Summary of Study ST002790

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 ID	ST002790
Study Title	Community metabolomes reflect taxon-specific fingerprints of phytoplankton and heterotrophic bacteria in the ocean (expanded)
Study Type	Metabolomic survey of 46 phytoplankton and heterotrophic bacteria species
Study Summary	This study is an updated version of the prior study in this project, ST001514. With this update we introduce additional marine species, in particular the heterotrophic bacteria, and include our expanded library of authentic standards (available at https://github.com/IngallsLabUW/Ingalls_Standards/blob/430992e10c0464a817c69d22e3905d73f2ea196f/Ingalls_Lab_Standards.csv) for improved targeted coverage.
Institute	University of Washington
Last Name	Kumler
First Name	William
Address	1501 NE Boat St, Seattle, WA, 98105, USA
Email	wkumler@uw.edu
Phone	9095551234
Submit Date	2023-07-20
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2023-08-07
Release Version	1

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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:	SU002897
Subject Type:	Other organism
Subject Species:	Marine plankton
Species Group:	Plankton

Factors:

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

mb_sample_id	local_sample_id	Sample_type	Species_strain	Broad_taxon	MS_run
SA299298	211218_Blk_MediaBlk_21_pos.mzML	Blank	NA	NA	NA
SA299299	211218_Blk_MediaBlk_3430_pos.mzML	Blank	NA	NA	NA
SA299300	211218_Blk_MediaBlk_49_pos.mzML	Blank	NA	NA	NA
SA299301	211218_Blk_MediaBlk_71_pos.mzML	Blank	NA	NA	NA
SA299302	220111_Blk_MediaBlk_A_pos.mzML	Blank	NA	NA	NA
SA299303	220111_Blk_MediaBlk_AMS_pos.mzML	Blank	NA	NA	NA
SA299304	211215_Blk_MediaBlk_Z_pos.mzML	Blank	NA	NA	NA
SA299305	220111_Blk_MediaBlk_B_pos.mzML	Blank	NA	NA	NA
SA299306	220111_Blk_MediaBlk_AOA_pos.mzML	Blank	NA	NA	NA
SA299307	211218_Blk_MediaBlk_N_pos.mzML	Blank	NA	NA	NA
SA299308	211218_Blk_MediaBlk_O_pos.mzML	Blank	NA	NA	NA
SA299309	211221_Blk_MediaBlk_C_pos.mzML	Blank	NA	NA	NA
SA299310	211221_Blk_MediaBlk_1314P_pos.mzML	Blank	NA	NA	NA
SA299311	211221_Blk_MediaBlk_A_pos.mzML	Blank	NA	NA	NA
SA299312	211221_Blk_MediaBlk_Nat_pos.mzML	Blank	NA	NA	NA
SA299313	220104_Blk_MediaBlk_C_pos.mzML	Blank	NA	NA	NA
SA299314	220104_Blk_MediaBlk_RAC5_pos.mzML	Blank	NA	NA	NA
SA299315	220104_Blk_MediaBlk_LInoSi_pos.mzML	Blank	NA	NA	NA
SA299316	220104_Blk_MediaBlk_H_pos.mzML	Blank	NA	NA	NA
SA299317	211215_Blk_MediaBlk_Pc55x_pos.mzML	Blank	NA	NA	NA
SA299318	211221_Blk_MediaBlk_As9601_pos.mzML	Blank	NA	NA	NA
SA299319	211215_Blk_MediaBlk_B_pos.mzML	Blank	NA	NA	NA
SA299320	211215_Blk_MediaBlk_A_pos.mzML	Blank	NA	NA	NA
SA299321	211215_Blk_MediaBlk_Fc_pos.mzML	Blank	NA	NA	NA
SA299322	220111_Poo_TruePooBacteria_Full1.mzML	QC Pooled	NA	NA	Bacteria
SA299323	220111_Poo_TruePooBacteria_Full2.mzML	QC Pooled	NA	NA	Bacteria
SA299324	220111_Poo_TruePooBacteria_Half3.mzML	QC Pooled	NA	NA	Bacteria
SA299325	220111_Poo_TruePooBacteria_Half1.mzML	QC Pooled	NA	NA	Bacteria
