Summary of Study ST001372

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 PR000938. The data can be accessed directly via it's Project DOI: 10.21228/M8FM4N 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.

Show all samples  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST001372
Study TitlePatterns in metabolite pools show that phytoplankton leave a taxon-specific signature on particulate carbon: North Pacific Subtropical Gyre depth profile
Study TypeMarine metabolomics depth profile
Study SummaryIn the surface ocean, carbon is fixed by phytoplankton and respired by the entire marine community at an astonishingly high rate. At any point in time, the difference between these two processes yields a carbon pool in surface particles that is a combination of both freshly fixed and partially degraded material. On a molecular level, we have a limited knowledge of the small molecules, or metabolites, within this pool. Specific metabolites have been shown to be responsible for fueling respiration, maintaining organismal interactions, and transferring energy throughout the microbial community. Metabolomics, or the direct observation and quantification of the small molecules that are the result of cellular activity, provides an important lens through which we can begin to assess the standing stocks of small compounds that likely fuel a great deal of heterotrophic activity in the surface ocean. Here we describe community metabolomes of particulate material into the North Pacific Ocean and compare the metabolomes to a variety of phytoplankton grown in the lab. Using both targeted and untargeted metabolomics, we identify metabolites in the particulate carbon pool and explore their latitudinal and phylogenetic distributions. This analysis reveals several compounds that have not been previously recognized as abundant components of the marine organic carbon pool. We found that the community metabolome showed distinct differences between the regimes that likely reflects the phytoplankton community present. The community metabolome in surface waters of the subtropical domain was remarkably consistent even when sampled weeks apart, while the northern regions showed a patichier and less reproducible community metabolome. Some individual compounds showed distinct patterns between oceanographic regimes, including homarine, an abundant molecule that can contribute up to 4\% of the total particulate carbon pool in marine surface waters. Glutamic acid and glutamine showed opposite patterns in the oceanographic regimes, suggesting differences in community-level nitrogen assimilation in these different regimes. Overall, this study offers a new perspective into particulate carbon composition in oceanographic research, reveals important carbon pools that may fuel the microbial loop, and suggests an altered community-level nitrogen assimilation capacity over the North Pacific transition zone.
Institute
University of Washington
DepartmentSchool of Oceanography
LaboratoryIngalls Lab
Last NameHeal
First NameKatherine
Address1501 NE Boat Street, Marine Science Building, Room G
Emailkheal@uw.edu
Phone612-616-4840
Submit Date2020-04-28
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2020-10-28
Release Version1
Katherine Heal Katherine Heal
https://dx.doi.org/10.21228/M8FM4N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000938
Project DOI:doi: 10.21228/M8FM4N
Project Title:Patterns in metabolite pools show that phytoplankton leave a taxon-specific signature on particulate carbon: North Pacific Subtropical Gyre depth profile
Project Type:Marine Metabolomics
Project Summary:In the surface ocean, carbon is fixed by phytoplankton and respired by the entire marine community at an astonishingly high rate. At any point in time, the difference between these two processes yields a carbon pool in surface particles that is a combination of both freshly fixed and partially degraded material. On a molecular level, we have a limited knowledge of the small molecules, or metabolites, within this pool. Specific metabolites have been shown to be responsible for fueling respiration, maintaining organismal interactions, and transferring energy throughout the microbial community. Metabolomics, or the direct observation and quantification of the small molecules that are the result of cellular activity, provides an important lens through which we can begin to assess the standing stocks of small compounds that likely fuel a great deal of heterotrophic activity in the surface ocean. Here we describe community metabolomes of particulate material into the North Pacific Ocean and compare the metabolomes to a variety of phytoplankton grown in the lab. Using both targeted and untargeted metabolomics, we identify metabolites in the particulate carbon pool and explore their latitudinal and phylogenetic distributions. This analysis reveals several compounds that have not been previously recognized as abundant components of the marine organic carbon pool. We found that the community metabolome showed distinct differences between the regimes that likely reflects the phytoplankton community present. The community metabolome in surface waters of the subtropical domain was remarkably consistent even when sampled weeks apart, while the northern regions showed a patchier and less reproducible community metabolome. Some individual compounds showed distinct patterns between oceanographic regimes, including homarine, an abundant molecule that can contribute up to 4% of the total particulate carbon pool in marine surface waters. Glutamic acid and glutamine showed opposite patterns in the oceanographic regimes, suggesting differences in community-level nitrogen assimilation in these different regimes. Overall, this study offers a new perspective into particulate carbon composition in oceanographic research, reveals important carbon pools that may fuel the microbial loop, and suggests an altered community-level nitrogen assimilation capacity over the North Pacific transition zone.
Institute:University of Washington
Department:School of 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:SU001446
Subject Type:Other
Subject Species:Natural mixed marine microbial community
Species Group:Algae

