Summary of Study ST001514

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 PR001021. The data can be accessed directly via it's Project DOI: 10.21228/M8QM5H 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.

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Study IDST001514
Study TitleCommunity metabolomes reflect taxon-specific fingerprints of phytoplankton in the ocean
Study TypeMetabolomic survey of 21 phytoplankton species
Study SummaryPhytoplankton transform inorganic carbon into thousands of biomolecules, including polar metabolites that represent an important pool of labile fixed carbon, nitrogen, and sulfur. Metabolite production is not identical among phytoplankton, and the flux of these molecules through the microbial loop depends on compound-specific bioavailability to a wider microbial community. Yet relatively little is known about the diversity or concentration of polar metabolites within marine plankton. Here we evaluate 313 metabolites in 21 phytoplankton species and in natural marine particles across environmental gradients to show that bulk community metabolomes reflect the phytoplankton community on a chemical level.
Institute
University of Washington
DepartmentOceanography
LaboratoryIngalls Lab
Last NameHeal
First NameKatherine
Address1501 NE Boat Street, Marine Science Building, Room G, Seattle, WA, 98195, USA
Emailkheal@uw.edu
Phone612-616-4840
Submit Date2020-10-22
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2021-01-25
Release Version1
Katherine Heal Katherine Heal
https://dx.doi.org/10.21228/M8QM5H
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001021
Project DOI:doi: 10.21228/M8QM5H
Project Title:Community metabolomes reflect taxon-specific fingerprints of phytoplankton in the ocean
Project Type:Marine Metabolomics
Project Summary:Phytoplankton transform inorganic carbon into thousands of biomolecules, including polar metabolites that represent an important pool of labile fixed carbon, nitrogen, and sulfur. Metabolite production is not identical among phytoplankton, and the flux of these molecules through the microbial loop depends on compound-specific bioavailability to a wider microbial community. Yet relatively little is known about the diversity or concentration of polar metabolites within marine plankton. Here we evaluate 313 metabolites in 21 phytoplankton species and in natural marine particles across environmental gradients to show that bulk community metabolomes reflect the phytoplankton community on a chemical level.
Institute:University of Washington
Department:Oceanography
Laboratory:Ingalls Lab
Last Name:Heal
First Name:Katherine
Address:1501 NE Boat Street, Marine Science Building, Room G, Seattle, WA, 98195, USA
Email:kheal@uw.edu
Phone:612-616-4840

Subject:

Subject ID:SU001588
Subject Type:Other
Subject Species:Marine Plankton
Gender:Not applicable

Factors:

Subject type: Other; Subject species: Marine Plankton (Factor headings shown in green)

mb_sample_id local_sample_id Species Strain Broad taxon
SA1271341771_AAlexandrium tamarense 1771 Dinoflagellate
SA1271351771_BAlexandrium tamarense 1771 Dinoflagellate
SA1271361771_CAlexandrium tamarense 1771 Dinoflagellate
SA1271371314_BAmphidinium carterae 1314 Dinoflagellate
SA1271381314_CAmphidinium carterae 1314 Dinoflagellate
SA1271391314_AAmphidinium carterae 1314 Dinoflagellate
SA1271408501_CCrocosphaera watsonii 8501 Cyanobacteria
SA1271418501_DCrocosphaera watsonii 8501 Cyanobacteria
SA1271428501_BCrocosphaera watsonii 8501 Cyanobacteria
SA127143Cy_CCyclotella meneghiniana 338 Diatom
SA127144Cy_ACyclotella meneghiniana 338 Diatom
SA127145Cy_BCyclotella meneghiniana 338 Diatom
SA1271462090_AEmiliania huxleyi 2090 Haptophyte
SA1271472090_CEmiliania huxleyi 2090 Haptophyte
SA1271482090_BEmiliania huxleyi 2090 Haptophyte
SA127149371_BEmiliania huxleyi 371 Haptophyte
SA127150371_CEmiliania huxleyi 371 Haptophyte
SA127151371_AEmiliania huxleyi 371 Haptophyte
SA127152449_BHeterocapsa triquetra 449 Dinoflagellate
SA127153449_AHeterocapsa triquetra 449 Dinoflagellate
SA127154449_CHeterocapsa triquetra 449 Dinoflagellate
SA1271552021_BLingulodinium polyedra 2021 Dinoflagellate
SA1271562021_CLingulodinium polyedra 2021 Dinoflagellate
SA1271572021_ALingulodinium polyedra 2021 Dinoflagellate
SA1271581545_BMicromonas pusilla 1545 Prasinophyte
SA1271591545_AMicromonas pusilla 1545 Prasinophyte
SA1271601545_CMicromonas pusilla 1545 Prasinophyte
SA127161Np_ANavicula pelliculosa 543 Diatom
SA127162Np_FNavicula pelliculosa 543 Diatom
SA127163Np_CNavicula pelliculosa 543 Diatom
SA127164Nmar_2Nitrosopumilus maritimus SCM1 Archaea
SA127165Nmar_3Nitrosopumilus maritimus SCM1 Archaea
SA127166Nmar_1Nitrosopumilus maritimus SCM1 Archaea
SA1271673430_BOstreococcus lucimarinus 3430 Prasinophyte
SA1271683430_COstreococcus lucimarinus 3430 Prasinophyte
SA1271693430_AOstreococcus lucimarinus 3430 Prasinophyte
SA127170Pt_CPhaeodactylum tricornutum 2561 Diatom
SA127171Pt_FPhaeodactylum tricornutum 2561 Diatom
SA1271721314P_CProchlorococcus marinus 1314 Cyanobacteria
SA1271731314P_BProchlorococcus marinus 1314 Cyanobacteria
SA1271741314P_AProchlorococcus marinus 1314 Cyanobacteria
SA127175As9601_BProchlorococcus marinus AS9601 Cyanobacteria
SA127176As9601_CProchlorococcus marinus AS9601 Cyanobacteria
SA127177As9601_AProchlorococcus marinus AS9601 Cyanobacteria
SA127178MED4_FProchlorococcus marinus MED4 Cyanobacteria
SA127179MED4_EProchlorococcus marinus MED4 Cyanobacteria
SA127180MED4_DProchlorococcus marinus MED4 Cyanobacteria
SA127181Nat_AProchlorococcus marinus NATL2A Cyanobacteria
SA127182Nat_CProchlorococcus marinus NATL2A Cyanobacteria
SA127183Nat_BProchlorococcus marinus NATL2A Cyanobacteria
SA127184Pc55x_BPseudo-nitzschia pungens Pc55x Diatom
SA127185Pc55x_APseudo-nitzschia pungens Pc55x Diatom
SA127186Pc55x_CPseudo-nitzschia pungens Pc55x Diatom
SA1271877803_FSynechococcus sp. 7803 Cyanobacteria
SA1271887803_BSynechococcus sp. 7803 Cyanobacteria
SA1271898102_FSynechococcus sp. 8102 Cyanobacteria
SA1271908102_ASynechococcus sp. 8102 Cyanobacteria
SA127191To_AThalassiosira oceanica 1005 Diatom
SA127192To_BThalassiosira oceanica 1005 Diatom
SA127193To_CThalassiosira oceanica 1005 Diatom
SA127194Tp_EThalassiosira pseudonana 1335 Diatom
SA127195Tp_AThalassiosira pseudonana 1335 Diatom
SA127196Tp_FThalassiosira pseudonana 1335 Diatom
Showing results 1 to 63 of 63

