Summary of Study ST004081
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 PR002562. The data can be accessed directly via it's Project DOI: 10.21228/M8GJ95 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004081 |
| Study Title | Remodeling of Prochlorococcus metabolism during viral infection |
| Study Type | Marine Microbial Metabolomics |
| Study Summary | The marine cyanobacterium Prochlorococcus is the most abundant photoautotroph in the world and is a major contributor to oceanic primary productivity. Viruses are important controls on Prochlorococcus populations with up to 10% of Prochlorococcus cells infected. During infection, viruses remodel their host’s metabolic machinery, creating metabolically distinct cells, termed virocells. However, the specific consequences of viral infection on Prochlorococcus metabolism remain poorly understood. Here, we characterize the infection of non-axenic cultures of Prochlorococcus MED4 by the T7-like virus P-SSP7 using a combination of metabolomics, transcriptomics, and population modeling approaches. Three biological replicates (Replicates A, B, and C) of Prochlorococcus MED4 and associated heterotrophic bacteria were inoculated with 3 different levels of the virus P-SSP7 at the beginning of the experiment. The treatments were as follows: Control (C), no virus added; Low Virus (LV), viruses added in a 1:0.001 host:virus ratio; and High Virus (HV), viruses add in a 1:0.7 host:virus ratio. The experiment was run for 48 hours with metabolomics samples collected at timepoints of 0, 12, 24, 36, and 48 hours for the LV and HV treatments and 0, 6, 12, 18, 24, 30, 36, 42, 48 hours for the C treatment. P-SSP7 infection dramatically altered the metabolome of Prochlorococcus with 25% of metabolites showing differential abundance. Infected cells exhibited decreased carbon fixation and the draw down of intracellular stores of carbon structures and energy such as glycogen and the osmolytes sucrose and aspartic acid. In contrast, another osmolyte, glucosylglycerol, was accumulated in high concentrations and came to dominate the virocell metabolome. Infected cells also experienced pseudocobalamin (pB12) stress, as evidenced by reduced pB12 concentrations, increased expression of genes to synthesize pB12, and depletion of metabolites whose synthesis relies on pB12 including S-adnosylmethionine (SAM) and the antioxidant glutathione. Collectively, our results suggest that the observed metabolic remodeling is driven by the demand for carbon and energy for virion production and infection-induced oxidative stress. Viral infection changes the substrate and vitamin pools provided by Prochlorococcus to the microbial community, potentially altering the speciation and flux of organic matter in marine systems and acting as a selective force on microbial community composition and function. |
| Institute | University of Washington |
| Department | School of Oceanography |
| Laboratory | Ingalls Lab |
| Last Name | Sacks |
| First Name | Joshua |
| Address | Box 355351 School of Oceanography University of Washington, Seattle WA 98115 |
| jssacks@uw.edu | |
| Phone | 4074090052 |
| Submit Date | 2025-07-03 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-08-19 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002562 |
| Project DOI: | doi: 10.21228/M8GJ95 |
| Project Title: | Remodeling of Prochlorococcus metabolism during viral infection |
| Project Type: | Marine Microbial Metabolomics |
| Project Summary: | The marine cyanobacterium Prochlorococcus is the most abundant photoautotroph in the world and is a major contributor to oceanic primary productivity. Viruses are important controls on Prochlorococcus populations with up to 10% of Prochlorococcus cells infected. During infection, viruses remodel their host’s metabolic machinery, creating metabolically distinct cells, termed virocells. However, the specific consequences of viral infection on Prochlorococcus metabolism remain poorly understood. Here, we characterize the infection of non-axenic cultures of Prochlorococcus MED4 by the T7-like virus P-SSP7 using a combination of metabolomics, transcriptomics, and population modeling approaches. P-SSP7 infection dramatically altered the metabolome of Prochlorococcus with 25% of metabolites showing differential abundance. Infected cells exhibited decreased carbon fixation and the draw down of intracellular stores of carbon structures and energy such as glycogen and the osmolytes sucrose and aspartic acid. In contrast, another osmolyte, glucosylglycerol, was accumulated in high concentrations and came to dominate the virocell metabolome. Infected