Metabolomic fingerprints of individual algal cells using the Single-Probe Mass Spectrometry technique from experiments conducted between May and August of 2017

Website: https://www.bco-dmo.org/dataset/746185
Data Type: experimental
Version: 1
Version Date: 2018-09-21

Project
» Collaborative Research: Creatine Cycling in Marine Bacterial and Phytoplankton Assemblages (Creatine Cycling)
ContributorsAffiliationRole
Wawrik, BorisUniversity of Oklahoma (OU)Principal Investigator
Yang, ZhiboUniversity of Oklahoma (OU)Co-Principal Investigator
York, Amber D.Woods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Abstract
Single-probe Mass Spectrometry was used to obtain mass to charge ratio (m/z) and relative intensity values of marine dinoflagellate Scrippsiella trochoidea cells grown under different illumination levels and under nitrogen (N) limiting conditions.


Coverage

Temporal Extent: 2017-05 - 2017-08

Dataset Description

These data were published in Sun et al., 2018.

A tabular version of this dataset is accessible by clicking the "Get Data" button on this page.  The columns of the tabular dataset are described in the "Parameters" section on this page.  This dataset is available as standard MS file format (.mzML) files within the following tar.gz file:
Algal_Cell_Data_mzML.tar.gz (2.4 GB, contains 20 .mzML files)

.mzML is a standard MS file format that can be viewed using freeware such as mMass (http://www.mmass.org/) and ProteoWizard (http://proteowizard.sourceforge.net/index.shtml).


Methods & Sampling

Methodology
The following are excerpts from Sun et al., 2018. Please refer to this publication for more details.

Non-axenic Scrippsiella trochoidea CCMP 3099 was originally obtained from the National Center for Marine Algae and Microbiota (Provasoil-Guillard NCMA, Boothbay Harbor, ME, United States). For maintenance, cultures were grown in L1 seawater media (Guillard and Ryther, 1962; Guillard et al., 1973; Guillard and Hargraves, 1993). Medium was prepared from natural seawater collected near Key West (salinity of 33), which was aged for at least 6 month in the dark and autoclaved. Maintenance and experimental cultures were grown in a light/dark incubator at 23–24°C and 30–40 μmol quanta⋅m-2 s-1 light under a 12-h light:12-h dark cycle.

For the light/dark comparisons, cultures were grown under replete conditions in full L1 media containing 880 μM NaNO3 and 36 μM NaH2PO4 (N/P ratio 24:1). Experimental cultures were started as a 1:10 inoculum from exponentially growing cultures into 1 L of media in 2.5 L Pyrex Fernbach flasks without shaking and monitored daily via cell counts and chlorophyll measurements. Cell counts were conducted by addition of 1% Lugol’s iodine and direct counting of cells in 96-well microtiter plates using a dissection microscope. Dilutions were made as necessary and at least 10 wells containing 100 μL diluted culture were counted to average cell counts. Chlorophyll a was measured via fluorometry (Welschmeyer, 1994) by filtering 5 mL of culture in triplicate onto GF/F filters, over-night extraction with methanol, and quantification using a Turner Trilogy Laboratory Fluorometer. Cultures were grown into late-log phase (data not shown) and then sampled 3 h before and 3 h after the light was turned on. Cultures were sub-sampled for MS analysis, making sure to keep ‘dark’ sample exposure to light to a minimum by wrapping sampling tubes in aluminum foil.

N-deplete cultures were generated by first growing cells on L1 media with an N:P ratio of 2.4:1 (88 mM nitrate: 36 mM phosphate) analogous what has been previously described (Harke et al., 2017). This lower ratio stoichiometrically limited cultures in nitrogen and at least three transfers were performed to ensure no carryover from higher nutrient full L1 medium. Cultures were monitored daily via cell counts (see above), chlorophyll a quantification (see above), and quantification of nitrate/nitrite via a Vanadium reduction method (Miranda et al., 2001). Parallel cultures were set up in which one culture was allowed to run out of nitrogenous nutrients (N-deplete), while the culture (control) was fed additional nitrate every second day to bring total nitrate/nitrite concentrations back to starting levels. Once nitrate/nitrite levels dropped below the limit of detection (∼1–2 μM) in the N-deplete culture, cultures were grown for an additional 24 h before sampling to ensure that N-depletion was complete. Both the N-deplete and replete cultures were then sampled for MS analysis of single cells.

