Summary of Study ST003653
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 PR002263. The data can be accessed directly via it's Project DOI: 10.21228/M83V6Q 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 | ST003653 |
Study Title | Marine community metabolomes in the eastern tropical North Pacific Oxygen Deficient Zone |
Study Summary | Oxygen deficient zones (ODZs) are subsurface marine systems that harbor distinct microbial communities, including populations of the picocyanobacteria Prochlorococcus that can form a secondary chlorophyll maxima (SCM), and low-oxygen tolerant strains of the globally abundant heterotroph Pelagibacter (SAR11). Yet, the small labile molecules (metabolites) responsible for maintaining these ODZ communities are unknown. Here, we compared the metabolome of an ODZ to that of an oxygenated site by quantifying 87 metabolites across depth profiles in the eastern tropical North Pacific ODZ and the oxygenated waters of the North Pacific Gyre. We further use transcriptomes to identify taxa involved in production and subsequent transformation of glycine betaine (GBT), a metabolite we suggest is involved in microbial interdependencies in this community, and elsewhere in the ocean. |
Institute | University of Washington, School of Oceanography |
Last Name | Kellogg |
First Name | Natalie |
Address | 1503 NE Boat Street, Seattle, WA, 98195, USA |
nak01@uw.edu | |
Phone | 6517958717 |
Submit Date | 2024-12-05 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzXML |
Analysis Type Detail | LC-MS |
Release Date | 2025-01-12 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR002263 |
Project DOI: | doi: 10.21228/M83V6Q |
Project Title: | Marine community metabolomes in the eastern tropical North Pacific Oxygen Deficient Zone |
Project Summary: | Oxygen deficient zones (ODZs) are subsurface marine systems that harbor distinct microbial communities, including populations of the picocyanobacteria Prochlorococcus that can form a secondary chlorophyll maxima (SCM), and low-oxygen tolerant strains of the globally abundant heterotroph Pelagibacter (SAR11). Yet, the small labile molecules (metabolites) responsible for maintaining these ODZ communities are unknown. Here, we compared the metabolome of an ODZ to that of an oxygenated site by quantifying 87 metabolites across depth profiles in the eastern tropical North Pacific ODZ and the oxygenated waters of the North Pacific Gyre. We further use transcriptomes to identify taxa involved in production and subsequent transformation of glycine betaine (GBT), a metabolite we suggest is involved in microbial interdependencies in this community, and elsewhere in the ocean. |
Institute: | University of Washington |
Last Name: | Kellogg |
First Name: | Natalie |
Address: | 1502 NE Boat St, Seattle, WA, 98105, USA |
Email: | nak01@uw.edu |
Phone: | 6517958717 |
Subject:
Subject ID: | SU003783 |
Subject Type: | Other organism |
Subject Species: | Marine microbes |
Factors:
Subject type: Other organism; Subject species: Marine microbes (Factor headings shown in green)
mb_sample_id | local_sample_id | Latitude | Longitude | Sample source | Depth (m) |
---|---|---|---|---|---|
SA398468 | MP2C44D0_A | 16.5562 | -107.0091 | Marine particulate organic matter | 10 |
SA398469 | MP2C44D0_B | 16.5562 | -107.0091 | Marine particulate organic matter | 10 |
SA398470 | MP2C44D0_C | 16.5562 | -107.0091 | Marine particulate organic matter | 10 |
SA398471 | MP2C49D105_B | 16.5562 | -107.0091 | Marine particulate organic matter | 105 |
SA398472 | MP2C49D105_C | 16.5562 | -107.0091 | Marine particulate organic matter | 105 |
SA398473 | MP2C49D105_A | 16.5562 | -107.0091 | Marine particulate organic matter | 105 |
SA398474 | MP2C50D110_B | 16.5562 | -107.0091 | Marine particulate organic matter | 110 |
SA398475 | MP2C44D110_A | 16.5562 | -107.0091 | Marine particulate organic matter | 110 |
SA398476 | MP2C44D110_B | 16.5562 | -107.0091 | Marine particulate organic matter | 110 |
SA398477 | MP2C44D110_C | 16.5562 | -107.0091 | Marine particulate organic matter | 110 |
