Summary of Study ST004351
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 PR002760. The data can be accessed directly via it's Project DOI: 10.21228/M8WR9Z This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004351 |
| Study Title | Interactions with bacteria shape diatom adaptation to carbon concentration changes |
| Study Summary | Diatoms are key contributors to global primary production, and have developed intricate partnerships with bacteria through long-term co-evolution. Here, we uncover a syntrophic relationship between the model obligate photoautotroph Phaeodactylum tricornutum and Loktanella vestfoldensis, which enables the diatom to indirectly utilize glucose. Reanalysis of Tara Oceans metagenomic data shows frequent co-occurrence of Loktanella with diatoms including Chaetoceros and Thalassiosira, indicating the ecological relevance of this partnership. Co-culture with L. vestfoldensis supports robust growth of Chaetoceros muelleri and Thalassiosira pseudonana in the presence of glucose as the sole carbon source. Transcriptomic and metabolomic analyses reveal that P. tricornutum maintains a photoautotrophic metabolism in co-culture, as indicated by the up-regulation of genes involved in inorganic carbon concentration and photosynthesis, while the co-cultured bacterium likely supplies CO2 and growth-stimulating metabolites such as indole-3-acetic acid. Our findings demonstrate that bacterial-algal interactions may shape diatom adaptation to carbon changes and contribute to marine carbon cycling. |
| Institute | Chinese Academy of Sciences |
| Department | Institute of Hydrobiology |
| Last Name | Li |
| First Name | Chenjie |
| Address | No. 7 Donghu South Road, Wuhan City, Hubei Province, 430072, China |
| 1159958986@qq.com | |
| Phone | 86-027-68780078 |
| Submit Date | 2025-11-14 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-11-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002760 |
| Project DOI: | doi: 10.21228/M8WR9Z |
| Project Title: | Interactions with bacteria shape diatom adaptation to carbon concentration changes |
| Project Summary: | Diatoms are key contributors to global primary production, and have developed intricate partnerships with bacteria through long-term co-evolution. Here, we uncover a syntrophic relationship between the model obligate photoautotroph Phaeodactylum tricornutum and Loktanella vestfoldensis, which enables the diatom to indirectly utilize glucose. Reanalysis of Tara Oceans metagenomic data shows frequent co-occurrence of Loktanella with diatoms including Chaetoceros and Thalassiosira, indicating the ecological relevance of this partnership. Co-culture with L. vestfoldensis supports robust growth of Chaetoceros muelleri and Thalassiosira pseudonana in the presence of glucose as the sole carbon source. Transcriptomic and metabolomic analyses reveal that P. tricornutum maintains a photoautotrophic metabolism in co-culture, as indicated by the up-regulation of genes involved in inorganic carbon concentration and photosynthesis, while the co-cultured bacterium likely supplies CO2 and growth-stimulating metabolites such as indole-3-acetic acid. Our findings demonstrate that bacterial-algal interactions may shape diatom adaptation to carbon changes and contribute to marine carbon cycling. |
| Institute: | Chinese Academy of Sciences |
| Department: | Institute of Hydrobiology |
| Last Name: | Li |
| First Name: | Chenjie |
| Address: | No. 7 Donghu South Road, Wuhan City, Hubei Province, 430072, China |
| Email: | 1159958986@qq.com |
| Phone: | 86-027-68780078 |
Subject:
| Subject ID: | SU004510 |
| Subject Type: | Bacteria |
| Subject Species: | Phaeodactylum tricornutum, Loktanella vestfoldensis |
| Taxonomy ID: | 2850, 245188 |
Factors:
Subject type: Bacteria; Subject species: Phaeodactylum tricornutum, Loktanella vestfoldensis (Factor headings shown in green)
| mb_sample_id | local_sample_id | group | Sample source |
|---|---|---|---|
| SA517184 | Blank | Blank | Methanol |
| SA517185 | Co-culture_1 | Co-culture | Supernatant |
| SA517186 | Co-culture_2 | Co-culture | Supernatant |
| SA517187 | Co-culture_3 | Co-culture | Supernatant |
| SA517188 | Monoculture_1 | Monoculture | Supernatant |
| SA517189 | Monoculture_2 | Monoculture | Supernatant |
| SA517190 | Monoculture_3 | Monoculture | Supernatant |
| SA517191 | QC1 | QC | Supernatant mixture |
| SA517192 | QC2 | QC | Supernatant mixture |
| SA517193 | QC3 | QC | Supernatant mixture |
| SA517194 | QC4 | QC | Supernatant mixture |
| Showing results 1 to 11 of 11 |
Collection:
| Collection ID: | CO004503 |
| Collection Summary: | Co-cultured samples were obtained from the supernatant after centrifugation of Phaeodactylum tricornutum and Loktanella vestfoldensis co-culture medium. Monocultured samples were obtained from the supernatant after centrifugation of Loktanella vestfoldensis monoculture medium. QC samples were obtained from a mixture of co-cultured and monocultured supernatants, and were used to test the stability of the data. All cell cultures were centrifuged at 2000 × g for 10 min, and 30 mL supernatant was collected and stored at -80 °C. |