Individual cells of S. trochoidea were analyzed via the ‘Single-probe’ MS techniques.
For the analysis, cells were deposited onto 0.2 μm polycarbonate membranes by gentle filtration, and the cells were rinsed with phosphate buffered saline (PBS; 137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO4, 1.47 mM KH2PO4; pH of 7.4) to remove culture medium. Filters were then placed on a home-built XYZ-translation stage system and spatial motion was controlled by a custom designed LabView software package (Lanekoff et al., 2012). The Single-probe tip (<10 μm) was then precisely insert into single S. trochoidea cells (typically ∼20–30 μm cellular diameter) using a microscope as a guide. During the experiment, a syringe (250 μl; Hamilton, Co., Reno, NV, United States) was used to continuously provide the sampling solvent (acetonitrile; Sigma-Aldrich, St. Louis, MO, United States), and a liquid junction formed at the Single-probe tip to perform highly efficient extraction of cellular contents. The analytes were withdrawn by capillary action toward the nano-ESI emitter, and ionized for analysis using a Thermo LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Waltham, MA, United States). Mass analyze parameters were as follows: mass resolution 60,000, +4 kV ionization voltage at positive ion mode (0.05–0.07 μA of ion current), 1 microscan, 100 ms max injection time, and automatic gain control on.

Data processing:
The Thermo Xcalibur Qual Browser (Thermo Scientific, Waltham, MA, United States) was used to export MS data (m/z values with relative intensities) as tab-delimited data files. As a conservative approach, only relatively abundant peaks with ion intensities > 103 were exported. This approach excluded 6% of low signal peaks as background while retaining 94% of total signal intensity. The relative ion intensities were normalized to the total ion current to minimize the influence induced by fluctuations of ion signals during experiments. The Geena 2 online software tool1 was then used for peak alignment (Romano et al., 2016), and the aligned m/z values were then used for comparisons. Parameters used in Geena 2 include analysis range (from 100 to 1500 m/z), maximum number of isotopic replicas (5), maximum delta between isotopic peaks (0.05 Da), and maximum delta for aligning replicates (0.01 Da). Metaboanalyst 3.02 was used to conduct statistical data analysis, including PLS-DA (partial least squares discriminant analysis) and t-tests (Xia et al., 2015; Xia and Wishart, 2016). PLS-DA was used to visualize differences in chemical composition profiles among treatment groups, while t-tests were applied to extract molecular peaks with significant abundance changes (p < 0.05). Finally, the online database METLIN3 was used to tentatively label all ions of interest (Smith et al., 2005; Guijas et al., 2018), to perform hierarchical clustering, and to generate heat maps. Lastly, Pathos4 was used to attempt identification of significantly regulated metabolic pathways by considering all KEGG maps in all organisms (Leader et al., 2011).

Single-Probe description:
Detailed fabrication protocols of the Single-probe have been previously described (Pan et al., 2014; Rao et al., 2015; Sun et al., 2017). Briefly, a Single-probe has three components: a dual-bore quartz tubing [outer diameter (OD) 500 μm; inner diameter (ID) 127 μm, Friedrich & Dimmock, Inc., Millville, NJ, United States] pulled using a laser pipette puller (P-2000 micropipette puller, Sutter Instrument, Novato, CA, United States), a fused silica capillary (OD 105 μm; ID 40 μm, Polymicro Technologies, Phoenix, AZ, United States), and a nano-ESI emitter made from the same type of fused silica capillary. A Single-probe is fabricated by embedding a fused silica capillary and a nano-ESI emitter into both of the channels of the laser-pulled dual-bore quartz needle.