SA398478 | MP2C50D110_A | 16.5562 | -107.0091 | Marine particulate organic matter | 110 |
SA398479 | MP2C50D110_C | 16.5562 | -107.0091 | Marine particulate organic matter | 110 |
SA398480 | MP2C44D150_A | 16.5562 | -107.0091 | Marine particulate organic matter | 150 |
SA398481 | MP2C44D150_C | 16.5562 | -107.0091 | Marine particulate organic matter | 150 |
SA398482 | MP2C44D150_B | 16.5562 | -107.0091 | Marine particulate organic matter | 150 |
SA398483 | MP2C48D150_A | 16.5562 | -107.0091 | Marine particulate organic matter | 150 |
SA398484 | MP2C48D150_B | 16.5562 | -107.0091 | Marine particulate organic matter | 150 |
SA398485 | MP2C48D150_C | 16.5562 | -107.0091 | Marine particulate organic matter | 150 |
SA398486 | MP2C44D200_C | 16.5562 | -107.0091 | Marine particulate organic matter | 200 |
SA398487 | MP2C44D200_A | 16.5562 | -107.0091 | Marine particulate organic matter | 200 |
SA398488 | MP2C44D200_B | 16.5562 | -107.0091 | Marine particulate organic matter | 200 |
SA398489 | MP2C44D275_B | 16.5562 | -107.0091 | Marine particulate organic matter | 275 |
SA398490 | MP2C44D275_C | 16.5562 | -107.0091 | Marine particulate organic matter | 275 |
SA398491 | MP2C44D275_A | 16.5562 | -107.0091 | Marine particulate organic matter | 275 |
SA398492 | MP2C44D400_A | 16.5562 | -107.0091 | Marine particulate organic matter | 400 |
SA398493 | MP2C44D400_B | 16.5562 | -107.0091 | Marine particulate organic matter | 400 |
SA398494 | MP2C44D400_C | 16.5562 | -107.0091 | Marine particulate organic matter | 400 |
SA398495 | MP2C44D50_C | 16.5562 | -107.0091 | Marine particulate organic matter | 50 |
SA398496 | MP2C44D50_A | 16.5562 | -107.0091 | Marine particulate organic matter | 50 |
SA398497 | MP2C44D50_B | 16.5562 | -107.0091 | Marine particulate organic matter | 50 |
SA398498 | MP2C44D75_C | 16.5562 | -107.0091 | Marine particulate organic matter | 75 |
SA398499 | MP2C44D75_B | 16.5562 | -107.0091 | Marine particulate organic matter | 75 |
SA398500 | MP2C44D75_A | 16.5562 | -107.0091 | Marine particulate organic matter | 75 |
SA398501 | MP1C62D10_3 | 20.1236 | -106.0308 | Marine particulate organic matter | 10 |
SA398502 | MP1C62D10_1 | 20.1236 | -106.0308 | Marine particulate organic matter | 10 |
SA398503 | MP1C62D10_2 | 20.1236 | -106.0308 | Marine particulate organic matter | 10 |
SA398504 | MP1C62D1000_1 | 20.1236 | -106.0308 | Marine particulate organic matter | 1000 |
SA398505 | MP1C62D1000_2 | 20.1236 | -106.0308 | Marine particulate organic matter | 1000 |
SA398506 | MP1C62D1000_3 | 20.1236 | -106.0308 | Marine particulate organic matter | 1000 |
SA398507 | MP1C62D150_1 | 20.1236 | -106.0308 | Marine particulate organic matter | 150 |
SA398508 | MP1C62D150_2 | 20.1236 | -106.0308 | Marine particulate organic matter | 150 |
SA398509 | MP1C62D150_3 | 20.1236 | -106.0308 | Marine particulate organic matter | 150 |
SA398510 | MP1C62D1500_2 | 20.1236 | -106.0308 | Marine particulate organic matter | 1500 |
SA398511 | MP1C62D1500_3 | 20.1236 | -106.0308 | Marine particulate organic matter | 1500 |
SA398512 | MP1C62D1500_1 | 20.1236 | -106.0308 | Marine particulate organic matter | 1500 |
SA398513 | MP1C62D25_1 | 20.1236 | -106.0308 | Marine particulate organic matter | 25 |
SA398514 | MP1C62D25_3 | 20.1236 | -106.0308 | Marine particulate organic matter | 25 |
SA398515 | MP1C62D25_2 | 20.1236 | -106.0308 | Marine particulate organic matter | 25 |
SA398516 | MP1C62D40_2 | 20.1236 | -106.0308 | Marine particulate organic matter | 40 |
SA398517 | MP1C62D40_3 | 20.1236 | -106.0308 | Marine particulate organic matter | 40 |
SA398518 | MP1C62D40_1 | 20.1236 | -106.0308 | Marine particulate organic matter | 40 |
SA398519 | MP1C62D500_3 | 20.1236 | -106.0308 | Marine particulate organic matter | 500 |
SA398520 | MP1C62D500_2 | 20.1236 | -106.0308 | Marine particulate organic matter | 500 |
SA398521 | MP1C62D500_1 | 20.1236 | -106.0308 | Marine particulate organic matter | 500 |
SA398522 | MP1C62D75_3 | 20.1236 | -106.0308 | Marine particulate organic matter | 75 |
SA398523 | MP1C62D75_2 | 20.1236 | -106.0308 | Marine particulate organic matter | 75 |