Factors:

Subject type: Other; Subject species: Natural mixed marine microbial community (Factor headings shown in green)

mb_sample_id local_sample_id Depth_m Vol_L
SA099855KM1513-125m_C125 12.17
SA099856KM1513-125m_B125 12.17
SA099857KM1513-125m_A125 12.17
SA099858KM1513-15m_C15 10.7
SA099859KM1513-15m_A15 10.7
SA099860KM1513-15m_B15 10.7
SA099861KM1513-45m_C45 9
SA099862KM1513-45m_B45 9
SA099863KM1513-45m_A45 9
SA099864KM1513-75m_C75 12.7
SA099865KM1513-75m_B75 12.7
SA099866KM1513-75m_A75 12.7
SA099867April11AqExtractsFull_2NA NA
SA099868April11AqExtractsFull_3NA NA
SA099869FilterBNA NA
SA099870April11AqExtractsFull_1NA NA
SA099871April11AqExtractsHalf_2NA NA
SA099872April11AqExtractsHalf_1NA NA
SA099873FilterANA NA
SA099874April11AqExtractsHalf_3NA NA
Showing results 1 to 20 of 20

Collection:

Collection ID:CO001441
Collection Summary:Samples for particulate metabolites were collected from different water depths by niskin bottles attached to a conductivity, temperature, depth array (CTD). Metabolite samples were filtered onto 142 mm 0.2 µm Durapore filters using peristaltic pumps, polycarbonate filter holders, and Masterflex PharMed BPT tubing (Cole-Parmer). Filters were quenched in liquid nitrogen immediately after filtration and stored at -80°C until extraction. Each sample was 30-40 L filtered seawater; each filter was split into three equal parts for triplicate extractions. A blank PTFE filter was extracted alongside samples as a methodological blank.
Sample Type:Suspended Marine Particulate Matter
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR001461
Treatment Summary:No treatment - this was a study of the natural marine microbial population at different depths in the North Pacific Subtropical Gyre.

Sample Preparation:

Sampleprep ID:SP001454
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 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.
Processing Storage Conditions:On ice
Extraction Method:Bligh-Dyer
Extract Storage:-80℃

Combined analysis:

Analysis ID AN002290 AN002291 AN002292
Analysis type MS MS MS
Chromatography type Reversed phase HILIC HILIC
Chromatography system Waters Acquity I-Class Waters Acquity I-Class Waters Acquity I-Class
Column Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um) SeQuant ZIC-pHILIC (150 x 2.1mm,5um) SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
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 Adjusted and normalized peak areas Adjusted and normalized peak areas Adjusted and normalized peak areas

Chromatography:

Chromatography ID:CH001682
Chromatography Summary:See attached summary
Methods Filename:CH_Ingalls_Lab_LC_Methods.txt
MS_Ingalls_Lab_MS_Methods.txt
Instrument Name:Waters Acquity I-Class
Column Name:Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um)
Column Temperature:35
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
  
Chromatography ID:CH001683
Chromatography Summary:See attached summary
Methods Filename:CH_Ingalls_Lab_LC_Methods.txt
MS_Ingalls_Lab_MS_Methods.txt
Instrument Name:Waters Acquity I-Class
Column Name:SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
Column Temperature:30
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

MS:

MS ID:MS002134
Analysis ID:AN002290
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:MS_Ingalls_Lab_MS_Methods.txt
  
MS ID:MS002135
Analysis ID:AN002291
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:MS_Ingalls_Lab_MS_Methods.txt
  
MS ID:MS002136
Analysis ID:AN002292
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:MS_Ingalls_Lab_MS_Methods.txt
  logo