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 |
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Treatment:
| Treatment ID: | TR002101 |
| Treatment Summary: | In order to determine the kinetics of GBT (glycine betaine) uptake, whole seawater was spiked with varying concentrations of 13C5, 15N1-GBT and incubated for 25–42 minutes. Water was collected into 2 L bottles around 8:00 am local time for both experiments. In order to minimize the biological transformation of 13C5, 15N1-GBT into other molecules and to limit the induction of enzymatic activity, the incubation time with 13C5, 15N1-GBT was kept short. The short incubation time necessitated that samples be spiked throughout the course of the day since only six samples could be processed at a time. Before and after the addition of 13C5, 15N1-GBT, bottles were kept in flow-through incubators with blue shading to be at in situ temperature and approximately mixed layer light conditions. Samples were spiked to have final concentrations of 0, 2, 5, 10, 50, 200, or 2000 nM 13C5, 15N1-GBT. Triplicates of each 13C5, 15N1-GBT concentration were processed for both experiments, with replicates spread throughout the sampling period. After incubation with the spiked molecule, seawater was filtered onto 47 mm diameter, 0.2 µm pore size PTFE (Omnipore) filters using a peristaltic pump, polycarbonate filter holder, and Masterflex PharMed BPT tubing (Cole-Parmer). Filtering time was 10–42 minutes with an average time of 22 minutes. Experimental blanks were collected for each spike concentration during the northern experiment by collecting filtrate from one replicate of each treatment and re-filtering filtrate onto a new filter. This provided a measure of dissolved organic compounds adsorbed onto the filter during processing. Filters were frozen in liquid nitrogen immediately after filtration and stored at -80 °C until the filters were extracted using the metabolite extraction method described in Boysen et al. (2018). For the GBT fate experiments, two time course incubation experiments were performed, one at each of the stations described above. For each experiment, 2 L bottles were filled with seawater collected with the CTD from 15 m depth (within the mixed layer) at approximately 6:00 am local time. All 2 L bottles were spiked with 500 nM 13C5, 15N1-GBT and incubated in temperature-controlled incubators at 10 °C and 14 °C for the north and south experiments, respectively. Samples for the initial timepoint (T0) were filtered directly after being spiked, resulting in actual incubation times of approximately 20 minutes. At each time point triplicate 2 L bottles were sampled for analysis of bacterial and picophytoplankton abundance and biomass via flow cytometry, metabolites, and total hydrolyzable amino acids. Timepoints sampled in the north experiment were 0, 4.5, 9, 12.5, 36, 50, and 98 hours. Timepoints sampled in the south experiment were 0, 6, 13, 25, 51, and 100 hours. For all samples, incubation time was calculated by taking the difference between the time the bottle was spiked and the midpoint time of sample filtration. |
| Treatment: | Isotopically labeled glycine betaine additions to natural seawater |
| Treatment Compound: | 13C5, 15N1 GBT (glycine betaine labeled with 5 carbon-13 atoms and one nitrogen-15 atom) |
| Treatment Dosevolume: | 0, 2, 5, 10, 50, 200, 2000 nM; 500nM |
| Treatment Doseduration: | 25-42 minutes; 0, 4.5, 6, 9,12.5, 13, 25, 36, 50, 51, 98, 100 hours |