SA398524 | MP1C62D75_1 | 20.1236 | -106.0308 | Marine particulate organic matter | 75 |
SA398525 | DOS-1070m_2 | 32.00046 | -157.599966 | Marine particulate organic matter | 1070 |
SA398526 | DOS-1070m_3 | 32.00046 | -157.599966 | Marine particulate organic matter | 1070 |
SA398527 | DOS-1070m_1 | 32.00046 | -157.599966 | Marine particulate organic matter | 1070 |
SA398528 | DOS-120m_1 | 32.00046 | -157.599966 | Marine particulate organic matter | 120 |
SA398529 | DOS-120m_2 | 32.00046 | -157.599966 | Marine particulate organic matter | 120 |
SA398530 | DOS-120m_3 | 32.00046 | -157.599966 | Marine particulate organic matter | 120 |
SA398531 | DOS-15m_1 | 32.00046 | -157.599966 | Marine particulate organic matter | 15 |
SA398532 | DOS-15m_2 | 32.00046 | -157.599966 | Marine particulate organic matter | 15 |
SA398533 | DOS-15m_3 | 32.00046 | -157.599966 | Marine particulate organic matter | 15 |
SA398534 | DOS-300m_3 | 32.00046 | -157.599966 | Marine particulate organic matter | 300 |
SA398535 | DOS-300m_2 | 32.00046 | -157.599966 | Marine particulate organic matter | 300 |
SA398536 | DOS-300m_1 | 32.00046 | -157.599966 | Marine particulate organic matter | 300 |
SA398537 | DOS-3000m_3 | 32.00046 | -157.599966 | Marine particulate organic matter | 3000 |
SA398538 | DOS-3000m_1 | 32.00046 | -157.599966 | Marine particulate organic matter | 3000 |
SA398539 | DOS-3000m_2 | 32.00046 | -157.599966 | Marine particulate organic matter | 3000 |
SA398540 | DOS-45m_1 | 32.00046 | -157.599966 | Marine particulate organic matter | 45 |
SA398541 | DOS-45m_2 | 32.00046 | -157.599966 | Marine particulate organic matter | 45 |
SA398542 | DOS-45m_3 | 32.00046 | -157.599966 | Marine particulate organic matter | 45 |
SA398543 | DOS-590m_3 | 32.00046 | -157.599966 | Marine particulate organic matter | 590 |
SA398544 | DOS-590m_1 | 32.00046 | -157.599966 | Marine particulate organic matter | 590 |
SA398545 | DOS-590m_2 | 32.00046 | -157.599966 | Marine particulate organic matter | 590 |
SA398546 | DOS-90m_2 | 32.00046 | -157.599966 | Marine particulate organic matter | 90 |
SA398547 | DOS-90m_3 | 32.00046 | -157.599966 | Marine particulate organic matter | 90 |
SA398548 | DOS-90m_1 | 32.00046 | -157.599966 | Marine particulate organic matter | 90 |
Showing results 1 to 81 of 81 |
Collection:
Collection ID: | CO003776 |
Collection Summary: | Samples were collected in the North Pacific for metabolomics analysis of particulate material within the upper 3000 m. Samples for the oxic North Pacific gyre (NPG) depth profile were collected during the MGL1704 cruise (Gradients II) aboard the R/V Marcus Langseth at eight depths between 15 and 3000 m on June 10, 2017 (St 17; 32ºN 157.6ºW). During the RR1805 cruise (POMZ 2018), samples for the eastern tropical North Pacific (ETNP) ODZ depth profiles were taken at two stations, one coastal (St. P1; 20.3 ºN 106.1ºW) at eight depths between 10 and 1500 m and one offshore (St. P2; 16.9ºN 107ºW) at eight depths between 10 and 400 m, from April 14, 2018 to May 2, 2018 aboard the R/V Roger Revelle. At each sampling location, single or triplicate filters were collected for environmental metabolomics, using 10-L Niskin bottles on a CTD-rosette. Each sample set was collected between 1 and 4 PM. Cast numbers were recorded according to the order of deployments during each sampling event to ensure traceability and organization. At each depth, 10 L of seawater was collected into polycarbonate carboys and the seawater particulates were harvested by gentle filtration onto 147 mm 0.2-µm PTFE Omnipore Membrane filters using a peristaltic pump, flash frozen in liquid N2, and stored at -80°C. Additional ancillary measurements were collected to characterize the environmental and biological setting. For both cruises, Salinity (PSU), Temperature (degC), Oxygen (umol/kg), and Chlorophyll a (ug/L) were collected using a Seabird 911 Conductivity Temperature Density meter, a Seabird SBE 43 Dissolved Oxygen Sensor, and a WETLabs ECO Chlorophyll Fluorometer. Differences in sample types were grouped a priori by measured