Summary of Study ST001912

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 PR001206. The data can be accessed directly via it's Project DOI: 10.21228/M8TD6R 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.

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Study IDST001912
Study TitleIdentification of effector metabolites using exometabolite profiling of diverse microalgae
Study SummaryWe conducted an untargeted metabolomic analysis of non-polar exometabolites from four phylogenetically and ecologically diverse eukaryotic microalgal strains grown in the laboratory: freshwater Chlamydomonas reinhardtii, brackish Desmodesmus sp., marine Phaeodactylum tricornutum, and marine Microchloropsis salina. We analyzed both exometabolomes and cell pellet metabolomes to identify released metabolites based on relative enrichment in the exometabolomes.
Institute
Lawrence Berkeley National Laboratory
Last NameBrisson
First NameVanessa
Address7000 East Ave, Livermore, CA, 94550, USA
Emailbrisson2@llnl.gov
Phone5107177560
Submit Date2021-08-23
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2021-09-10
Release Version1
Vanessa Brisson Vanessa Brisson
https://dx.doi.org/10.21228/M8TD6R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001206
Project DOI:doi: 10.21228/M8TD6R
Project Title:LLNL Biofuels SFA
Project Summary:The LLNL Biofuels SFA brings a systems biology approach to understanding interactions and resource allocation in bioenergy-relevant microbial communities.
Institute:Lawrence Berkeley National Laboratory
Last Name:Brisson
First Name:Vanessa
Address:7000 East Ave, Livermore, CA, 94550, USA
Email:vlbrisson@lbl.gov
Phone:510-717-7560
Funding Source:DOE

Subject:

Subject ID:SU001990
Subject Type:Algae
Subject Species:Chlamydomonas reinhardtii;Desmodesmus sp.;Phaeodactylum tricornutum;Microchloropsis salina
Taxonomy ID:3055;91202;2950;2511165

Factors:

Subject type: Algae; Subject species: Chlamydomonas reinhardtii;Desmodesmus sp.;Phaeodactylum tricornutum;Microchloropsis salina (Factor headings shown in green)

