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.

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Study IDST003653
Study TitleMarine community metabolomes in the eastern tropical North Pacific Oxygen Deficient Zone
Study SummaryOxygen 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 NameKellogg
First NameNatalie
Address1503 NE Boat Street, Seattle, WA, 98195, USA
Emailnak01@uw.edu
Phone6517958717
Submit Date2024-12-05
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2025-01-12
Release Version1
Natalie Kellogg Natalie Kellogg
https://dx.doi.org/10.21228/M83V6Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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)
SA398468MP2C44D0_A16.5562 -107.0091 Marine particulate organic matter 10
SA398469MP2C44D0_B16.5562 -107.0091 Marine particulate organic matter 10
SA398470MP2C44D0_C16.5562 -107.0091 Marine particulate organic matter 10
SA398471MP2C49D105_B16.5562 -107.0091 Marine particulate organic matter 105
SA398472MP2C49D105_C16.5562 -107.0091 Marine particulate organic matter 105
SA398473MP2C49D105_A16.5562 -107.0091 Marine particulate organic matter 105
SA398474MP2C50D110_B16.5562 -107.0091 Marine particulate organic matter 110
SA398475MP2C44D110_A16.5562 -107.0091 Marine particulate organic matter 110
SA398476MP2C44D110_B16.5562 -107.0091 Marine particulate organic matter 110
SA398477MP2C44D110_C16.5562 -107.0091 Marine particulate organic matter 110
SA398478MP2C50D110_A16.5562 -107.0091 Marine particulate organic matter 110
SA398479MP2C50D110_C16.5562 -107.0091 Marine particulate organic matter 110
SA398480MP2C44D150_A16.5562 -107.0091 Marine particulate organic matter 150
SA398481MP2C44D150_C16.5562 -107.0091 Marine particulate organic matter 150
SA398482MP2C44D150_B16.5562 -107.0091 Marine particulate organic matter 150
SA398483MP2C48D150_A16.5562 -107.0091 Marine particulate organic matter 150
SA398484MP2C48D150_B16.5562 -107.0091 Marine particulate organic matter 150
SA398485MP2C48D150_C16.5562 -107.0091 Marine particulate organic matter 150
SA398486MP2C44D200_C16.5562 -107.0091 Marine particulate organic matter 200
SA398487MP2C44D200_A16.5562 -107.0091 Marine particulate organic matter 200
SA398488MP2C44D200_B16.5562 -107.0091 Marine particulate organic matter 200
SA398489MP2C44D275_B16.5562 -107.0091 Marine particulate organic matter 275
SA398490MP2C44D275_C16.5562 -107.0091 Marine particulate organic matter 275
SA398491MP2C44D275_A16.5562 -107.0091 Marine particulate organic matter 275
SA398492MP2C44D400_A16.5562 -107.0091 Marine particulate organic matter 400
SA398493MP2C44D400_B16.5562 -107.0091 Marine particulate organic matter 400
SA398494MP2C44D400_C16.5562 -107.0091 Marine particulate organic matter 400
SA398495MP2C44D50_C16.5562 -107.0091 Marine particulate organic matter 50
SA398496MP2C44D50_A16.5562 -107.0091 Marine particulate organic matter 50
SA398497MP2C44D50_B16.5562 -107.0091 Marine particulate organic matter 50
SA398498MP2C44D75_C16.5562 -107.0091 Marine particulate organic matter 75
SA398499MP2C44D75_B16.5562 -107.0091 Marine particulate organic matter 75
SA398500MP2C44D75_A16.5562 -107.0091 Marine particulate organic matter 75
SA398501MP1C62D10_320.1236 -106.0308 Marine particulate organic matter 10
SA398502MP1C62D10_120.1236 -106.0308 Marine particulate organic matter 10
SA398503MP1C62D10_220.1236 -106.0308 Marine particulate organic matter 10
SA398504MP1C62D1000_120.1236 -106.0308 Marine particulate organic matter 1000