SA299326	220111_Poo_TruePooBacteria_Half2.mzML	QC Pooled	NA	NA	Bacteria
SA299327	220111_Poo_TruePooBacteria_Full3.mzML	QC Pooled	NA	NA	Bacteria
SA299328	211102_Poo_TruePooCyanos_Full1.mzML	QC Pooled	NA	NA	Cyanos
SA299329	211102_Poo_TruePooCyanos_Full2.mzML	QC Pooled	NA	NA	Cyanos
SA299330	211102_Poo_TruePooCyanos_Half3.mzML	QC Pooled	NA	NA	Cyanos
SA299331	211102_Poo_TruePooCyanos_Half2.mzML	QC Pooled	NA	NA	Cyanos
SA299332	211102_Poo_TruePooCyanos_Half1.mzML	QC Pooled	NA	NA	Cyanos
SA299333	211102_Poo_TruePooCyanos_Full3.mzML	QC Pooled	NA	NA	Cyanos
SA299334	211102_Poo_TruePooDiatoms_Half3.mzML	QC Pooled	NA	NA	Diatom
SA299335	211102_Poo_TruePooDiatoms_Half1.mzML	QC Pooled	NA	NA	Diatom
SA299336	211102_Poo_TruePooDiatoms_Half2.mzML	QC Pooled	NA	NA	Diatom
SA299337	211102_Poo_TruePooDiatoms_Full2.mzML	QC Pooled	NA	NA	Diatom
SA299338	211102_Poo_TruePooDiatoms_Full1.mzML	QC Pooled	NA	NA	Diatom
SA299339	211102_Poo_TruePooDiatoms_Full3.mzML	QC Pooled	NA	NA	Diatom
SA299340	211102_Poo_TruePooDinosGreens_Full2.mzML	QC Pooled	NA	NA	DinosGreens
SA299341	211102_Poo_TruePooDinosGreens_Full1.mzML	QC Pooled	NA	NA	DinosGreens
SA299342	211102_Poo_TruePooDinosGreens_Half1.mzML	QC Pooled	NA	NA	DinosGreens
SA299343	211102_Poo_TruePooDinosGreens_Full3.mzML	QC Pooled	NA	NA	DinosGreens
SA299344	211102_Poo_TruePooDinosGreens_Half3.mzML	QC Pooled	NA	NA	DinosGreens
SA299345	211102_Poo_TruePooDinosGreens_Half2.mzML	QC Pooled	NA	NA	DinosGreens
SA299346	220104_Poo_TruePooHaptophytes_Half1.mzML	QC Pooled	NA	NA	Haptophytes
SA299347	220104_Poo_TruePooHaptophytes_Half2.mzML	QC Pooled	NA	NA	Haptophytes
SA299348	220104_Poo_TruePooHaptophytes_Full3.mzML	QC Pooled	NA	NA	Haptophytes
SA299349	220104_Poo_TruePooHaptophytes_Full2.mzML	QC Pooled	NA	NA	Haptophytes
SA299350	220104_Poo_TruePooHaptophytes_Half3.mzML	QC Pooled	NA	NA	Haptophytes
SA299351	220104_Poo_TruePooHaptophytes_Full1.mzML	QC Pooled	NA	NA	Haptophytes
SA299352	211218_Smp_1771_A_pos.mzML	Sample	Alexandrium tamarense CCMP1771	Dinoflagellates	DinosGreens
SA299353	211218_Smp_1771_C_pos.mzML	Sample	Alexandrium tamarense CCMP1771	Dinoflagellates	DinosGreens
SA299354	211218_Smp_1771_B_pos.mzML	Sample	Alexandrium tamarense CCMP1771	Dinoflagellates	DinosGreens
SA299355	211221_Smp_1314P_B_pos.mzML	Sample	Amphidinium carterae CCMP1314	Dinoflagellates	DinosGreens
SA299356	211221_Smp_1314P_C_pos.mzML	Sample	Amphidinium carterae CCMP1314	Dinoflagellates	DinosGreens
SA299357	211221_Smp_1314P_A_pos.mzML	Sample	Amphidinium carterae CCMP1314	Dinoflagellates	DinosGreens
SA299358	211218_Smp_1314_C_pos.mzML	Sample	Amphidinium carterae CCMP1314	Dinoflagellates	DinosGreens
SA299359	211218_Smp_1314_A_pos.mzML	Sample	Amphidinium carterae CCMP1314	Dinoflagellates	DinosGreens
SA299360	211218_Smp_1314_B_pos.mzML	Sample	Amphidinium carterae CCMP1314	Dinoflagellates	DinosGreens
SA299361	220104_Smp_Ca_A_pos.mzML	Sample	Chrysochromulina acantha	Haptophytes	Haptos
SA299362	220104_Smp_Ca_C_pos.mzML	Sample	Chrysochromulina acantha	Haptophytes	Haptos
SA299363	220104_Smp_Ca_B_pos.mzML	Sample	Chrysochromulina acantha	Haptophytes	Haptos
