Summary of Study ST002957
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 PR001837. The data can be accessed directly via it's Project DOI: 10.21228/M88B0T 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 | ST002957 |
| Study Title | Metabolite flux from temperature-acclimated diatom strains (main experiment) |
| Study Summary | The temperature increase occurring in the surface ocean has fundamental implications for physiological rates and processes of marine microbes. Here we asked whether the temperature at which a marine diatom strain is acclimated affects carbon transfer to a co-cultured heterotrophic bacterium. Model systems were established in which the diatom Thalassiosira pseudonana was acclimated for three months at temperatures below (14°C), equal to (20°C), and above (28°C) the temperature of optimal growth, and then inoculated with the heterotrophic bacterium Ruegeria pomeroyi. This deposition is for the results of diatom endometabolites obtained from the main experiment of this study. |
| Institute | University of Georgia |
| Laboratory | Moran Lab, Edison Lab |
| Last Name | Uchimiya |
| First Name | Mario |
| Address | 315 Riverbend Rd, Athens, GA, 30602, USA |
| mario.uchimiya@uga.edu | |
| Phone | (706) 542-8387 |
| Submit Date | 2023-10-29 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2023-11-23 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001837 |
| Project DOI: | doi: 10.21228/M88B0T |
| Project Title: | Metabolite flux from temperature-acclimated diatom strains |
| Project Summary: | The temperature increase occurring in the surface ocean has fundamental implications for physiological rates and processes of marine microbes. Here we asked whether the temperature at which a marine diatom strain is acclimated affects carbon transfer to a co-cultured heterotrophic bacterium. Model systems were established in which the diatom Thalassiosira pseudonana was acclimated for three months at temperatures below (14°C), equal to (20°C), and above (28°C) the temperature of optimal growth, and then inoculated with the heterotrophic bacterium Ruegeria pomeroyi. This Project contains results obtained from main and drawdown experiments. |
| Institute: | University of Georgia |
| Last Name: | Uchimiya |
| First Name: | Mario |
| Address: | 315 Riverbend Rd, Athens, GA, 30602, USA |
| Email: | mario.uchimiya@uga.edu |
| Phone: | (706) 542-8387 |
| Project Comments: | See also Metabolomics Workbench_UGA_temp_Oct2023_drawdown.docx for details about this deposition. |
Subject:
| Subject ID: | SU003070 |
| Subject Type: | Plant |
| Subject Species: | Thalassiosira pseudonana |
| Taxonomy ID: | 296543 |
Factors:
Subject type: Plant; Subject species: Thalassiosira pseudonana (Factor headings shown in green)
| mb_sample_id | local_sample_id | Temperature | Bacteria presence |
|---|---|---|---|
| SA321996 | 15 | 14 | 0 |
| SA321997 | 16 | 14 | 0 |
| SA321998 | 14 | 14 | 0 |
| SA321999 | 13 | 14 | 0 |
| SA322000 | 3 | 14 | 1 |
| SA322001 | 2 | 14 | 1 |
| SA322002 | 1 | 14 | 1 |
| SA322003 | 4 | 14 | 1 |
| SA322004 | 19 | 20 | 0 |
| SA322005 | 20 | 20 | 0 |
| SA322006 | 18 | 20 | 0 |
| SA322007 | 17 | 20 | 0 |
| SA322008 | 5 | 20 | 1 |
| SA322009 | 8 | 20 | 1 |
| SA322010 | 7 | 20 | 1 |
| SA322011 | 6 | 20 | 1 |
| SA322012 | 21 | 28 | 0 |
| SA322013 | 23 | 28 | 0 |
| SA322014 | 22 | 28 | 0 |
| SA322015 | 24 | 28 | 0 |
| SA322016 | 12 | 28 | 1 |
| SA322017 | 10 | 28 | 1 |
| SA322018 | 9 | 28 | 1 |
| SA322019 | 11 | 28 | 1 |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO003063 |
| Collection Summary: | Based on pre-experimental axenic growth curves, harvests occurred at days 3 (28°C), 4 (20°C), and 6 (14°C), starting 7 h into the light cycle. At each harvest, subsamples of 600 mL were filtered onto 2.0-µm Isopore filters (Millipore, Burlington, MA) for diatom endometabolite analysis and stored in 50-mL centrifuge tubes at -80°C. |
| Collection Protocol Filename: | 2_Collection protocol_UGA_temp_Oct2023_main.docx |
| Sample Type: | Algae |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003079 |
| Treatment Summary: | Six treatment combinations of a marine diatom strain Thalassiosira pseudonana CCMP1335 were prepared: treatments incubated axenically at either 14, 20, or 28 oC, and treatments co-cultured with a bacterial strain Ruegeria pomeroyi DSS-3 at the corresponding temperatures (four replicates for each). L1 media was used with NaH13CO3 as a source of bicarbonate and a salinity of 35 ppt. The diatom used for the co-cultured treatments was B12 stressed to emphasize the known co-existing system. The light cycle consisted of 16 h light (120 µmol photons m-2 s-1) and 8 h of dark. |
| Treatment Protocol Filename: | 3_Treatment protocol_UGA_temp_Oct2023_main.docx |
Sample Preparation:
| Sampleprep ID: | SP003076 |
| Sampleprep Summary: | Filter samples were transferred into 15-mL of ultrapure MilliQ water in 50-mL tubes, and diatom cells were removed from the filters by sonication in an ice-water bath for 7 min (cycle: 50 s on and 10 s off). The liquid fraction was subsequently collected in new tubes and the procedure repeated three times, after which fractions were combined and stored at -80°C until further processing. Samples were lyophilized (Labconco, Kansas City, MO, USA) and pellets mixed with 600 μL of phosphate buffer (30 mmol L-1 phosphate in deuterated water, pH 7.4) and 1 mmol L-1 internal standard 2,2-dimethyl-2-silapentane-5-sulfonate (DSS). Samples were vortexed for 5 min, centrifuged at 20,800 relative centrifugal force (RCF) for 10 min, and supernatants were transferred to 5-mm NMR tubes (Bruker, Billerica, MA, USA). Extraction and buffer blank controls were also prepared. Additionally, one pooled control sample was prepared by combining aliquots of all the samples and used for annotation. |
| Sampleprep Protocol Filename: | 4_Sample preparation protocol_UGA_temp_Oct2023_main.docx |
Analysis:
| Analysis ID: | AN004857 |
| Analysis Type: | NMR |
| Analysis Protocol File: | 5_Analysis protocol_UGA_temp_Oct2023_main.docx |
| Software Version: | TopSpin version 3.5 |
| Num Factors: | 6 |
| Num Metabolites: | 16 |
| Units: | Intensity |
NMR:
| NMR ID: | NM000269 |
| Analysis ID: | AN004857 |
| Instrument Name: | AVANCE III HD instrument (Bruker) |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 2D-1H-13C |
| Spectrometer Frequency: | 600 MHz |
| NMR Probe: | TCI cryoprobe |
| NMR Tube Size: | 5-mm |