mb_sample_id local_sample_id Type Medium Algal strain or abiotic control condition Incubation
SA17693579_E-FW-Cr-Inc_4E - exometabolome FW - freshwater Cr - Chlamydomonas reinhardtii Inc - incubated
SA17693678_E-FW-Cr-Inc_3E - exometabolome FW - freshwater Cr - Chlamydomonas reinhardtii Inc - incubated
SA17693776_E-FW-Cr-Inc_1E - exometabolome FW - freshwater Cr - Chlamydomonas reinhardtii Inc - incubated
SA17693880_E-FW-Cr-Inc_5E - exometabolome FW - freshwater Cr - Chlamydomonas reinhardtii Inc - incubated
SA17693977_E-FW-Cr-Inc_2E - exometabolome FW - freshwater Cr - Chlamydomonas reinhardtii Inc - incubated
SA17694086_E-FW-DF-Inc_1E - exometabolome FW - freshwater DF - Desmodesmus sp. Inc - incubated
SA17694190_E-FW-DF-Inc_5E - exometabolome FW - freshwater DF - Desmodesmus sp. Inc - incubated
SA17694288_E-FW-DF-Inc_3E - exometabolome FW - freshwater DF - Desmodesmus sp. Inc - incubated
SA17694389_E-FW-DF-Inc_4E - exometabolome FW - freshwater DF - Desmodesmus sp. Inc - incubated
SA17694487_E-FW-DF-Inc_2E - exometabolome FW - freshwater DF - Desmodesmus sp. Inc - incubated
SA17694567_E-FW-TxCtrl-Inc_2E - exometabolome FW - freshwater TxCtrl - treatment control Inc - incubated
SA17694666_E-FW-TxCtrl-Inc_1E - exometabolome FW - freshwater TxCtrl - treatment control Inc - incubated
SA17694768_E-FW-TxCtrl-Inc_3E - exometabolome FW - freshwater TxCtrl - treatment control Inc - incubated
SA17694870_E-FW-TxCtrl-Inc_5E - exometabolome FW - freshwater TxCtrl - treatment control Inc - incubated
SA17694969_E-FW-TxCtrl-Inc_4E - exometabolome FW - freshwater TxCtrl - treatment control Inc - incubated
SA17695057_E-FW-TxCtrl-noInc_2E - exometabolome FW - freshwater TxCtrl - treatment control noInc - not incubated
SA17695156_E-FW-TxCtrl-noInc_1E - exometabolome FW - freshwater TxCtrl - treatment control noInc - not incubated
SA17695258_E-FW-TxCtrl-noInc_3E - exometabolome FW - freshwater TxCtrl - treatment control noInc - not incubated
SA17695359_E-FW-TxCtrl-noInc_4E - exometabolome FW - freshwater TxCtrl - treatment control noInc - not incubated
SA17695460_E-FW-TxCtrl-noInc_5E - exometabolome FW - freshwater TxCtrl - treatment control noInc - not incubated
SA17695547_E-SW-DS-Inc_2E - exometabolome SW - saltwater DS - Desmodesmus sp. Inc - incubated
SA17695649_E-SW-DS-Inc_4E - exometabolome SW - saltwater DS - Desmodesmus sp. Inc - incubated
SA17695746_E-SW-DS-Inc_1E - exometabolome SW - saltwater DS - Desmodesmus sp. Inc - incubated
SA17695850_E-SW-DS-Inc_5E - exometabolome SW - saltwater DS - Desmodesmus sp. Inc - incubated
SA17695948_E-SW-DS-Inc_3E - exometabolome SW - saltwater DS - Desmodesmus sp. Inc - incubated
SA17696038_E-SW-Ms-Inc_3E - exometabolome SW - saltwater Ms - Microchloropsis salina Inc - incubated
SA17696139_E-SW-Ms-Inc_4E - exometabolome SW - saltwater Ms - Microchloropsis salina Inc - incubated
SA17696240_E-SW-Ms-Inc_5E - exometabolome SW - saltwater Ms - Microchloropsis salina Inc - incubated
SA17696336_E-SW-Ms-Inc_1E - exometabolome SW - saltwater Ms - Microchloropsis salina Inc - incubated
SA17696437_E-SW-Ms-Inc_2E - exometabolome SW - saltwater Ms - Microchloropsis salina Inc - incubated
SA17696527_E-SW-Pt-Inc_2E - exometabolome SW - saltwater Pt - Phaeodactylum trocornutum Inc - incubated
SA17696628_E-SW-Pt-Inc_3E - exometabolome SW - saltwater Pt - Phaeodactylum trocornutum Inc - incubated
SA17696726_E-SW-Pt-Inc_1E - exometabolome SW - saltwater Pt - Phaeodactylum trocornutum Inc - incubated
SA17696830_E-SW-Pt-Inc_5E - exometabolome SW - saltwater Pt - Phaeodactylum trocornutum Inc - incubated
SA17696929_E-SW-Pt-Inc_4E - exometabolome SW - saltwater Pt - Phaeodactylum trocornutum Inc - incubated
SA17697016_E-SW-TxCtrl-Inc_1E - exometabolome SW - saltwater TxCtrl - treatment control Inc - incubated
SA17697118_E-SW-TxCtrl-Inc_3E - exometabolome SW - saltwater TxCtrl - treatment control Inc - incubated
SA17697219_E-SW-TxCtrl-Inc_4E - exometabolome SW - saltwater TxCtrl - treatment control Inc - incubated
SA17697317_E-SW-TxCtrl-Inc_2E - exometabolome SW - saltwater TxCtrl - treatment control Inc - incubated
SA17697420_E-SW-TxCtrl-Inc_5E - exometabolome SW - saltwater TxCtrl - treatment control Inc - incubated
SA1769758_E-SW-TxCtrl-noInc_3E - exometabolome SW - saltwater TxCtrl - treatment control noInc - not incubated
SA1769769_E-SW-TxCtrl-noInc_4E - exometabolome SW - saltwater TxCtrl - treatment control noInc - not incubated
SA1769777_E-SW-TxCtrl-noInc_2E - exometabolome SW - saltwater TxCtrl - treatment control noInc - not incubated
SA17697810_E-SW-TxCtrl-noInc_5E - exometabolome SW - saltwater TxCtrl - treatment control noInc - not incubated
SA1769796_E-SW-TxCtrl-noInc_1E - exometabolome SW - saltwater TxCtrl - treatment control noInc - not incubated
SA1770252_none-none-ExCtrl-noInc_2none none ExCtrl - extraxtion control noInc - not incubated
