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.

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Study IDST001393
Study TitleSea-ice diatom compatible solute shifts
Study TypeCompatible solutes were quantified in sea-ice diatoms
Study SummarySea-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
DepartmentSchool of Oceanography
LaboratoryIngalls Lab
Last NameDawson
First NameHannah
Address1501 NE Boat Street, Marine Science Building, Room G, Seattle, WA 98195
Emailhmdawson@uw.edu
Phone2062216750
Submit Date2020-03-24
PublicationsDawson et al., Elementa
Raw Data AvailableYes
Raw Data File Type(s).mzXML
Analysis Type DetailLC-MS
Release Date2020-09-29
Release Version1
Hannah Dawson Hannah Dawson
https://dx.doi.org/10.21228/M84386
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA113432MediaBlk_ppt32Blk 32 NA
SA113433MediaBlk_ppt40Blk 40 NA
SA113434ASWFilterBlk_1Blk NA NA
SA113435ASWFilterBlk_2Blk NA NA
SA113436ASWFilterBlk_3Blk NA NA
SA11343732ppt-1C_ASmp 32 -1
SA11343832ppt-1C_BSmp 32 -1
SA11343932ppt-1C_CSmp 32 -1
SA11344032ppt4C_CSmp 32 4
SA11344132ppt4C_ASmp 32 4
SA11344232ppt4C_BSmp 32 4
SA11344340ppt-1C_BSmp 40 -1
SA11344440ppt-1C_ASmp 40 -1
SA11344540ppt-1C_CSmp 40 -1
SA11344640ppt4C_BSmp 40 4
SA11344740ppt4C_CSmp 40 4
SA11344840ppt4C_ASmp 40 4
SA113449S2C_6Smp NA NA
SA113450S2C_5Smp NA NA
SA113451S2C_4Smp 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
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