environmental characteristics. The surface is defined as the upper water column, where chlorophyll remains relatively constant. The deep chlorophyll maximum (DCM) represents the highest fluorescence point near the surface. The oxycline is described as a sharp drop in oxygen from >200 µmol kg-1 in the surface to zero, while the secondary chlorophyll maximum (SCM) corresponds to the point where peak fluorescence occurs below the DCM, with no detectable oxygen. The mid-anoxic and mid-oxic zones extend from 120 to 600 meters, with the mid-anoxic zone lacking oxygen and the mid-oxic zone containing measurable levels. Deep oxic samples were taken from depths of 1,000 meters and beyond, where oxygen is present. |
Sample Type: | Suspended Marine Particulate Matter |
Treatment:
Treatment ID: | TR003792 |
Treatment Summary: | No treatments - this was a study of the natural marine microbial population within the upper 3000 meters in the North Pacific Gyre (32ºN 157.6ºW) and the Eastern Tropical North Pacific Oxygen Deficient Zone (20.3 ºN 106.1ºW and 16.9ºN 107ºW) |
Sample Preparation:
Sampleprep ID: | SP003790 |
Sampleprep Summary: | Each sample was extracted using a modified Bligh-Dyer extraction. Filters were cut up and split between Teflon centrifuge tubes containing a mixture of 100 µm and 400 µm silica beads. Heavy isotope-labeled internal standards were added to each sample along with ~2mL of cold aqueous solvent (50:50 methanol:water) and ~3 mL of cold organic solvent (dichloromethane). Samples were shaken on a FastPrep-24 Homogenizer for 30 seconds, followed by chilling in a -20°C freezer. This process was repeated for three bead-beating cycles, totaling 30 minutes of chilling. Organic and aqueous layers were separated by centrifugation (4,300 rpm for 2 minutes or 5,000 rpm for 90 seconds at 4°C). The aqueous layer was transferred to a new glass tube and rinsed three times with additional cold aqueous solvent. Combined aqueous fractions were extracted with cold dichloromethane, centrifuged, and dried under N2 gas. The remaining organic layer in the bead-beating tube was rinsed two additional times with cold organic solvent, combined, centrifuged, transferred to a new glass tube, and dried under N2 gas. Dried aqueous fractions were re-dissolved in 380 µL of water, while organic fractions were re-dissolved in 380 µL of 1:1 water:acetonitrile. To both fractions, 20 µL of isotope-labeled injection standards were added. Blank filters or media blanks were extracted alongside samples as methodological controls. |
Processing Storage Conditions: | On ice |
Extraction Method: | Bligh-Dyer |
Extract Storage: | -80℃ |
Combined analysis:
Analysis ID | AN006001 | AN006002 | AN006003 |
---|---|---|---|
Analysis type | MS | MS | MS |
Chromatography type | HILIC | HILIC | Reversed phase |
Chromatography system | 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) | Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um) |
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 | NEGATIVE | POSITIVE |
Units | Normalized Peak Area per Liter of Sea Water filtered | Normalized Peak Area per Liter of Sea Water filtered | Normalized Peak Area per Liter of Sea Water filtered |
Chromatography:
Chromatography ID: | CH004560 |
Methods Filename: | Ingalls_Lab_LC_Methods_2019.txt |
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 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 |
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 |
Chromatography ID: | CH004561 |
Methods Filename: | Ingalls_Lab_LC_Methods_2019.txt |
Instrument Name: | Waters Acquity I-Class |
Column Name: | Waters Acquity UPLC HSS Cyano (100 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 |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS005713 |
Analysis ID: | AN006001 |
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_2019.txt |
MS ID: | MS005714 |
Analysis ID: | AN006002 |
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_2019.txt |
MS ID: | MS005715 |
Analysis ID: | AN006003 |
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_2019.txt |