SA1770264_none-none-ExCtrl-noInc_4none none ExCtrl - extraxtion control noInc - not incubated
SA1770271_none-none-ExCtrl-noInc_1none none ExCtrl - extraxtion control noInc - not incubated
SA1770285_none-none-ExCtrl-noInc_5none none ExCtrl - extraxtion control noInc - not incubated
SA1770293_none-none-ExCtrl-noInc_3none none ExCtrl - extraxtion control noInc - not incubated
SA17698081_P-FW-Cr-Inc_1P - pellet FW - freshwater Cr - Chlamydomonas reinhardtii Inc - incubated
SA17698183_P-FW-Cr-Inc_3P - pellet FW - freshwater Cr - Chlamydomonas reinhardtii Inc - incubated
SA17698285_P-FW-Cr-Inc_5P - pellet FW - freshwater Cr - Chlamydomonas reinhardtii Inc - incubated
SA17698384_P-FW-Cr-Inc_4P - pellet FW - freshwater Cr - Chlamydomonas reinhardtii Inc - incubated
SA17698482_P-FW-Cr-Inc_2P - pellet FW - freshwater Cr - Chlamydomonas reinhardtii Inc - incubated
SA17698591_P-FW-DF-Inc_1P - pellet FW - freshwater DF - Desmodesmus sp. Inc - incubated
SA17698692_P-FW-DF-Inc_2P - pellet FW - freshwater DF - Desmodesmus sp. Inc - incubated
SA17698794_P-FW-DF-Inc_4P - pellet FW - freshwater DF - Desmodesmus sp. Inc - incubated
SA17698895_P-FW-DF-Inc_5P - pellet FW - freshwater DF - Desmodesmus sp. Inc - incubated
SA17698993_P-FW-DF-Inc_3P - pellet FW - freshwater DF - Desmodesmus sp. Inc - incubated
SA17699071_P-FW-TxCtrl-Inc_1P - pellet FW - freshwater TxCtrl - treatment control Inc - incubated
SA17699195_P-FW-TxCtrl-Inc_5P - pellet FW - freshwater TxCtrl - treatment control Inc - incubated
SA17699272_P-FW-TxCtrl-Inc_2P - pellet FW - freshwater TxCtrl - treatment control Inc - incubated
SA17699374_P-FW-TxCtrl-Inc_4P - pellet FW - freshwater TxCtrl - treatment control Inc - incubated
SA17699473_P-FW-TxCtrl-Inc_3P - pellet FW - freshwater TxCtrl - treatment control Inc - incubated
SA17699565_P-FW-TxCtrl-noInc_5P - pellet FW - freshwater TxCtrl - treatment control noInc - not incubated
SA17699664_P-FW-TxCtrl-noInc_4P - pellet FW - freshwater TxCtrl - treatment control noInc - not incubated
SA17699761_P-FW-TxCtrl-noInc_1P - pellet FW - freshwater TxCtrl - treatment control noInc - not incubated
SA17699862_P-FW-TxCtrl-noInc_2P - pellet FW - freshwater TxCtrl - treatment control noInc - not incubated
SA17699963_P-FW-TxCtrl-noInc_3P - pellet FW - freshwater TxCtrl - treatment control noInc - not incubated
SA17700053_P-SW-DS-Inc_3P - pellet SW - saltwater DS - Desmodesmus sp. Inc - incubated
SA17700152_P-SW-DS-Inc_2P - pellet SW - saltwater DS - Desmodesmus sp. Inc - incubated
SA17700251_P-SW-DS-Inc_1P - pellet SW - saltwater DS - Desmodesmus sp. Inc - incubated
SA17700355_P-SW-DS-Inc_5P - pellet SW - saltwater DS - Desmodesmus sp. Inc - incubated
SA17700454_P-SW-DS-Inc_4P - pellet SW - saltwater DS - Desmodesmus sp. Inc - incubated
SA17700543_P-SW-Ms-Inc_3P - pellet SW - saltwater Ms - Microchloropsis salina Inc - incubated
SA17700644_P-SW-Ms-Inc_4P - pellet SW - saltwater Ms - Microchloropsis salina Inc - incubated
SA17700742_P-SW-Ms-Inc_2P - pellet SW - saltwater Ms - Microchloropsis salina Inc - incubated
SA17700841_P-SW-Ms-Inc_1P - pellet SW - saltwater Ms - Microchloropsis salina Inc - incubated
SA17700945_P-SW-Ms-Inc_5P - pellet SW - saltwater Ms - Microchloropsis salina Inc - incubated
SA17701031_P-SW-Pt-Inc_1P - pellet SW - saltwater Pt - Phaeodactylum trocornutum Inc - incubated
SA17701134_P-SW-Pt-Inc_4P - pellet SW - saltwater Pt - Phaeodactylum trocornutum Inc - incubated
SA17701232_P-SW-Pt-Inc_2P - pellet SW - saltwater Pt - Phaeodactylum trocornutum Inc - incubated
SA17701333_P-SW-Pt-Inc_3P - pellet SW - saltwater Pt - Phaeodactylum trocornutum Inc - incubated
SA17701435_P-SW-Pt-Inc_5P - pellet SW - saltwater Pt - Phaeodactylum trocornutum Inc - incubated
SA17701524_P-SW-TxCtrl-Inc_4P - pellet SW - saltwater TxCtrl - treatment control Inc - incubated
SA17701621_P-SW-TxCtrl-Inc_1P - pellet SW - saltwater TxCtrl - treatment control Inc - incubated
SA17701722_P-SW-TxCtrl-Inc_2P - pellet SW - saltwater TxCtrl - treatment control Inc - incubated
SA17701823_P-SW-TxCtrl-Inc_3P - pellet SW - saltwater TxCtrl - treatment control Inc - incubated
SA17701955_P-SW-TxCtrl-Inc_5P - pellet SW - saltwater TxCtrl - treatment control Inc - incubated
SA17702013_P-SW-TxCtrl-noInc_3P - pellet SW - saltwater TxCtrl - treatment control noInc - not incubated
SA17702115_P-SW-TxCtrl-noInc_5P - pellet SW - saltwater TxCtrl - treatment control noInc - not incubated
SA17702212_P-SW-TxCtrl-noInc_2P - pellet SW - saltwater TxCtrl - treatment control noInc - not incubated
SA17702314_P-SW-TxCtrl-noInc_4P - pellet SW - saltwater TxCtrl - treatment control noInc - not incubated
SA17702411_P-SW-TxCtrl-noInc_1P - pellet SW - saltwater TxCtrl - treatment control noInc - not incubated
Showing results 1 to 95 of 95

