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:
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 |
