Summary of Study ST001480
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 PR001004. The data can be accessed directly via it's Project DOI: 10.21228/M8X98D This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST001480 |
| Study Title | Large diversity in nitrogen- and sulfur-containing compatible solute profiles in polar and temperate diatoms |
| Study Type | Intracellular metabolites were quantified in diatom species |
| Study Summary | Intense bottom-ice algal blooms, often dominated by diatoms, are an important source of food for grazers, organic matter for export during sea ice melt, and dissolved organic carbon. Sea-ice diatoms have a number of adaptations, including accumulation of compatible solutes, that allow them to inhabit this highly variable environment characterized by extremes in temperature, salinity, and light. In addition to protecting them from extreme conditions, these compounds present a labile, nutrient-rich source of organic matter and include precursors to climate active compounds (e.g. DMS), which are likely regulated with environmental change. Here, intracellular concentrations of 45 metabolites were quantified in three sea-ice diatom species and were compared to two temperate diatom species, with a focus on compatible solutes and free amino acid pools. There was a large diversity of metabolite concentrations between diatoms with no clear pattern identifiable for sea-ice species. Concentrations of some compatible solutes (isethionic acid, homarine) approached 1 M in the sea-ice diatoms, Fragilariopsis cylindrus and Navicula cf. perminuta, but not in the larger sea-ice diatom, Nitzschia lecointei or in the temperate diatom species. The differential use of compatible solutes in sea-ice diatoms suggest different adaptive strategies and highlights which small organic compounds may be important in polar biogeochemical cycles. |
| Institute | University of Washington |
| Department | Oceanography |
| Laboratory | Ingalls Lab |
| Last Name | Dawson |
| First Name | Hannah |
| Address | 1501 NE Boat Street, Marine Science Building, Room G, Seattle, WA, 98195, USA |
| hmdawson@uw.edu | |
| Phone | 206-543-0744 |
| Submit Date | 2020-09-09 |
| Publications | Dawson et al, 2020, Integrative and Comparative Biology |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-12-09 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001004 |
| Project DOI: | doi: 10.21228/M8X98D |
| Project Title: | Large diversity in nitrogen- and sulfur-containing compatible solute profiles in polar and temperate diatoms |
| Project Type: | Marine Metabolomics |
| Project Summary: | Intense bottom-ice algal blooms, often dominated by diatoms, are an important source of food for grazers, organic matter for export during sea ice melt, and dissolved organic carbon. Sea-ice diatoms have a number of adaptations, including accumulation of compatible solutes, that allow them to inhabit this highly variable environment characterized by extremes in temperature, salinity, and light. In addition to protecting them from extreme conditions, these compounds present a labile, nutrient-rich source of organic matter and include precursors to climate active compounds (e.g. DMS), which are likely regulated with environmental change. Here, intracellular concentrations of 45 metabolites were quantified in three sea-ice diatom species and were compared to two temperate diatom species, with a focus on compatible solutes and free amino acid pools. There was a large diversity of metabolite concentrations between diatoms with no clear pattern identifiable for sea-ice species. Concentrations of some compatible solutes (isethionic acid, homarine) approached 1 M in the sea-ice diatoms, Fragilariopsis cylindrus and Navicula cf. perminuta, but not in the larger sea-ice diatom, Nitzschia lecointei or in the temperate diatom species. The differential use of compatible solutes in sea-ice diatoms suggest different adaptive strategies and highlights which small organic compounds may be important in polar biogeochemical cycles. |
| Institute: | University of Washington |
| Department: | Oceanography |
| Laboratory: | Ingalls Lab |
| Last Name: | Dawson |
| First Name: | Hannah |
| Address: | 1501 NE Boat Street, Marine Science Building, Room G, Seattle, WA, 98195, USA |
| Email: | hmdawson@uw.edu |
| Phone: | 206-543-0744 |
| Publications: | Dawson et al, 2020, Integrative and Comparative Biology |
Subject:
| Subject ID: | SU001554 |
| Subject Type: | Other |
| Subject Species: | Nitzschia lecointei;Fragilariopsis cylindrus;Navicula cf. perminuta;Navicula pelliculosa |