Data Processing Description

BCO-DMO Data Manager Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions


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Data Files

File
algae_cell_data.csv
(Comma Separated Values (.csv), 20.92 MB)
MD5:08a1374d7d0dc85ab2d14a2e34fbeaed
Primary data file for dataset ID 746185

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Related Publications

Guijas, C., Montenegro-Burke, J. R., Domingo-Almenara, X., Palermo, A., Warth, B., Hermann, G., … Siuzdak, G. (2018). METLIN: A Technology Platform for Identifying Knowns and Unknowns. Analytical Chemistry, 90(5), 3156–3164. doi:10.1021/acs.analchem.7b04424
Methods
Guillard, R. R. L., & Hargraves, P. E. (1993). Stichochrysis immobilis is a diatom, not a chrysophyte. Phycologia, 32(3), 234–236. doi:10.2216/i0031-8884-32-3-234.1
Methods
Guillard, R. R. L., & Ryther, J. H. (1962). STUDIES OF MARINE PLANKTONIC DIATOMS: I. CYCLOTELLA NANA HUSTEDT, AND DETONULA CONFERVACEA (CLEVE) GRAN. Canadian Journal of Microbiology, 8(2), 229–239. doi:10.1139/m62-029
Methods
Guillard, R. R. L., Kilham, P., & Jackson, T. A. (1973). KINETICS OF SILICON-LIMITED GROWTH IN THE MARINE DIATOM THALASSIOSIRA PSEUDONANA HASLE AND HEIMDAL (= CYCLOTELLA NANA HUSTEDT)2. Journal of Phycology, 9(3), 233–237. doi:10.1111/j.1529-8817.1973.tb04086.x
Methods
Harke, M. J., Juhl, A. R., Haley, S. T., Alexander, H., & Dyhrman, S. T. (2017). Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae. Frontiers in Microbiology, 8. doi:10.3389/fmicb.2017.01279
Methods
Lanekoff, I., Heath, B. S., Liyu, A., Thomas, M., Carson, J. P., & Laskin, J. (2012). Automated Platform for High-Resolution Tissue Imaging Using Nanospray Desorption Electrospray Ionization Mass Spectrometry. Analytical Chemistry, 84(19), 8351–8356. doi:10.1021/ac301909a
Methods
Leader, D. P., Burgess, K., Creek, D., & Barrett, M. P. (2011). Pathos: A web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry. Rapid Communications in Mass Spectrometry, 25(22), 3422–3426. doi:10.1002/rcm.5245
Methods
Miranda, K. M., Espey, M. G., & Wink, D. A. (2001). A Rapid, Simple Spectrophotometric Method for Simultaneous Detection of Nitrate and Nitrite. Nitric Oxide, 5(1), 62–71. doi:10.1006/niox.2000.0319
Methods
Pan, N., Rao, W., Kothapalli, N. R., Liu, R., Burgett, A. W. G., & Yang, Z. (2014). The Single-Probe: A Miniaturized Multifunctional Device for Single Cell Mass Spectrometry Analysis. Analytical Chemistry, 86(19), 9376–9380. doi:10.1021/ac5029038
Methods
Pan, N., Rao, W., Standke, S. J., & Yang, Z. (2016). Using Dicationic Ion-Pairing Compounds To Enhance the Single Cell Mass Spectrometry Analysis Using the Single-Probe: A Microscale Sampling and Ionization Device. Analytical Chemistry, 88(13), 6812–6819. doi:10.1021/acs.analchem.6b01284
Methods
Rao, W., Pan, N., & Yang, Z. (2016). Applications of the Single-probe: Mass Spectrometry Imaging and Single Cell Analysis under Ambient Conditions. Journal of Visualized Experiments, (112). doi:10.3791/53911
Methods
Smith, C. A., Maille, G. O., Want, E. J., Qin, C., Trauger, S. A., Brandon, T. R., … Siuzdak, G. (2005). METLIN. Therapeutic Drug Monitoring, 27(6), 747–751. doi:10.1097/01.ftd.0000179845.53213.39
Methods
Sun, M., Tian, X., & Yang, Z. (2017). Microscale Mass Spectrometry Analysis of Extracellular Metabolites in Live Multicellular Tumor Spheroids. Analytical Chemistry, 89(17), 9069–9076. doi:10.1021/acs.analchem.7b01746
Methods
Sun, M., Yang, Z., & Wawrik, B. (2018). Metabolomic Fingerprints of Individual Algal Cells Using the Single-Probe Mass Spectrometry Technique. Frontiers in Plant Science, 9. doi:10.3389/fpls.2018.00571
Results
Welschmeyer, N. A. (1994). Fluorometric analysis of chlorophyll a in the presence of chlorophyll b and pheopigments. Limnology and Oceanography, 39(8), 1985–1992. doi:10.4319/lo.1994.39.8.1985
Methods
Xia, J., & Wishart, D. S. (2016). Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis. Current Protocols in Bioinformatics, 55(1), 14.10.1–14.10.91. doi:10.1002/cpbi.11
Methods
Xia, J., Sinelnikov, I. V., Han, B., & Wishart, D. S. (2015). MetaboAnalyst 3.0—making metabolomics more meaningful. Nucleic Acids Research, 43(W1), W251–W257. doi:10.1093/nar/gkv380
Methods

