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.

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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.

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Study IDST001480
Study TitleLarge diversity in nitrogen- and sulfur-containing compatible solute profiles in polar and temperate diatoms
Study TypeIntracellular metabolites were quantified in diatom species
Study SummaryIntense 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
DepartmentOceanography
LaboratoryIngalls Lab
Last NameDawson
First NameHannah
Address1501 NE Boat Street, Marine Science Building, Room G, Seattle, WA, 98195, USA
Emailhmdawson@uw.edu
Phone206-543-0744
Submit Date2020-09-09
PublicationsDawson et al, 2020, Integrative and Comparative Biology
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2020-12-09
Release Version1
Hannah Dawson Hannah Dawson
https://dx.doi.org/10.21228/M8X98D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
Species Group:Algae

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
SA125004Fc_2Fragilariopsis cylindrus 31 -1
SA125005Fc_1Fragilariopsis cylindrus 31 -1
SA125006Nperm_1Navicula cf. perminuta 31 -1
SA125007Nperm_2Navicula cf. perminuta 31 -1
SA125008Npell_1Navicula pelliculosa 35 13
SA125009Npell_3Navicula pelliculosa 35 13
SA125010Npell_2Navicula pelliculosa 35 13
SA125011Nl_1Nitzschia lecointei 31 -1
SA125012Nl_2Nitzschia lecointei 31 -1
SA125013Nl_32ppt-1C_3Nitzschia lecointei 32 -1
SA125014Nl_32ppt-1C_1Nitzschia lecointei 32 -1
SA125015Nl_32ppt-1C_2Nitzschia lecointei 32 -1
SA125016Nl_32ppt4C_1Nitzschia lecointei 32 4
SA125017Nl_32ppt4C_2Nitzschia lecointei 32 4
SA125018Nl_32ppt4C_3Nitzschia lecointei 32 4
SA125019Nl_41ppt-1C_2Nitzschia lecointei 41 -1
SA125020Nl_41ppt-1C_1Nitzschia lecointei 41 -1
SA125021Nl_41ppt-1C_3Nitzschia lecointei 41 -1
SA125022Nl_41ppt4C_2Nitzschia lecointei 41 4
SA125023Nl_41ppt4C_1Nitzschia lecointei 41 4
SA125024Nl_41ppt4C_3Nitzschia 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
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