SA299370	220104_Smp_P3_A_pos.mzML	Sample	Chrysochromulina	Haptophytes	Haptos
SA299371	220104_Smp_116-1_B_pos.mzML	Sample	Chrysochromulina	Haptophytes	Haptos
SA299372	220104_Smp_116-1_A_pos.mzML	Sample	Chrysochromulina	Haptophytes	Haptos
SA299373	220104_Smp_P5-5_C_pos.mzML	Sample	Chrysochromulina	Haptophytes	Haptos
SA299374	220104_Smp_P3_B_pos.mzML	Sample	Chrysochromulina	Haptophytes	Haptos
SA299375	220104_Smp_116-1_C_pos.mzML	Sample	Chrysochromulina	Haptophytes	Haptos
SA299376	220104_Smp_P3_C_pos.mzML	Sample	Chrysochromulina	Haptophytes	Haptos
SA299377	220104_Smp_P5-5_A_pos.mzML	Sample	Chrysochromulina	Haptophytes	Haptos
SA299378	220104_Smp_P5-5_B_pos.mzML	Sample	Chrysochromulina	Haptophytes	Haptos
SA299364	220104_Smp_Cr_A_pos.mzML	Sample	Chrysochromulina rotalis	Haptophytes	Haptos
SA299365	220104_Smp_Cr_C_pos.mzML	Sample	Chrysochromulina rotalis	Haptophytes	Haptos
SA299366	220104_Smp_Cr_B_pos.mzML	Sample	Chrysochromulina rotalis	Haptophytes	Haptos
SA299367	220104_Smp_Cs_C_pos.mzML	Sample	Chrysochromulina simplex	Haptophytes	Haptos
SA299368	220104_Smp_Cs_A_pos.mzML	Sample	Chrysochromulina simplex	Haptophytes	Haptos
SA299369	220104_Smp_Cs_B_pos.mzML	Sample	Chrysochromulina simplex	Haptophytes	Haptos
SA299379	220111_Smp_SA60_A_pos.mzML	Sample	Croceibacter (CFB) SA60	Heterotrophic Bacteria	Bacteria
SA299380	220111_Smp_SA60_B_pos.mzML	Sample	Croceibacter (CFB) SA60	Heterotrophic Bacteria	Bacteria
SA299381	220111_Smp_SA60_C_pos.mzML	Sample	Croceibacter (CFB) SA60	Heterotrophic Bacteria	Bacteria
SA299382	211221_Smp_8501_D_pos.mzML	Sample	Crocosphaera watsonii WH8501	Cyanos	Cyanos
SA299383	211221_Smp_8501_C_pos.mzML	Sample	Crocosphaera watsonii WH8501	Cyanos	Cyanos
SA299384	211221_Smp_8501_B_pos.mzML	Sample	Crocosphaera watsonii WH8501	Cyanos	Cyanos
SA299385	211215_Smp_Cy_B_pos.mzML	Sample	Cyclotella meneghiniana CCMP 338	Diatoms	Diatom
SA299386	211215_Smp_Cy_C_pos.mzML	Sample	Cyclotella meneghiniana CCMP 338	Diatoms	Diatom
SA299387	211215_Smp_Cy_A_pos.mzML	Sample	Cyclotella meneghiniana CCMP 338	Diatoms	Diatom
SA299388	220104_Smp_2090_B_pos.mzML	Sample	Emiliana huxleyi CCMP2090 (baller)	Haptophytes	Haptos
SA299389	220104_Smp_2090_A_pos.mzML	Sample	Emiliana huxleyi CCMP2090 (baller)	Haptophytes	Haptos
SA299390	220104_Smp_2090_C_pos.mzML	Sample	Emiliana huxleyi CCMP2090 (baller)	Haptophytes	Haptos
SA299391	220104_Smp_371_C_pos.mzML	Sample	Emiliana huxleyi CCMP371 (c)	Haptophytes	Haptos
SA299392	220104_Smp_371_A_pos.mzML	Sample	Emiliana huxleyi CCMP371 (c)	Haptophytes	Haptos
SA299393	220104_Smp_371_B_pos.mzML	Sample	Emiliana huxleyi CCMP371 (c)	Haptophytes	Haptos
SA299394	211215_Smp_Fc_B_pos.mzML	Sample	Fragilariopsis cylindrus CCMP3383	Diatoms	Diatom
SA299395	211215_Smp_Fc_A_pos.mzML	Sample	Fragilariopsis cylindrus CCMP3383	Diatoms	Diatom
SA299396	211215_Smp_Fc_C_pos.mzML	Sample	Fragilariopsis cylindrus CCMP3383	Diatoms	Diatom
SA299397	211218_Smp_449_C_pos.mzML	Sample	Heterocapsa triquetra CCMP449	Dinoflagellates	DinosGreens

