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.
Study ID | ST001356 |
Study Title | Diel Metabolites in the North Pacific Subtropical Gyre (KM1513) |
Study Type | Diel metabolomics |
Study 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 | Oceanography |
Laboratory | Ingalls Lab |
Last Name | Boysen |
First Name | Angela |
Address | 1502 NE Boat St |
aboysen@uw.edu | |
Phone | 3037461944 |
Submit Date | 2020-03-23 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzXML |
Analysis Type Detail | LC-MS |
Release Date | 2020-07-21 |
Release Version | 1 |
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: | Ilyonectria mors-panacis;Ilyonectria rufa;Ilyonectria robusta;Ilyonectria torresensis;Ilyonectria estremocensis;Neonectria obtusispora |
Taxonomy ID: | 1079131;1079113;1079257;1199091;1079267;78417 |
Species Group: | Fungi |
Factors:
Subject type: Other; Subject species: Ilyonectria mors-panacis;Ilyonectria rufa;Ilyonectria robusta;Ilyonectria torresensis;Ilyonectria estremocensis;Neonectria obtusispora (Factor headings shown in green)
mb_sample_id | local_sample_id | Time | Station and Cast |
---|---|---|---|
SA098553 | S2R3 | 1000 | S07C001 |
SA098554 | S2R1 | 1000 | S07C001 |
SA098555 | S2R2 | 1000 | S07C001 |
SA098556 | S8R1 | 1000 | S17C001 |
SA098557 | S8R2 | 1000 | S17C001 |
SA098558 | S8R3 | 1000 | S17C001 |
SA098559 | S14R2 | 1000 | S23C001 |
SA098560 | S14R3 | 1000 | S23C001 |
SA098561 | S14R1 | 1000 | S23C001 |
SA098562 | S20R1 | 1000 | S31C001 |
SA098563 | S20R2 | 1000 | S31C001 |
SA098564 | S20R3 | 1000 | S31C001 |
SA098565 | S30R3 | 1000 | S53C001 |
SA098566 | S30R2 | 1000 | S53C001 |
SA098567 | S30R1 | 1000 | S53C001 |
SA098568 | S36R3 | 1000 | S60C001 |
SA098569 | S36R2 | 1000 | S60C001 |
SA098570 | S36R1 | 1000 | S60C001 |
SA098571 | S42R1 | 1000 | S68C001 |
SA098572 | S42R2 | 1000 | S68C001 |
SA098573 | S42R3 | 1000 | S68C001 |
SA098574 | S3R3 | 1400 | S08C001 |
SA098575 | S3R2 | 1400 | S08C001 |
SA098576 | S3R1 | 1400 | S08C001 |
SA098577 | S9R3 | 1400 | S18C001 |
SA098578 | S9R1 | 1400 | S18C001 |
SA098579 | S9R2 | 1400 | S18C001 |
SA098580 | S15R1 | 1400 | S24C001 |
SA098581 | S15R3 | 1400 | S24C001 |
SA098582 | S15R2 | 1400 | S24C001 |
SA098583 | S21R2 | 1400 | S32C001 |
SA098584 | S21R1 | 1400 | S32C001 |
SA098585 | S21R3 | 1400 | S32C001 |
SA098586 | S31R3 | 1400 | S54C001 |
SA098587 | S31R1 | 1400 | S54C001 |
SA098588 | S37R1 | 1400 | S61C001 |
SA098589 | S37R3 | 1400 | S61C001 |
SA098590 | S37R2 | 1400 | S61C001 |
SA098591 | S43R3 | 1400 | S69C001 |
SA098592 | S43R2 | 1400 | S69C001 |
SA098593 | S43R1 | 1400 | S69C001 |
SA098594 | S4R2 | 1800 | S11C001 |
SA098595 | S4R1 | 1800 | S11C001 |
SA098596 | S4R3 | 1800 | S11C001 |
SA098597 | S10R3 | 1800 | S19C001 |
SA098598 | S10R2 | 1800 | S19C001 |
SA098599 | S10R1 | 1800 | S19C001 |
SA098600 | S16R2 | 1800 | S26C001 |
SA098601 | S16R3 | 1800 | S26C001 |
SA098602 | S16R1 | 1800 | S26C001 |
SA098603 | S22R1 | 1800 | S33C001 |
SA098604 | S22R2 | 1800 | S33C001 |
SA098605 | S22R3 | 1800 | S33C001 |
