Summary of study ST001356

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 PR000926. The data can be accessed directly via it's Project DOI: 10.21228/M80H4K 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 IDST001356
Study TitleDiel Metabolites in the North Pacific Subtropical Gyre (KM1513)
Study TypeDiel metabolomics
Study SummaryDiverse organisms within the marine microbial communities show 24-hour cycles of gene expression, likely driven by the need to harness energy from sunlight and to cope with dramatic fluctuations in solar radiation over the course of the day. Metabolites are the direct product of metabolic activity; they are therefore expected to both reflect and influence the daily cycle of the microbial community. Here we measure the intracellular metabolome of the microbial community of the North Pacific Subtropical Gyre, sampled at 4-hour intervals for 8 days. Concentrations of some metabolites common to many organisms exhibit diel periodicity, revealing synchrony of community-level metabolism. Comparing these data to gene expression data reveals temporal offsets between gene transcription and cellular activity, and ties some metabolites to the activities of specific organisms. For example, the dramatic fluctuations of the disaccharide trehalose likely reflect the daily cycles of {Crocosphaera}, a photosynthesizing cyanobacteria that needs to store energy during the day to fuel nighttime nitrogen-fixation. This study illustrates how pairing multiple types of 'omics and environmental data can provide insight into how the activities of individual organisms lead to community functions such as net primary productivity and nitrogen fixation.
Institute
University of Washington
DepartmentOceanography
LaboratoryIngalls Lab
Last NameBoysen
First NameAngela
Address1502 NE Boat St
Emailaboysen@uw.edu
Phone3037461944
Submit Date2020-03-23
Raw Data AvailableYes
Raw Data File Type(s).mzXML
Analysis Type DetailLC-MS
Release Date2020-07-21
Release Version1
Angela Boysen Angela Boysen
https://dx.doi.org/10.21228/M80H4K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000926
Project DOI:doi: 10.21228/M80H4K
Project Title:Diel Metabolites in the North Pacific Subtropical Gyre
Project Type:Marine Metabolomics
Project Summary:Diverse organisms within the marine microbial communities show 24-hour cycles of gene expression, likely driven by the need to harness energy from sunlight and to cope with dramatic fluctuations in solar radiation over the course of the day. Metabolites are the direct product of metabolic activity; they are therefore expected to both reflect and influence the daily cycle of the microbial community. Here we measure the intracellular metabolome of the microbial community of the North Pacific Subtropical Gyre, sampled at 4-hour intervals for 8 days. Concentrations of some metabolites common to many organisms exhibit diel periodicity, revealing synchrony of community-level metabolism. Comparing these data to gene expression data reveals temporal offsets between gene transcription and cellular activity, and ties some metabolites to the activities of specific organisms. For example, the dramatic fluctuations of the disaccharide trehalose likely reflect the daily cycles of Crocosphaera, a photosynthesizing cyanobacteria that needs to store energy during the day to fuel nighttime nitrogen-fixation. This study illustrates how pairing multiple types of 'omics and environmental data can provide insight into how the activities of individual organisms lead to community functions such as net primary productivity and nitrogen fixation.
Institute:University of Washington
Department:School of Oceanography
Laboratory:Ingalls Lab
Last Name:Boysen
First Name:Angela
Address:1503 NE Boat Street, Box 357940, Seattle, WA, 98195, USA
Email:aboysen@uw.edu
Phone:3037461944
Funding Source:Simons Foundation, NSF

Subject:

Subject ID:SU001430
Subject Type:Other
Subject Species:Natural Mixed Marine Microbial Community

Factors:

Subject type: Other; Subject species: Natural Mixed Marine Microbial Community (Factor headings shown in green)