cells also experienced pseudocobalamin (pB12) stress, as evidenced by reduced pB12 concentrations, increased expression of genes to synthesize pB12, and depletion of metabolites whose synthesis relies on pB12 including S-adnosylmethionine (SAM) and the antioxidant glutathione. Collectively, our results suggest that the observed metabolic remodeling is driven by the demand for carbon and energy for virion production and infection-induced oxidative stress. Viral infection changes the substrate and vitamin pools provided by Prochlorococcus to the microbial community, potentially altering the speciation and flux of organic matter in marine systems and acting as a selective force on microbial community composition and function. |
| Institute: | University of Washington |
| Department: | School of Oceanography |
| Laboratory: | Ingalls Lab |
| Last Name: | Sacks |
| First Name: | Joshua |
| Address: | Box 355351 School of Oceanography University of Washington, Seattle WA 98115 |
| Email: | jssacks@uw.edu |
| Phone: | 206 221 6750 |
| Funding Source: | Simons Foundation |
| Publications: | Sacks et al. in prep |
Subject:
| Subject ID: | SU004227 |
| Subject Type: | Bacteria |
| Subject Species: | Prochlorococcus marinus |
| Taxonomy ID: | 59919 |
| Genotype Strain: | MED4 |
| Gender: | Not applicable |
Factors:
Subject type: Bacteria; Subject species: Prochlorococcus marinus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Treatment | Timepoint_h |
|---|---|---|---|---|
| SA473513 | B_C_0 | Marine Microbe Culture | C | 0 |
| SA473514 | C_C_0 | Marine Microbe Culture | C | 0 |
| SA473515 | A_C_0 | Marine Microbe Culture | C | 0 |
| SA473516 | B_C_12 | Marine Microbe Culture | C | 12 |
| SA473517 | C_C_12 | Marine Microbe Culture | C | 12 |
| SA473518 | A_C_12 | Marine Microbe Culture | C | 12 |
| SA473519 | C_C_18 | Marine Microbe Culture | C | 18 |
| SA473520 | A_C_18 | Marine Microbe Culture | C | 18 |
| SA473521 | B_C_18 | Marine Microbe Culture | C | 18 |
| SA473522 | C_C_24 | Marine Microbe Culture | C | 24 |
| SA473523 | B_C_24 | Marine Microbe Culture | C | 24 |
| SA473524 | A_C_24 | Marine Microbe Culture | C | 24 |
| SA473525 | A_C_30 | Marine Microbe Culture | C | 30 |
| SA473526 | C_C_30 | Marine Microbe Culture | C | 30 |
| SA473527 | B_C_30 | Marine Microbe Culture | C | 30 |
| SA473528 | C_C_36 | Marine Microbe Culture | C | 36 |
| SA473529 | A_C_36 | Marine Microbe Culture | C | 36 |
| SA473530 | B_C_36 | Marine Microbe Culture | C | 36 |
| SA473531 | C_C_42 | Marine Microbe Culture | C | 42 |
| SA473532 | B_C_42 | Marine Microbe Culture | C | 42 |
| SA473533 | A_C_42 | Marine Microbe Culture | C | 42 |
| SA473534 | C_C_48 | Marine Microbe Culture | C | 48 |
| SA473535 | A_C_48 | Marine Microbe Culture | C | 48 |
| SA473536 | B_C_48 | Marine Microbe Culture | C | 48 |
| SA473537 | C_C_6 | Marine Microbe Culture | C | 6 |
| SA473538 | B_C_6 | Marine Microbe Culture | C | 6 |
| SA473539 | A_C_6 | Marine Microbe Culture | C | 6 |
| SA473540 | B_HV_0 | Marine Microbe Culture | HV | 0 |
| SA473541 | A_HV_0 | Marine Microbe Culture | HV | 0 |
| SA473542 | C_HV_0 | Marine Microbe Culture | HV | 0 |
| SA473543 | B_HV_12 | Marine Microbe Culture | HV | 12 |
| SA473544 | A_HV_12 | Marine Microbe Culture | HV | 12 |
| SA473545 | C_HV_12 | Marine Microbe Culture | HV | 12 |
| SA473546 | B_HV_24 | Marine Microbe Culture | HV | 24 |
| SA473547 | C_HV_24 | Marine Microbe Culture | HV | 24 |
| SA473548 | A_HV_24 | Marine Microbe Culture | HV | 24 |
| SA473549 | A_HV_36 | Marine Microbe Culture | HV | 36 |
| SA473550 | B_HV_36 | Marine Microbe Culture | HV | 36 |
| SA473551 | C_HV_36 | Marine Microbe Culture | HV | 36 |
| SA473552 | B_HV_48 | Marine Microbe Culture | HV | 48 |
| SA473553 | C_HV_48 | Marine Microbe Culture | HV | 48 |
| SA473554 | A_HV_48 | Marine Microbe Culture | HV | 48 |
| SA473555 | A_LV_0 | Marine Microbe Culture | LV | 0 |
| SA473556 | B_LV_0 | Marine Microbe Culture | LV | 0 |
| SA473557 | C_LV_0 | Marine Microbe Culture | LV | 0 |
| SA473558 | C_LV_12 | Marine Microbe Culture | LV | 12 |
| SA473559 | B_LV_12 | Marine Microbe Culture | LV | 12 |
| SA473560 | A_LV_12 | Marine Microbe Culture | LV | 12 |
| SA473561 | C_LV_24 | Marine Microbe Culture | LV | 24 |
| SA473562 | B_LV_24 | Marine Microbe Culture | LV | 24 |
| SA473563 | A_LV_24 | Marine Microbe Culture | LV | 24 |
| SA473564 | C_LV_36 | Marine Microbe Culture | LV | 36 |
| SA473565 | A_LV_36 | Marine Microbe Culture | LV | 36 |
| SA473566 | B_LV_36 | Marine Microbe Culture | LV | 36 |
| SA473567 | B_LV_48 | Marine Microbe Culture | LV | 48 |
| SA473568 | C_LV_48 | Marine Microbe Culture | LV | 48 |
