Summary of Study ST002008
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 PR001273. The data can be accessed directly via it's Project DOI: 10.21228/M85D8M 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 | ST002008 |
| Study Title | Glycine betaine uptake and metabolism in marine microbial communities |
| Study Type | Quantitative and qualitative exploration of isotope-labeled glycine betaine uptake and use in natural marine microbial communities |
| Study Summary | Glycine betaine (GBT) is a component of labile dissolved organic matter and a compatible solute in high concentrations in marine microbial populations. GBT has complex biochemical potential, but, once taken up from the environment, the cellular fate of the carbon and nitrogen from GBT is unknown. Here we determine the uptake kinetics and metabolism of GBT in two natural microbial communities characterized by different nitrate concentrations in the North Pacific transition zone. Dissolved GBT had maximum uptake rates of 0.36 and 0.56 nM hr -1 and half-saturation constants of 79 and 11 nM in the high nitrate and low nitrate stations, respectively. GBT taken into cells was predominantly retained as an untransformed compatible solute. A portion of GBT was transformed into other metabolites, through characterized and uncharacterized pathways. Where nitrate was scarce, GBT was primarily catabolized via the demethylation to glycine. Resulting metabolites were used to build protein biomass, and remineralized ammonia was re-assimilated into cells. Gene expression data from this region show that bacteria, especially SAR11, are the dominant organisms expressing the demethylation genes. Where nitrate concentrations were higher, more GBT was used for choline synthesis. Our data highlight undiscussed metabolic pathways and potential routes of microbial metabolite exchange. |
| Institute | University of Washington |
| Department | School of Oceanography |
| Laboratory | Ingalls Lab |
| Last Name | Kumler |
| First Name | William |
| Address | 1501 NE Boat St, Seattle, WA 98105 |
| wkumler@uw.edu | |
| Phone | 2062216732 |
| Submit Date | 2021-12-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Waters) |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-01-17 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003271 | AN003272 | AN003273 | AN003274 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | HILIC | HILIC | HILIC | Reversed phase |
| Chromatography system | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class |
| Column | SeQuant ZIC-HILIC (150 x 2.1mm,5um) | SeQuant ZIC-HILIC (150 x 2.1mm,5um) | SeQuant ZIC-HILIC (150 x 2.1mm,5um) | Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Triple quadrupole | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Waters Xevo-TQ-S | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | POSITIVE |
| Units | nmol/L | Peak area | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH002415 |
| Chromatography Summary: | See protocol wkumler_20211201_100602_PR_CH_CH_Ingalls_Lab_LC_Methods.txt |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH002416 |
| Chromatography Summary: | See protocol wkumler_20211201_100602_PR_CH_CH_Ingalls_Lab_LC_Methods.txt |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um) |
| Chromatography Type: | Reversed phase |
