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.

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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.

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Study IDST002008
Study TitleGlycine betaine uptake and metabolism in marine microbial communities
Study TypeQuantitative and qualitative exploration of isotope-labeled glycine betaine uptake and use in natural marine microbial communities
Study SummaryGlycine 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
DepartmentSchool of Oceanography
LaboratoryIngalls Lab
Last NameKumler
First NameWilliam
Address1501 NE Boat St, Seattle, WA 98105
Emailwkumler@uw.edu
Phone2062216732
Submit Date2021-12-01
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Waters)
Analysis Type DetailLC-MS
Release Date2022-01-17
Release Version1
William Kumler William Kumler
https://dx.doi.org/10.21228/M85D8M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Sample Preparation:

Sampleprep ID:SP002095
Sampleprep Summary:Polar and nonpolar metabolites were extracted using a modified Bligh−Dyer extraction using 1:1 methanol/water (aqueous phase) and dichloromethane (organic phase). Methodological blanks were extracted and analyzed along with each sample set. Each sample was aliquotted into two vials and isotope-labeled internal standards were added either before or after the extraction to one vial for all samples, blanks, and pooled samples. To evaluate the effect of obscuring variation due to different matrix strengths and analytical drift, pooled samples were run at both full and half concentration (diluted with water) at least three times throughout a sample set.
Processing Storage Conditions:On ice
Extraction Method:Bligh-Dyer
Extract Storage:-80℃
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