mb_sample_id local_sample_id Time Station and Cast
SA098553S2R31000 S07C001
SA098554S2R11000 S07C001
SA098555S2R21000 S07C001
SA098556S8R11000 S17C001
SA098557S8R21000 S17C001
SA098558S8R31000 S17C001
SA098559S14R21000 S23C001
SA098560S14R31000 S23C001
SA098561S14R11000 S23C001
SA098562S20R11000 S31C001
SA098563S20R21000 S31C001
SA098564S20R31000 S31C001
SA098565S30R31000 S53C001
SA098566S30R21000 S53C001
SA098567S30R11000 S53C001
SA098568S36R31000 S60C001
SA098569S36R21000 S60C001
SA098570S36R11000 S60C001
SA098571S42R11000 S68C001
SA098572S42R21000 S68C001
SA098573S42R31000 S68C001
SA098574S3R31400 S08C001
SA098575S3R21400 S08C001
SA098576S3R11400 S08C001
SA098577S9R31400 S18C001
SA098578S9R11400 S18C001
SA098579S9R21400 S18C001
SA098580S15R11400 S24C001
SA098581S15R31400 S24C001
SA098582S15R21400 S24C001
SA098583S21R21400 S32C001
SA098584S21R11400 S32C001
SA098585S21R31400 S32C001
SA098586S31R31400 S54C001
SA098587S31R11400 S54C001
SA098588S37R11400 S61C001
SA098589S37R31400 S61C001
SA098590S37R21400 S61C001
SA098591S43R31400 S69C001
SA098592S43R21400 S69C001
SA098593S43R11400 S69C001
SA098594S4R21800 S11C001
SA098595S4R11800 S11C001
SA098596S4R31800 S11C001
SA098597S10R31800 S19C001
SA098598S10R21800 S19C001
SA098599S10R11800 S19C001
SA098600S16R21800 S26C001
SA098601S16R31800 S26C001
SA098602S16R11800 S26C001
SA098603S22R11800 S33C001
SA098604S22R21800 S33C001
SA098605S22R31800 S33C001
SA098606S26R11800 S47C001
SA098607S26R21800 S47C001
SA098608S26R31800 S47C001
SA098609S32R21800 S55C001
SA098610S32R31800 S55C001
SA098611S32R11800 S55C001
SA098612S38R31800 S63C001
SA098613S38R11800 S63C001
SA098614S38R21800 S63C001
SA098615S44R11800 S70C001
SA098616S44R21800 S70C001
SA098617S44R31800 S70C001
SA098618S6R2200 S15C001
SA098619S6R1200 S15C001
SA098620S6R3200 S15C001
SA098621S12R2200 S21C001
SA098622S12R3200 S21C001
SA098623S12R1200 S21C001
SA098624S18R2200 S29C001
SA098625S18R3200 S29C001
SA098626S18R1200 S29C001
SA098627S24R2200 S35C001
SA098628S24R3200 S35C001
SA098629S24R1200 S35C001
SA098630S28R3200 S51C001
SA098631S28R2200 S51C001
SA098632S28R1200 S51C001
SA098633S34R1200 S57C001
SA098634S34R3200 S57C001
SA098635S34R2200 S57C001
SA098636S40R2200 S66C001
SA098637S40R3200 S66C001
SA098638S40R1200 S66C001
SA098639S5R22200 S14C001
SA098640S5R12200 S14C001
SA098641S5R32200 S14C001
SA098642S11R32200 S20C001
SA098643S11R12200 S20C001
SA098644S11R22200 S20C001
SA098645S17R32200 S28C001
SA098646S17R22200 S28C001
SA098647S17R12200 S28C001
SA098648S23R32200 S34C001
SA098649S23R22200 S34C001
SA098650S23R12200 S34C001
SA098651S27R32200 S49C001
SA098652S27R12200 S49C001
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Collection:

Collection ID:CO001425
Collection Summary:Samples for particulate metabolites were collected from 15 m water depth by niskin bottles attached to a conductivity, temperature, depth array (CTD). Metabolite samples were collected in triplicate at each time point by filtering approximately 3.5 L of seawater onto 47 mm 0.2 micron Omnipore filters using peristaltic pumps, polycarbonate filter holders, and Masterflex PharMed BPT tubing (Cole-Parmer). Filters were frozen in liquid nitrogen immediately after filtration and stored in a -80 C freezer until extraction.
Sample Type:Suspended Marine Particulate Matter

Treatment:

Treatment ID:TR001445
Treatment Summary:No treatments - this was a study of the natural marine microbial population in the surface ocean at approximately 24.5 degrees N, 156.5 degrees W.