Collection:

Collection ID:CO001583
Collection Summary:Axenic phytoplankton were cultured in controlled laboratory settings and harvested under exponential growth using a gentle vacuum filtration onto 47 mm Durapore filters (pore size 0.2 µm). Samples were flash frozen in liquid N2 and stored at -80°C until extraction for metabolites.
Sample Type:Cultured plankton cells
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR001603
Treatment Summary:Media, light, and temperature were chosen for optimal growth of each phytoplankton species. In short, axenic phytoplankton were cultured in controlled laboratory settings and harvested under exponential growth using a gentle vacuum filtration onto 47 mm Durapore filters (pore size 0.2 µm). Samples were flash frozen in liquid N2 and stored at -80°C until extraction. In addition to samples, media blanks corresponding to each media type were harvested and served as a matrix blank to each corresponding phytoplankton sample.

Sample Preparation:

Sampleprep ID:SP001596
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 cold 50:50 methanol:water. All aqueous rinses were combined for each sample and ~2mL of cold dichloromethane was added to the combined aqueous layer. Tubes were shaken and centrifuged at 4,300 rpm for 2 minutes at 4°C. The aqueous layer was removed to a new glass vial and dried under N2 gas. The remaining organic layer in the bead beating tubes was transferred into the glass centrifuge tube and the bead beating tube was rinsed two more times with cold organic solvent. The combined organic rinses were centrifuged, transferred to a new glass vial, 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. Media blanks were extracted alongside samples as methodological blanks.
Processing Storage Conditions:On ice
Extraction Method:Bligh-Dyer
Extract Storage:-80℃

Combined analysis:

Analysis ID AN002508 AN002509 AN002510
Analysis type MS MS MS
Chromatography type Reversed phase HILIC HILIC
Chromatography system Waters Acquity I-Class Waters Acquity I-Class Waters Acquity I-Class
Column Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um) SeQuant ZIC-pHILIC (150 x 2.1mm,5um) SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
MS Type ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE POSITIVE NEGATIVE
Units Adjusted and normalized peak areas Adjusted and normalized peak areas Adjusted and normalized peak areas

Chromatography:

Chromatography ID:CH001833
Chromatography Summary:See attached summary.
Methods Filename:Ingalls_Lab_LC_Methods.txt
Instrument Name:Waters Acquity I-Class
Column Name:Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um)
Column Temperature:35
Flow Rate:0.4 ml/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH001834
Chromatography Summary:See attached summary
Methods Filename:Ingalls_Lab_LC_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:MS002326
Analysis ID:AN002508
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:Ingalls_Lab_MS_Methods.txt
  
MS ID:MS002327
Analysis ID:AN002509
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:Ingalls_Lab_MS_Methods.txt
  
MS ID:MS002328
Analysis ID:AN002510
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:Ingalls_Lab_MS_Methods.txt
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