SA098606 | S26R1 | 1800 | S47C001 |
SA098607 | S26R2 | 1800 | S47C001 |
SA098608 | S26R3 | 1800 | S47C001 |
SA098609 | S32R2 | 1800 | S55C001 |
SA098610 | S32R3 | 1800 | S55C001 |
SA098611 | S32R1 | 1800 | S55C001 |
SA098612 | S38R3 | 1800 | S63C001 |
SA098613 | S38R1 | 1800 | S63C001 |
SA098614 | S38R2 | 1800 | S63C001 |
SA098615 | S44R1 | 1800 | S70C001 |
SA098616 | S44R2 | 1800 | S70C001 |
SA098617 | S44R3 | 1800 | S70C001 |
SA098618 | S6R2 | 200 | S15C001 |
SA098619 | S6R1 | 200 | S15C001 |
SA098620 | S6R3 | 200 | S15C001 |
SA098621 | S12R2 | 200 | S21C001 |
SA098622 | S12R3 | 200 | S21C001 |
SA098623 | S12R1 | 200 | S21C001 |
SA098624 | S18R2 | 200 | S29C001 |
SA098625 | S18R3 | 200 | S29C001 |
SA098626 | S18R1 | 200 | S29C001 |
SA098627 | S24R2 | 200 | S35C001 |
SA098628 | S24R3 | 200 | S35C001 |
SA098629 | S24R1 | 200 | S35C001 |
SA098630 | S28R3 | 200 | S51C001 |
SA098631 | S28R2 | 200 | S51C001 |
SA098632 | S28R1 | 200 | S51C001 |
SA098633 | S34R1 | 200 | S57C001 |
SA098634 | S34R3 | 200 | S57C001 |
SA098635 | S34R2 | 200 | S57C001 |
SA098636 | S40R2 | 200 | S66C001 |
SA098637 | S40R3 | 200 | S66C001 |
SA098638 | S40R1 | 200 | S66C001 |
SA098639 | S5R2 | 2200 | S14C001 |
SA098640 | S5R1 | 2200 | S14C001 |
SA098641 | S5R3 | 2200 | S14C001 |
SA098642 | S11R3 | 2200 | S20C001 |
SA098643 | S11R1 | 2200 | S20C001 |
SA098644 | S11R2 | 2200 | S20C001 |
SA098645 | S17R3 | 2200 | S28C001 |
SA098646 | S17R2 | 2200 | S28C001 |
SA098647 | S17R1 | 2200 | S28C001 |
SA098648 | S23R3 | 2200 | S34C001 |
SA098649 | S23R2 | 2200 | S34C001 |
SA098650 | S23R1 | 2200 | S34C001 |
SA098651 | S27R3 | 2200 | S49C001 |
SA098652 | S27R1 | 2200 | S49C001 |
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) ( 50 x 2.1mm,1.8um) | Waters Acquity UPLC HSS Cyano (CN) ( 50 x 2.1mm,1.8um) | 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_MS_Parameters_2015.pdf |
Instrument Name: | Waters Acquity I-Class |
Column Name: | Waters Acquity UPLC HSS Cyano (CN) ( 50 x 2.1mm,1.8um) |
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: | 100% water; 0.1% formic acid |
Solvent B: | 100% acetonitrile; 0.1% formic acid |
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_MS_Parameters_2015.pdf |
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: | 85% acetonitrile/15% water; 10 mM ammonium carbonate |
Solvent B: | 40% acetonitrile/60% water; 10 mM ammonium carbonate |
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 |
Acquisition Parameters File: | Ingalls_Metabolomics_MS_Parameters_2015.txt |
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 |
Acquisition Parameters File: | Ingalls_Metabolomics_MS_Parameters_2015.txt |
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 |
Acquisition Parameters File: | Ingalls_Metabolomics_MS_Parameters_2015.txt |
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 |
Acquisition Parameters File: | Ingalls_Metabolomics_MS_Parameters_2015.txt |
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 |
Acquisition Parameters File: | Ingalls_Metabolomics_MS_Parameters_2015.txt |