Summary of Study ST001944
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 PR001231. The data can be accessed directly via it's Project DOI: 10.21228/M8KT3K 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 | ST001944 |
| Study Title | Growth-stage related diatom-bacteria interactions |
| Study Summary | Phytoplankton-derived metabolites fuel a large fraction of heterotrophic bacterial production in the global ocean, yet methodological challenges have limited our knowledge of organic molecules transferred between these two microbial groups. In an experimental bloom study in which the diatom Thalassiosira pseudonana was co-cultured with three heterotrophic marine bacteria, we concurrently measured diatom endometabolites (i.e., potential exometabolite supply) by nuclear magnetic resonance (NMR) spectroscopy and bacterial gene expression (i.e., potential exometabolite uptake) by metatranscriptomic sequencing. |
| Institute | University of Georgia |
| Department | Department of Marine Sciences; Complex Carbohydrate Research Center |
| Laboratory | Moran Lab, Edison Lab |
| Last Name | Mario |
| First Name | Uchimiya |
| Address | 315 Riverbend Rd, Athens, GA 30602 |
| mario.uchimiya@uga.edu | |
| Phone | (706) 542-8387 |
| Submit Date | 2021-08-31 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2021-11-04 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001231 |
| Project DOI: | doi: 10.21228/M8KT3K |
| Project Title: | Growth-stage related diatom-bacteria interactions |
| Project Summary: | Phytoplankton-derived metabolites fuel a large fraction of heterotrophic bacterial production in the global ocean, yet methodological challenges have limited our knowledge of organic molecules transferred between these two microbial groups. In an experimental bloom study in which the diatom Thalassiosira pseudonana was co-cultured with three heterotrophic marine bacteria, we concurrently measured diatom endometabolites (i.e., potential exometabolite supply) by nuclear magnetic resonance (NMR) spectroscopy and bacterial gene expression (i.e., potential exometabolite uptake) by metatranscriptomic sequencing. |
| Institute: | University of Georgia |
| Department: | Department of Marine Sciences; Complex Carbohydrate Research Center |
| Laboratory: | Moran Lab, Edison Lab |
| Last Name: | Mario |
| First Name: | Uchimiya |
| Address: | 315 Riverbend Rd, Athens, GA 30602 |
| Email: | mario.uchimiya@uga.edu |
| Phone: | (706) 542-8387 |
| Funding Source: | National Science Foundation (OCE-1948104); Swedish Research Council (2018-06571) |
| Contributors: | Malin Olofsson |
Subject:
| Subject ID: | SU002022 |
| Subject Type: | Other organism |
| Subject Species: | Thalassiosira pseudonana |
| Taxonomy ID: | 296543 |
| Genotype Strain: | CCMP1335 |
Factors:
Subject type: Other organism; Subject species: Thalassiosira pseudonana (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor-1 | Factor-2 |
|---|---|---|---|
| SA183459 | 61 | Early Growth phase | With bacteria |
| SA183460 | 17 | Early Growth phase | With bacteria |
| SA183461 | 15 | Early Growth phase | With bacteria |
| SA183462 | 29 | Late Growth phase | With bacteria |
| SA183463 | 25 | Late Growth phase | With bacteria |
| SA183464 | 27 | Late Growth phase | With bacteria |
| SA183465 | 35 | Late Growth phase | Without bacteria |
| SA183466 | 31 | Late Growth phase | Without bacteria |
| SA183467 | 33 | Late Growth phase | Without bacteria |
| SA183468 | 57 | NA | NA |
| SA183469 | 51 | NA | NA |
| SA183470 | 43 | NA | NA |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO002015 |
| Collection Summary: | During this synthetic bloom experiment, axenic cultures of the diatom Thalssiosira pseudonana CCMP1335 (National Center for Marine Algae) were inoculated with equal cell numbers of the heterotrophic bacteria Ruegeria pomeroyi DSS-3 (Rhodobacterales), Stenotrophomonas sp. SKA-14 (Xanthomonadales), and Polaribacter dokdonensis MED-152 (Flavobacteriales) and co-cultured for 20 d. Co-cultured diatoms were harvested at day 3 and day 15, as well as axenic cultures (diatom only) day 15. Subsamples of 700-1000 ml were filtered onto 2.0 µm pore-size Isopore (Millipore, Burlington, MA) filters. Filters were stored in 50 ml falcon tubes at -80°C until processing. |