| SA473569 | A_LV_48 | Marine Microbe Culture | LV | 48 |
| Showing results 1 to 57 of 57 |
Collection:
| Collection ID: | CO004220 |
| Collection Summary: | Particulate metabolites were sampled using gentle vacuum filtration onto 47 mm 0.2-mm polytetrafluoroethylene (PTFE) omnipore filters (Omnipore Membrane Filters, Merck Millipore Ltd). Glass and polysulfone filtration rigs were used. Glass rigs were combusted at 450 ˚C for 4 hours before and between experiments. The polysulfone filtration setups were soaked in 10% HCl for 24 hours and triple rinsed with MiliQ water before and between experiments. In between sampling different treatments, timepoints, and biological replicates, the filtration setups were triple rinsed with MiliQ water, rinsed with 10% HCl, and then triple rinsed again with MiliQ water. After filtration, samples were wrapped in combusted foil and flash frozen in liquid nitrogen before storage at -80˚C until analysis. Sample volumes ranged from 50–300 mL to account for variations in biomass throughout the experiment and filtration times ranged from 5–15 minutes. |
| Sample Type: | Bacterial cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR004236 |
| Treatment Summary: | Three biological replicates (Replicates A, B, and C) of Prochlorococcus MED4 and associated heterotrophic bacteria were inoculated with 3 different levels of the virus P-SSP7 at the beginning of the experiment. The treatments were as follows: Control (C), no virus added; Low Virus (LV), viruses added in a 1:0.001 host:virus ratio; and High Virus (HV), viruses add in a 1:0.7 host:virus ratio. The experiment was run for 48 hours with samples collected at timepoints (timepoint_h) of 0, 12, 24, 36, and 48 hours for the LV and HV treatments and 0, 6, 12, 18, 24, 30, 36, 42, 48 hours for the C treatment. |
Sample Preparation:
| Sampleprep ID: | SP004233 |
| Sampleprep Summary: | Each sample was extracted using a modified Bligh-Dyer extraction. Briefly, filters were cut up and put into 15 mL teflon centrifuge tubes containing a mixture of 100 µm and 400 µm silica beads. Heavy isotope-labeled internal standards were added along with ~2 mL of cold aqueous solvent (50:50 methanol:water) and ~3 mL of cold organic solvent (dichloromethane). The samples were shaken on a FastPrep-24 Homogenizer for 30 seconds and chilled in a -20 °C freezer repeatedly for three cycles of bead-beating and a total of 30 minutes of chilling. The organic and aqueous layers were separated by spinning samples in a centrifuge at 4,300 rpm for 2 minutes at 4 °C. The aqueous layer was removed to a new glass centrifuge tube. The remaining organic fraction was rinsed three more times with additions of 1 to 2 mL of 50:50 methanol:water. All aqueous rinses were combined for each sample and dried down under N2 gas. The remaining organic layer was transferred into a clean glass centrifuge tube and the remaining bead beating tube was rinsed two more times with cold organic solvent. The combined organic rinses were centrifuged, transferred to a new tube, and dried under N2 gas. Dried aqueous fractions were re-dissolved in 380 µL of water. Dried organic fractions were re-dissolved in 380 µL of 1:1 water:acetonitrile. 20 µL of isotope-labeled injection standards in water were added to both fractions. Blank filters were extracted alongside samples as methodological blanks. |
| Processing Storage Conditions: | On ice |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN006755 | AN006756 | AN006757 | AN006758 |
|---|---|---|---|---|
| Chromatography ID | CH005133 | CH005134 | CH005134 | CH005135 |
| MS ID | MS006454 | MS006455 | MS006456 | MS006457 |
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | HILIC | HILIC | Reversed phase |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters ACQUITY UPLC HSS CN (100 x 2.1mm,1.8um) | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) | Waters ACQUITY UPLC HSS CN (100 x 2.1mm,1.8um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Triple quadrupole |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Waters Xevo-TQ-S |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | POSITIVE |
| Units | Peak Area/mL | nmol/L | nmol/L | nmol/L |
Chromatography:
| Chromatography ID: | CH005133 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC HSS CN (100 x 2.1mm,1.8um) |
| Column Temperature: | 35 C |
| Flow Gradient: | The column was held at 5% B for 2 minutes, ramped to 100% B over 16 minutes, held at 100% B for 2 minutes, and equilibrated at 5% B for 5 minutes (25 minutes total) |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH005134 |
| Instrument Name: | Waters Acquity |
