Summary of Study ST001410
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 PR000966. The data can be accessed directly via it's Project DOI: 10.21228/M8TM42 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 | ST001410 |
| Study Title | Patterns in metabolite pools show that phytoplankton leave a taxon-specific signature on particulate carbon: Surface samples from the North Pacific Subtropical Gyre to North Pacific Transition Zone |
| Study Type | Marine metabolomics surface samples from the North Pacific Subtropical Gyre to North Pacific Transition Zone |
| Study 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 |
| kheal@uw.edu | |
| Phone | 206-616-4658 |
| Submit Date | 2020-06-25 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-03-31 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000966 |
| Project DOI: | doi: 10.21228/M8TM42 |
| Project Title: | Patterns in metabolite pools show that phytoplankton leave a taxon-specific signature on particulate carbon: Surface samples from the North Pacific Subtropical Gyre to North Pacific Transition Zone |
| 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 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 |
| 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: | 206-616-4658 |
Subject:
| Subject ID: | SU001484 |
| 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 | Depth_m | Vol_L |
|---|---|---|---|
| SA115661 | U7_B | 15 | 10 |
| SA115662 | U8_A | 15 | 10 |
| SA115663 | U8_B | 15 | 10 |
| SA115664 | U7_A | 15 | 10 |
| SA115665 | U6_A | 15 | 10 |
| SA115666 | S9C2_B | 15 | 10 |
| SA115667 | S11C1_A | 15 | 10 |
| SA115668 | U9_B | 15 | 10 |
| SA115669 | S12C1_A | 15 | 10 |
| SA115670 | S14C1_B | 15 | 10 |
| SA115671 | S14C1_C | 15 | 10 |
| SA115672 | S14C1_A | 15 | 10 |
| SA115673 | S13C1_B | 15 | 10 |
| SA115674 | S12C1_B | 15 | 10 |
| SA115675 | S13C1_A | 15 | 10 |
| SA115676 | S9C2_A | 15 | 10 |
| SA115677 | U9_A | 15 | 10 |
| SA115678 | S4C2_B | 15 | 10 |
| SA115679 | S4C2_A | 15 | 10 |
| SA115680 | U6_B | 15 | 10.5 |
| SA115681 | S6C2_A | 15 | 10.5 |
| SA115682 | S6C2_B | 15 | 10.5 |
| SA115683 | S8C1_A | 15 | 10.5 |
| SA115684 | S6C1_C | 15 | 11 |
| SA115685 | S6C1_B | 15 | 11 |
| SA115686 | S9C1_B | 15 | 11 |
| SA115687 | S2C1_C | 15 | 11 |
| SA115688 | S6C1_A | 15 | 11 |
| SA115689 | S2C1_B | 15 | 11 |
| SA115690 | S4C1_B | 15 | 11.5 |
| SA115691 | S4C1_A | 15 | 11.5 |
| SA115692 | S4C1_C | 15 | 11.5 |
| SA115693 | S9C1_A | 15 | 11.5 |
| SA115694 | U4_B | 15 | 12 |
| SA115695 | U4_A | 15 | 13.5 |
| SA115696 | U3_B | 15 | 15 |
| SA115697 | U3_A | 15 | 15.5 |
| SA115698 | S2C3_A | 15 | 9.5 |
| SA115699 | TruePoo_Half2 | NA | NA |
| SA115700 | TruePoo_Half3 | NA | NA |
| SA115701 | TruePoo_Half1 | NA | NA |
| SA115702 | QC_Full3 | NA | NA |
| SA115703 | TruePoo_Half4 | NA | NA |
| SA115704 | QC_Full4 | NA | NA |
| SA115705 | TruePoo_Full4 | NA | NA |
| SA115706 | QC_Full2 | NA | NA |
| SA115707 | FilterBlk_B | NA | NA |
| SA115708 | TruePoo_Full3 | NA | NA |
| SA115709 | TruePoo_Full2 | NA | NA |
| SA115710 | TruePoo_Full1 | NA | NA |
| SA115711 | April1718AqExtracts_1 | NA | NA |
| SA115712 | April21AqExtracts_1 | NA | NA |
| SA115713 | April1718AqExtracts_3 | NA | NA |
| SA115714 | April1718AqExtracts_2 | NA | NA |
| SA115715 | FilterBlk_A | NA | NA |
| SA115716 | April21AqExtracts_2 | NA | NA |
| SA115717 | April21AqExtracts_3 | NA | NA |
| SA115718 | QC_Half4 | NA | NA |
| SA115719 | QC_Half3 | NA | NA |
| SA115720 | QC_Half2 | NA | NA |
| SA115721 | QC_Half1 | NA | NA |
| SA115722 | QC_Full1 | NA | NA |
| Showing results 1 to 62 of 62 |
Collection:
| Collection ID: | CO001479 |
| Collection Summary: | Samples for particulate metabolites from cruise KOK1606 were collected aboard the Ka’imikai-O- Kanoloa research vessel from April 20 to May 2, 2016, all at 15 m. At each sampling location, single, duplicate, or triplicate filters were collected using either niskins attached to a conductivity, temperature, depth array (CTD) or the underway intake. Samples (10-15 L) were collected into polycarbonate carboys, filtered onto 147 mm 0.2 μm PTFE filters using peristaltic pumps, polycarbonate filter holders, and Masterflex PharMed BPT tubing (Cole-Parmer). Filters were flash frozen in liquid nitrogen and stored at -80°C until extraction. Blank PTFE filters were extracted alongside samples as methodological blanks. |
| Sample Type: | Suspended Marine Particulate Matter |
| Storage Conditions: | Described in summary |
Treatment:
| Treatment ID: | TR001499 |
| Treatment Summary: | No treatment - this was a study of the of natural marine microbial population in the surface ocean from the North Pacific Subtropical Gyre to North Pacific Transition Zone. |
Sample Preparation:
| Sampleprep ID: | SP001492 |
| 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 | AN002358 | AN002359 | AN002360 |
|---|---|---|---|
| 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 | POSITIVE | NEGATIVE |
| Units | Adjusted and normalized peak areas | Adjusted and normalized peak areas | Adjusted and normalized peak areas |
Chromatography:
| Chromatography ID: | CH001729 |
| Chromatography Summary: | See attached protocol |
| 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: | CH001730 |
| Chromatography Summary: | See attached protocol |
| 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: | MS002200 |
| Analysis ID: | AN002358 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See attached protocol. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002201 |
| Analysis ID: | AN002359 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See attached protocol. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002202 |
| Analysis ID: | AN002360 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See attached protocol. |
| Ion Mode: | NEGATIVE |
