Summary of Study ST001512
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 PR001019. The data can be accessed directly via it's Project DOI: 10.21228/M80408 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 | ST001512 |
| Study Title | Diel investments in phytoplankton metabolite production influenced by associated heterotrophic bacteria |
| Study Type | Incubation experiment |
| Study Summary | Organic substrate transfer between photoautotrophic and heterotrophic microbes in the surface ocean is a central but poorly understood process in the global carbon cycle. This study developed a co-culture system of marine diatom Thalassiosira pseudonana and heterotrophic bacterium Ruegeria pomeroyi, and addressed diel changes in phytoplankton endometabolite production using nuclear magnetic resonance (NMR) and bacterial metabolite consumption using gene expression. Here we deposit data for NMR analysis from the study. Samples were collected every 6 hours over two days under a diel light cycle. During the course of the study, we observed an increase in some phytoplankton endometabolites presumably due to the effects of the associated bacteria. We introduced an additional experiment and tested this possibility by comparing phytoplankton endometabolite accumulation between axenic treatments and bacteria coculture treatments. |
| Institute | University of Georgia |
| Department | Department of Marine Sciences; Complex Carbohydrate Research Center |
| Laboratory | Moran Lab; Edison Lab |
| Last Name | Uchimiya |
| First Name | Mario |
| Address | 315 Riverbend Rd, Athens, GA 30602 |
| mario.uchimiya@uga.edu | |
| Phone | (706) 542-8387 |
| Submit Date | 2020-10-18 |
| Raw Data Available | Yes |
| Analysis Type Detail | NMR |
| Release Date | 2020-11-02 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001019 |
| Project DOI: | doi: 10.21228/M80408 |
| Project Title: | Diel investments in phytoplankton metabolite production influenced by associated heterotrophic bacteria |
| Institute: | University of Georgia |
| Department: | Department of Marine Sciences; Complex Carbohydrate Research Center |
| Laboratory: | Moran Lab; Edison Lab |
| Last Name: | Uchimiya |
| First Name: | Mario |
| Address: | 315 Riverbend Rd, Athens, GA 30602 |
| Email: | mario.uchimiya@uga.edu |
| Phone: | (706) 542-8387 |
| Funding Source: | The Gordon and Betty Moore Foundation (5503); NSF (IOS-1656311); The Simons Foundation (542391); JSPS (Research Fellowship for Young Scientists and Grant-in-Aid for JSPS Fellows); Swedish Research Council (2018-06571) |
Subject:
| Subject ID: | SU001586 |
| Subject Type: | Plant |
| Subject Species: | Thalassiosira pseudonana CCMP1335 |
| Taxonomy ID: | 296543 |
| Genotype Strain: | CCMP1335 |
Factors:
Subject type: Plant; Subject species: Thalassiosira pseudonana CCMP1335 (Factor headings shown in green)
| mb_sample_id | local_sample_id | Collection time | Prediction Model (Coculture vs Axenic) |
|---|---|---|---|
| SA127023 | 18 | 12 | - |
| SA127024 | 20 | 12 | - |
| SA127025 | 22 | 12 | - |
| SA127026 | 28 | 18 | - |
| SA127027 | 24 | 18 | - |
| SA127028 | 26 | 18 | - |
| SA127029 | 34 | 24.5 | - |
| SA127030 | 30 | 24.5 | - |
| SA127031 | 32 | 24.5 | - |
| SA127032 | 36 | 30.6 | - |
| SA127033 | 38 | 30.6 | - |
| SA127034 | 40 | 30.6 | - |
| SA127035 | 46 | 35.8 | - |
| SA127036 | 44 | 35.8 | - |
| SA127037 | 42 | 35.8 | - |
| SA127038 | 50 | 40.9 | - |
| SA127039 | 48 | 40.9 | - |
| SA127040 | 52 | 40.9 | - |
| SA127041 | 54 | 44.9 | - |
| SA127042 | 56 | 44.9 | - |
| SA127043 | 58 | 44.9 | - |
| SA127044 | 12 | 5.9 | - |
| SA127045 | 16 | 5.9 | - |
| SA127046 | 14 | 5.9 | - |
| SA127007 | 6 | - | - |
| SA127008 | 103 | - | - |
| SA127009 | 3 | - | - |
| SA127010 | 60 | - | - |
| SA127011 | 43 | - | - |
| SA127012 | 51 | - | - |
| SA127013 | 8 | - | - |
| SA127014 | 10 | - | - |
| SA127015 | 57 | - | - |
| SA127016 | 2 | - | - |
| SA127017 | 35 | - | Axenic |
| SA127018 | 31 | - | Axenic |
| SA127019 | 33 | - | Axenic |
| SA127020 | 27 | - | Coculture |
| SA127021 | 29 | - | Coculture |
| SA127022 | 25 | - | Coculture |
| Showing results 1 to 40 of 40 |
Collection:
| Collection ID: | CO001581 |
| Collection Summary: | Diel experiment – Samples were collected every 6 h over 2 days. 500 mL of diatom cells were collected by filtering the culture onto 2.0-µm-pore-size PCTE membrane filters (MilliporeSigma Isopore). Filters were kept in 50 mL tubes (Falcon) and stored at -80oC until processing. Test of model prediction experiment – The same procedure was used except that samples were collected at day 15 and 700 mL of the culture was filtered. |