SA398505MP1C62D1000_220.1236 -106.0308 Marine particulate organic matter 1000
SA398506MP1C62D1000_320.1236 -106.0308 Marine particulate organic matter 1000
SA398507MP1C62D150_120.1236 -106.0308 Marine particulate organic matter 150
SA398508MP1C62D150_220.1236 -106.0308 Marine particulate organic matter 150
SA398509MP1C62D150_320.1236 -106.0308 Marine particulate organic matter 150
SA398510MP1C62D1500_220.1236 -106.0308 Marine particulate organic matter 1500
SA398511MP1C62D1500_320.1236 -106.0308 Marine particulate organic matter 1500
SA398512MP1C62D1500_120.1236 -106.0308 Marine particulate organic matter 1500
SA398513MP1C62D25_120.1236 -106.0308 Marine particulate organic matter 25
SA398514MP1C62D25_320.1236 -106.0308 Marine particulate organic matter 25
SA398515MP1C62D25_220.1236 -106.0308 Marine particulate organic matter 25
SA398516MP1C62D40_220.1236 -106.0308 Marine particulate organic matter 40
SA398517MP1C62D40_320.1236 -106.0308 Marine particulate organic matter 40
SA398518MP1C62D40_120.1236 -106.0308 Marine particulate organic matter 40
SA398519MP1C62D500_320.1236 -106.0308 Marine particulate organic matter 500
SA398520MP1C62D500_220.1236 -106.0308 Marine particulate organic matter 500
SA398521MP1C62D500_120.1236 -106.0308 Marine particulate organic matter 500
SA398522MP1C62D75_320.1236 -106.0308 Marine particulate organic matter 75
SA398523MP1C62D75_220.1236 -106.0308 Marine particulate organic matter 75
SA398524MP1C62D75_120.1236 -106.0308 Marine particulate organic matter 75
SA398525DOS-1070m_232.00046 -157.599966 Marine particulate organic matter 1070
SA398526DOS-1070m_332.00046 -157.599966 Marine particulate organic matter 1070
SA398527DOS-1070m_132.00046 -157.599966 Marine particulate organic matter 1070
SA398528DOS-120m_132.00046 -157.599966 Marine particulate organic matter 120
SA398529DOS-120m_232.00046 -157.599966 Marine particulate organic matter 120
SA398530DOS-120m_332.00046 -157.599966 Marine particulate organic matter 120
SA398531DOS-15m_132.00046 -157.599966 Marine particulate organic matter 15
SA398532DOS-15m_232.00046 -157.599966 Marine particulate organic matter 15
SA398533DOS-15m_332.00046 -157.599966 Marine particulate organic matter 15
SA398534DOS-300m_332.00046 -157.599966 Marine particulate organic matter 300
SA398535DOS-300m_232.00046 -157.599966 Marine particulate organic matter 300
SA398536DOS-300m_132.00046 -157.599966 Marine particulate organic matter 300
SA398537DOS-3000m_332.00046 -157.599966 Marine particulate organic matter 3000
SA398538DOS-3000m_132.00046 -157.599966 Marine particulate organic matter 3000
SA398539DOS-3000m_232.00046 -157.599966 Marine particulate organic matter 3000
SA398540DOS-45m_132.00046 -157.599966 Marine particulate organic matter 45
SA398541DOS-45m_232.00046 -157.599966 Marine particulate organic matter 45
SA398542DOS-45m_332.00046 -157.599966 Marine particulate organic matter 45
SA398543DOS-590m_332.00046 -157.599966 Marine particulate organic matter 590
SA398544DOS-590m_132.00046 -157.599966 Marine particulate organic matter 590
SA398545DOS-590m_232.00046 -157.599966 Marine particulate organic matter 590
SA398546DOS-90m_232.00046 -157.599966 Marine particulate organic matter 90
SA398547DOS-90m_332.00046 -157.599966 Marine particulate organic matter 90
SA398548DOS-90m_132.00046 -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
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