Collection:

Collection ID:CO001983
Collection Summary:Axenic algal were grown in glass 125 mL Erlenmeyer flasks that had previously been baked in a muffle furnace at 550°C for two hours to remove trace organics that could contaminate metabolomics analyses. Each flask contained 50 mL of the appropriate medium (defined freshwater or saltwater medium) and was capped with a foam stopper and covered with aluminum foil to avoid contamination during the experiment. Flasks were incubated with shaking at 90 rpm in a light incubator, with a 12-hour day/night light cycle. Daytime illumination was 3500 lux, and the incubator temperature was maintained at 22°C. Algal inocula were prepared by first growing algal stock cultures under experimental conditions (flasks, media, incubation) for one week to acclimate cultures to those conditions. Experimental flasks were inoculated by transferring 2 mL of inoculum culture to flasks with the appropriate medium. Cultures were harvested for metabolomic analysis from five replicate flasks for each alga after 8 days of incubation. Spent medium and cell pellets were separated by centrifugation. Half of the culture was transferred to a 50 mL falcon tube and centrifuged at 5000 g for eight minutes at 4°C. The supernatant was carefully transferred to a clean Falcon tube, and the remainder of the culture was added to the tube containing the pellet and the centrifugation procedure was repeated. After separation by centrifugation, the supernatant was filtered through a 0.45µm pore size syringe filter to remove residual algal cells. Filtered spent medium and cell pellets were frozen on dry ice and stored at -80°C until extraction.
Sample Type:Algae
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002002
Treatment Summary:Treatments consisted of 4 different axenic algal strains growth separately for comparison: Chlamydomonas reinhardtii, Desmodesmus sp., Phaeodactylum tricornutum, and Microchloropsis salina. C. reinhartdii was grown in defined freshwater mediunm. Desmodesmus was grown separately in defined freshwater and saltwater medium. P. tricornutum and M. salina were grown separately in defined saltwater medium. Separate axenic controls were conducted for the defined freshwater and saltwater media. Metabolite extraction controls were also prepared using the same extraction protocol.

