doi: 10.21228/M84386 |
| 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 |
Subject:
| Subject ID: | SU001467 |
| Subject Type: | Other |
| Subject Species: | Nitzschia lecointei |
| Taxonomy ID: | 186028 |
| Gender: | Not applicable |
Factors:
Subject type: Other; Subject species: Nitzschia lecointei (Factor headings shown in green)
| mb_sample_id | local_sample_id | Type | Salinity | Temp_degC |
|---|---|---|---|---|
| SA113432 | MediaBlk_ppt32 | Blk | 32 | NA |
| SA113433 | MediaBlk_ppt40 | Blk | 40 | NA |
| SA113434 | ASWFilterBlk_1 | Blk | NA | NA |
| SA113435 | ASWFilterBlk_2 | Blk | NA | NA |
| SA113436 | ASWFilterBlk_3 | Blk | NA | NA |
| SA113437 | 32ppt-1C_A | Smp | 32 | -1 |
| SA113438 | 32ppt-1C_B | Smp | 32 | -1 |
| SA113439 | 32ppt-1C_C | Smp | 32 | -1 |
| SA113440 | 32ppt4C_C | Smp | 32 | 4 |
| SA113441 | 32ppt4C_A | Smp | 32 | 4 |
| SA113442 | 32ppt4C_B | Smp | 32 | 4 |
| SA113443 | 40ppt-1C_B | Smp | 40 | -1 |
| SA113444 | 40ppt-1C_A | Smp | 40 | -1 |
| SA113445 | 40ppt-1C_C | Smp | 40 | -1 |
| SA113446 | 40ppt4C_B | Smp | 40 | 4 |
| SA113447 | 40ppt4C_C | Smp | 40 | 4 |
| SA113448 | 40ppt4C_A | Smp | 40 | 4 |
| SA113449 | S2C_6 | Smp | NA | NA |
| SA113450 | S2C_5 | Smp | NA | NA |
| SA113451 | S2C_4 | Smp | NA | NA |
| Showing results 1 to 20 of 20 |
Collection:
| Collection ID: | CO001462 |
| 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 ID: | TR001482 |
| 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. |
Sample Preparation:
| Sampleprep ID: | SP001475 |
| 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℃ |
Combined analysis:
| Analysis ID | AN002323 | AN002324 | AN002325 | AN002326 | AN002327 | AN002328 | AN002329 | AN002330 | AN002331 |
|---|---|---|---|---|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS | MS | MS | MS | MS | MS |
| Chromatography type | HILIC | HILIC | HILIC | HILIC | HILIC | HILIC | HILIC | HILIC | Reversed phase |
| Chromatography system | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class |
| Column | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um) |
| MS Type | ESI | ESI | ESI | ESI | ESI | ESI | ESI | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole | Triple quadrupole | Orbitrap | Orbitrap | Orbitrap | Orbitrap | Triple quadrupole |
| MS instrument name | Waters Xevo-TQ-S | Waters Xevo-TQ-S | Waters Xevo-TQ-S | Waters Xevo-TQ-S | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Waters Xevo-TQ-S |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE | POSITIVE |
| Units | Normalized Peak Area Per L Seawater | Normalized Peak Area Per RFU | Normalized Peak Area Per L Seawater | Normalized Peak Area Per RFU | Normalized Peak Area Per L Seawater | Normalized Peak Area Per RFU | Normalized Peak Area Per L Seawater | Normalized Peak Area Per RFU | Normalized Peak Area Per RFU |
Chromatography:
| Chromatography ID: | CH001707 |
| Chromatography Summary: | See attached summary |
| Methods Filename: | TruxalCarlson_LC_Methods_HD.txt TruxalCarlson_MS_Methods_HD.txt |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH001708 |
| Chromatography Summary: | See attached summary |
| Methods Filename: | TruxalCarlson_LC_Methods_HD.txt TruxalCarlson_MS_Methods_HD.txt |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002165 |
| Analysis ID: | AN002323 |
| Instrument Name: | Waters Xevo-TQ-S |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | See protocol, data from culture samples |
| Ion Mode: | POSITIVE |
| MS ID: | MS002166 |
| Analysis ID: | AN002324 |
| Instrument Name: | Waters Xevo-TQ-S |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | See protocol, data from field samples |
| Ion Mode: | POSITIVE |
| MS ID: | MS002167 |
| Analysis ID: | AN002325 |
| Instrument Name: | Waters Xevo-TQ-S |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | See protocol, data from culture samples |
| Ion Mode: | NEGATIVE |
| MS ID: | MS002168 |
| Analysis ID: | AN002326 |
| Instrument Name: | Waters Xevo-TQ-S |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | See protocol, data from field samples |
| Ion Mode: | NEGATIVE |
| MS ID: | MS002169 |
| Analysis ID: | AN002327 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See protocol, data from culture samples |
| Ion Mode: | POSITIVE |
| MS ID: | MS002170 |
| Analysis ID: | AN002328 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See protocol, data from field samples |
| Ion Mode: | POSITIVE |
| MS ID: | MS002171 |
| Analysis ID: | AN002329 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See protocol, data from culture samples |
| Ion Mode: | NEGATIVE |
| MS ID: | MS002172 |
| Analysis ID: | AN002330 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See protocol, data from field samples |
| Ion Mode: | NEGATIVE |
| MS ID: | MS002173 |
| Analysis ID: | AN002331 |
| Instrument Name: | Waters Xevo-TQ-S |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | See protocol, data from culture samples |
| Ion Mode: | POSITIVE |