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Collection:

Collection ID:	CO002890
Collection Summary:	Cultures were 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 cells

Treatment:

Treatment ID:	TR002906
Treatment Summary:	Media, light, and temperature were chosen for optimal growth of each phytoplankton species. In short, cultures were grown 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.

Treatment ID:

TR002906

Treatment Summary:

Media, light, and temperature were chosen for optimal growth of each phytoplankton species. In short, cultures were grown 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:	SP002903
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	AN004540
Analysis type	MS
Chromatography type	HILIC
Chromatography system	Waters Acquity I-Class
Column	SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive HF hybrid Orbitrap
Ion Mode	POSITIVE
Units	normalized peak area per liter seawater filtered

Chromatography:

Chromatography ID:	CH003410
Chromatography Summary:	A SeQuant ZIC-pHILIC column (5 um particle size, 2.1 mm x 150 mm, from Millipore) was used with 10 mM ammonium carbonate in 85:15 acetonitrile to water (Solvent A) and 10 mM ammonium carbonate in 85:15 water to acetonitrile (Solvent B) at a flow rate of 0.15 mL/min. This column was compared with a Waters UPLC BEH amide and a Millipore cHILIC column; the pHILIC showed superior reproducibility and peak shapes. The column was held at 100% A for 2 minutes, ramped to 64% B over 18 minutes, ramped to 100% B over 1 minute, held at 100% B for 5 minutes, and equilibrated at 100% A for 25 minutes (50 minutes total). The column was maintained at 30 C. The injection volume was 2 µL for samples and standard mixes. When starting a batch, the column was equilibrated at the starting conditions for at least 30 minutes. To improve the performance of the HILIC column, we maintained the same injection volume, kept the instrument running water blanks between samples as necessary, and injected standards in a representative matrix in addition to standards in water. After each batch, the column was flushed with 10 mM ammonium carbonate in 85:15 water to acetonitrile for 20 to 30 minutes.
Instrument Name:	Waters Acquity I-Class
Column Name:	SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
Column Temperature:	30
Flow Gradient:	100% A for 2 minutes, ramped to 64% B over 18 minutes, ramped to 100% B over 1 minute, held at 100% B for 5 minutes, and equilibrated at 100% A for 25 minutes (50 minutes total)
Flow Rate:	0.15mL/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:	MS004287
Analysis ID:	AN004540
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Metabolomic data was collected on a Thermo Q Exactive HF hybrid Orbitrap mass spectrometer. The capillary and auxiliary gas heater temperatures were maintained at 320°C and 100°C, respectively. The S-lens RF level was kept at 65, the H-ESI voltage was set to 3.3 kV and sheath gas, auxiliary gas, and sweep gas flow rates were set at 16, 3, and 1, respectively. Polarity switching was used with a scan range of 60 to 900 m/z and a resolution of 60,000. Calibration was performed every 3-4 days at a target mass of 200 m/z. All files were then converted to an open-source mzML format and centroided via Proteowizard’s msConvert tool. Skyline was used to for manual integration and QC of quantified data, while XCMS was used with a custom QC method for peak area data and each feature manually reviewed.
Ion Mode:	POSITIVE