Sample Preparation:

Sampleprep ID:SP001996
Sampleprep Summary:In order to disrupt cells for metabolite extraction, cell pellets were resuspended in 1 mL sterile water, frozen at -80°C, and lyophilized. Lyophilized pellets were disrupted using a sterilized steel ball and vortexing three times for five seconds. Disrupted pellets were then resuspended in 50 mL sterile water and filtered and frozen in the same manner as spent medium. Thus, the spent medium and cell pellet samples corresponded to the same original sample volume. Samples for LC-MS/MS metabolomics analysis were extracted by solid phase extraction using Waters Sep-Pak C18 3 mL cartridges. Because chlorophyll and biomass content were similar across samples, samples were normalized to the same volume (30 mL). Cartridges were first preconditioned with 3 mL methanol, and the rinsed with 6 mL ultrapure water. Metabolites were extracted by passing 30 mL of sample through the cartridge. Columns with extracted metabolites were rinsed with 6 mL ultrapure water. Metabolites were eluted with 1 mL methanol into a 1.5 mL polypropylene tube and the dried in a vacuum centrifuge with a refrigerated vapor trap. Dried metabolite extracts resuspended in 150 µL methanol with matrix control internal standards, vortexed for 5 to 10 seconds, and sonicated in a water bath sonicator with ice for ten minutes. Samples were centrifuged at 10,000 g for five minutes at 4°C to pellet insoluble salts and proteins. Supernatant was transferred to a 0.2 µm pore size centrifuge filter device, and centrifuged at 5,000 g for five minutes at 4°C. Filtrate was transferred to an autosampler vial for LC-MS/MS analysis.

Combined analysis:

Analysis ID AN003109 AN003110
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 1290 Agilent 1290
Column Agilent Sorbax Eclipse Plus C18 RRHD (50 x 2.1 mm, 1.8 um) Agilent Sorbax Eclipse Plus C18 RRHD (50 x 2.1 mm, 1.8 um)
MS Type ESI ESI
MS instrument type Single quadrupole Single quadrupole
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode NEGATIVE POSITIVE
Units peak height peak height

Chromatography:

Chromatography ID:CH002296
Instrument Name:Agilent 1290
Column Name:Agilent Sorbax Eclipse Plus C18 RRHD (50 x 2.1 mm, 1.8 um)
Chromatography Type:Reversed phase

MS:

MS ID:MS002891
Analysis ID:AN003109
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Single quadrupole
MS Type:ESI
MS Comments:Feature detection conducted using MZmine 2
Ion Mode:NEGATIVE
  
MS ID:MS002892
Analysis ID:AN003110
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Single quadrupole
MS Type:ESI
MS Comments:Feature detection conducted using MZmine 2
Ion Mode:POSITIVE
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