| Taxonomy ID: | 186028;186039;908978;913975 |
Factors:
Subject type: Other; Subject species: Nitzschia lecointei;Fragilariopsis cylindrus;Navicula cf. perminuta;Navicula pelliculosa (Factor headings shown in green)
| mb_sample_id | local_sample_id | Species | Salinity | Temp_degC |
|---|---|---|---|---|
| SA125004 | Fc_2 | Fragilariopsis cylindrus | 31 | -1 |
| SA125005 | Fc_1 | Fragilariopsis cylindrus | 31 | -1 |
| SA125006 | Nperm_1 | Navicula cf. perminuta | 31 | -1 |
| SA125007 | Nperm_2 | Navicula cf. perminuta | 31 | -1 |
| SA125008 | Npell_1 | Navicula pelliculosa | 35 | 13 |
| SA125009 | Npell_3 | Navicula pelliculosa | 35 | 13 |
| SA125010 | Npell_2 | Navicula pelliculosa | 35 | 13 |
| SA125011 | Nl_1 | Nitzschia lecointei | 31 | -1 |
| SA125012 | Nl_2 | Nitzschia lecointei | 31 | -1 |
| SA125013 | Nl_32ppt-1C_3 | Nitzschia lecointei | 32 | -1 |
| SA125014 | Nl_32ppt-1C_1 | Nitzschia lecointei | 32 | -1 |
| SA125015 | Nl_32ppt-1C_2 | Nitzschia lecointei | 32 | -1 |
| SA125016 | Nl_32ppt4C_1 | Nitzschia lecointei | 32 | 4 |
| SA125017 | Nl_32ppt4C_2 | Nitzschia lecointei | 32 | 4 |
| SA125018 | Nl_32ppt4C_3 | Nitzschia lecointei | 32 | 4 |
| SA125019 | Nl_41ppt-1C_2 | Nitzschia lecointei | 41 | -1 |
| SA125020 | Nl_41ppt-1C_1 | Nitzschia lecointei | 41 | -1 |
| SA125021 | Nl_41ppt-1C_3 | Nitzschia lecointei | 41 | -1 |
| SA125022 | Nl_41ppt4C_2 | Nitzschia lecointei | 41 | 4 |
| SA125023 | Nl_41ppt4C_1 | Nitzschia lecointei | 41 | 4 |
| SA125024 | Nl_41ppt4C_3 | Nitzschia lecointei | 41 | 4 |
| Showing results 1 to 21 of 21 |
Collection:
| Collection ID: | CO001549 |
| Collection Summary: | Axenic cultures of three Antarctic sea-ice diatoms (N. lecointei, N. cf. perminuta, and F. cylindrus) and two temperate diatoms (T. pseudonana and N. pelliculosa) were chosen for study. Cells were harvested during exponential growth onto 47 mm 0.2 µm PTFE filters (Omnipore) using combusted glassware and gentle filtration and stored at –80 °C until extraction. For each biological replicate (n = 2 for Antarctic species, n = 3 for temperate species), two 35 mL cultures were harvested onto each filter . An un-inoculated media blank was prepared and treated in the same manner as samples. |
| Sample Type: | Cultured diatom cells |
| Storage Conditions: | Described in summary |
Treatment:
| Treatment ID: | TR001569 |
| Treatment Summary: | Antarctic species were grown at −1°C and a PAR irradiance of 45 𝜇mol photons m−2 s−1 (16:8 light:dark cycle) using cool white lights. Temperate species were grown at 13°C and a PAR irradiance of 120 𝜇mol photons m−-2 s−-1(12:12 light:dark cycle). In both cases, light was saturating. Cultures were grown in artificial seawater (ESAW, salinity 31, for Antarctic species and Instant Ocean, salinity ~35 for temperate species). Cobalamin (vitamin B12) was replete in all cultures. To explore the effect of growth conditions on metabolic profiles using non-metric dimensional scaling analysis, samples were included of N. lecointei grown at temperatures of −1 and 4˚C and salinities of 32 and 41. |
Sample Preparation:
| Sampleprep ID: | SP001562 |
| 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. An un-inoculated media blank was prepared and treated in the same manner as the samples. |
| Processing Storage Conditions: | On ice |
| Extraction Method: | Bligh-Dyer |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN002456 | AN002457 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | 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) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | mM (intracellular concentration) | mM (intracellular concentration) |
Chromatography:
| Chromatography ID: | CH001799 |
| Chromatography Summary: | See attached summary. |
| Methods Filename: | CH_Ingalls_Lab_LC_Methods.txt MS_Ingalls_Lab_MS_Methods.txt |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
| Column Temperature: | 30 |
| Flow Rate: | 0.15 mL/min |
| Solvent A: | 85% acetonitrile/15% water; 10 mM ammonium carbonate |
| Solvent B: | 15% acetonitrile/85% water; 10 mM ammonium carbonate |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS002276 |
| Analysis ID: | AN002456 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See attached protocol. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | MS_Ingalls_Lab_MS_Methods.txt |
| MS ID: | MS002277 |
| Analysis ID: | AN002457 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See attached protocol. |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | MS_Ingalls_Lab_MS_Methods.txt |
