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 |
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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℃ |