| Collection Protocol Filename: | uchimiya_20201018_2_Collection protocol_UGA_phytoplankton_Oct2020.docx |
| Collection Protocol Comments: | Collection summary is in 2_Collection protocol_UGA_phytoplankton_Oct2020.docx |
| Sample Type: | Algae |
Treatment:
| Treatment ID: | TR001601 |
| Treatment Summary: | Diel experiment – An axenic strain of marine diatom Thalassiosira pseudonana CCMP1335 was cultured at 18 oC in three replicate 15-L polycarbonate bottles containing 10 L of L1 medium in which NaH13CO3 (Cambridge Isotope Laboratories, CLM-441) was used for sodium bicarbonate. The light cycle consisted of 16 h light, during which light intensity varied gradually between 0 and 150 µmol photon m-2 s-1 with a maximum intensity at noon, followed by 8 h of dark. Bacterial strain Ruegeria pomeroyi DSS-3 was grown at 30oC on ½ YTSS agar and transferred to ½ YTSS liquid2 medium for overnight growth. Axenic T. pseudonana cultures grown for 6 days were inoculated with bacterial cells washed in L1 medium three times (final concentration, 106 bacterial cells mL-1). Co-cultures were pre-incubated for two days. Test of model prediction experiment – T. pseudonana was inoculated into L1 as described above. Triplicate samples were inoculated with three heterotrophic bacteria (R. pomeroyi DSS-3, Stenotrophomonas sp. SKA-14, and Polaribacter dokdonensis MED-152). Another set of triplicate samples was kept axenic (diatom only). The cultures were maintained under 16 h of light period (160 µmol photons m-2 s-1) and 8 h of dark period cycles. |
| Treatment Protocol Filename: | uchimiya_20201018_3_Treatment_protocol_UGA_phytoplankton_Oct2020.docx |
| Treatment Protocol Comments: | Treatment protocol is in 3_Treatment protocol_UGA_phytoplankton_Oct2020.docx |
| Treatment: | Test of model prediction experiment: with/without bacteria |
| Plant Light Period: | Light period: 16 hr, dark period: 8 hr |
| Plant Temp: | 18oC |
Sample Preparation:
| Sampleprep ID: | SP001594 |
| Sampleprep Summary: | Phytoplankton cells were removed from filters using a sonicator SLPe (Branson) in ultra-pure water (Millipore), concentrated by a lyophilizer (Labconco), and kept -80oC until further processing. The samples were mixed with 600 µL of 30 mmol L-1 sodium phosphate buffer (18 mmol L-1 NaHPO4, 12 mmol L-1, pH 7.4) and an internal standard of 2,2-dimethyl-2-silapentane-5-sulfonate-d6 (DSS, 1 mmol L-1), vortexed at 4oC for 5 minutes, and centrifuged at 20,800 rcf using an ultracentrifuge (Eppendorf) at 4oC for 10 minutes, and supernatants were transferred to 5-mm NMR tubes (Bruker). For the test of model prediction experiment, 300 µL of supernatants were further diluted with 250 µL of the buffer and transferred to NMR tubes. All the sample preparation steps were done on ice or in a cold room (4oC). |
| Sampleprep Protocol Filename: | uchimiya_20201018_4_Sample_preparation_protocol_UGA_phytoplankton_Oct2020.docx |
| Sampleprep Protocol Comments: | Sample preparation protocol is in 4_Sample preparation protocol_UGA_phytoplankton_Oct2020.docx |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | Water |
| Extract Enrichment: | Lyophilization |
| Extract Storage: | -80℃ |
| Sample Resuspension: | Sodium phosphate buffer |
Analysis:
| Analysis ID: | AN002506 |
| Laboratory Name: | Complex Carbohydrate Research Center |
| Analysis Type: | NMR |
| Analysis Protocol File: | 5_Analysis protocol_UGA_phytoplankton_Oct2020.docx |
| Acquisition Parameters File: | 6_Acquisition and processing parameters_UGA_phytoplankton_Oct2020.xlsx |
| Software Version: | TopSpin 3.5.7, 4.0.1, and 4.0.4 |
| Operator Name: | Mario Uchimiya |
| Processing Parameters File: | 6_Acquisition and processing parameters_UGA_phytoplankton_Oct2020.xlsx |
| Data Format: | Bruker |
NMR:
| NMR ID: | NM000185 |
| Analysis ID: | AN002506 |
| Instrument Name: | Bruker Avance lll |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 2D-1H-13C |
| NMR Comments: | Analysis protocol is in 5_Analysis protocol_UGA_phytoplankton_Oct2020.docx; detailed aquisition and processing parameters are in 6_Acquisition and processing parameters_UGA_phytoplankton_Oct2020.xlsx |
| Standard Concentration: | 1 mmol L-1 |
| Spectrometer Frequency: | 600 and 800 MHz |
| NMR Probe: | 800 MHz 5 mm TCI, 800 MHz 1.7 mm TCI and 600 MHz 5 mm TXI |
| NMR Solvent: | Sodium phosphate buffer in D2O |
| NMR Tube Size: | 5 mm |
| Shimming Method: | TopShim |
| Pulse Sequence: | hsqcetgpprsisp2.2, hsqcdietgpsisp.2, and hmbcetgpl2nd |
| Chemical Shift Ref Std: | DSS |
| Binned Data Protocol File: | Folder 'rNMR' |