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Related Datasets

Different Version
Mei, S., Yang, Z., & Wawrik, B. (2018). Mass Spectra For Single Scrippsiella Trochoidea Cells: Light Vs. Dark & Replete Vs. N Limiting Conditions (Version 1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.1188486

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Parameters

ParameterDescriptionUnits
light1_cell1_mzMass to charge ratio (m/z) of light contition experiment replicate 1 cell 1 dimensionless
light1_cell1_intensityRelative intensity of light contition experiment replicate 1 cell 1 unitless
light1_cell2_mzMass to charge ratio (m/z) of light contition experiment replicate 1 cell 2 dimensionless
light1_cell2_intensityRelative intensity of light contition experiment replicate 1 cell 2 unitless
light1_cell3_mzMass to charge ratio (m/z) of light contition experiment replicate 1 cell 3 dimensionless
light1_cell3_intensityRelative intensity of light contition experiment replicate 1 cell 3 unitless
light1_cell4_mzMass to charge ratio (m/z) of light contition experiment replicate 1 cell 4 dimensionless
light1_cell4_intensityRelative intensity of light contition experiment replicate 1 cell 4 unitless
light1_cell5_mzMass to charge ratio (m/z) of light contition experiment replicate 1 cell 5 dimensionless
light1_cell5_intensityRelative intensity of light contition experiment replicate 1 cell 5 unitless
light1_cell6_mzMass to charge ratio (m/z) of light contition experiment replicate 1 cell 6 dimensionless
light1_cell6_intensityRelative intensity of light contition experiment replicate 1 cell 6 unitless
light2_cell1_mzMass to charge ratio (m/z) of light contition experiment replicate 2 cell 1 dimensionless
light2_cell1_intensityRelative intensity of light contition experiment replicate 2 cell 1 unitless
light2_cell2_mzMass to charge ratio (m/z) of light contition experiment replicate 2 cell 2 dimensionless
light2_cell2_intensityRelative intensity of light contition experiment replicate 2 cell 2 unitless
light3_cell1_mzMass to charge ratio (m/z) of light contition experiment replicate3 cell1 dimensionless
light3_cell1_intensityRelative intensity of light contition experiment replicate3 cell1 unitless
light3_cell2_mzMass to charge ratio (m/z) of light contition experiment replicate3 cell2 dimensionless
light3_cell2_intensityRelative intensity of light contition experiment replicate3 cell2 unitless
light3_cell3_mzMass to charge ratio (m/z) of light contition experiment replicate3 cell 3 dimensionless
light3_cell3_intensityRelative intensity of light contition experiment replicate 3 cell 3 unitless
light3_cell4_mzMass to charge ratio (m/z) of light contition experiment replicate 3 cell 4 dimensionless
light3_cell4_intensityRelative intensity of light contition experiment replicate 3 cell 4 unitless
light3_cell5_mzMass to charge ratio (m/z) of light contition experiment replicate 3 cell 5 dimensionless
light3_cell5_intensityRelative intensity of light contition experiment replicate 3 cell 5 unitless
light3_cell6_mzMass to charge ratio (m/z) of light contition experiment replicate 3 cell 6 dimensionless
light3_cell6_intensityRelative intensity of light contition experiment replicate 3 cell 6 unitless
light4_cell1_mzMass to charge ratio (m/z) of light contition experiment replicate4 cell1 dimensionless
light4_cell1_intensityRelative intensity of light contition experiment replicate4 cell1 unitless
light4_cell2_mzMass to charge ratio (m/z) of light contition experiment replicate4 cell2 dimensionless
light4_cell2_intensityRelative intensity of light contition experiment replicate4 cell2 unitless
light4_cell3_mzMass to charge ratio (m/z) of light contition experiment replicate4 cell 3 dimensionless
light4_cell3_intensityRelative intensity of light contition experiment replicate 4 cell 3 unitless
light4_cell4_mzMass to charge ratio (m/z) of light contition experiment replicate 4 cell 4 dimensionless
light4_cell4_intensityRelative intensity of light contition experiment replicate 4 cell 4 unitless