| Collection Protocol Filename: | LiChenjie_Protocol.pdf |
| Sample Type: | Media |
Treatment:
| Treatment ID: | TR004519 |
| Treatment Summary: | One mL (OD600 ≈ 0.4) of PtCr epiphytic bacterium was inoculated into 50 mL plug-seal cap culture flasks containing 30 mL of f/2-enriched artificial seawater (without NaHCO3) with 3 g/L glucose as the sole carbon source, and then Pt1 (6 × 106 cells) (co-culture) or bicarbonate-free artificial seawater (designated as “bacterial monoculture”) of an equal volume was added to the bacterial cultures. Subsequently, the cultures were maintained at 22 °C with shaking (120 rpm) under continuous illumination of 100 μmol photons m-2 s-1 for 6 days. |
| Treatment Protocol Filename: | LiChenjie_Protocol.pdf |
Sample Preparation:
| Sampleprep ID: | SP004516 |
| Sampleprep Summary: | One mL of samples centrifuged at 4 ℃, 13000 rpm for 5 minutes, collect the supernatant and filter it through a 0.22 µm aqueous membrane. Take 80 µL of filtrate and add 20 µL of 300 µg/mL internal standard for sample analysis. A mixture of 200 µL per sample was divided into 4 replicates, and the first three pooled samples were used to monitor the precision of the instrument, and the last one was used to monitor the stability of the instrument. |
| Sampleprep Protocol Filename: | LiChenjie_Protocol.pdf |
Combined analysis:
| Analysis ID | AN007263 | AN007264 |
|---|---|---|
| Chromatography ID | CH005512 | CH005513 |
| MS ID | MS006957 | MS006958 |
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak Intensity | Peak intensity |
Chromatography:
| Chromatography ID: | CH005512 |
| Chromatography Summary: | The injection volume for each sample was 2 μL, and methanol was used as a blank sample to deduct baseline features from the mobile phase. |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 300 |
| Flow Gradient: | 0-1 min, 10% B; 1-13 min, linear increase to 98% B; 13-18 min, 98% B; 18-18.5 min, linear decrease to 10% B; 18.5-20 min, 10% B |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH005513 |
| Chromatography Summary: | The injection volume for each sample was 2 μL, and methanol was used as a blank sample to deduct baseline features from the mobile phase. |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 300 |
| Flow Gradient: | 0-1 min, 10% B; 1-13 min, linear increase to 98% B; 13-18 min, 98% B; 18-18.5 min, linear decrease to 10% B; 18.5-20 min, 10% B |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 100% water; 10 mM ammonium formate |
| Solvent B: | 95% methanol/5% water; 10 mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS006957 |
| Analysis ID: | AN007263 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Mass spectrometry parameters included: capillary temperature, 300 °C; sheath gas flow, 40 arbitrary units; nebulizer temperature, 350 °C. Samples were maintained at 4 °C in the autosampler during analysis. Raw LC-MS data were converted to Analysis Base File (ABF) format using the ABF Converter tool. MS-DIAL software (version 4.70) was used to perform blank deduction (peak intensity [Sample/Blank] >= 3), feature peak screening (at least 2 feature peaks appearing in repeated samples), and normalization (LOWESS method) on the data of positive and negative ion modes separately. A comprehensive feature matrix was generated, containing metabolite identifiers, RT, mass-to-charge ratio (m/z), ion patterns, and peak intensities. Metabolite annotation was achieved by matching experimental RT and m/z values against the MassBank database with the following parameters: RT tolerance = ± 0.1 min, MS1 mass tolerance = 0.005 Da, MS2 mass tolerance = 0.0025 Da, and MS2 spectral match score > 0.7. Missing values were imputed using 20% of the minimum value within each experimental group. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | LiChenjie_Protocol.pdf |
| MS ID: | MS006958 |
| Analysis ID: | AN007264 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Mass spectrometry parameters included: capillary temperature, 300 °C; sheath gas flow, 40 arbitrary units; nebulizer temperature, 350 °C. Samples were maintained at 4 °C in the autosampler during analysis. Raw LC-MS data were converted to Analysis Base File (ABF) format using the ABF Converter tool. MS-DIAL software (version 4.70) was used to perform blank deduction (peak intensity [Sample/Blank] >= 3), feature peak screening (at least 2 feature peaks appearing in repeated samples), and normalization (LOWESS method) on the data of positive and negative ion modes separately. A comprehensive feature matrix was generated, containing metabolite identifiers, RT, mass-to-charge ratio (m/z), ion patterns, and peak intensities. Metabolite annotation was achieved by matching experimental RT and m/z values against the MassBank database with the following parameters: RT tolerance = ± 0.1 min, MS1 mass tolerance = 0.005 Da, MS2 mass tolerance = 0.0025 Da, and MS2 spectral match score > 0.7. Missing values were imputed using 20% of the minimum value within each experimental group. |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | LiChenjie_Protocol.pdf |