| Collection Protocol Filename: | 2_Collection protocol_UGA_phytoplankton_ Aug2021.docx |
| Collection Protocol Comments: | Details are in 2_Collection protocol_UGA_phytoplankton_ Aug2021.docx. |
| Sample Type: | Algae |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002034 |
| Treatment Summary: | The diatom was grown in organic-carbon free L1 medium (Guillard and Hargraves 1993) prepared in acid washed glass containers at a salinity of 35 (Harrison et al. 1980) for one week prior to the start of the experiment. Cultures were grown with a 16:8 h light:dark cycle under 160 µmol photons m-2 s-1 at 18°C and checked for bacterial contamination by plating on rich medium (½ YTSS). On Day 0 of the experiment, diatoms were transferred into 1.9 L culture flasks containing 1000 ml of medium made with 13C-bicarbonate (final concentration of ~ 2x103 cells ml-1). One flask was kept as an L1 medium control without organisms. The three strains of heterotrophic bacteria were grown overnight in rich medium made with artificial seawater, either ½ YTSS medium (R. pomeroyi and Stenotrophomonas) or 1/10 YTSS medium (P. dokdonensis). Cells were harvested in exponential growth phase and washed five times in the same artificial sea water used for preparing the L1 medium. The bacteria were inoculated in equal proportions of OD600 into 15 flasks containing diatoms, with a final combined concentration of ca. 1x105 cells ml-1. One set of three flasks remained axenic. Three co-culture flasks were sacrificed at 4 pm days 3 and 15, and the axenic flasks day 15. |
| Treatment Protocol Filename: | 3_Treatment protocol_UGA_phytoplankton_ Aug2021.docx |
| Treatment Protocol Comments: | Details are in 3_Treatment protocol_UGA_phytoplankton_ Aug2021.docx. |
| Treatment: | Incubation of a diatom strain with and without bacterial strains |
Sample Preparation:
| Sampleprep ID: | SP002028 |
| 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, centrifuged at 20,800 rcf using an ultracentrifuge (Eppendorf) at 4oC for 10 minutes, and supernatants were transferred to 5-mm NMR tubes (Bruker). All the sample preparation steps were done on ice or in a cold room (4oC). |
| Sampleprep Protocol Filename: | 4_Sample preparation protocol_UGA_phytoplankton_ Aug2021.docx |
| Sampleprep Protocol Comments: | Details are in 4_Sample preparation protocol_UGA_phytoplankton_ Aug2021.docx. |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | Water |
| Extract Enrichment: | Lyophilization |
| Extract Storage: | -80℃ |
| Sample Resuspension: | Sodium phosphate buffer |
Analysis:
| Analysis ID: | AN003166 |
| Laboratory Name: | Complex Carbohydrate Research Center |
| Analysis Type: | NMR |
| Analysis Protocol File: | 5_Analysis protocol_UGA_phytoplankton_ Aug2021.docx |
| Acquisition Parameters File: | 6_Acquisition and processing parameters_UGA_phytoplankton_ Aug2021.xlsx |
| Processing Parameters File: | 6_Acquisition and processing parameters_UGA_phytoplankton_ Aug2021.xlsx |
| Data Format: | Bruker |
| Results File: | roiSummary200811_flipped.txt |
| Units: | Intensity |
NMR:
| NMR ID: | NM000216 |
| Analysis ID: | AN003166 |
| Instrument Name: | AVANCE Ⅲ |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 2D-1H-13C |
| NMR Comments: | Details are in 5_Analysis protocol_UGA_phytoplankton_ Aug2021.docx. All the experiment and processing parameters are in 6_Acquisition and processing parameters_UGA_phytoplankton_ Aug2021.xlsx. |
| Standard Concentration: | 1 mmol L-1 |
| Spectrometer Frequency: | 600 MHz |
| NMR Probe: | 5 mm TXI |
| NMR Solvent: | Sodium phosphate buffer |
| NMR Tube Size: | 5 mm |
| Shimming Method: | topshim |
| Pulse Sequence: | hsqcetgpprsisp2.2; hsqcdietgpsisp.2 |
| Water Suppression: | Yes |
| Chemical Shift Ref Cpd: | 2,2-dimethyl-2-silapentane-5-sulfonate-d6 |
| Temperature: | 25 |