light5_cell1_mzMass to charge ratio (m/z) of light contition experiment replicate5 cell1 dimensionless
light5_cell1_intensityRelative intensity of light contition experiment replicate5 cell1 unitless
light5_cell2_mzMass to charge ratio (m/z) of light contition experiment replicate5 cell2 dimensionless
light5_cell2_intensityRelative intensity of light contition experiment replicate5 cell2 unitless
light5_cell3_mzMass to charge ratio (m/z) of light contition experiment replicate5 cell 3 dimensionless
light5_cell3_intensityRelative intensity of light contition experiment replicate 5 cell 3 unitless
light5_cell4_mzMass to charge ratio (m/z) of light contition experiment replicate 5 cell 4 dimensionless
light5_cell4_intensityRelative intensity of light contition experiment replicate 5 cell 4 unitless
light5_cell5_mzMass to charge ratio (m/z) of light contition experiment replicate 5 cell 5 dimensionless
light5_cell5_intensityRelative intensity of light contition experiment replicate 5 cell 5 unitless
light5_cell6_mzMass to charge ratio (m/z) of light contition experiment replicate 5 cell 6 dimensionless
light5_cell6_intensityRelative intensity of light contition experiment replicate 5 cell 6 unitless
dark1_cell1_mzMass to charge ratio (m/z) of dark contition experiment replicate1 cell1 dimensionless
dark1_cell1_intensityRelative intensity of dark contition experiment replicate1 cell1 unitless
dark1_cell2_mzMass to charge ratio (m/z) of dark contition experiment replicate1 cell2 dimensionless
dark1_cell2_intensityRelative intensity of dark contition experiment replicate1 cell2 unitless
dark2_cell1_mzMass to charge ratio (m/z) of dark contition experiment replicate2 cell1 dimensionless
dark2_cell1_intensityRelative intensity of dark contition experiment replicate2 cell1 unitless
dark2_cell2_mzMass to charge ratio (m/z) of dark contition experiment replicate2 cell2 dimensionless
dark2_cell2_intensityRelative intensity of dark contition experiment replicate2 cell2 unitless
dark2_cell3_mzMass to charge ratio (m/z) of dark contition experiment replicate2 cell3 dimensionless
dark2_cell3_intensityRelative intensity of dark contition experiment replicate2 cell3 unitless
dark2_cell4_mzMass to charge ratio (m/z) of dark contition experiment replicate2 cell4 dimensionless
dark2_cell4_intensityRelative intensity of dark contition experiment replicate2 cell4 unitless
dark2_cell5_mzMass to charge ratio (m/z) of dark contition experiment replicate2 cell5 dimensionless
dark2_cell5_intensityRelative intensity of dark contition experiment replicate2 cell5 unitless
dark2_cell6_mzMass to charge ratio (m/z) of dark contition experiment replicate2 cell6 dimensionless
dark2_cell6_intensityRelative intensity of dark contition experiment replicate2 cell6 unitless
dark2_cell7_mzMass to charge ratio (m/z) of dark contition experiment replicate2 cell7 dimensionless
dark2_cell7_intensityRelative intensity of dark contition experiment replicate2 cell7 unitless
dark2_cell8_mzMass to charge ratio (m/z) of dark contition experiment replicate2 cell8 dimensionless
dark2_cell8_intensityRelative intensity of dark contition experiment replicate2 cell8 unitless
dark3_cell1_mzMass to charge ratio (m/z) of dark contition experiment replicate3 cell1 dimensionless
dark3_cell1_intensityRelative intensity of dark contition experiment replicate3 cell1 unitless
dark3_cell2_mzMass to charge ratio (m/z) of dark contition experiment replicate3 cell2 dimensionless
dark3_cell2_intensityRelative intensity of dark contition experiment replicate3 cell2 unitless
dark3_cell3_mzMass to charge ratio (m/z) of dark contition experiment replicate3 cell3 dimensionless
dark3_cell3_intensityRelative intensity of dark contition experiment replicate3 cell3 unitless
dark3_cell4_mzMass to charge ratio (m/z) of dark contition experiment replicate3 cell4 dimensionless
dark3_cell4_intensityRelative intensity of dark contition experiment replicate3 cell4 unitless
dark3_cell5_mzMass to charge ratio (m/z) of dark contition experiment replicate3 cell5 dimensionless