| Column Name: | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) |
| Column Temperature: | 30 C |
| Flow Gradient: | The column was held at 100% A for 2 minutes, ramped to 100% B over 18 minutes, held at 100% B for 5 minutes, and equilibrated at 100% A for 25 minutes (50 minutes total). |
| Flow Rate: | 0.15 mL/min |
| Solvent A: | 85% acetonitrile/15% water; 10 mM ammonium carbonate |
| Solvent B: | 60% water/40% acetonitrile; 10 mM ammonium carbonate |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH005135 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC HSS CN (100 x 2.1mm,1.8um) |
| Column Temperature: | 35C |
| Flow Gradient: | The column was held at 2% B for 0.5 minutes, ramped to 25% B for 7.8 minutes, ramped to 95% B, held at 95% B for 1 minute, and equilibrated back to 2% B for 1.7 minutes (total run time is 11 minutes) |
| Flow Rate: | 0.6 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 20mM ammonium formate |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS006454 |
| Analysis ID: | AN006755 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS acquisition Comments: A full scan method was used with a scan range of 90 to 900 m/z and a resolution of 120,000. A DDA method was used with a scan range of 90 to 900 m/z. Data processing: Data was processed as in Boysen and Heal et al. 2018. Analytical Chemistry (DOI: 10.1021/acs.analchem.7b04400). Software/procedures used for feature assignments: Peaks were integrated using Skyline. Data was processed using quality control and best-matched internal standard normalization. MS parameters were as follows: capillary temperature was 320C, the H-ESI spray voltage was 3.8 kV, and the auxiliary gas heater temperature was 90C. The S-lens RF level was 65. Sheath gas, auxiliary gas, and sweep gas flow rates were maintained at 40, 10, and 1, respectively. |
| Ion Mode: | POSITIVE |
| MS ID: | MS006455 |
| Analysis ID: | AN006756 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS acquisition Comments: Polarity switching was used with a scan range of 60 to 900 m/z and a resolution of 60,000. A DDA method was used with a scan range of 60 to 900 m/z. Data processing Comments: Data was processed as in Boysen and Heal et al. 2018 (DOI: 10.1021/acs.analchem.7b04400). Analytical Chemistry. Software/procedures used for feature assignments: Peaks were integrated using Skyline. Data was processed using quality control and best-matched internal standard normalization. MS parameters were as follows: capillary temperature was 320C, the H-ESI spray voltage was 3.5 kV, and the auxiliary gas heater temperature was 90C. The S-lens RF level was 65. Sheath gas, auxiliary gas, and sweep gas flow rates were maintained at 16, 3, and 1, respectively. |
| Ion Mode: | POSITIVE |
| MS ID: | MS006456 |
| Analysis ID: | AN006757 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS acquisition Comments: Polarity switching was used with a scan range of 60 to 900 m/z and a resolution of 60,000. A DDA method was used with a scan range of 60 to 900 m/z. Data processing Comments: Data was processed as in Boysen and Heal et al. 2018 (DOI: 10.1021/acs.analchem.7b04400). Analytical Chemistry. Software/procedures used for feature assignments: Peaks were integrated using Skyline. Data was processed using quality control and best-matched internal standard normalization. MS parameters were as follows: capillary temperature was 320C, the H-ESI spray voltage was 3.5 kV, and the auxiliary gas heater temperature was 90C. The S-lens RF level was 65. Sheath gas, auxiliary gas, and sweep gas flow rates were maintained at 16, 3, and 1, respectively. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS006457 |
| Analysis ID: | AN006758 |
| Instrument Name: | Waters Xevo-TQ-S |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | MS acquisition Comments: The selected reaction monitoring (SRM) transitions were monitored over a 5 to 10 minute window around the retention time. For most metabolites, two SRM transitions were monitored, one for quantification and an additional for compound confirmation. Scheduling was set up to ensure at least 12 data points per peak were collected. Data processing Comments: Data was processed as in Heal et al. 2014 (DOI: 10.1021/acs.analchem.7b04400). Software/procedures used for feature assignments: Peaks were integrated using Skyline. Data was processed using quality control, and best-matched internal standard normalization. MS parameters were as follows: capillary voltage of 0.5 kV, source temperature of 130C, cone gas flow at 150 L/h and desolvation gas flow at 1000 L/h, Desolvation temperature was 500C |
| Ion Mode: | POSITIVE |