Sample Preparation:

Sampleprep ID:SP001438
Sampleprep Summary:Each sample was extracted using a modified Bligh-Dyer extraction. Briefly, filters were cut up and split between two bead beating tubes containing a mixture of 100 µm and 400 µm silica beads. Heavy isotope-labeled internal standards were added along with 750 µL of cold aqueous solved (50:50 methanol:water) and 750 µL 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 microcentrifuge at 5,000 rpm for 90 seconds 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 750 µL 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.
Sampleprep Protocol Filename:Ingalls_Metabolomics_Sample_Processing_2015.txt
Processing Storage Conditions:On ice
Extract Storage:-80℃

Combined analysis:

Analysis ID AN002255 AN002256 AN002257 AN002258 AN002259
Analysis type MS MS MS MS MS
Chromatography type Reversed phase Reversed phase HILIC HILIC HILIC
Chromatography system Waters Acquity I-Class Waters Acquity I-Class Waters Acquity I-Class Waters Acquity I-Class Waters Acquity I-Class
Column Waters Acquity UPLC HSS Cyano (CN) (2.1 mm X 50 mm, 1.8 µm) Waters Acquity UPLC HSS Cyano (CN) (2.1 mm X 50 mm, 1.8 µm) SeQuant ZIC- pHILIC (150 x 2.1mm, 5um) SeQuant ZIC- pHILIC (150 x 2.1mm, 5um) SeQuant ZIC- pHILIC (150 x 2.1mm, 5um)
MS Type ESI ESI ESI ESI ESI
MS instrument type Triple quadrupole Orbitrap Triple quadrupole Triple quadrupole Orbitrap
MS instrument name Waters Xevo-TQ-S Thermo Q Exactive HF hybrid Orbitrap Waters Xevo-TQ-S Waters Xevo-TQ-S Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE POSITIVE POSITIVE NEGATIVE POSITIVE
Units Normalized Peak Area Per L Seawater Filtered Normalized Peak Area Per L Seawater Filtered Normalized Peak Area Per L Seawater Filtered Normalized Peak Area Per L Seawater Filtered Normalized Peak Area per L of SW filtered

Chromatography:

Chromatography ID:CH001657
Chromatography Summary:RP
Methods Filename:Ingalls_Metabolomics_LC_Parameters_2015.txt
Instrument Name:Waters Acquity I-Class
Column Name:Waters Acquity UPLC HSS Cyano (CN) (2.1 mm X 50 mm, 1.8 µm)
Column Temperature:35 C
Flow Gradient:5% B for 2 minutes, ramped to 100% B over 16 minutes, held at 100% B for 2 minutes, and equilibrated at 5% B for 5 minutes
Flow Rate:0.4 mL/min
Solvent A:0.1% formic acid in water
Solvent B:0.1% formic acid in acetonitrile
Analytical Time:20 min
Preconditioning:equilibrated at the starting conditions for at least 10 minutes; several water blanks were run before
Chromatography Type:Reversed phase
  
Chromatography ID:CH001658
Chromatography Summary:HILIC
Methods Filename:Ingalls_Metabolomics_LC_Parameters_2015.txt
Chromatography Comments:In marine samples, a major salt peak elutes at approximately 23 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.
Instrument Name:Waters Acquity I-Class
Column Name:SeQuant ZIC- pHILIC (150 x 2.1mm, 5um)
Column Temperature:30 C
Flow Gradient:100% A for 2 minutes, ramped to 100% B over 18 minutes, held at 100% B for 5 minutes, and equilibrated at 100% A for 25 minutes
Flow Rate:0.15 mL/min
Solvent A:10 mM ammonium carbonate in 85:15 acetonitrile to water
Solvent B:10 mM ammonium carbonate in 60:40 water to acetonitrile
Analytical Time:25 min
Preconditioning:, the column was equilibrated at the starting conditions for at least 30 minutes
Chromatography Type:HILIC

MS:

MS ID:MS002099
Analysis ID:AN002255
Instrument Name:Waters Xevo-TQ-S
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:See File
Ion Mode:POSITIVE
  
MS ID:MS002100
Analysis ID:AN002256
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:See File
Ion Mode:POSITIVE
  
MS ID:MS002101
Analysis ID:AN002257
Instrument Name:Waters Xevo-TQ-S
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:See File
Ion Mode:POSITIVE
  
MS ID:MS002102
Analysis ID:AN002258
Instrument Name:Waters Xevo-TQ-S
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:See File
Ion Mode:NEGATIVE
  
MS ID:MS002103
Analysis ID:AN002259
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:See File
Ion Mode:POSITIVE
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