dark3_cell5_intensityRelative intensity of dark contition experiment replicate3 cell5 unitless
dark3_cell6_mzMass to charge ratio (m/z) of dark contition experiment replicate3 cell6 dimensionless
dark3_cell6_intensityRelative intensity of dark contition experiment replicate3 cell6 unitless
dark3_cell7_mzMass to charge ratio (m/z) of dark contition experiment replicate3 cell7 dimensionless
dark3_cell7_intensityRelative intensity of dark contition experiment replicate3 cell7 unitless
dark4_cell1_mzMass to charge ratio (m/z) of dark contition experiment replicate4 cell1 dimensionless
dark4_cell1_intensityRelative intensity of dark contition experiment replicate4 cell1 unitless
dark4_cell2_mzMass to charge ratio (m/z) of dark contition experiment replicate4 cell2 dimensionless
dark4_cell2_intensityRelative intensity of dark contition experiment replicate4 cell2 unitless
dark4_cell3_mzMass to charge ratio (m/z) of dark contition experiment replicate4 cell3 dimensionless
dark4_cell3_intensityRelative intensity of dark contition experiment replicate4 cell3 unitless
dark4_cell4_mzMass to charge ratio (m/z) of dark contition experiment replicate4 cell4 dimensionless
dark4_cell4_intensityRelative intensity of dark contition experiment replicate4 cell4 unitless
dark4_cell5_mzMass to charge ratio (m/z) of dark contition experiment replicate4 cell5 dimensionless
dark4_cell5_intensityRelative intensity of dark contition experiment replicate4 cell5 unitless
n-limited1_cell1_mzMass to charge ratio (m/z) of n-limited contition experiment replicate1 cell1 dimensionless
n-limited1_cell1_intensityRelative intensity of n-limited contition experiment replicate1 cell1 unitless
n-limited1_cell2_mzMass to charge ratio (m/z) of n-limited contition experiment replicate1 cell2 dimensionless
n-limited1_cell2_intensityRelative intensity of n-limited contition experiment replicate1 cell2 unitless
n-limited1_cell3_mzMass to charge ratio (m/z) of n-limited contition experiment replicate1 cell3 dimensionless
n-limited1_cell3_intensityRelative intensity of n-limited contition experiment replicate1 cell3 unitless
n-limited1_cell4_mzMass to charge ratio (m/z) of n-limited contition experiment replicate1 cell4 dimensionless
n-limited1_cell4_intensityRelative intensity of n-limited contition experiment replicate1 cell4 unitless
n-limited1_cell5_mzMass to charge ratio (m/z) of n-limited contition experiment replicate1 cell5 dimensionless
n-limited1_cell5_intensityRelative intensity of n-limited contition experiment replicate1 cell5 unitless
n-limited1_cell6_mzMass to charge ratio (m/z) of n-limited contition experiment replicate1 cell6 dimensionless
n-limited1_cell6_intensityRelative intensity of n-limited contition experiment replicate1 cell6 unitless
n-limited1_cell7_mzMass to charge ratio (m/z) of n-limited contition experiment replicate1 cell7 dimensionless
n-limited1_cell7_intensityRelative intensity of n-limited contition experiment replicate1 cell7 unitless
n_limited2_cell1_mzMass to charge ratio (m/z) of n-limited contition experiment replicate2 cell1 dimensionless
n-limited2_cell1_intensityRelative intensity of n-limited contition experiment replicate2 cell1 unitless
n-limited2_cell2_mzMass to charge ratio (m/z) of n-limited contition experiment replicate2 cell2 dimensionless
n-limited2_cell2_intensityRelative intensity of n-limited contition experiment replicate2 cell2 unitless
n_limited3_cell1_mzMass to charge ratio (m/z) of n-limited contition experiment replicate3 cell1 dimensionless
n-limited3_cell1_intensityRelative intensity of n-limited contition experiment replicate3 cell1 unitless
n_limited4_cell1_mzMass to charge ratio (m/z) of n-limited contition experiment replicate4 cell1 dimensionless
n-limited4_cell1_intensityRelative intensity of n-limited contition experiment replicate4 cell1 unitless
n-limited4_cell2_mzMass to charge ratio (m/z) of n-limited contition experiment replicate4 cell2 dimensionless
n-limited4_cell2_intensityRelative intensity of n-limited contition experiment replicate4 cell2 unitless
n_limited5_cell1_mzMass to charge ratio (m/z) of n-limited contition experiment replicate5 cell1 dimensionless
n-limited5_cell1_intensityRelative intensity of n-limited contition experiment replicate5 cell1 unitless
n-limited5_cell2_mzMass to charge ratio (m/z) of n-limited contition experiment replicate5 cell2 dimensionless
n-limited5_cell2_intensityRelative intensity of n-limited contition experiment replicate5 cell2 unitless
n_limited6_cell1_mzMass to charge ratio (m/z) of n-limited contition experiment replicate6 cell1 dimensionless
n-limited6_cell1_intensityRelative intensity of n-limited contition experiment replicate6 cell1 unitless
n-limited6_cell2_mzMass to charge ratio (m/z) of n-limited contition experiment replicate6 cell2 dimensionless
n-limited6_cell2_intensityRelative intensity of n-limited contition experiment replicate6 cell2 unitless
replete1_cell1_mzMass to charge ratio (m/z) of replte contition experiment replicate1 cell1 dimensionless
replete1_cell1_intensityRelative intensity of replete contition experiment replicate1 cell1 unitless
replete1_cell2_mzMass to charge ratio (m/z) of replete contition experiment replicate1 cell2 dimensionless
replete1_cell2_intensityRelative intensity of replete contition experiment replicate1 cell2 unitless
replete2_cell1_mzMass to charge ratio (m/z) of replte contition experiment replicate2 cell1 dimensionless
replete2_cell1_intensityRelative intensity of replete contition experiment replicate2 cell1 unitless
replete3_cell1_mzMass to charge ratio (m/z) of replte contition experiment replicate3 cell1 dimensionless
replete3_cell1_intensityRelative intensity of replete contition experiment replicate3 cell1 unitless
replete3_cell2_mzMass to charge ratio (m/z) of replete contition experiment replicate3 cell2 dimensionless
replete3_cell2_intensityRelative intensity of replete contition experiment replicate3 cell2 unitless
replete3_cell3_mzMass to charge ratio (m/z) of replte contition experiment replicate3 cell3 dimensionless
replete3_cell3_intensityRelative intensity of replete contition experiment replicate3 cell3 unitless
replete4_cell1_mzMass to charge ratio (m/z) of replte contition experiment replicate4 cell1 dimensionless
replete4_cell1_intensityRelative intensity of replete contition experiment replicate4 cell1 unitless
replete4_cell2_mzMass to charge ratio (m/z) of replete contition experiment replicate4 cell2 dimensionless
replete4_cell2_intensityRelative intensity of replete contition experiment replicate4 cell2 unitless
replete4_cell3_mzMass to charge ratio (m/z) of replte contition experiment replicate4 cell3 dimensionless
replete4_cell3_intensityRelative intensity of replete contition experiment replicate4 cell3 unitless
replete5_cell1_mzMass to charge ratio (m/z) of replte contition experiment replicate5 cell1 dimensionless
replete5_cell1_intensityRelative intensity of replete contition experiment replicate5 cell1 unitless
replete5_cell2_mzMass to charge ratio (m/z) of replete contition experiment replicate5 cell2 dimensionless
replete5_cell2_intensityRelative intensity of replete contition experiment replicate5 cell2 unitless
replete5_cell3_mzMass to charge ratio (m/z) of replte contition experiment replicate5 cell3 dimensionless
replete5_cell3_intensityRelative intensity of replete contition experiment replicate5 cell3 unitless
replete5_cell4_mzMass to charge ratio (m/z) of replte contition experiment replicate5 cell4 dimensionless
replete5_cell4_intensityRelative intensity of replete contition experiment replicate5 cell4 unitless
replete5_cell5_mzMass to charge ratio (m/z) of replete contition experiment replicate5 cell5 dimensionless
replete5_cell5_intensityRelative intensity of replete contition experiment replicate5 cell5 unitless
replete5_cell6_mzMass to charge ratio (m/z) of replte contition experiment replicate6 cell6 dimensionless
replete5_cell6_intensityRelative intensity of replete contition experiment replicate6 cell6 unitless


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Instruments

Dataset-specific Instrument Name
Thermo LTQ Orbitrap XL mass spectrometer
Generic Instrument Name
Mass Spectrometer
Dataset-specific Description
Thermo LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Waltham, MA, United States). Mass analyze parameters were as follows: mass resolution 60,000, +4 kV ionization voltage at positive ion mode (0.05–0.07 μA of ion current), 1 microscan, 100 ms max injection time, and automatic gain control on.
Generic Instrument Description
General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.


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Project Information

Collaborative Research: Creatine Cycling in Marine Bacterial and Phytoplankton Assemblages (Creatine Cycling)

Coverage: Atlantic bight


NSF Award Abstract:
High rates of dissolved organic nitrogen (DON) production and utilization in aquatic systems are typically attributed to microbial activity. Though it is known that there is a tight coupling between the production and consumption of biologically available DON, the composition, dynamics, and ecological significance of this rapidly cycled DON pool are less well understood. This proposal focuses on a component of the DON pool, creatine, which is historically understood as a product of metazoan activity, but appears to be both produced by phytoplankton and consumed by marine bacteria. Creatine is present in seawater in measurable quantities, which led to the hypothesis that creatine may be a significant component of the marine DON cycle. DON cycling likely has a bearing on fundamental marine ecosystem processes with large implications for carbon and nitrogen turnover on a global scale. Broader impacts of this project will include outreach that focuses on connecting scientists with K-12 students through research experiences for teachers and lesson development in collaboration with the K20 Center for Educational and Community Renewal, a statewide education research and development center at the University of Oklahoma. The project will integrate the research with inquiry-based teaching of rural secondary science teachers through Authentic Research Experiences in oceanographic science and microbial ecology. The K20 network includes 96% of Oklahoma schools, providing a unique opportunity to impact STEM education in Oklahoma.

The results of this project will help develop a better understanding of DON cycling, the ecological context of creatine uptake activity, and identify both creatine-producing and consuming organisms in the marine environment. The importance of creatine cycling will be assessed via 15N tracer studies along the natural coastal-to-offshore productivity gradient observed in the North Atlantic. Tracer and molecular approaches will be used to investigate the importance of phytoplankton vs. bacteria in creatine uptake and, the taxonomic identities of creatine-utilizing bacteria will be interrogated via molecular, stable isotope probing (SIP), and RT-qPCR approaches.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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